title: Patient 206 4684

description:
4684
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 201 4679

status: Public on Oct 26 2018

type: genomic

city: Cantanhede

first: Helena

last: Vazao

address: Biocant Park Nucleo4, 4A

department: HeartGenetics

country: Portugal

institute: HeartGenetics

description:
4679
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

hyb_protocol: Not applicable

scan_protocol: The status of 171 mutations (by the reading of 61 positions) in 6 genes (OncoAlvo® Panel) was assessed using a high-throughput DNA Microchip platform, the iPLEX® system (Agena Bioscience, Inc). This array platform allows an optimal genetic analysis by combining the benefits of accurate primer extension chemistry with MALDI-TOF mass spectrometry. The different masses of each generated PCR product are then converted into mutational status information.

data_processing: The processed data (attached as 14 .txt files) were generated by software computing analysis. The processing was made by normalizing the peak intensity (converted into fraction of mutant alleles) of each genetic variant of each sample by the peak intensity of the correspondent variant of the average of 96 baseline samples. As the baseline samples serve as the minimum threshold, the computer software does not give a processed data file for them; thus, there are no processed data .txt files for these 96 samples. The processed data files only show the positive results.

molecule: genomic DNA

organism: Homo sapiens

source_name: metastatic colorectal carcinoma

label_protocol: Not applicable

growth_protocol: FFPE human colon adenocarcinoma.

extract_protocol: A commercial kit was used to perform DNA extraction and purification from FFPE colon adenocarcinoma. DNA concentration and quality were evaluated with MultiskanGo spectrophotometer (Thermo Scientific).

treatment_protocol: No treatment applied.

tag: tissue

value: FFPE colon adenocarcinoma


title: Patient 200 4678

description:
4678
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 199 4642

description:
4642
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 202 4680

description:
4680
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 197 4640

description:
4640
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 192 4635

description:
4635
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 191 4634

description:
4634
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 195 4638

description:
4638
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 193 4636

description:
4636
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 194 4637

description:
4637
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 189 4632

description:
4632
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 187 4630

description:
4630
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 196 4639

description:
4639
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 188 4631

description:
4631
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 186 4629

description:
4629
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 185 4628

description:
4628
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 184 4627

description:
4627
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 182 4625

description:
4625
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 183 4626

description:
4626
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 181 4624

description:
4624
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 198 4641

description:
4641
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 180 4623

description:
4623
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: FourSU_293T_shMYC_6hFP_15min_rep3

type: SRA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

description:
nuclear RNA
4SU-seq 15min after Flavopiridol treatment

library_source: transcriptomic

data_processing:
Library strategy: 4sU-seq
4sU-seq reads were aligned to the human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm) for each strand. Genes used for calculating elongation rates were required to have an observed transcription start site with 4sU RNA signals, a minimum gene length of 50 kb and must be at least 2kb away from the transcription start site of another gene. Genes were further filtered for activity/coverage by filtering on the reads-per-million count within each gene body (+400 to TES) in our untreated, wildtype data. Thus, the read coverage must be present at levels above background (RPM > 1). Elongation rates were calculated in two ways. 1. Advancing waves were identified using a three state Hidden Markov Model (HMM) that was previously developed and implemented on GRO-seq data from a human cell line (Danko et al., 2013). 2. Peaks were called with SICER version 1.1 (Zang et al., 2009) with the following options --windowSize 150 --fragSize 150 --gapSize 3 with strand separated reads over input. These strand-specific peaks were filtered for an FDR < 0.01. Peaks were merged together if there was a gap less than 2kb. Peaks were then overlapped with TSS’s of genes on the same strand that were greater than 50kb. The distance traveled was calculated from the TSS to the 3’ end of the merged peak and the elongation rate in kb/min was calculated using the time after release.
Genome_build: hg19
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

molecule: total RNA

growth_protocol: HEK293T (ATCC), HCT116 (ATCC), Flag-AFF1 and Flag-AFF4 stable cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, catalog No. F6178, Sigma). NCI-H2171 [H2171] (ATCC CRL-5929) and SW1271 (ATCC CRL-2177) small cell lung cancer cells were maintained in RPMI-1640 and DMEM/F12 medium supplemented with 20% FBS. The Jurkat J-Lat full-length cells (6.3) (Cat # 9846) were provided by the NIH AIDS Reagent Program and cultured in RPMI-1640 medium with 10% FBS. Drosophila S2 cells were maintained in Schneider's medium. The wild-type Pol II, slow Pol II (R749H) and fast Pol II (E1126G) mutant HEK293T cell lines (Fong et al., 2014) were provided by Dr. David Bentley (University of Colorado School of Medicine) and cultured in DMEM with 10% FBS.  After induction with doxycycline (2.0 μg/mL) for 16 hr, speed-mutant cells were treated with α-amanitin (2.5 μg/mL, Sigma) for 42 hr prior to ChIP-seq analysis.

