title: Nuclear HK2 NLS2 overexpression 3 (ChIP-seq)

data_processing:
Chip-seq data has been aligned to the human genome using bowtie2.
Duplicated reads and multiple loci aligned reads have been discarded
Peaks were called using MACS2 peak caller.
Differentiallly binding peaks have been analyzed using edgeR package.
Genome coverage tracks have been created using the bamCoverage tool in the deeptools package.
Genome_build: hg38
Supplementary_files_format_and_content: Narrow peaks were identified from the alignment files using MACS2 v.2.1.1 with a cutoff score FDR 0.01

growth_protocol: NB4 cells were cultured in IMDM supplemented with 20% FCS, 100  units/mL streptomycin, 100 µg/mL penicillin,SCF (20 ng/mL), IL-3 (2 ng/mL), and L-glutamine (2 mM).

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with anti-HK2 (Santa Cruz, sc-374091)  antibody.
Samples were prepared as outlined by Takara Bio USA Inc’s ThruPLEX DNA-seq Kit user guide. Briefly, samples were normalized to 10ng of DNA input and topped up to 10ul with nuclease-free water. Samples were then mixed with 3ul of template preparation master mix and incubated at 22°C for 25 minutes, then 55°C for 20 minutes in a Veriti 96-well thermocycler (Thermo Fisher). Following template preparation, samples were mixed with 2ul of library synthesis master mix and incubated at 22°C for 40 minutes on the same cycler. Samples were prepared for library amplification as outlined in the user guide and indexed individually. From here, PCR cycles were optimized by adding 0.75ul of 10x SYBR green I nucleic acid gel stain (Thermo Fisher) to each sample. Once mixed, 10ul from each sample was removed and run on a CFX96 Touch Real-Time PCR cycler (Bio-Rad). Samples were normalized to 1/3 of their amplification curve and amplified on a Veriti 96-well thermocycler. Samples were topped up to 50ul with nuclease-free water prior to bead cleanup with AMPure XP beads (Beckman Coulter). Final library sizing and QC was evaluated on Agilent’s high sensitivity DNA kit run on the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Overexpression was performed with lentiviral infections. 2 mL of virus was added to 3 mL of media containing 5.0 x 10e6 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2).The next day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium and the 3rd day cells are transferred to Blasticidin (10 ug/ml) and subjected to selection.

value: Acute Myeloid leukemia cell line NB4

value: Nuclear HK2 NLS2 overexpression

value: anti-HK2 (Santa Cruz, sc-374091)


title: CC_4

status: Public on Mar 15 2022

type: SRA

city: Munich

first: Maria

middle: Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic

data_processing:
Quality control of the sequencing was analyzed with FastQC
Demultiplexed reads were aligned using STAR (version 2.7.3a) with the default parameters, the gene counts were produced with the same command using the option “--quantMode GeneCounts”. The annotation used was downloaded from iGenomes (UCSC as the source), the ERCC genes and mitochondrial genes (from ENSEMBL) were added to the annotation for quality control metrics.
Using unix commands, a count matrix was created by joining the individual count files produced by STAR
The count matrix was processed with custom R (version 4.0.2) scripts. The scripts were used for the quality control, cleaning of the matrix, and principal component analyses
Genome_build: mm10
Supplementary_files_format_and_content: Txt, named counts and FPKM table ready to load in R with rows as genes, and columns as samples

molecule: total RNA

organism: Mus musculus

source_name: Cumulus cell

growth_protocol: MII oocytes were collected and enucleated in CZB medium and were then let to recover in KSOM until they were used for nuclear transfer. The nuclei of donor cumulus cells were injected into the enucleated oocytes using a Piezo-driven micromanipulator. After reconstruction, oocytes were cultured for 1 h in KSOM and activated for 6 h in KSOM containing 10 mM Sr2+ and 5 ug/ml CB supplemented with 2 mM EGTA.

extract_protocol:
Individual cells were manually picked into the lysis solution with macrocapilary pipettes and cDNA was synthesized acording to the Smart-seq2 protocol. Quality of cDNA was checked by the bioanalyzer both after and before the tagmentation.
Libraries were prepared with Smart-seq2 protocol.

treatment_protocol: Embryos were then randomly distributed in medium with or without HU (10uM), which was replaced by fresh medium without HU after 24 h.

