Date received at UCSF

Number received

(EXAMPLE) 3/25/2024

IMMRSE MTA (use dropdown)

Zumba_Zambia_DBS Household positive samples carried by Amy

Zumba_Zambia_HF_DBS shipment carried by Amy

Recrudescence from Indiana U

Jenny carried, Faith will scan to develop manifest

EPPIcenter received shipments/ 2025.02.10 Zumba DBS_carried by Jessica

WGS requiring larger sequencer -- need a second spot, because we sent extracted DNA but troubleshooting assay at UCSF (IMMRSE WGS), Extended MIPs panel requiring larger sequencer (Melissa request - IMMRSE)

EPPIcenter received shipments/ 2025.02.10 Zumba DBS_IMMRSE WGS_Melissa request - IMMRSE_carried by Jessica

For Zumba (2 spots - 2 will remain in Uganda), for IMMRSE WGS (second spot - 2 will remain in Uganda)

Recrudescence from Indiana U

EPPIcenter received shipments/ 2025.1.10 Recrudescence from Indiana U

Biohub returning prepandemic boxes

2024.12.09 boxes from Biohub freezer

PRISM RNA 08/27/19
PRISM Subset 2
PRISM DNA/RNA Extractions

2024.10.30 returning Musical aliquots (Pras borrowed)

2024.10.24 IDRC to UCSF 12 boxes ZUMBA and PBC

Huang, Liusheng <liusheng.huang@ucsf.edu>

EPPIcenter received shipments/ 2024-07-17 Teun 13DNAplates & Liesheing plate

SPARTAN Uganda Plasma Plasma from Heparin vacutainer collection. Assessment of Lumefantrine levels (1 plate)

EPPIcenter received shipments/ 2024-07-17 Teun 13DNAplates & Liesheing plate

Indie1b Gambia Transmission network analysis (10 plates), for AMA-1 sequencing
SPARTAN Uganda WholeBlood Total NA extracted from wholeblood samples (preserved in RNA protect). Assessment of MOI and durg resistance markers (3 plates)

DNA Gambia Plt 1/ DNA Gambia Plt 2 /DNA Gambia Plt 3/ AMA-1 selection 1/ AMA-1 selection 2 / AMA-1 selection 3 / Gambia Indie1b y3 Total NA KT230524/ plt 50/ plt 51/ KT060922 / KT260822/ Total NA Gambia Indie b1/ Total NA Gambia Indie b1

EPPIcenter received shipments/ 2024-07-18 Zumba DBS carried by Jessica

barcode format= Z20001

IDRC Stephen Orena Kseries in LN2 shippers

about 1417

EPPIcenter received shipments/ 2024-07-16 LN2 4 carriers cryopreserved cells

K1011 is half full because we already shipped the other half.
K1012 K2001 K2002 K2003 K2004 K2005 K2006 K2007 K2008 K2009 K2010 K2011 K2012

AHRI Ethiopia carried by Izzy

EPPIcenter received shipments/ 2024-06-18 Zamb Ethiop DBS carried by Izzy

AHRI Ethiopia carried by Izzy

EPPIcenter received shipments/ 2024-06-18 Zamb Ethiop DBS carried by Izzy

3 boxes Luminex + controls for RDTs UPLOADED (871 DBS total)
Sufrakara Luminex+ controls for RDTs carried by Izzy June 2024 (219 DBS)
Arebia Luminex+ controls for RDTs carried by Izzy June 2024 (349 DBS)
Firqa dangurie Luminex+ controls for RDTs carried by Izzy June 2024 (303 DBS)

EPPIcenter received shipments/ 2024-05-29 IDRC 17plates 20vag&stool 2paxgene

2 paxgene handed tp Pras within hours

EPPIcenter received shipments/ 2024-05-29 IDRC 17plates 20vag&stool 2paxgene

vaginal swabs VSB-1022-VSB1031.