extract_protocol:
Cell Labeling with 4sU, RNA Extraction and Fragmentation 20-50 million cells were treated with flavopiridol for 1 hour and washed with PBS twice. The cells were labeled in media with 500 μM 4-thiouridine (4sU, Sigma-Aldrich, St. Louis, MO, USA.) and harvested through centrifugation for 3 min at 3,000 rpm. RNA was extracted with 4 mL Trizol (Invitrogen) and 5 μL 20 mg/mL glycogen. The extracted RNA was further fragmented by base hydrolysis in 0.2 M NaOH on ice for 18 min, neutralized by adding 1x volume of 1 M Tris-HCl pH 6.8 and precipitated with isopropanol.
RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

treatment_protocol: Treatment withKL-1 or KL-2 inhibitors was administrated only once

tag: cell type

value: Human embryonic kidney cells

tag: mutation

value: cells lentiviral infected with shRNA targeting MYC


title: FourSU_293T_GFP_6hFP_15min_rep2

value: cells lentiviral infected with control vector


title: Patient 178 4621

description:
4621
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: FourSU_293T_shMYC_6hFP_15min_rep2


title: Patient 179 4622

description:
4622
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: FourSU_293T_shMYC_6hFP_15min_rep1


title: PolII_468_2.5uM_6h_293T_rep1

description: ChIP-seq PolII

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the Drosophila genome (UCSC dm3) or human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm). Peaks were called using MACS (model based analysis of ChIP-Seq) (Zhang et al., 2008) version 1.4.2 using default parameters. Ensembl version 75 transcripts were chosen with the highest total coverage from the annotated TSS to 200 nt downstream for protein coding genes that also have a refseq identifier, were at least 2 kb long, and 2 kb away from the nearest gene. For pausing indexes, the promoter region was defined as -200 bp upstream to 400 bp downstream, and the body region was the remainder of the entire gene body. The ratio of the average coverage (r.p.m) of the promoter over the average coverage of the gene body was then taken to be the Pausing Index. ECDF plots were made in R version 3.3.3 using the ecdf function. P-values were calculated with a one-sided Kolmogorov-Smirnov test. Heatmaps tables were made for the indicated windows around the TSS or TES using the average coverage (r.p.m) in 25bp & 50bp bins (50bp bins for 50kb downstream of the TSS). Meta gene tables were made by approximating the coverage across all genes to the same length. All ChIP-seq heatmaps were sorted by the decreasing coverage in indicated windows by the control sample and visualized using JavaTreeView version 1.6.4 (Saldanha, 2004). Average profile plots were made by averaging the coverage for all genes using colMeans in R.
Genome_build: hg19
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

extract_protocol:
ChIP-seq was done according to a previously published protocol (Liang et al., 2015). Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultrasonicator for 6 minutes and immunoprecipitated with the indicated antibody. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: drug treatment


title: FourSU_293T_GFP_6hFP_15min_rep1


title: Patient 177 4620

description:
4620
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 176 4619

description:
4619
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_5uM_6h_293T_rep1

description: ChIP-seq PolII


title: Patient 175 4563

description:
4563
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_20uM_6h_293T_rep1

description: ChIP-seq PolII


title: PolII_468_10uM_6h_293T_rep1

description: ChIP-seq PolII


title: Patient 172 4560

description:
4560
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_20uM_2h_293T_rep1

description: ChIP-seq PolII


title: Patient 171 4559

description:
4559
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_20uM_4h_293T_rep1

description: ChIP-seq PolII


title: Patient 173 4561

description:
4561
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 174 4562

description:
4562
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_20uM_1h_293T_rep1

description: ChIP-seq PolII


title: FourSU_293T_GFP_6hFP_15min_rep3


title: PolII_DMSO_6h_293T_rep1

description: ChIP-seq PolII

value: DMSO


title: ELL2_shMYC_293T_rep1

description: ChiP-seq ELL2


title: Patient 190 4633

description:
4633
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 170 4558

description:
4558
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: ELL2_shGFP_293T_rep1

description: ChiP-seq ELL2


title: Patient 169 4557

description:
4557
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 168 4556

description:
4556
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 167 4553

description:
4553
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 166 4552

description:
4552
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 164 4550

description:
4550
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: AFF1_shMYC_293T_rep1

description: ChiP-seq AFF1


title: Patient 165 4551

description:
4551
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: AFF4_shMYC_293T_rep1

description: ChiP-seq AFF4


title: AFF4_shGFP_293T_rep1

description: ChiP-seq AFF4


title: AFF1_shGFP_293T_rep1

description: ChiP-seq AFF1


title: MYC_shGFP_293T_rep1

description: ChIP-seq MYC


title: Patient 163 4549

description:
4549
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MLL-AF9/NrasG12D_sgZFP64e5.1

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were mapped into reference human genome hg38 or mouse genome mm10 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
RNA-seq files of two sgRNAs for each target gene were treated as replicates
Genome_build: hg38, mm10
Supplementary_files_format_and_content: txt, normalized RPKM. Processed data files are included in a tar archive on the series record.

molecule: polyA RNA

source_name: acute myeloid leukemia

growth_protocol: MOLM13, NOMO1, MV4-11, THP1, RN2 were cultured in RPMI with 1XP/S and 10% FBS, OCIAML3 cells were cultured in a-MEM plus 10% FBS and 1XP/S, MLL-AF9/NrasG12D cells were cultured in IMDM with 20%FBS and 1XP/S.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout

tag: cell line

tag: treatment

value: day9 after sgZFP64e5.1 guide RNA infection


title: MLL-AF9/NrasG12D_sgZFP64e2

value: day9 after sgZFP64e2 guide RNA infection


title: Patient 159 4545

description:
4545
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 161 4547

description:
4547
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MLL-AF9/NrasG12D_sgNeg2

value: day9 after sgNeg2 guide RNA infection


title: Patient 158 4544

description:
4544
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgMLLe5.2_Rep2

value: day9 after sgMLLe5.2 guide RNA infection


title: OCIAML3_sgMLLe5.1_Rep2

value: day9 after sgMLLe5.1 guide RNA infection


title: Patient 160 4546

description:
4546
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgZFP64e5.1_Rep2


title: Patient 155 4541

description:
4541
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgNeg1_Rep2

