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Transcriptome of CD4+ T cells and CD8+ T cells in glioblastoma multiforme

Patients included in this study were over 18 years of age and had a histology-confirmed diagnosis of glioblastoma multiforme (GBM). Exclusion criteria were the previous administration of any anti-tumor therapy including radiation therapy. All patients gave written informed consent. The study was approved by the local ethics committee (TUM Medical school) and conducted following the Declaration of Helsinki. During resection of the tumors, tumor tissue and tissue from normal appearing brain within the operative channel was collected. Blood was drawn during the surgical procedure. Single cell suspensions were prepared from the tumor tissue, the normal appearing brain, and the blood. CD4+ T cells and CD8+ T cells were sorted by flow cytometry. Only patients with a complete set of specimens (CD4+ tumor infiltrating lymphocytes (TIL), CD8+ TIL, CD4+ T cells from normal appearing brain, CD8+ T cells from normal appearing brain, blood-derived CD4+ and CD8+ T cells) containing a minimum of 1000 cells in each sorted sample were further analyzed (n=9). Total RNA was isolated from sorted cell populations using the RNAeasy Plus micro kit (Qiagen, 74034). Quality and integrity of total RNA was controlled on a Bioanalyzer 2100 (Agilent Technologies). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (ThermoFisher Scientific, EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated and 3'-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to previous descriptions (Parekh et al., 2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read 1 and barcodes and UMIs in read 2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 59 cycles for the cDNA in read 1 and 16 cycles for the barcodes and UMIs in read 2. Data were processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to the Genecode Annotation Version 35.

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Study ID Study Title Study Type
EGAS50000000156 RNASeq