tag: strain

tag: tissue

value: cumulus cell


title: CC_3


title: OMMLS CONTROL 2 (RNA-seq)

city: Toronto

first: Aaron

middle: D

last: Schimmer

state: CA-ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Reads adapters were removed using Trim Galore v. 0.4.0 and reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.
After removing genes whose cpm (counts per million reads) were less than 0.5, edgeR R package v.3.8.6 was used to normalize the data using the TMM (trimmed mean of M values) method and to estimate differential expression by applying a generalized linear model between the control vs knockdown cells.A score that ranks genes in nuclear HK2 knockdown samples from the most upregulated to the most downregulated compared to control shRNA samples was calculated using the formula ‘-log10(pvalue) * sign(logFC)‘.
Genome_build: hg38 (RefSeq gene models)
Supplementary_files_format_and_content: Htseq read counts

organism: Homo sapiens

source_name: OCI AML 8227 Cells

growth_protocol: 8227 cells were cultured in X-VIVO 10 (Lonza 04-380Q) with 20% bovine serum albumin (BSA)–insulin-transferrin (STEMCELL Technologies 09500), human Fms-related tyrosine kinase 3 ligand (Flt3-L; 50 ng/ml) (PeproTech 300-19), IL-6 (10 ng/ml) (PeproTech 200-06), SCF (50 ng/ml) (PeproTech 300-07), thrombopoietin (25 ng/ml) (PeproTech 300-18), IL-3 (10 ng/ml) (PeproTech 200-03), and granulocyte colony-stimulating factor (G-CSF; 10 ng/ml) (Amgen 121181-53-1).

extract_protocol:
RNeasy Plus Mini Kit. Quality of total RNA samples were checked on an Agilent Bioanalyzer 2100 RNA Nano chip following Agilent Technologies’ recommendation. Concentration was measured by Qubit RNA HS Assay ona Qubit fluorometer (ThermoFisher)
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol

treatment_protocol: Nuclear HK2 knockdown was performed by expressing mitochondrial tethered HK2 (OMMLS-HK2) and knocking down native HK2 using UTR shRNA performed with lentiviral infections.

tag: cell line

value: Engineered leukemic stem cell line OCI AML 8227

value: Blood

tag: genotype

value: control


title: OMMLS CONTROL 1 (RNA-seq)


title: Nuclear HK2 NLS2 overexpression  1 (ChIP-seq)

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: chip antibody


title: HU_NT_8

source_name: Nuclear transferred embryo

tag: treatment

value: hydroxyurea treated

value: embryo


title: CC_1


title: sgCtr9-1 Ctr9KD RNA-seq

city: Beijing

first: wei

middle: zi

last: guo

state: Beijing

address: ZhongGuanCun

country: China

institute: tsinghua university

data_processing:
The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Reads were aligned to mouse genome mm10 and Drosophila genome dm6 from GENCODE using STAR (version 2.7.1a).
Aligned reads stored in BAM format were filtered using SAMtools (version 1.9) with parameter is “samtools view –b –h –F 4 –f 3”.
featureCounts (version 1.6.4) counted reads stored in BAM format to exon sites of genes included in GTF file from GENCODE.
Spike-in normalized bigwig files were created with deepTools (bamCoverage). We used spike-in read counts to calculate size factors by EdgeR. Then we used these size factors to normalize of mm10 read counts and calculated differentially expressed regions by EdgeR.
Genome_build: mm10; dm6
Supplementary_files_format_and_content: bigwig files were generated using deeptools

source_name: pancreatic ductal adenocarcinoma

growth_protocol: Pancreatic cancer cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol:
Before RNA extraction, 0.2% Drosophila S2 cells were mixed with PDAC cells as spike-in. RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual
500ng RNA of each sample was used to prepare libraries. Total RNA-seq libraries were prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NR603-01).

treatment_protocol: 1μg/mL doxycycline was added into medium for 72hr before harvesting cells to induced dCas9-KRAB expression

value: pancreatic ductal adenocarcinoma cells

value: treated with Ctr9KD

tag: genotypes

value: Ctr9 knockdown


title: sgCtr9-5 Ctr9KD RNA-seq


title: sg9270 Ctr9KD RNA-seq

value: untreated

value: WT


title: Nuclear HK2 NLS2 overexpression 2 (ChIP-seq)


title: sgDis3-2  Dis3KD RNA-seq

description: chromatin RNA

value: treated with Dis3KD

value: Dis3 knockdown


title: sg4841 Ctr9KD RNA-seq


title: HU_NT_7


title: HU_NT_6


title: sgDis3-1 Dis3KD RNA-seq

description: chromatin RNA


title: Nuclear HK2 NLS1 overexpression  2 (ChIP-seq)

value: Nuclear HK2 NLS1 overexpression


title: HU_NT_4


title: HU_NT_5


title: sg9270 Dis3KD RNA-seq

description: chromatin RNA


title: Nuclear HK2 NLS1 overexpression 1 (ChIP-seq)