value: day9 after sgNeg1 guide RNA infection


title: Patient 157 4543

description:
4543
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 156 4542

description:
4542
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgMLLe5.2_Rep1


title: Patient 154 4540

description:
4540
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgMLLe5.1_Rep1


title: MYC1_shMYC_293T_rep1

description: ChIP-seq MYC


title: Patient 151 4364

description:
4364
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 150 4363

description:
4363
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgZFP64e2_Rep1


title: Patient 162 4548

description:
4548
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgZFP64e5.1_Rep1


title: THP1_sgMLLe5.2_Rep2


title: OCIAML3_sgNeg1_Rep1


title: THP1_sgMLLe5.1_Rep2


title: Patient 147 4360

description:
4360
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 148 4361

description:
4361
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 146 4359

description:
4359
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: THP1_sgZFP64e5.1_Rep2

value: day11 after sgZFP64e5.1 guide RNA infection


title: THP1_sgZFP64e2_Rep2

value: day11 after sgZFP64e2 guide RNA infection


title: Patient 145 4358

description:
4358
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: OCIAML3_sgZFP64e2_Rep2


title: THP1_sgMLLe5.1_Rep1


title: Patient 143 4356

description:
4356
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 142 4355

description:
4355
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: THP1_sgMLLe5.2_Rep1


title: THP1_sgZFP64e5.1_Rep1


title: THP1_sgZFP64e2_Rep1


title: Patient 153 4366

description:
4366
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: THP1_sgNeg1_Rep1

value: day11 after sgNeg1 guide RNA infection


title: Patient 141 4354

description:
4354
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 140 4353

description:
4353
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MV411_sgMLLe5.2_Rep2

value: day4 after sgMLLe5.2 guide RNA infection


title: Patient 139 4352

description:
4352
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 149 4362

description:
4362
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 138 4351

description:
4351
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MV411_sgMLLe5.1_Rep2

value: day4 after sgMLLe5.1 guide RNA infection


title: Patient 137 4349

description:
4349
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MV411_sgZFP64e2_Rep2

value: day4 after sgZFP64e2 guide RNA infection


title: Patient 135 4347

description:
4347
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: Patient 136 4348

description:
4348
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 144 4357

description:
4357
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MV411_sgNeg1_Rep2

value: day4 after sgNeg1 guide RNA infection


title: Patient 134 4346

description:
4346
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MV411_sgMLLe5.2_Rep1


title: Patient 133 4345

description:
4345
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MV411_sgZFP64e5.1_Rep1

value: day4 after sgZFP64e5.1 guide RNA infection


title: MV411_sgZFP64e2_Rep1


title: MV411_sgZFP64e5.1_Rep2


title: MV411_sgMLLe5.1_Rep1


title: Patient 132 4344

description:
4344
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: THP1_sgNeg1_Rep2


title: MV411_sgNeg1_Rep1


title: Patient 130 4342

description:
4342
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 129 4340

description:
4340
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 131 4343

description:
4343
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgZFP64e5.1_Rep3

value: day6 after sgZFP64e5.1 guide RNA infection


title: NOMO1_sgZFP64e2_Rep3

value: day6 after sgZFP64e2 guide RNA infection


title: Patient 128 4339

description:
4339
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgNeg1_Rep3


title: Patient 127 4338

description:
4338
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgMLLe5.2_Rep2


title: Patient 126 4337

description:
4337
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 125 4336

description:
4336
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgMLLe5.1_Rep2


title: NOMO1_sgNeg1_Rep2


title: Patient 123 4332

description:
4332
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 122 4331

description:
4331
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgMLLe5.1_Rep1


title: Patient 152 4365

description:
4365
Raw data file: G1129619.xml
Processed data file: G1129619_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 124 4335

description:
4335
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgZFP64e5.1_Rep1


title: Patient 121 4330

description:
4330
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 119 4328

description:
4328
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_sgNeg1_Rep1


title: MOLM13_sgZFP64e5.1_Rep4


title: Patient 115 4324

description:
4324
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgRUNX1e6.1_Rep5

value: day5 after sgRUNX1e6.1 guide RNA infection


title: MOLM13_sgZFP64e2_Rep4


title: Patient 117 4326

description:
4326
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgRUNX1e4.2_Rep5

value: day5 after sgRUNX1e4.2 guide RNA infection


title: Patient 116 4325

description:
4325
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 118 4327

description:
4327
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 114 4323

description:
4323
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 113 4322

description:
4322
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgZFP64e2_Rep3


title: Patient 112 4321

description:
4321
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgZFP64e5.1_Rep3


title: MOLM13_sgNeg1_Rep3


title: Patient 111 4320

description:
4320
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 110 4319

description:
4319
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgMLLe5.2_Rep2


title: NOMO1_sgMLLe5.2_Rep1


title: Patient 109 4318

description:
4318
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgMLLe5.1_Rep2


title: Patient 108 4313

description:
4313
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 120 4329

description:
4329
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgNeg1_Rep2


title: NOMO1_sgZFP64e2_Rep1


title: MOLM13_sgMLLe5.2_Rep1


title: Patient 107 4312

description:
4312
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgMLLe5.1_Rep1


title: Patient 106 4311

description:
4311
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgNeg1_Rep4


title: Patient 105 4310

description:
4310
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 103 4308

description:
4308
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 104 4309

description:
4309
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_sgZFP64e2_Rep1


title: MOLM13_sgNeg1_Rep1


title: Input_Mll-AF9_ZFP64_Rep2

data_processing:
Sequence reads were mapped into reference human genome hg19 or mouse genome mm10 by using Bowtie2.
Peakcalling was done by using MACS2 FDR cut off 5% with narrow peak option for ZFP64.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: bigwig contains normalized tag count calculated by MACS2.0.

