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TSCA-LI amplicon sequencing of called variants in WXS data of DSALL.

Targeted resequencing of samples was done with TruSeq custom amplicon low input kit (TSCA-LI, Illumina). The oligo capture probes were designed to include a prefix of 8 random nucleotides at the 5 end of each probe. The assay is designed such that each targeted locus is annealed with two probes, resulting in amplicons tagged with unique molecular identifiers (UMI) (22) of 16 bases. Raw FASTQ sequencing files were processed as following: (a) The first 8 bases were trimmed from each read and recorded with the corresponding base quality scores (BQ) in the attribute field. (b) Reads were aligned with BWA. (c) First round of PCR duplicate cleaning was performed with picard tools markDuplicates using the parameters BARCODE_TAG=BC TAGGING_POLICY=All REMOVE_DUPLICATES=true (d) Since in the previous step only duplicate reads with identical UMIs were removed, a second pass of filtering was done. Reads with identical mapping were considered unique only if their corresponding UMIs were different in at least 3 positions (i.e., UMI edit distance > 2). (e) Paired-end read pairs overlapping genomic positions were clipped to avoid overestimation of the sequencing coverage using bamUtils clipOverlap.

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Access to genomic data of Down Syndrome acute lymphoblastic leukemia samples.

A submitted request for research addressing leukemia-related questions – for which we have explicit consent – accompanied by a positive IRB vote from the request-submitting institution would be reviewed by a data access committee. Upon positive review, a material transfer agreement would need to be signed by the requesting researcher and the data transfer to third parties could proceed.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00001590268 bam 153.9 MB
EGAF00001590269 bam 43.4 MB
EGAF00001590270 bam 31.2 MB
EGAF00001590271 bam 50.2 MB
EGAF00001590272 bam 52.6 MB
EGAF00001590273 bam 69.0 MB
EGAF00001590274 bam 14.9 MB
EGAF00001590275 bam 32.9 MB
EGAF00001590276 bam 60.0 MB
EGAF00001590277 bam 64.8 MB
EGAF00001590278 bam 85.9 MB
EGAF00001590279 bam 67.0 MB
EGAF00001590280 bam 49.3 MB
EGAF00001590281 bam 104.2 MB
EGAF00001590282 bam 138.7 MB
EGAF00001590283 bam 38.0 MB
EGAF00001590284 bam 44.1 MB
EGAF00001590285 bam 37.3 MB
EGAF00001590286 bam 40.3 MB
EGAF00001590287 bam 31.8 MB
EGAF00001590288 bam 61.9 MB
EGAF00001590289 bam 49.2 MB
EGAF00001590290 bam 43.7 MB
EGAF00001590291 bam 60.2 MB
EGAF00001590292 bam 32.4 MB
EGAF00001590293 bam 59.9 MB
EGAF00001590294 bam 98.4 MB
EGAF00001590295 bam 27.1 MB
EGAF00001590296 bam 50.1 MB
EGAF00001590297 bam 73.1 MB
EGAF00001590298 bam 37.9 MB
EGAF00001590299 bam 37.9 MB
EGAF00001590300 bam 41.6 MB
EGAF00001590301 bam 38.0 MB
EGAF00001590302 bam 47.9 MB
EGAF00001590303 bam 41.4 MB
EGAF00001590304 bam 42.1 MB
EGAF00001590305 bam 8.4 MB
EGAF00001590306 bam 51.0 MB
EGAF00001590307 bam 28.4 MB
EGAF00001590308 bam 88.7 MB
EGAF00001590309 bam 39.7 MB
EGAF00001590310 bam 28.8 MB
EGAF00001590311 bam 77.2 MB
EGAF00001590312 bam 18.1 MB
EGAF00001590313 bam 13.9 MB
EGAF00001590314 bam 85.3 MB
EGAF00001590315 bam 37.5 MB
EGAF00001590316 bam 42.5 MB
EGAF00001590317 bam 71.8 MB
EGAF00001590318 bam 162.7 MB
EGAF00001590319 bam 51.9 MB
EGAF00001590320 bam 42.3 MB
EGAF00001590321 bam 43.6 MB
EGAF00001590322 bam 5.9 MB
EGAF00001590323 bam 38.1 MB
EGAF00001590324 bam 13.1 MB
EGAF00001590325 bam 26.0 MB
EGAF00001590326 bam 13.0 MB
EGAF00001590327 bam 53.2 MB
EGAF00001590328 bam 44.3 MB
EGAF00001590329 bam 53.0 MB
EGAF00001590330 bam 23.8 MB
EGAF00001590331 bam 43.4 MB
EGAF00001590332 bam 33.1 MB
EGAF00001590333 bam 49.3 MB
EGAF00001590334 bam 39.8 MB
EGAF00001590335 bam 74.8 MB
EGAF00001590336 bam 37.3 MB
EGAF00001590337 bam 47.5 MB
EGAF00001590338 bam 6.2 MB
EGAF00001590339 bam 62.1 MB
EGAF00001590340 bam 53.8 MB
EGAF00001590341 bam 48.3 MB
74 Files (3.7 GB)