value: Acute Myeloid leukemia cell line NB4


title: sg4841 Dis3KD RNA-seq

description: chromatin RNA


title: CC_2


title: Empty Vector Control 2 (ChIP-seq)

value: Empty Vector Control


title: Empty Vector Control 3 (ChIP-seq)

value: anti-HK2 (Santa Cruz, sc-374091)


title: HU_NT_3


title: HU_NT_2


title: Nuclear HK2 NLS1 overexpression  3 (ChIP-seq)


title: sgInts11-3 Ints11KD RNA-seq

value: treated with Ints11KD

value: Ints11 knockdown


title: sgInts11-1 Ints11KD RNA-seq


title: Nuclear HK2 knockdown 3 (RNA-seq)

value: Engineered leukemic stem cell line OCI AML 8227

value: Blood

value: Nuclear HK2 knockdown


title: Nuclear HK2 knockdown 3 (ATAC-seq)

data_processing:
ATAC-seq data has been aligned to the human genome using bowtie2.
Duplicated reads and multiple loci aligned reads have been discarded
Peaks were called using MACS2 peak caller.
Differentiallly binding peaks have been analyzed using edgeR package.
Genome coverage tracks have been created using the bamCoverage tool in the deeptools package.
Genome_build: hg38
Supplementary_files_format_and_content: Narrow peaks were identified from the alignment files using MACS2 v.2.1.1 with a cutoff score FDR 0.01

extract_protocol:
60,000 viable cells per sample were pelleted at 500 RCF at 4°C for 5 min. Supernatant was removed and cells were re-suspended in 50ul of cold resuspension buffer (RSB) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin. Cell suspension was incubated on ice for 3 minutes before being washed out with 1 ml of cold RSB containing 0.1% Tween-20. Cells were mixed by inversion prior to pelleting at 500 RCF at 4°C for 5 min. Supernatant was removed, cells were re-suspended in 50µl of transposition mix and incubated at 37°C for 1 hour in a thermomixer (Eppendorf) set to 1000 RPM. Transposition mix was purified using the Qiagen MinElute Reaction Cleanup Kit (Qiagen) and eluted in 20µl of water.
1µl of sample was taken into a qPCR reaction to determine the optimal number of PCR cycles required for amplification without reaching saturation and based off the measured cycle number, the remaining 19ul of each sample was amplified. Libraries were purified using AMPure XP beads (Beckman Coulter) using a double-sided bead cleanup protocol set to 0.7x-1.0x. This cleanup was performed twice to remove the large molecular fragments.

treatment_protocol: Overexpression and knockdown was performed with lentiviral infections. 2 mL of virus was added to 3 mL of media containing 5.0 x 10e6 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2).The next day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium and the 3rd day cells are transferred to Blasticidin (10 ug/ml) or puromycin (2 ug/ml) and subjected to selection.


title: HU_NT_1

value: hydroxyurea treated

value: embryo


title: sg4841 Ints11KD RNA-seq

value: pancreatic ductal adenocarcinoma cells


title: Con_NT_8

value: control


title: Con_NT_9


title: Nuclear HK2 knockdown 2 (ATAC-seq)


title: Nuclear HK2 knockdown 1 (ATAC-seq)


title: Con_NT_7


title: Knockdown control 2 (ATAC-seq)

value: Knockdown control


title: X-ten87-sg4841

value: untreated

value: WT


title: sgPaf1-1 Paf1KD RNA-seq

value: treated with Paf1KD

value: Paf1 knockdown


title: Con_NT_6


title: Knockdown control 3 (ATAC-seq)

value: Acute Myeloid leukemia cell line NB4


title: X-ten87-Setd1a

value: treated with Setd1a

value: Setd1a knockdown


title: Con_NT_4


title: sg9270 Paf1KD RNA-seq


title: Knockdown control 1 (ATAC-seq)


title: Input ChIP

data_processing:
The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Trimmed reads were aligned to mouse genome mm10 from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”.
Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with parameter is “samtools view –b –h –F 1028 –f 3”.
BPM normalized bigwig files were created with deepTools (bamCoverage).
Peak detection was done using MACS2. BPM normalized bigwig files were created with deepTools (bamCoverage).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

source_name: pancreatic ductal adenocarcinoma cells

extract_protocol:
Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde,  washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140  mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease  inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six  times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton  X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer  and reverse-crosslinked for 6 h at 65 ºC
DNA samples were treated sequentially with   RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5  (Zymo Research, D4014).The End-It DNA End-Repair Kit (Lucigen, ER81050) was used to convert purified DNA to 5′-phosphorylated, blunt-end DNA. After treated with Klenow Fragment (3'→5' exo-), barcodes (BIOO Scientific, 514120) were ligated with Quick Ligation kit (NEB, M2200). After size selection, 15 cycles of PCR were used to amplify the library.