growth_protocol: MOLM-13 and NOMO-1 cells were cultured in RPM1 with 10% FBS and penicillin/streptomycin,Mll-AF9 cells were cultrured in IMDM supplemented 10% FBS, 1XP/S, 10ng/ml mSCF, mGM-CSF, mIL3, mIL6 each.

extract_protocol:
Cell lysates were clarified from sonicated nulcei and ZFP64-DNA or histone-DNA complexs were isolated with ZFP64 or histone antibody.
Libraries were prepared using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end-repaired, 3’-adenylated, and then ligated with indexed adaptor. These DNA was size selected (200-400 bp) via agarose gel electrophoresis, and PCR amplified. Final products were purified using AMPure XP beads.

treatment_protocol: For FLAG ChIP-seq, MOLM-13 and NOMO-1 cells were infected with ZFP64 cDNA with fusion to triple FLAG

value: Mll-AF9 knock in

tag: chip antibody


title: Patient 101 4306

description:
4306
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 102 4307

description:
4307
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Input_Mll-AF9_ZFP64_Rep1


title: NOMO1_FLAGXZFP64_Rep2

value: NOMO-1 expressing FLAG_ZFP64

value: Stable cell line was generated by infecting NOMO-1 with FLAG-ZFP64 lentivirus

value: FLAG(Sigma-Aldrich,F1804, )


title: Patient 100 4305

description:
4305
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 99 4304

description:
4304
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_FLAGXZFP64_Rep1


title: Patient 97 4302

description:
4302
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Input_NOMO1_FLAGXZFP64_Rep2


title: Input_NOMO1_FLAGXZFP64_Rep1


title: Patient 96 4301

description:
4301
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 95 4300

description:
4300
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: NOMO1_ZFP64_Rep2

value: ZFP64(Proteintech Group,17187-1-AP)


title: NOMO1_ZFP64_Rep1


title: Patient 94 4299

description:
4299
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 92 4297

description:
4297
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Input_NOMO1_ZFP64_Rep1


title: Input_NOMO1_ZFP64_Rep2


title: MOLM13_FLAGXZFP64_Rep2

value: MOLM-13 expressing FLAG_ZFP64

value: Stable cell line was generated by infecting MOLM-13 with FLAG-ZFP64 lentivirus


title: MOLM13_sgZFP64e5.1_Rep1


title: Patient 91 4296

description:
4296
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 90 4295

description:
4295
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 89 4294

description:
4294
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Input_MOLM13_FLAGXZFP64_Rep1


title: MOLM13_ZFP64_Rep2


title: Patient 88 4293

description:
4293
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MOLM13_FLAGXZFP64_Rep1


title: Patient 87 4292

description:
4292
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 98 4303

description:
4303
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Input_MOLM13_FLAGXZFP64_Rep2


title: MOLM13_ZFP64_Rep1


title: Input_MOLM13_ZFP64_Rep1


title: Patient 85 4290

description:
4290
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Input_MOLM13_ZFP64_Rep2


title: Patient 84 4289

description:
4289
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 93 4298

description:
4298
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: 293T_INPUT

description: INPUT ChIP-seq

data_processing:
ChIP-seq was done according to a previously published protocol (Liang et al., 2015). Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultrasonicator for 6 minutes and immunoprecipitated with the indicated antibody. Libraries were prepared with the HTP Library Preparation Kit for Illumina (KAPA Biosystems) and sequenced on a NextSeq 500. ChIP-seq reads were aligned to the Drosophila genome (UCSC dm3) or human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm). Peaks were called using MACS (model based analysis of ChIP-Seq) (Zhang et al., 2008) version 1.4.2 using default parameters. Ensembl version 75 transcripts were chosen with the highest total coverage from the annotated TSS to 200 nt downstream for protein coding genes that also have a refseq identifier, were at least 2 kb long, and 2 kb away from the nearest gene. For pausing indexes, the promoter region was defined as -200 bp upstream to 400 bp downstream, and the body region was the remainder of the entire gene body. The ratio of the average coverage (r.p.m) of the promoter over the average coverage of the gene body was then taken to be the Pausing Index. ECDF plots were made in R version 3.3.3 using the ecdf function. P-values were calculated with a one-sided Kolmogorov-Smirnov test. Heatmaps tables were made for the indicated windows around the TSS or TES using the average coverage (r.p.m) in 25bp & 50bp bins (50bp bins for 50kb downstream of the TSS). Meta gene tables were made by approximating the coverage across all genes to the same length. All ChIP-seq heatmaps were sorted by the decreasing coverage in indicated windows by the control sample and visualized using JavaTreeView version 1.6.4 (Saldanha, 2004). Average profile plots were made by averaging the coverage for all genes using colMeans in R.
PRO-seq was performed according to the previously published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 µM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp. After sequencing, adaptors were removed with cutadapt version 1.14 (Martin, 2011). Reads were trimmed from the 3prime end to 36bp with removing low quality bases using Trimmomatic version 0.33 (Bolger et al., 2014) requiring a minimal read length of 16nt. Reads were then mapped to the human genome (UCSC hg19) using Bowtie version 1.1.2 (Langmead et al., 2009). Only uniquely mapped reads with up to 2 mismatches in the entire read were used for further analysis. Read where then converted to single nucleotide 3prime BigWig strand specific tracks by taking 5prime positions of the read (using bedtools genomecov version 2.17 (Quinlan and Hall, 2010) with options -strand -bg -5. Strands were then swapped to give the correct orientation with the 5prime end now becoming the 3prime end of the read (Mahat et al., 2016a). PRO-seq genome browser track examples show coverage of the entire length of the read for easier visualization. For the Pol II-selected genes described above, we found the site of maximum coverage, in the region from the annotated TSS to 500bp downstream, to which we assign the pausing site. Heatmap tables were made as described above but instead centering at this calculated pausing site.
4sU-seq reads were aligned to the human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm) for each strand. Genes used for calculating elongation rates were required to have an observed transcription start site with 4sU RNA signals, a minimum gene length of 50 kb and must be at least 2kb away from the transcription start site of another gene. Genes were further filtered for activity/coverage by filtering on the reads-per-million count within each gene body (+400 to TES) in our untreated, wildtype data. Thus, the read coverage must be present at levels above background (RPM > 1). Elongation rates were calculated in two ways. 1. Advancing waves were identified using a three state Hidden Markov Model (HMM) that was previously developed and implemented on GRO-seq data from a human cell line (Danko et al., 2013). 2. Peaks were called with SICER version 1.1 (Zang et al., 2009) with the following options --windowSize 150 --fragSize 150 --gapSize 3 with strand separated reads over input. These strand-specific peaks were filtered for an FDR < 0.01. Peaks were merged together if there was a gap less than 2kb. Peaks were then overlapped with TSS’s of genes on the same strand that were greater than 50kb. The distance traveled was calculated from the TSS to the 3’ end of the merged peak and the elongation rate in kb/min was calculated using the time after release.
Total RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33 (Bolger et al., 2014) and then aligned to the human genome (UCSC hg19, using Tophat version 2.1.0) with the following options -no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 10 --max-multihits 20 then post filtering for uniquely mapped reads using the NH flag. Protein coding genes from Ensembl version 75 that also had a refseq identifier were only considered for analysis. Raw read counts were normalized to r.p.m. per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Exonic reads were assigned to specific genes from Ensembl release 75 using Bioconductor package GenomicRanges countOverlaps. We used the R Bioconductor package edgeR, version 3.12.0 to fit the data to a negative binomial generalized log–linear model and estimate a dispersion parameter. We used an adjusted P value threshold of 0.001 and a log2 r.p.m cut off of 3 to identify genes significantly differentially expressed in one experimental condition relative to another. GO term analysis was done using Metascape
Genome_build: hg19, dm3
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

