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SRX027415: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 17,307 spots, 8.8M bases, 20.5Mb downloads

Design: 270 HapMap human genomic DNA samples of known HLA type were amplified by PCR with six different exon-specific primer pairs. The six amplicons for each individual were pooled, and underwent barcoded 454 library construction. A total of 96 unique barcodes were utilized, thus, sets of 96 individuals could be pooled prior to sequencing.
Submitted by: Broad Institute (BI)
Study: Homo sapiens
PRJNA50323 • SRP003652 • All experiments • All runs
show Abstracthide Abstract
The human leukocyte antigen system (HLA) is the name of the major histocompatibility complex (MHC) in humans. HLA variation plays a role in infectious and autoimmune disease.
Samples: pool of 24 samples • Homo sapiens
Library:
Name: 454-3442
Instrument: 454 GS FLX Titanium
Strategy: OTHER
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
          barcode
Group tagBasecalls
AccraAGTCGAC
AmmanTAGGAATC
AthensACGGCTC
BerlinTATTGAC
BissauCCAGGAC
BudapestACTCCTC
CairoTCTTGGC
ConakryTCTCGAC
CopenhagenAACCAGC
DublinAAGGCAC
GuatemalaTGCGTTC
HelsinkiTCACCTC
JakartaTTCCTGC
KingstonTGCCGAAC
NairobiCCGGCCAC
PyongyangTCTCCGTC
QuitoAAGGTGC
RigaTTCGTGGC
RomeACACGGAC
SeoulAACCTGGC
SuvaTAATCTC
TarawaAATGGTAC
TehranTTCATAC
TokyoTATTCGTC
 primer
Group tagBasecalls
HLA_A_exon2_30018486-30018849_ForwardCRGGTCTCAGCCACTSCTC
HLA_A_exon2_30018486-30018849_ReverseCTCGGACCCGGAGACTGT
HLA_A_exon3_30018988-30019360_ForwardCTYGGGGGACYGGGCTGAC
HLA_A_exon3_30018988-30019360_ReverseCCCAATTGTCTCCCCTCCTTG
HLA_B_exon2_31432401-31432811_ForwardGGATGGGGAGTCGTGACCT
HLA_B_exon2_31432401-31432811_ReverseGGSAGGGAAATGGCCTCT
HLA_B_exon3_31431877-31432282_ForwardCGGCGACCTATAGGAGATGG
HLA_B_exon3_31431877-31432282_ReverseGCGTTTACCCGGTTTCATT
HLA_C_exon2_31347190-31347707_ForwardTGAAACCGGGTAAAGGYGACT
HLA_C_exon2_31347190-31347707_ReverseCTCTGSGGAGAGGARCGAGG
HLA_C_exon3_31346739-31347191_ForwardAGYGCTGATCCCATTTTCCT
HLA_C_exon3_31346739-31347191_ReverseAGTCRCCTTTACCCGGTTTC
  forward

Experiment attributes: (show all 4 attributes...) (hide...)
4 BI attributes: (show...)(hide...)
BI GSSR sample IDs: 40733.1 40734.1 40735.1 40736.1 40737.1 40738.1 40739.1 40740.1 40741.1 40742.1 40743.1 40744.1 40745.1 40746.1 40747.1 40748.1 40749.1 40750.1 40751.1 40752.1 40753.1 40754.1 40755.1 40756.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40733.1 BROAD:SEQUENCING_SAMPLE:40734.1 BROAD:SEQUENCING_SAMPLE:40735.1 BROAD:SEQUENCING_SAMPLE:40736.1 BROAD:SEQUENCING_SAMPLE:40737.1 BROAD:SEQUENCING_SAMPLE:40738.1 BROAD:SEQUENCING_SAMPLE:40739.1 BROAD:SEQUENCING_SAMPLE:40740.1 BROAD:SEQUENCING_SAMPLE:40741.1 BROAD:SEQUENCING_SAMPLE:40742.1 BROAD:SEQUENCING_SAMPLE:40743.1 BROAD:SEQUENCING_SAMPLE:40744.1 BROAD:SEQUENCING_SAMPLE:40745.1 BROAD:SEQUENCING_SAMPLE:40746.1 BROAD:SEQUENCING_SAMPLE:40747.1 BROAD:SEQUENCING_SAMPLE:40748.1 BROAD:SEQUENCING_SAMPLE:40749.1 BROAD:SEQUENCING_SAMPLE:40750.1 BROAD:SEQUENCING_SAMPLE:40751.1 BROAD:SEQUENCING_SAMPLE:40752.1 BROAD:SEQUENCING_SAMPLE:40753.1 BROAD:SEQUENCING_SAMPLE:40754.1 BROAD:SEQUENCING_SAMPLE:40755.1 BROAD:SEQUENCING_SAMPLE:40756.1
BI project name: G2399
BI work request ID: 20247
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-11-23 15:53:31.0454BaseCaller2.0.01.12
Runs: 24 runs, 17,307 spots, 8.8M bases, 20.5Mb
Run# of Spots# of BasesSizePublished
SRR066872830428,9851,029,944b2010-10-01
SRR066945858439,1991Mb2010-10-01
SRR0669591,019506,4151.2Mb2010-10-01
SRR066965795398,233971,120b2010-10-01
SRR066981764395,219955,215b2010-10-01
SRR06698716382,708233,587b2010-10-01
SRR067008325161,021419,907b2010-10-01
SRR0670121,071555,0691.3Mb2010-10-01
SRR067037923464,1511.1Mb2010-10-01
SRR0670461,438737,9931.7Mb2010-10-01
SRR0670541,357693,3071.6Mb2010-10-01
SRR067058851431,3761,044,674b2010-10-01
SRR067081925472,2901.1Mb2010-10-01
SRR067115875450,2301Mb2010-10-01
SRR067116854435,9011Mb2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000061 : Copenhagen_AACCAGC537272,782
2SRS000063 : Suva_TAATCTC923464,151
3SRS000064 : Accra_AGTCGAC764395,219
4SRS000065 : Athens_ACGGCTC1,019506,415
5SRS000066 : Kingston_TGCCGAAC16382,708
6SRS000067 : Tokyo_TATTCGTC14572,930
7SRS000068 : Pyongyang_TCTCCGTC369184,408
8SRS000072 : Guatemala_TGCGTTC1,438737,993
9SRS000073 : Conakry_TCTCGAC854435,901
10SRS000075 : Budapest_ACTCCTC925472,290
11SRS000076 : Jakarta_TTCCTGC1,094567,267
12SRS000077 : Rome_ACACGGAC875450,230
13SRS000598 : Quito_AAGGTGC795398,233
14SRS000599 : Cairo_TCTTGGC919465,350
15SRS000600 : Berlin_TATTGAC1,071555,069
16SRS000601 : Nairobi_CCGGCCAC241119,509
17SRS000602 : Tarawa_AATGGTAC17990,604
18SRS000603 : Seoul_AACCTGGC325161,021
19SRS002007 : Helsinki_TCACCTC858439,199
20SRS003533 : Amman_TAGGAATC16982,437
21SRS003544 : Riga_TTCGTGGC606309,934
22SRS003547 : Bissau_CCAGGAC830428,985
23SRS003548 : Tehran_TTCATAC851431,376
24SRS003549 : Dublin_AAGGCAC1,357693,307
25 : defaultn/an/a

ID:
33276

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