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SRX027414: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 10,041 spots, 5.1M bases, 12.3Mb 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
AnkaraACACCGGTC
ApiaTTCAGGTTC
BanguiAGTTGGC
BeijingAGGCGGC
BogotaCGGTATC
BrazzavilleACAAGGC
BrusselsAGACAC
CanberraACTTGC
CaracasACGTGGAAC
FreetownTTCGCCGTC
KampalaTTCGGTGTC
KhartoumACCTTGGTC
KigaliAGTCCGTC
MadridTTCGTTATC
MinskACTCAC
NassauACGCGC
ParamariboACCAACCAC
RioAGCTTC
SanaaCGGTTCGAC
TashkentACCACCTTC
TunisAGGAGGAAC
VictoriaAGGAAGGTC
WashingtonACCGCGGTC
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: 40709.1 40710.1 40711.1 40712.1 40713.1 40714.1 40715.1 40716.1 40717.1 40718.1 40719.1 40720.1 40721.1 40722.1 40723.1 40724.1 40725.1 40726.1 40727.1 40728.1 40729.1 40730.1 40731.1 40732.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40709.1 BROAD:SEQUENCING_SAMPLE:40710.1 BROAD:SEQUENCING_SAMPLE:40711.1 BROAD:SEQUENCING_SAMPLE:40712.1 BROAD:SEQUENCING_SAMPLE:40713.1 BROAD:SEQUENCING_SAMPLE:40714.1 BROAD:SEQUENCING_SAMPLE:40715.1 BROAD:SEQUENCING_SAMPLE:40716.1 BROAD:SEQUENCING_SAMPLE:40717.1 BROAD:SEQUENCING_SAMPLE:40718.1 BROAD:SEQUENCING_SAMPLE:40719.1 BROAD:SEQUENCING_SAMPLE:40720.1 BROAD:SEQUENCING_SAMPLE:40721.1 BROAD:SEQUENCING_SAMPLE:40722.1 BROAD:SEQUENCING_SAMPLE:40723.1 BROAD:SEQUENCING_SAMPLE:40724.1 BROAD:SEQUENCING_SAMPLE:40725.1 BROAD:SEQUENCING_SAMPLE:40726.1 BROAD:SEQUENCING_SAMPLE:40727.1 BROAD:SEQUENCING_SAMPLE:40728.1 BROAD:SEQUENCING_SAMPLE:40729.1 BROAD:SEQUENCING_SAMPLE:40730.1 BROAD:SEQUENCING_SAMPLE:40731.1 BROAD:SEQUENCING_SAMPLE:40732.1
BI project name: G2399
BI work request ID: 20246
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-11-23 15:53:31.0454BaseCaller2.0.01.12
Runs: 24 runs, 10,041 spots, 5.1M bases, 12.3Mb
Run# of Spots# of BasesSizePublished
SRR066869396203,454512,014b2010-10-01
SRR066880501253,541630,298b2010-10-01
SRR066881521264,606656,675b2010-10-01
SRR066897775402,075970,106b2010-10-01
SRR066952350179,029456,202b2010-10-01
SRR066969335170,594434,983b2010-10-01
SRR066982319161,400417,425b2010-10-01
SRR067018485245,060610,464b2010-10-01
SRR067063283142,884375,277b2010-10-01
SRR067065630324,331793,527b2010-10-01
SRR067080365186,863474,797b2010-10-01
SRR067092320160,523415,529b2010-10-01
SRR0670972512,38570,345b2010-10-01
SRR067136269135,038356,339b2010-10-01
SRR067143527269,561666,156b2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000041 : Washington_ACCGCGGTC2512,385
2SRS000042 : Bangui_AGTTGGC545276,299
3SRS000043 : Brussels_AGACAC396203,454
4SRS000044 : Zagreb_AGACCTC521264,606
5SRS000045 : Tunis_AGGAGGAAC469238,273
6SRS000046 : Victoria_AGGAAGGTC411214,721
7SRS000052 : Canberra_ACTTGC630324,331
8SRS000053 : Apia_TTCAGGTTC253128,195
9SRS000054 : Freetown_TTCGCCGTC335170,594
10SRS000055 : Madrid_TTCGTTATC527269,561
11SRS000056 : Kampala_TTCGGTGTC501253,541
12SRS000057 : Bogota_CGGTATC350179,029
13SRS000058 : Sanaa_CGGTTCGAC283142,884
14SRS000059 : Rio_AGCTTC320160,523
15SRS000060 : Kigali_AGTCCGTC319161,400
16SRS000595 : Beijing_AGGCGGC485245,060
17SRS000596 : Minsk_ACTCAC493255,014
18SRS003522 : Ankara_ACACCGGTC365186,863
19SRS003523 : Brazzaville_ACAAGGC517256,163
20SRS003524 : Nassau_ACGCGC269135,038
21SRS003525 : Caracas_ACGTGGAAC208103,164
22SRS003526 : Khartoum_ACCTTGGTC573293,794
23SRS003527 : Tashkent_ACCACCTTC775402,075
24SRS003528 : Paramaribo_ACCAACCAC471241,005
25 : defaultn/an/a

ID:
33275

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