extract_protocol:
Total RNA was extracted using Trizol and QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
PRO-seq was performed according to the previously published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 μM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp.
4sU-seq Cell Labeling with 4sU, RNA Extraction and Fragmentation 20-50 million cells were treated with flavopiridol for 1 hour and washed with PBS twice. The cells were labeled in media with 500 μM 4-thiouridine (4sU, Sigma-Aldrich, St. Louis, MO, USA.) and harvested through centrifugation for 3 min at 3,000 rpm. RNA was extracted with 4 mL Trizol (Invitrogen) and 5 μL 20 mg/mL glycogen. The extracted RNA was further fragmented by base hydrolysis in 0.2 M NaOH on ice for 18 min, neutralized by adding 1x volume of 1 M Tris-HCl pH 6.8 and precipitated with isopropanol.

value: Human embryonic kidney cells


title: Patient 82 4287

description:
4287
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: SW1271_INPUT

description: INPUT ChIP-seq

value: small cell lung cancer

value: No MYC amplifcation


title: Patient 81 4286

description:
4286
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: Ser2P_DMSO_293T_rep1

description: ChIP-seq Ser2P

value: DMSO

tag: antibody

value: Anti-RNA polymerase II subunit B1 (phospho CTD Ser-2) Antibody, clone 3E12


title: Patient 79 4284

description:
4284
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 80 4285

description:
4285
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Ser2P_522_293T_rep1

description: ChIP-seq Ser2P

value: Anti-RNA polymerase II subunit B1 (phospho CTD Ser-2) Antibody, clone 3E11


title: Patient 78 4283

description:
4283
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Ser2P_468_293T_rep1

description: ChIP-seq Ser2P

value: Anti-RNA polymerase II subunit B1 (phospho CTD Ser-2) Antibody, clone 3E10


title: RNA_shGFP_293T_rep2

description: Total RNA-seq

value: cells lentiviral infected with control vector


title: Patient 77 4282

description:
4282
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 86 4291

description:
4291
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 76 4281

description:
4281
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RNA_shELL2_274361_293T_rep2

description: Total RNA-seq

value: cells lentiviral infected with shRNA targeting ELL2


title: Patient 74 4279

description:
4279
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 75 4280

description:
4280
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 73 4278

description:
4278
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 72 4277

description:
4277
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 83 4288

description:
4288
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 71 4276

description:
4276
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RNA_shAFF14_21975_426769_293T_rep2

description: Total RNA-seq

value: cells lentiviral infected with shRNA targeting AFF4 and AFF1


title: Patient 70 4275

description:
4275
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RNA_DMSO_24h_293T_rep1

description: Total RNA-seq


title: RNA_522_24h_293T_rep3

description: Total RNA-seq


title: RNA_DMSO_24h_293T_rep2

description: Total RNA-seq


title: Patient 67 4272

description:
4272
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RNA_DMSO_24h_293T_rep3

description: Total RNA-seq


title: RNA_shGFP_293T_rep1

description: Total RNA-seq


title: Patient 66 4271

description:
4271
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 65 4270

description:
4270
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 64 4269

description:
4269
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RNA_shELL2_274361_293T_rep1