treatment_protocol: For PAF1 KD H3K27ac ChIP-seq, 1μg/mL doxycycline was added into medium for 72hr before harvesting cells to induced dCas9-KRAB expression. For HQ461 treatment PAF1 ChIP-seq, 10μM HQ461 was added into medium for 8h before harvesting cells


title: Con_NT_3


title: Con_NT_5


title: Nuclear HK2 overexpression 3 (ATAC-seq)

value: Nuclear HK2 overexpression


title: Pol II ChIP Paf1-KD

value: Pol II


title: Con_NT_1


title: Empty Vector Control 1 (ChIP-seq)

value: Empty Vector Control

value: anti-HK2 (Santa Cruz, sc-374091)


title: Nuclear HK2 overexpression 1 (ATAC-seq)


title: Empty vector Control 2 (ATAC-seq)

value: Empty vector Control


title: Pol II ChIP WT


title: sg9270 Ints11KD RNA-seq


title: Nuclear HK2 overexpression 2 (ATAC-seq)


title: HCT116_siYAP/TAZ_2

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

description: YAP/TAZ Knock down

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic ( 0.36 ), then mapped to GR38p7 whole genome using Hisat2 ( 2.0.5 ) with parameters ( --rna-strandness RF --fr  )
FPKM value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count (  0.9.1 )
Genome_build: GR38p7
Supplementary_files_format_and_content: FPKM

source_name: HCT116 CELL LINE

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: knockdown

value: YAP/TAZ Knock down


title: HCT116_siYAP/TAZ_1

description: YAP/TAZ Knock down


title: Con_NT_2

value: embryo


title: DMSO-Paf1 ChIP

value: pancreatic ductal adenocarcinoma cells

value: DMSO


title: pancreatic ductal adenocarcinoma cells, Paf1-KD input


title: Empty vector Control 1 (ATAC-seq)


title: HCT116_siTEAD1/2/3/4

description: TEAD1/2/3/4 Knock down

value: TEAD1/2/3/4 Knock down


title: Paf1 ChIP

value: untreated


title: CAG-OE_Input

city: nanjing

first: Wenren

last: Zuo

address: xianlin road

institute: nanjing university of chinese medicine

data_processing:
Fastp 0.19.11 software performs basic quality statistics for raw reads
burrows Wheeler aligner(0.7.12-r1039) can  compare reads to reference genome
Peak calling was performed by MACS22.1.0
The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peaks file

source_name: Multiple Myeloma cells

growth_protocol: Human multiple myeloma cell lines CAG were cultured in RPMI 1640 Medium  with 10% fetal bovine serum 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured in a humidified atmosphere of 5 % CO2 at 37℃.

extract_protocol:
~5-20 x 10e06 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of HA and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using a phenol-chloroform lysate to obtain a purified product.
RNA samples were fragmented by RNA fragmentation buffer (10 mM Tris-HCl [pH 7.0], 10 mM ZnCl2). Fragmented RNA was  incubated for 2 hr at 4C with 0.5 mg/mL antim6A polyclonal antibody in IP buffer (150  mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl [pH 7.4]) supplemented with RNasin  Plus RNase inhibitor (Promega). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase（RNase H - ）. Second strand cDNA  synthesis was subsequently performed using DNA Polymerase I and RNase H.  Remaining overhangs were converted into blunt ends via exonuclease/polymerase  activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with  hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA  fragments of preferentially 150~200 bp in length, the library fragments were purified  with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µL USER Enzyme  (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min  followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion  High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last,  PCR products were purified (AMPure XP system) and library quality was assessed on  the Agilent Bioanalyzer 2100 system.