EPPIcenter received shipments/ 2024-05-29 IDRC 17plates 20vag&stool 2paxgene

stool ST-1022 through ST-1031

EPPIcenter received shipments/ 2024-05-29 IDRC 17plates 20vag&stool 2paxgene

no- these were immediately extracted, I presume the extractions are in DB

CIGASS Senegal (Awa Deme)

EPPIcenter received shipments/ 2024-05-6 DRC DBS from Senegal

These were punched and extracted immediately by Kore and Charles, and remnants will go to basket 14

UNAM Davis Mumbengegwi

EPPIcenter received shipments/ 2024-04-28 Lydia DBS in suitcase

UNAM Davis Mumbengegwi

EPPIcenter received shipments/ 2024-04-28 Lydia DBS in suitcase

AHRI Ethiopia (endalamaw.gadisa@ahri.gov.et)

EPPIcenter received shipments/ 24.1.18 DNA from Ethiopia

shipment arranged by Sylvia Jebiwott in MEI, PO# B002725533

Ifakara TZ (Deb Sumari)

EPPIcenter received shipments/ 2024.4.9 CHILD swab.Plasma from IfakaraTZ

CHILD Plasma 1-23

Ifakara TZ (Deb Sumari)

EPPIcenter received shipments/ 2024.4.9 CHILD swab.Plasma from IfakaraTZ

These smNGS Plasma were immediately sent to Maira Phelps <maira.phelps@czbiohub.org>

Ifakara TZ (Deb Sumari)

EPPIcenter received shipments/ 2024.4.9 CHILD swab.Plasma from IfakaraTZ

These swabs were immediately sent to Maira Phelps <maira.phelps@czbiohub.org>

IDRC Uganda (David Masiga)

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

IDRC Uganda (David Masiga)

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

Plasma_1 for Jared and Arefin 22 boxes

IDRC Uganda (David Masiga)

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

IDRC Uganda (David Masiga)

Saki mNGS swabs

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

J1019
J2008
H1019
H2008 in Sample DB

IDRC Uganda (David Masiga)

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

"PV1812-065 IM-WGS-004
IM-WGS-003"
"none IM-WGS-001
IM-WGS-002"
"none PBC-SMT-107
PBC-SMT-108"
"none PBC SMT-109
PBC-SMT-110"
"none PBC- SPP shipment-01
PBC-SMT-113"
"none PBC-SMT-112
PBC-SMT-111"
none IM-WGS-005

IDRC Uganda (David Masiga)

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

IDRC Uganda (David Masiga)

EPPIcenter received shipments/ 2024.4.2Last PBC shipment off PRISM grant

AHRI Ethiopia (endalamaw.gadisa@ahri.gov.et)

EPPIcenter received shipments/ 24.1.18 DBS from Ethiopia

These were carried in Endeshaw's luggage HRP study uploaded into Sample DB

Antibodies Temp box rack 18 not able to add to DB yet- TM 9/24

RadboudUMC antibodies

EPPIcenter received shipments/ 2024-02.Radboud Teun antibodies

These were picked up by Jared

EPPIcenter received shipments/2023-08-31 LN2 RBCs PRISM BC K1008,9,10 K3006, 7, 8

EPPIcenter received shipments/2023-08-29 7musicplasma 4metagenomic 8DNAextract JennyRNA

MUSICAL. 10 boxes in two dry liquid nitrogen cryo shippers.

EPPIcenter received shipments/2023-07-31 LN2 RBCs PRISM BC K1003-7 K3001-5

see LN2 tab of -80 inventory

37x 96 well plates

EPPIcenter received shipments/2023-07 14 boxes of Prism samples for Saki

mNGS samples tested by Saj/Sophie

UG coord US requestor # samples Description
Peter/David Saki 195 PBC plasma for Isabel/Saki serology - requested March & didn't make shipment
Stephen/David Jared 209 PRISM plasma aliquots for S3TIMULATE - [TENTATIVE]
Peter/David Saki/Jared 32 PRISM-1 pellets & DBS for S3TIMULATE
Peter/David Saki PBC boxes with samples for mNGS
Peter/David Saki 18 PBC plasma samples for MUSICAL (annual draws) - requested in March & still in Tororo
Feli/Peter Pras 729 vials MICDroP TLR
Feli/Peter Pras 1452 vials DPSP Paxgene
Peter/Johnie Pras/Maggie 39plates BC3 Extracted DNA
Feli/Peter Pras 1944 vials MICDroP Paxgene
Bakar Michelle 810 DPSP Stool and vaginal swab samples