description: Total RNA-seq


title: RNA_shAFF14_21975_426769_293T_rep1

description: Total RNA-seq


title: PRO_DMSO_293T_rep1

description: PRO-seq

data_processing:
Library strategy: PRO-seq
ChIP-seq was done according to a previously published protocol (Liang et al., 2015). Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultrasonicator for 6 minutes and immunoprecipitated with the indicated antibody. Libraries were prepared with the HTP Library Preparation Kit for Illumina (KAPA Biosystems) and sequenced on a NextSeq 500. ChIP-seq reads were aligned to the Drosophila genome (UCSC dm3) or human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm). Peaks were called using MACS (model based analysis of ChIP-Seq) (Zhang et al., 2008) version 1.4.2 using default parameters. Ensembl version 75 transcripts were chosen with the highest total coverage from the annotated TSS to 200 nt downstream for protein coding genes that also have a refseq identifier, were at least 2 kb long, and 2 kb away from the nearest gene. For pausing indexes, the promoter region was defined as -200 bp upstream to 400 bp downstream, and the body region was the remainder of the entire gene body. The ratio of the average coverage (r.p.m) of the promoter over the average coverage of the gene body was then taken to be the Pausing Index. ECDF plots were made in R version 3.3.3 using the ecdf function. P-values were calculated with a one-sided Kolmogorov-Smirnov test. Heatmaps tables were made for the indicated windows around the TSS or TES using the average coverage (r.p.m) in 25bp & 50bp bins (50bp bins for 50kb downstream of the TSS). Meta gene tables were made by approximating the coverage across all genes to the same length. All ChIP-seq heatmaps were sorted by the decreasing coverage in indicated windows by the control sample and visualized using JavaTreeView version 1.6.4 (Saldanha, 2004). Average profile plots were made by averaging the coverage for all genes using colMeans in R.
PRO-seq was performed according to the previously published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 µM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp. After sequencing, adaptors were removed with cutadapt version 1.14 (Martin, 2011). Reads were trimmed from the 3prime end to 36bp with removing low quality bases using Trimmomatic version 0.33 (Bolger et al., 2014) requiring a minimal read length of 16nt. Reads were then mapped to the human genome (UCSC hg19) using Bowtie version 1.1.2 (Langmead et al., 2009). Only uniquely mapped reads with up to 2 mismatches in the entire read were used for further analysis. Read where then converted to single nucleotide 3prime BigWig strand specific tracks by taking 5prime positions of the read (using bedtools genomecov version 2.17 (Quinlan and Hall, 2010) with options -strand -bg -5. Strands were then swapped to give the correct orientation with the 5prime end now becoming the 3prime end of the read (Mahat et al., 2016a). PRO-seq genome browser track examples show coverage of the entire length of the read for easier visualization. For the Pol II-selected genes described above, we found the site of maximum coverage, in the region from the annotated TSS to 500bp downstream, to which we assign the pausing site. Heatmap tables were made as described above but instead centering at this calculated pausing site.
4sU-seq reads were aligned to the human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm) for each strand. Genes used for calculating elongation rates were required to have an observed transcription start site with 4sU RNA signals, a minimum gene length of 50 kb and must be at least 2kb away from the transcription start site of another gene. Genes were further filtered for activity/coverage by filtering on the reads-per-million count within each gene body (+400 to TES) in our untreated, wildtype data. Thus, the read coverage must be present at levels above background (RPM > 1). Elongation rates were calculated in two ways. 1. Advancing waves were identified using a three state Hidden Markov Model (HMM) that was previously developed and implemented on GRO-seq data from a human cell line (Danko et al., 2013). 2. Peaks were called with SICER version 1.1 (Zang et al., 2009) with the following options --windowSize 150 --fragSize 150 --gapSize 3 with strand separated reads over input. These strand-specific peaks were filtered for an FDR < 0.01. Peaks were merged together if there was a gap less than 2kb. Peaks were then overlapped with TSS’s of genes on the same strand that were greater than 50kb. The distance traveled was calculated from the TSS to the 3’ end of the merged peak and the elongation rate in kb/min was calculated using the time after release.
Total RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33 (Bolger et al., 2014) and then aligned to the human genome (UCSC hg19, using Tophat version 2.1.0) with the following options -no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 10 --max-multihits 20 then post filtering for uniquely mapped reads using the NH flag. Protein coding genes from Ensembl version 75 that also had a refseq identifier were only considered for analysis. Raw read counts were normalized to r.p.m. per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Exonic reads were assigned to specific genes from Ensembl release 75 using Bioconductor package GenomicRanges countOverlaps. We used the R Bioconductor package edgeR, version 3.12.0 to fit the data to a negative binomial generalized log–linear model and estimate a dispersion parameter. We used an adjusted P value threshold of 0.001 and a log2 r.p.m cut off of 3 to identify genes significantly differentially expressed in one experimental condition relative to another. GO term analysis was done using Metascape
Genome_build: hg19, dm3
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

molecule: nuclear RNA


title: RNA_522_24h_293T_rep2

description: Total RNA-seq


title: RNA_468_24h_293T_rep1

description: Total RNA-seq


title: Patient 69 4274

description:
4274
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PRO_522_293T_rep1

description: PRO-seq


title: PRO_468_293T_rep1

description: PRO-seq


title: RNA_468_24h_293T_rep3

description: Total RNA-seq


title: Patient 61 4266

description:
4266
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 63 4268

description:
4268
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_shELL2_293T_974_NO81

description: ChIP-seq PolII

value: Rpb1 NTD (D8L4Y) Rabbit mAb


title: Patient 60 4265

description:
4265
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 68 4273

description:
4273
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_shELL2_293T_974_274361