value: circHNRNPU_603aa overexpression

value: multiple myeloma cell line CAG

tag: rip antibody

value: input


title: HQ461-Paf1 ChIP

value: WT


title: CAG-EV_Input

value: empty vector


title: HCT116_siHHEX_2

description: HHEX Knock down

value: HHEX Knock down


title: siSP140 IP TOP2A_Replicate 2

city: Boston

first: Kate

middle: L

last: Jeffrey

state: MA

address: 50 Blossom Street

department: Medicine

country: USA

institute: Massachusetts General Hospital

data_processing:
Sequences were aligned using bwa version 0.7.1 with default parameter
homer version 4.10.3 was used to call peaks
diffBind R package was used for the analysis of differential chromatin accessibility between knockdown and control samples
Genome_build: hg19
Supplementary_files_format_and_content: peak bed file

source_name: Peripheral Blood-derived Macrophages

growth_protocol: Peripheral blood mononuclear cells were isolated from  buffy coats of healthy donors and differentiated into macrophages with 100ng/mL M-CSF for 7 days

extract_protocol:
100,000 cells were used for each CUT&TAG reaction according to protocol by Epicypher.
Library was constructed as part of CUT&TAG protocol. Sequencing was done on a NovaSeq SP 100 flow cell.

treatment_protocol: On Day 7, Cells were treated with siControl and siSP140 for 48 hours in the presence of IFN-g (100ng/mL)

value: Healthy donor

value: Blood

value: Human Macrophages

value: Unstimulated siSP140


title: pancreatic ductal adenocarcinoma cells, WT- input


title: pancreatic ductal adenocarcinoma cells, WT- H3K27ac

value: H3K27ac (ActiveMotif, #39133)


title: Ints11 ChIP


title: HCT116_siHHEX_1

description: HHEX Knock down


title: HCT116_siNC_2

description: control

value: control


title: pancreatic ductal adenocarcinoma cells, Paf1-KD H3K27ac

value: treated with Paf1KD

value: Paf1 knockdown


title: pancreatic ductal adenocarcinoma cells, sgPaf1-2 Paf1KD RNA-seq

value: pancreatic ductal adenocarcinoma cells


title: HCT116_siNC_1

description: control


title: CAG-OE_IP

value: HNRNPA2B1/ILF3, Proteintech


title: siControl IP TOP2A_Replicate 2

value: siControl

value: Unstimulated siControl


title: HCT116_siHHEX_3

description: HHEX Knock down


title: pancreatic ductal adenocarcinoma cells, sg4841 Paf1KD RNA-seq

value: untreated


title: Empty vector Control 3 (ATAC-seq)

value: Acute Myeloid leukemia cell line NB4

value: Empty vector Control


title: siSP140 IP TOP1_Replicate 2


title: siSP140 IP TOP2A_Replicate 1


title: Ythdf2-vKO rep1

first: xin

middle: xi

last: zhao

address: Yueyang Road, 320#, new building 615

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Adaptor sequences and read sequences on both ends with Phred quality scores below 30 were trimmed.
Trimmed reads were then mapped with the Hisat2 algorithm (Hisat2 v2.1.0) to target sequences.
Gene expression levels were quantified by the software package HTSeq (v0.6.1p1).
Differentially expressed genes were generated by asking for a log2 (-fold change) ＞ 1.5 with P < 0.05.

source_name: Testis

extract_protocol:
Testes were collected, flash frozen, and RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared according to the protocol for use with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760).

tag: genotype/variation

value: Testis

tag: age

value: post natal day 56


title: WT_2 H3K9ac

city: Wuhan

first: Binbin

last: Tao

address: No. 7 Donghu South Road

institute: Institute of Hydrobiology

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters: filter -l 5 -q 0.5 -n 0.1 -Q 2 -5 1 -c 50.
Cleaned reads were mapped to the reference genome of GRCz11 using SOAPaligner/SOAP2 (version: 2.2.5), whose parameters is -v 2 -s 35
The different enrichment peaks from different samples was plotted by MAnorm (v1.1)
Also the gene element annotation of peak or different enrichment peak from different samples was carry out by bedtools intersect mode with overlap 50%
To identify the characteristic of peak, motif discovery was analyzed using HOMER (v4.10.3).
Assembly: GRCz11
Supplementary files format and content: bw and excel files of peaks

organism: Danio rerio

source_name: zebrafish embryos

growth_protocol: Wild type and mutant zebrafish embryos were raised and maintained at 28.5℃.

extract_protocol:
About 600 36hpf wild type or sinhcaf mutant embryos were collected. Immunoprecipitation was carried out using ChIP Grade anti- acetyl-histone H3 (K9 9649T) antibody.Chromatin immunoprecipitation assays were carried out using a variation of the protocol (https://wiki.zfin.org/display/prot/ZFIN+Protocol+Wiki)
The DNA is combined with End Repair Mix, and incubate at 20℃ for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit (Qiagen), then add A-Tailing Mix, incubate at 37℃ for 30 min. Combine the purified Adenylate 3' Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20℃ for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected (about 100-300bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). The final library is quantitated in two ways: Determine the average molecule length and sample integrity as well as purity using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and quantify the library by real-time quantitative PCR (RT-qPCR).