PBC plasma for Isabel/Saki serology - requested March & didn't make shipment
PRISM plasma aliquots for S3TIMULATE - [TENTATIVE]
PRISM-1 pellets & DBS for S3TIMULATE
PBC boxes with samples for mNGS
PBC plasma samples for MUSICAL (annual draws) - requested in March & still in Tororo
MICDroP TLR
DPSP Paxgene
BC3 Extracted DNA
MICDroP Paxgene
DPSP Stool and vaginal swab samples

EPPIcenter received shipments/2023-04 Plasma, extracted DNA, mNGS samples from UG

Yes=Nasal swabs Yes 13 boxes= plasma NO=VSB+DPSP Vaginal Swabs. No=ST=DPSP stool

Nasal swabs, Vaginal Swabs, stool paxgene

J & H box=Nasal swabs VSB+DPSP Vaginal Swabs. ST=DPSP stool Saki 13 boxes= plasma
J011 H2004 VSB-2001 ST-2001 13 boxes starting with S, S001-S013
J012 H1012 VSB-2002 ST-2002
J013 H1013 VSB-2003 ST-2003
J014 H1014 VSB-2004
J015
J2004

EPPIcenter received shipments/2023-04 Plasma, extracted DNA, mNGS samples from UG

Paxgene, TLR boxes for Pras, Oriana's + Michelle Roh's samples wtih Rosenthal Lab.

No - Jareds upload blocked by longitudinal study issue

2023-02 plates from Teun

EPPIcenter received shipments/2023-02 plates from Teun

Cassias single cell samples from Orena Stephen <orenastphn@gmail.com>

in N2 tower 2 Box names are K1001 and K1002

EPPIcenter received shipments/2023-03 Cassia's N2 single cell samples

see LN2 tab of -80 inventory

Birkholtz South Africa DBS for microsat analyses

DBS : UPSB14_01 UPSB14_02 UPSB14_03 UPSB14_04 UPSB14_05 UPSB14_06 UPSB14_07 UPSB14_10 UPSB14_11 UPTD14_01 UPTD14_02 UPKF14_01

EPPIcenter received shipments/2023-02 DBS Birkholtz SAfrica microsat analyses

EPPIcenter received shipments/2023.2 Will Smith

EPPIcenter received shipments/2023.1 Teun

Samples from Fitsum Dire Dawa (thru Radboud) 2 plates DNA

EPPIcenter received shipments/2022-10 Samples from Fitsum Dire Dawa 2 plates DNA

Prass received samples via Carlton Maven a subset was sent to UCSF

Nasal swabs, Vaginal Swabs, stool paxgene buffy coats

16 boxes Paxgene F1008
F1009 F1010 F1011 F1012 F1013 F1014 F1015 F2016
H1009 H1010 H1011 H2003
J1009 J1010 J2003

16 Boxes named F1008, F1009, F1010, F1011, F1012, F1013, F1014, F1015, F2016, H1009, H1010, H1011, J1009, J1010, H2003, J2003. Note that boxes F1008- 15 do not have excel file of contents

EPPIcenter received shipments/2022-06.17 From Will Stone LSTM

Stored in the bottom of the -80 -Teresa Jared, Charles, while waiting for manifest (6/17/22)

The volume of the sample type 'SS' (Standard Prism1 samples) is set at 50, which is not be accurate 100% of the time. I can update this with more accurate volumes in future. Some of these samples may have been missing (Hristina is isolating and the plate maps made on the day of collection are clocked in her desk).

