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SRX027409: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 21,290 spots, 10.6M bases, 24.1Mb 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: 454-3416
Instrument: 454 GS FLX Titanium
Strategy: OTHER
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
          barcode
Group tagBasecalls
ApiaTTCAGGTTC
BangkokCAACCGTTC
BanguiAGTTGGC
BeijingAGGCGGC
BernTGGTTGGTC
BogotaCGGTATC
BrusselsAGACAC
CanberraACTTGC
DamascusTGTCCGGTC
FreetownTTCGCCGTC
HarareTAATTCCGC
KampalaTTCGGTGTC
KigaliAGTCCGTC
KinshasaTGACGAC
MadridTTCGTTATC
MinskACTCAC
OttawaCAAGAAC
RioAGCTTC
SanaaCGGTTCGAC
SantiagoTATCAAC
TunisAGGAGGAAC
VictoriaAGGAAGGTC
ViennaTCACAC
ZagrebAGACCTC
 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: 40637.1 40638.1 40639.1 40640.1 40641.1 40642.1 40643.1 40644.1 40645.1 40646.1 40647.1 40648.1 40649.1 40650.1 40651.1 40652.1 40653.1 40654.1 40655.1 40656.1 40657.1 40658.1 40659.1 40660.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40637.1 BROAD:SEQUENCING_SAMPLE:40638.1 BROAD:SEQUENCING_SAMPLE:40639.1 BROAD:SEQUENCING_SAMPLE:40640.1 BROAD:SEQUENCING_SAMPLE:40641.1 BROAD:SEQUENCING_SAMPLE:40642.1 BROAD:SEQUENCING_SAMPLE:40643.1 BROAD:SEQUENCING_SAMPLE:40644.1 BROAD:SEQUENCING_SAMPLE:40645.1 BROAD:SEQUENCING_SAMPLE:40646.1 BROAD:SEQUENCING_SAMPLE:40647.1 BROAD:SEQUENCING_SAMPLE:40648.1 BROAD:SEQUENCING_SAMPLE:40649.1 BROAD:SEQUENCING_SAMPLE:40650.1 BROAD:SEQUENCING_SAMPLE:40651.1 BROAD:SEQUENCING_SAMPLE:40652.1 BROAD:SEQUENCING_SAMPLE:40653.1 BROAD:SEQUENCING_SAMPLE:40654.1 BROAD:SEQUENCING_SAMPLE:40655.1 BROAD:SEQUENCING_SAMPLE:40656.1 BROAD:SEQUENCING_SAMPLE:40657.1 BROAD:SEQUENCING_SAMPLE:40658.1 BROAD:SEQUENCING_SAMPLE:40659.1 BROAD:SEQUENCING_SAMPLE:40660.1
BI project name: G2399
BI work request ID: 20166
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-10-18 22:44:10.0454BaseCaller2.0.01.12
Runs: 24 runs, 21,290 spots, 10.6M bases, 24.1Mb
Run# of Spots# of BasesSizePublished
SRR066862758381,443911,512b2010-10-01
SRR0668671,163583,8741.3Mb2010-10-01
SRR066871828405,757973,391b2010-10-01
SRR066874661334,180803,725b2010-10-01
SRR066917820409,858982,527b2010-10-01
SRR066932694337,590819,660b2010-10-01
SRR066957657327,979795,458b2010-10-01
SRR066964969480,0641.1Mb2010-10-01
SRR066973844421,2521,006,621b2010-10-01
SRR066995985485,2031.1Mb2010-10-01
SRR066999581291,503705,100b2010-10-01
SRR067028870431,8751,030,535b2010-10-01
SRR0670671,438704,5611.6Mb2010-10-01
SRR067096942473,8761.1Mb2010-10-01
SRR067114760382,101911,534b2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000141 : Harare_TAATTCCGC758381,443
2SRS000142 : Brussels_AGACAC1,163583,874
3SRS000143 : Freetown_TTCGCCGTC760382,101
4SRS000144 : Kigali_AGTCCGTC929463,259
5SRS000145 : Canberra_ACTTGC657327,979
6SRS000146 : Minsk_ACTCAC844421,252
7SRS000149 : Santiago_TATCAAC694337,590
8SRS000678 : Apia_TTCAGGTTC979488,497
9SRS000685 : Madrid_TTCGTTATC1,053521,913
10SRS000686 : Bogota_CGGTATC820409,858
11SRS000688 : Rio_AGCTTC885442,216
12SRS000689 : Vienna_TCACAC828405,757
13SRS000690 : Bangkok_CAACCGTTC1,438704,561
14SRS003571 : Damascus_TGTCCGGTC661334,180
15SRS003572 : Ottawa_CAAGAAC985485,203
16SRS003573 : Tunis_AGGAGGAAC581291,503
17SRS003574 : Bangui_AGTTGGC942473,876
18SRS003575 : Kampala_TTCGGTGTC870431,875
19SRS003576 : Sanaa_CGGTTCGAC564282,873
20SRS003577 : Bern_TGGTTGGTC598297,183
21SRS003578 : Kinshasa_TGACGAC1,332669,258
22SRS003580 : Victoria_AGGAAGGTC889450,505
23SRS003583 : Zagreb_AGACCTC1,091538,008
24SRS003584 : Beijing_AGGCGGC969480,064
25 : defaultn/an/a

ID:
33270

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