description: ChIP-seq PolII


title: PolII_shAFF4_shAFF1_293T_855_rep2

description: ChIP-seq PolII


title: RNA_522_24h_293T_rep1

description: Total RNA-seq


title: PolII_shAFF4_shAFF1_293T_855_rep1

description: ChIP-seq PolII


title: RNA_468_24h_293T_rep2

description: Total RNA-seq


title: Patient 55 4260

description:
4260
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 57 4262

description:
4262
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_GFP_293T_855

description: ChIP-seq PolII


title: Patient 56 4261

description:
4261
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_WT_293T_895

description: ChIP-seq PolII

value: WT Pol II


title: PolII_DMSO_SLOW_293T_894

description: ChIP-seq PolII

value: Slow Pol II mutant with R749H


title: Patient 62 4267

description:
4267
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 53 4258

description:
4258
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 52 4257

description:
4257
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_S2_37_rep1

description: ChIP-seq PolII

value: Schneider 2 cells

value: homemade Pol II NTD


title: PolII_DMSO_S2_25_rep2

description: ChIP-seq PolII


title: Patient 50 4255

description:
4255
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_GFP_293T_974_rep2

description: ChIP-seq PolII


title: PolII_DMSO_S2_37_rep2

description: ChIP-seq PolII


title: Patient 49 4254

description:
4254
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_JLAT63_rep1

description: ChIP-seq PolII

value: Jurkat cells from childhood T acute lymphoblastic leukemia

value: Intergration of modified HIV genome


title: Patient 48 4253

description:
4253
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_S2_25_rep1

description: ChIP-seq PolII


title: Patient 54 4259

description:
4259
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 47 4252

description:
4252
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_HCT116_42_rep1

description: ChIP-seq PolII

value: colorectal carcinoma


title: Patient 51 4256

description:
4256
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 45 4250

description:
4250
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 58 4263

description:
4263
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_293T_rep2

description: ChIP-seq PolII

value: Human embryonic kidney cells


title: Patient 44 4249

description:
4249
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: PolII_DMSO_HCT116_37_rep1

description: ChIP-seq PolII

value: DMSO


title: Patient 43 4248

description:
4248
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_293T_rep1

description: ChIP-seq PolII


title: Patient 42 4247

description:
4247
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 41 4246

description:
4246
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 40 4245

description:
4245
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_CST10_shGFP_293T_1020

description: ChIP-seq PolII


title: PolII_CST10_shELL2_NO81_293T_1020

description: ChIP-seq PolII


title: Patient 39 4244

description:
4244
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_522_WT_293T_895

description: ChIP-seq PolII


title: Patient 38 4243

description:
4243
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_CST10_shELL2_274361_293T_1020

description: ChIP-seq PolII


title: Patient 37 4242

description:
4242
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_522_SLOW_293T_894

description: ChIP-seq PolII


title: Patient 36 4241

description:
4241
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 35 4240

description:
4240
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 46 4251

description:
4251
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_DMSO_FAST_293T_895

description: ChIP-seq PolII

value: Fast Pol II mutant with E1126G


title: PolII_522_JLAT63_rep1

description: ChIP-seq PolII


title: Patient 34 4239

description:
4239
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 33 4238

description:
4238
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_522_293T_rep2

description: ChIP-seq PolII


title: PolII_522_HCT116_37_rep1

description: ChIP-seq PolII


title: PolII_522_FAST_293T_895

description: ChIP-seq PolII


title: PolII_522_HCT116_42_rep1

description: ChIP-seq PolII


title: Patient 32 4237

description:
4237
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_522_293T_rep1

description: ChIP-seq PolII


title: Patient 31 4236

description:
4236
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_WT_293T_895

description: ChIP-seq PolII


title: Patient 30 4235

description:
4235
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: GS526_Spleen3.4_KO_Tregs_ATAC

city: Munich

first: Thomas

last: Korn

state: Bavaria

address: Ismaninger Str. 22

department: Neurology

country: Germany

institute: Technical University of Munich

data_processing:
Raw reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -S”
ATAC peaks over Input background were identified using Homer (Heinz et al., 2010) findPeaks.pl with option “-style factor”
Peaks from all samples replicates were merged using mergePeaks resulting in a unified Peak set
The peak list was filtered for promoter-associated peaks (distance to TSS < 1000bp) with bedtools
annotatePeaks was used to obtain coverage counts within 500 pb across peak centers
Differential ATAC peaks were determined with the DESeq2 result function and filtered for padj < 0.05. Genomic feature annotation of ATAC-seq peaks was done using annotatePeaks.
Transcription factor motif prediction was done with Homer findMotifsGenome.pl
bigWig files were generated from homer tag directories using makeBigWig.pl
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are in bigWig format and contain differential ATAC peaks for each sample

organism: Mus musculus

source_name: Treg cells

growth_protocol: Animals were kept in a specific pathogen-free facility at the Technical University of Munich or at the Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. All experimental protocols were approved by the standing committee for experimentation with laboratory animals of the Bavarian state authorities or the animal ethics committee of the Walter and Eliza Hall Institute and carried out in accordance with the corresponding guidelines.

extract_protocol:
The cells were isolated from the CNS at the peak of the disease. The cells were digested with collagenase and DNAse to obtain single cell suspensions
Nextera DNA Sample Prep Kit FC-121-1030

treatment_protocol: The mice were immunized with MOG(35-55) and CFA at day 0. The mice received pertussis toxin at day0 and day2.