value: wild type

tag: developmental stage

tag: antibody


title: Ythdf2-vKO rep2


title: KO_3 H3K9ac

value: sinhcaf-/-


title: CAG-EV_IP

value: empty vector

value: multiple myeloma cell line CAG


title: control rep2


title: IVD organoid cells (scRNA-seq)

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

description: Single cell RNA-seq

data_processing:
scRNA-seq reads were aligned to merged genome reference (hg38 and mm10) using STAR software.
Uniquely mapped reads was use to run gene UMI quantification using Cellranger software.
Genome_build: hg38and mm10
Supplementary_files_format_and_content: 10X Cellranger gene quantification outputs: barcodes.tsv.gz. features.tsv.gz, matrix.mtx.gz

source_name: Human brain organoid cells

growth_protocol: The human induced PSC line were provided by iXCells Biotechnologies and cultured on Matrigel (BD Biosciences) coated dishes in mTeSR1 medium (Stem Cell Technologies).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kits v2 following the manufacturer’s protocol.
2 × 150 bp paired-end.

treatment_protocol: STEMdiff™ Cerebral Organoid Kit (Stem Cell Technologies) was used for generation of premature organoids.

value: In vivo development human brain organoid cells


title: control rep1

value: control


title: siControl IP TOP1_Replicate 1

value: Healthy donor

value: Blood

value: Human Macrophages


title: siSP140 IP TOP1_Replicate 1

value: Unstimulated siSP140


title: siControl IP TOP1_Replicate 2

value: siControl


title: 4_6_IC

status: Public on Mar 14 2022

city: Cardiff

first: Anthony

last: Isles

address: Hadyn Ellis Building

country: United Kingdom

institute: Cardiff University

data_processing:
sequencing reads were mapped to the mouse genome using the STAR software package
quantification of annotations was calculated with the GeneCounts option which outputs count reads per gene
featureCounts software was used to count the raw reads, which were subsequently analysed in R Studio 1.1.383 using the DESeq2 package, with genotype and litter as fixed effects into the statistical model
Differential isoform usage was pseudo-aligned to the mouse transcriptome with the Kallisto software which was also used to quantify the raw reads. The Kallisto files were then analysed in R studio via DEXSeq with the IsoformSwitchAnalyzeR package, which measures isoform usage by quantifying the fraction of isoform expression from the parent gene expression
Prediction of protein domains was run on EBI’s Pfam webserver, which performs bio sequence analysis using hidden Markov models
Assembly: mm10
Supplementary files format and content: raw count, FPKM, TPM, statistics

source_name: brain

extract_protocol:
The tissue was collected first thing in the morning (9–10:00 am) following birth and was snap-frozen on dry ice and stored at −80 °C until. RNA was extracted using the Direct-zol RNA Miniprep kit.
Libraries were prepared with the KAPA mRNA HyperPrep kit (Roche Sequencing solutions) from total RNA of RQN > 8.5 as assessed by the Fragment Analyser system (Agilent Technologies)

value: P0 brain

value: WT

tag: Sex

value: male


title: 1_10_IC

value: HET PWS-ICdel

value: female


title: 4_5_IC


title: 4_3_IC


title: 4_4_IC


title: 1_3_IC


title: 3_5_Cr

value: HET PWS-Cr


title: 4_2_Cr


title: siControl IP TOP2A_Replicate 1

value: Unstimulated siControl


title: 4_1_Cr


title: KO_1 H3K9ac

value: sinhcaf-/-


title: 4_3_Cr


title: 3_6_Cr


title: 1_5_IC


title: WT_3 H3K9ac

value: wild type


title: 1_5_Cr


title: 4_2_IC


title: KO_2 H3K9ac


title: 2_1_Cr


title: 1_7_IC


title: 1_1_IC


title: 1_1_Cr


title: 8h CX-5461 rep2

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

institute: MRC Laboratory of Medical Sciences

data_processing:
Reads were quality and adaptor trimmed using trim_galore v0.5.0, and standard parameters
Trimmed reads were aligned to mm10 using tophat2 v2.1.1, using standard parameters and g-1
Bam files were used to generate count data using Rsubread package feature-counts v1.6.4, parameters: -t exon -g gene_id
Count data was analyzed in R v4.0.5, using Bioconductor v3.12, Deseq2 v.1.30.1, edgeR v. 3.32.1, limma_3.46.0
Genome_build: mm10
Supplementary_files_format_and_content: Filtered and ERCC-normalised log2 expression counts

molecule: polyA RNA

source_name: E14 ESCs

growth_protocol: E14 ESCs were cultured in DMEM GlutaMAX with Na Pyruvate (Thermo Fisher Scientific), 15% FBS (Gibco), 0.1 mM Non-essential amino acids,  0.1 mM EmbryoMax 2-Mercaptoethanol (Millipore) and 2000 U/ml ESGRO supplement (LIF, Millipore).