One issue with the SS samples (which are in 7 PCR plates) is that the 'Jo' and 'STI' requests were grouped for our aliquoting. Apologies for this. If they need to be separated into a different deepwell you will have to fish them out yourselves based on the info in the attached files, but this should be strightforward.

The other sample types ('Immuno' and 'PRISM2') have accurate volumes and none were missing based on the samples we anticipated having here (all but 37 - as discussed previously).

Hope this all makes sense - any questions please ask.

Best wishes,

Will

Uganda (Carlton Maven)

Fran Aweeka/Megan Whalen, Sara (insect), PRISM-TOLAB/Shipped to UCSF/PRISM BORDER COHORT/PBC- 29.05.2022

EPPIcenter received shipments/2022-06 From IDRC 64 boxes

NO some HRP2 reference strins given to Andres

South Africa DBS for microsat analyses

13 DBS as follows: UPSB14_01 thru 07 , UPSB14_10 & 11 . UPTD14_01 & 02 , UPKF14_01

13 dried blood spots

EPPIcenter received shipments/2022.2 South Africa microsat analyses

NOT IN DB Prism1 (129)DBS 2 Cryo boxes -Saki /Jared JD-001 JD-002 (consumed)
NOT IN DB Prism1 Pellets 1 Cryo box -Saki /Jared JD-003 (consumed)
IN DB RNA Shield 2 Cryo boxes -Saki H1005 H1006
IN DB Nasal Swab 2 Cryo boxes -Saki J1005 J1006

From Ug to UCSF Many faculty

DPART STUDY for Pras
Prism DBS, Pellets, swabs H1006 J1005 J1006 not shipped: H1005.
S3timulate JD001 JD002 JD003

Total= 68 boxes
Prism-1 DBS 2 Cryo boxes -Saki /Jared JD-001 JD-002
Prism-1 Pellets 1 Cryo box -Saki /Jared JD-003
RNA Shield 2 Cryo boxes -Saki H1005 H1006
Nasal Swab 2 Cryo boxes -Saki J1005 J1006
PK DPART 14 Cryo boxes -Mary
Paxgene 8 Cryo boxes -Pras
TLR 39 Cryo boxes -Pras (Aliquot-1 and 2)

EPPIcenter received shipments/2022-03 From Ug to UCSF Many faculty

Pras, Meghan, Jared, Saki recieved stuff

EPPIcenter received shipments/2021 11_ Rcvd from Teun DNA Selection plts Gambia MRC samples 2021.xlsx

3x 96 well plates in ziplock in box 3 green freezer

plates are unlocated, but in DB. No key between manifest & micronic

Plasma-LIINC plasma for long COVID studies

EPPIcenter received shipments/2021-09 Samples from ASB (LIINC plasma for long COVID studies)

Uganda (Carlton Maven), organized by Erika

mNGS, H1002 H1003 H1004 J1002 J1003 J1004
plasma;
extracted DNA
RNA Boxes 005 and 006
Vaginal swabs box 00-VSB1001 thru 8
Frozen Placentas box 1-12

EPPIcenter received shipments/2021-09 Shipment from Uganda (PRISM Border Cohort mNGS and PRISM DNA)

Micronics in chest -20, PRISM samples in -80 see here for racks: https://ucsf.app.box.com/folder/144884435072; the original manifest for mNGS samples was incorrect and the correct version is: https://ucsf.box.com/s/n9o21pxap5q5glvavj4zeac21j2yxr7o