value: Spleen

tag: genotype


title: GS530_CNS1.4_KO_Treg_ATAC

value: CNS


title: GS529_CNS1.3_WT_Treg_ATAC

value: WT


title: PolII_468_HCT116_42_rep1

description: ChIP-seq PolII


title: Patient 29 4234

description:
4234
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: GS522_Spleen2.4_KO_Tregs_ATAC


title: PolII_468_JLAT63_rep1

description: ChIP-seq PolII


title: PolII_468_HCT116_37_rep1

description: ChIP-seq PolII


title: PolII_468_SLOW_293T_894

description: ChIP-seq PolII


title: GS521_Spleen2.3_WT_Tregs_ATAC


title: Patient 27 4232

description:
4232
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 26 4231

description:
4231
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 28 4233

description:
4233
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: GS525_Spleen3.3_WT_Tregs_ATAC


title: PolII_468_293T_rep2

description: ChIP-seq PolII


title: GS532_CNS2.2_KO_Tconv_ATAC

source_name: Tconv cells


title: GS519_Spleen1.3_WT_Tregs_ATAC


title: Patient 24 4229

description:
4229
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 25 4230

description:
4230
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_293T_rep1

description: ChIP-seq PolII


title: GS528_CNS1.2_KO_Tconv_ATAC


title: GS527_CNS1.1_WT_Tconv_ATAC


title: GS531_CNS2.1_WT_Tconv_ATAC


title: MYC_SW1271_rep1

description: ChIP-seq MYC

value: small cell lung cancer

value: No MYC amplifcation

value: c-Myc (D3N8F) Rabbit mAb


title: GS524_Spleen3.2_KO_Tconv_ATAC


title: Patient 23 4228

description:
4228
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: MYC_H2171_rep1

description: ChIP-seq MYC

value: MYC amplifcation


title: PolII_468_FAST_293T_895

description: ChIP-seq PolII

value: Rpb1 NTD (D8L4Y) Rabbit mAb


title: GS517_Spleen1.2_KO_Tconv_ATAC


title: Patient 21 4226

description:
4226
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: GS518_Spleen1.4_KO_Tregs_ATAC


title: Patient 22 4227

description:
4227
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_522_S2_37_rep2

description: ChIP-seq PolII

organism: Drosophila melanogaster

value: Schneider 2 cells


title: FourSU_293T_DMSO_6hFP_15min_rep2

description: 4SU-seq 15min after Flavopiridol treatment with DMSO treatment


title: GS516_Spleen1.1_WT_Tconv_ATAC


title: H2171_INPUT

description: INPUT ChIP-seq


title: GS523_Spleen3.1_WT_Tconv_ATAC


title: GS520_Spleen2.1_WT_Tconv_ATAC


title: Patient 20 4225

description:
4225
Raw data file: G1116577.xml
Processed data file: G1116577_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_522_S2_25_rep2

description: ChIP-seq PolII

value: homemade Pol II NTD


title: PolII_522_S2_25_rep1

description: ChIP-seq PolII


title: PolII_522_S2_37_rep1

description: ChIP-seq PolII


title: PolII_468_S2_37_rep2

description: ChIP-seq PolII


title: Patient 19 4224

description:
4224
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 18 4223

description:
4223
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: FourSU_293T_522_6hFP_15min_rep1

description: 4SU-seq 15min after Flavopiridol treatment with KL-1 drug treatment


title: FourSU_293T_522_6hFP_15min_rep2


title: FourSU_293T_DMSO_6hFP_15min_rep1


title: PolII_468_S2_25_rep1

description: ChIP-seq PolII


title: FourSU_293T_468_6hFP_15min_rep2

description: 4SU-seq 15min after Flavopiridol treatment with KL-2 drug treatment


title: Patient 17 4222

description:
4222
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: PolII_468_S2_37_rep1

description: ChIP-seq PolII


title: PolII_468_S2_25_rep2

description: ChIP-seq PolII


title: normal

type: RNA

city: Worcester

first: Guangping

last: Gao

state: Massachusetts

address: Albert Sherman Center (AS6-2011)

department: Gene Therapy Center

institute: University of Massachusetts, Medial School

description: untreated

data_processing:
Data were normalized to the top 100 most highly expressed miRNAs in each sample, and the average ± 2 SD of six internal negative control probes were used to determine background detection threshold. We computed the mean expression values of each miRNA across our cohort to filter for expressed miRNAs,
A threshold cutoff-point of 1.0 was selected based on background detection threshold. Values exceeding this cutoff-point were considered to be indicative of relevant miRNA expression.

label: biotinylated capture probe and color coded reporter probe pairs

source_name: cornea

label_protocol: Labeling was performed according to the manufacturer's instructions.

extract_protocol: A total of 100 ng of RNA was extracted from whole mouse corneas. Four corneas were pooled into one sample

value: cornea

tag: age

value: 6-8 week old

tag: gender

value: female

tag: strain


title: FourSU_293T_468_6hFP_15min_rep1

value: Human embryonic kidney cells


title: Patient 16 4221

description:
4221
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: d15_L2

description: 15 days post-treatment


title: ELL2_SW1271_rep2

description: ChiP-seq ELL2

value: homemade ELL2


title: Patient 15 4220

description:
4220
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: d10_L1

description: 10 days post-treatment


title: d10_L2

description: 10 days post-treatment


title: d5_L1

description: 5 days post-treatment


title: Patient 14 4219

description:
4219
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: d5_L2

description: 5 days post-treatment


title: ELL2_SW1271_rep1

description: ChiP-seq ELL2


title: d15_R1

description: 15 days post-treatment


title: d10_R2

description: 10 days post-treatment


title: d15_R2

description: 15 days post-treatment


title: ELL2_H2171_rep1

description: ChiP-seq ELL2


title: Patient 13 4218

description:
4218
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 12 4196

description:
4196
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: d10_R1

description: 10 days post-treatment