extract_protocol:
RNA was extracted using QiaGen Mini purifcation kit, according to standard protocols, including on-column DNAse I digestion
Libraries were generated using the NEBnext Ultra Directional II mRNA-seq kit using DNAse-1 treated RNA per sample, using NEBNex index primers

treatment_protocol: ESCs were plated the day before treatment at 500,000 cells per 6wp; next day media was changed for ESC media plus 1uM BMH-21 or CX-5461 for the indicated time period, cultured at 37oC, 5%CO2.

value: E14, 129 strain ESCs


title: 8h CX-5461 rep3


title: 1_3_Cr


title: 8h CX-5461 rep1


title: 4h CX-5461 rep3


title: 1_2_Cr


title: 4h CX-5461 rep2


title: 3_1_Cr


title: 2_2_Cr


title: gastric cancer cells SNU_exosome_rep3

city: Fuzhou

first: Sheng

last: Zhang

state: Fujian

address: 20 Cha Zhong Lu

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

description: non-coding RNA

data_processing:
remove adapter, poly Ns, reads samller than 17 nts with fastqc
using miRDeep2, we align clean reads against sequences in miRBase22 library to predict known miRNA expression.
The expression levels were normalized to RPM (Reads per Million), that is number of reads mapping to miRNA/ number of reads in Clean data)×1000000
Differential expressed miRNAs were calculated using edgeR, and filtered using |log2(Fold Change)| >= 1 and p-value < 0.05
Assembly: miRBase22(reads were blasted directly against library)
Supplementary files format and content: comma seprated values; expressions of human miRNAs in RPM
Supplementary files format and content: comma seprated values; expressions of EBV miRNAs in RPM

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: gastric epithelial cells

growth_protocol: SNU-719 (EBV positive gastric cancer cell line) and AGS (EBV negative gastric cancer cell line) were cultured in RPMI-1640 and F12, respectively. 5% fetal bovine serum without exosomes and penicillin and streptomycin (100U/ mL) were added into the culture medium before use. When the cells grow vigorously (with a degree of fusion up to about 70%), the supernatant is collected.

extract_protocol:
Total RNA was extracted from cells and exosomes using the high pure RNA extraction kit (TRIzol) in accordance with the manufaxturer’s protocol. The OD260 and OD280 values and ratios of 1μL extracted samples were determined by ultraviolet spectrophotometer to determine the concentration and purity of extracted samples.
Approximately 1 μg of total RNA from each sample was used to prepare the miRNA sequencing library. The strips between 17 and 32 nt were cut by polyacrylamide gel electmphoresis（PAGE) and the products were recycled. T4 RNA ligase (Epicenter, San Diego, CA, USA) was used to connect the isolated small RNA to the 3' end and then the isolated small RNA to the 5 'end using the same method. The sRNA connected by the connector was used as the template for RT-PCR, and the single-stranded cDNA template was amplified into double-stranded cDNA, and then PCR amplification was conducted. Then the gel was cut and the target fragment library was recycled. The constructed library was used to detect quality and yield using Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. The library with qualified quality test was sequenced.

treatment_protocol: No special treatment other than growth protocol described above was conducted.

tag: ebv status

value: positive

value: Stomach

value: untreated

tag: rna population

value: exosome


title: 4h CX-5461 rep1

tag: strain


title: gastric cancer cells SNU_exosome_rep2

description: non-coding RNA

tag: tissue


title: 2h CX-5461 rep3


title: S_100144

type: RNA

city: New York

first: Erik

middle: Roy

last: Rasmussen

state: NY

address: 430 East 29th Street

institute: Eli Lilly

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data was normalized using SCAN (SCAN.UPC package from Bioconductor).
Probe group file: Decipher-v1.r1.pgf
Meta-probeset file: Decipher-v1.r1.mps
Background probe file: Decipher-v1.r1.antigenomic.bgp
CEL layout file: Decipher-v1.r1.clf
Quality Control Content file: Decipher-v1.r1.qcc

label: biotin

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications.