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
EGAF50000065296 fastq.gz 110.8 MB
EGAF50000065297 fastq.gz 360.3 MB
EGAF50000065298 fastq.gz 144.6 MB
EGAF50000065299 fastq.gz 62.5 MB
EGAF50000065300 fastq.gz 150.0 MB
EGAF50000065301 fastq.gz 319.3 MB
EGAF50000065302 fastq.gz 63.4 MB
EGAF50000065303 fastq.gz 155.6 MB
EGAF50000065304 fastq.gz 293.0 MB
EGAF50000065305 fastq.gz 121.2 MB
EGAF50000065306 fastq.gz 290.1 MB
EGAF50000065307 fastq.gz 117.8 MB
EGAF50000065308 fastq.gz 243.0 MB
EGAF50000065309 fastq.gz 100.2 MB
EGAF50000065310 fastq.gz 214.5 MB
EGAF50000065311 fastq.gz 89.2 MB
EGAF50000065312 fastq.gz 275.3 MB
EGAF50000065313 fastq.gz 129.0 MB
EGAF50000065314 fastq.gz 186.8 MB
EGAF50000065315 fastq.gz 78.9 MB
EGAF50000065316 fastq.gz 72.3 MB
EGAF50000065317 fastq.gz 174.1 MB
EGAF50000065318 fastq.gz 384.9 MB
EGAF50000065319 fastq.gz 156.1 MB
EGAF50000065320 fastq.gz 222.2 MB
EGAF50000065321 fastq.gz 95.5 MB
EGAF50000065322 fastq.gz 303.0 MB
EGAF50000065323 fastq.gz 122.6 MB
EGAF50000065324 fastq.gz 285.7 MB
EGAF50000065325 fastq.gz 115.4 MB
EGAF50000065326 fastq.gz 329.3 MB
EGAF50000065327 fastq.gz 134.4 MB
EGAF50000065328 fastq.gz 307.5 MB
EGAF50000065329 fastq.gz 124.9 MB
EGAF50000065330 fastq.gz 237.9 MB
EGAF50000065331 fastq.gz 98.3 MB
EGAF50000065332 fastq.gz 270.6 MB
EGAF50000065333 fastq.gz 114.2 MB
EGAF50000065334 fastq.gz 395.9 MB
EGAF50000065335 fastq.gz 160.8 MB
EGAF50000065336 fastq.gz 144.2 MB
EGAF50000065337 fastq.gz 355.7 MB
EGAF50000065338 fastq.gz 350.7 MB
EGAF50000065339 fastq.gz 142.2 MB
EGAF50000065340 fastq.gz 359.4 MB
EGAF50000065341 fastq.gz 147.7 MB
EGAF50000065342 fastq.gz 492.6 MB
EGAF50000065343 fastq.gz 197.8 MB
EGAF50000065344 fastq.gz 308.4 MB
EGAF50000065345 fastq.gz 126.3 MB
EGAF50000065346 fastq.gz 156.1 MB
EGAF50000065347 fastq.gz 386.2 MB
EGAF50000065348 fastq.gz 401.4 MB
EGAF50000065349 fastq.gz 161.6 MB
EGAF50000065350 fastq.gz 170.4 MB
EGAF50000065351 fastq.gz 421.1 MB
EGAF50000065352 fastq.gz 222.0 MB
EGAF50000065353 fastq.gz 90.9 MB
EGAF50000065354 fastq.gz 201.8 MB
EGAF50000065355 fastq.gz 82.2 MB
EGAF50000065356 fastq.gz 255.3 MB
EGAF50000065357 fastq.gz 103.3 MB
EGAF50000065358 fastq.gz 330.0 MB
EGAF50000065359 fastq.gz 134.3 MB
EGAF50000065360 fastq.gz 324.5 MB
EGAF50000065361 fastq.gz 131.9 MB
EGAF50000065362 fastq.gz 331.2 MB
EGAF50000065363 fastq.gz 139.0 MB
EGAF50000065364 fastq.gz 352.7 MB
EGAF50000065365 fastq.gz 142.2 MB
EGAF50000065366 fastq.gz 149.1 MB
EGAF50000065367 fastq.gz 370.5 MB
EGAF50000065368 fastq.gz 207.0 MB
EGAF50000065369 fastq.gz 84.6 MB
EGAF50000065370 fastq.gz 156.3 MB
EGAF50000065371 fastq.gz 64.1 MB
EGAF50000065372 fastq.gz 214.3 MB
EGAF50000065373 fastq.gz 89.5 MB
EGAF50000065374 fastq.gz 259.1 MB
EGAF50000065375 fastq.gz 105.9 MB
EGAF50000065376 fastq.gz 120.6 MB
EGAF50000065377 fastq.gz 296.2 MB
EGAF50000065378 fastq.gz 459.7 MB
EGAF50000065379 fastq.gz 186.6 MB
EGAF50000065380 fastq.gz 373.5 MB
EGAF50000065381 fastq.gz 150.6 MB
EGAF50000065382 fastq.gz 371.9 MB
EGAF50000065383 fastq.gz 149.1 MB
EGAF50000065384 fastq.gz 380.3 MB
EGAF50000065385 fastq.gz 154.5 MB
EGAF50000065386 fastq.gz 396.8 MB
EGAF50000065387 fastq.gz 160.5 MB
EGAF50000065388 fastq.gz 349.5 MB
EGAF50000065389 fastq.gz 141.2 MB
EGAF50000065390 fastq.gz 295.2 MB
EGAF50000065391 fastq.gz 121.2 MB
EGAF50000065392 fastq.gz 142.4 MB
EGAF50000065393 fastq.gz 58.9 MB
EGAF50000065394 fastq.gz 359.9 MB
EGAF50000065395 fastq.gz 144.8 MB
EGAF50000065396 fastq.gz 369.1 MB
EGAF50000065397 fastq.gz 148.6 MB
EGAF50000065398 fastq.gz 279.0 MB
EGAF50000065399 fastq.gz 113.7 MB
EGAF50000065400 fastq.gz 404.1 MB
EGAF50000065401 fastq.gz 163.6 MB
EGAF50000065402 fastq.gz 258.1 MB
EGAF50000065403 fastq.gz 105.9 MB
EGAF50000065404 fastq.gz 255.3 MB
EGAF50000065405 fastq.gz 107.0 MB
EGAF50000065406 fastq.gz 315.0 MB
EGAF50000065407 fastq.gz 128.4 MB
EGAF50000065408 fastq.gz 390.5 MB
EGAF50000065409 fastq.gz 157.1 MB
EGAF50000065410 fastq.gz 365.3 MB
EGAF50000065411 fastq.gz 146.8 MB
EGAF50000065412 fastq.gz 172.7 MB
EGAF50000065413 fastq.gz 70.7 MB
EGAF50000065414 fastq.gz 312.6 MB
EGAF50000065415 fastq.gz 126.2 MB
120 Files (25.7 GB)