Ugandan Blood bank positives

Plasma F2016
H1009 H1010 H1011 H2003
J1009 J1010 J2003
Paxgene G1001 G1002
G1004 G1005 G1006 G1007 G1008 G1009 G1010 G1011 G1012 G1013 G1014
G1016 G1017
G1019 G1020 G1021 G1022
G1026 G1027 G1028
G1030 G1031 G1032 G1033 G1034 G1035 G1036
G1039 G1040 G1041 G1042
G1045 G1046 G1047 G1048 G1049 G1050
G1053 G1054 G1055 G1056
G1058
G1060 G1061 G1062 G1063 G1064
G1067 G1068 G1069
G1072
G1074 G1075
G1077 G1078 G1079 G1080 G1081
G1083 G1084 G1085 G1086 G1087 G1088 G1089 G1090
G1095
G1096 G1097
G1102 G1103 G1104 G1105
G1110 G1111 G1112
G1114 G1115 G1116 G1117 G1118 G1119
G1121 G1122 G1123 G1124 G1125 G1126 G1127 G1128 G1129 G1130
G1134 G1135 G1136 G1137
G1139 G1140 G1141 G1142 G1143
G1145
G1149
G1151 G1152
G1156 G1157
G1159
G1161 G1162
G1164 G1165 G1166
G1168 G1169

(8/13 plasma to Evelien Bunnik @ U Texas) Requested list from Diego

Box labeled "Donor Plasma" in -80 Row 2, Rack7, Box D4

Uganda (Carlton Maven)

Plasma. B-010, DPSP-88002, DPSP-88003, DPSP-88004, TLR-1001thru TLR-10013 donor samples 203000141
203000175
203000291
203000222
203102436
203000409

EPPIcenter received shipments/2021-08 Shipment from Uganda (PRISM Border Cohort plasma and TLR, paxgene)

London (DHL) from Will Stone

Plasma 4 plates of serum PRISM_July2021_GHA

EPPIcenter received shipments/2021-07 July shipment from London (PRISM plasma)

Uganda (World Courier)

PaxGene G1001 G1002 G1003 G1004 G1005 G1006 G1007 G1008 G1009 G1010 G1011 G1012 G1013 G1014 G1015 G1016 G1017 G1018 G1019 G1020 G1021
RNA shield H1001
RNA Swab J1001
BC1 FPs Box 1 Box 2 Box 3
Prism1 FP BG-001 BG-002 BG-003 BG-004 BG-005 BG-006 BG-007 BG-008 BG-009
Prism1_Pellets BG-010
GGS Wholeblood GGS WB #01 GGS WB #02 GGS WB #03 GGS WB #04 GGS WB #05 GGS WB #12
DNA Box #1 Box #2 Box #3

EPPIcenter received shipments/2021-03 March shipment from Uganda

EPPIcenter received shipments/2020-02 February shipment from Uganda (buffy coats P2)

Plasma 112 samples probably in Jo's samples

EPPIcenter received shipments/2019-12 Plasma sample retrieval from Jiangsu, China

Yes ICE_MR_PNG_series and Jos sample

Case Western - Chris King lab

Plasma 8 boxes probably in Jos samlpes

EPPIcenter received shipments/2019-08 PNG Sample retrieval from Case Western

Uganda by way of London

EPPIcenter received shipments/2019-03 SeroX plasma shipment from London

EPPIcenter received shipments/2019-01 shipment from Kampala

Yes- DBS are all extracted DNA with the format (studysubject)(date)

EPPIcenter received shipment/2018-09 shipment from Uganda (P1 pellets and DBS)

Not in sDB- have not found DBS yet, but file is linked here
check nodes_with_epi_data_20210217.csv in the 2019FinalDataAnalysis folder
https://ucsf.box.com/s/sc88odwc8f0t9z1qbzwbam29aec2wnoa

dbs barcode format looks like 17950, 21042, 41421

swaziland study folder

With Meghan Whalen, shipping 8-10 boxes for DPART study

Cannot find Bryans RNA. Jessicas DNA is in DB

EPPIcenter received shipments/2019-05 May shipment from Uganda (P2 pellets and BC1BC3 samples for Mary Prahl)

EPPIcenter received shipments/2008-10 U01 Plasma shipment from Uganda