growth_protocol: Not Applicable

extract_protocol: NOT PROVIDED

treatment_protocol: Not Applicable

value: Placebo + Docetaxel

tag: primary site

value: Non-Bladder


title: S_100141

value: LY3009806 + Docetaxel

value: Bladder


title: gastric cancer cells SNU_exosome_rep1

description: non-coding RNA

tag: cell line


title: S_100138


title: S_100140


title: S_100143


title: S_100145


title: S_100142


title: S_100135


title: S_100137


title: 0h Control rep3

value: 0h Control


title: S_100136


title: 2h CX-5461 rep1


title: gastric cancer cells SNU_cell_rep3

description: non-coding RNA

value: whole cell


title: S_100139


title: gastric cancer cells SNU_cell_rep2

description: non-coding RNA


title: 2h CX-5461 rep2


title: S_100126


title: S_100133


title: S_100129


title: gastric cancer cells SNU_cell_rep1

description: non-coding RNA


title: S_100128


title: S_100127


title: S_100123


title: S_100125


title: 0h Control rep1


title: S_100122


title: 0h Control rep2


title: Tumor cells, Late stage, IRF4;p53+/- fish 5_scRNA-Seq

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
Annotations from Ensembl (GRCz11) for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 (ENSG00000137265) gene information.  Single cell data were generated using mkref from cellranger package.
Alignment, barcode assignation, and generation of cell-gene-count matrices were all performed using cellranger count from 10x genomics version 3.1.0
cellranger count --id zv11_{sampleID} --fastqs={directory_scSeq} --sample={sampleID}--transcriptome={mkgtf generated STAR library}
Genome_build: GRCz11 Danio Rerio + mCherry + Human IRF4 (ENSG00000137265)
Supplementary_files_format_and_content: HDF5 Gene-Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze

source_name: Zebrafish cells, transgenic

growth_protocol: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  After the development of lymphoma phenotype, tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.

extract_protocol:
After sorting, the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell 3' Solution v2 kit following manufacturer's instructions.
Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.
Single cell RNA-Seq

treatment_protocol: No treatment

value: tumors driven by overexpression of human IRF4

tag: sorted cells

value: mCherry sorted cells

tag: genotype

value: IRF4 overexpression and p53 mutation

tag: time

value: Late stage


title: Tumor cells, Late stage, IRF4;p53+/- fish 4_scRNA-Seq


title: Tumor cells, Late stage, IRF4;p53+/- fish 3_scRNA-Seq


title: Tumor cells, Late stage, IRF4;p53+/- fish 2_scRNA-Seq


title: S_100119

tag: treatment


title: 8h BMH21 rep3

value: 8h BMH21


title: 8h BMH21 rep2


title: 4h BMH21 rep3

value: 4h BMH21


title: Tumor cells, Late stage, Ick:IRF4 fish 6_scRNA-Seq

value: IRF4 overexpression


title: Tumor cells, Late stage, IRF4;p53+/- fish 1_scRNA-Seq


title: S_100121


title: 8h BMH21 rep1

value: E14, 129 strain ESCs


title: Tumor cells, Late stage, Ick:IRF4 fish 5_scRNA-Seq


title: 4h BMH21 rep1


title: S_100120


title: 2h BMH21 rep3

value: 2h BMH21


title: S_100117


title: S_100114


title: S_100111


title: Tumor cells, Late stage, Ick:IRF4 fish 4_scRNA-Seq


title: S_100110


title: S_100113


title: S_100124


title: S_100115


title: S_100106


title: S_100109


title: S_100107


title: S_100112


title: S_100116


title: S_100118


title: S_100105


title: Tumor cells, Late stage, Ick:IRF4 fish 3_scRNA-Seq


title: S_100104


title: S_100103


title: S_100101


title: Tumor cells, Late stage, Ick:IRF4 fish 1_scRNA-Seq


title: 2h BMH21 rep2


title: Tumor cells, Late stage, Ick:IRF4 fish 2_scRNA-Seq


title: 4h BMH21 rep2


title: ZEB1 ChIP-seq, ZEB1R3

city: Geneva

first: Didier

last: Picard

address: Sciences III

country: Switzerland

institute: University of Geneva

description: stable cell line (with doxycycline)

data_processing:
The basecalling was performed using bcl2fastq v.2.20.0 for the ChIPSeq.
Sequences were aligned to the Human Reference Genome (assembly hg19, NCBI build 37, February 2009) with BWA-MEM. Peak calling was carried out using the MACS2 tool of the Galaxy tool suite.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including the genomic coordinates of peaks
Supplementary_files_format_and_content: bigwig file containing the peak signal and location.

source_name: breast; derived from metastatic site: pleural effusion

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) complemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells stably expressing a doxycycline-inducible construct to express ZEB1 were induced for ZEB1 expression with 2 µg/ml of doxycycline (DOX) supplemented every day in the medium.

extract_protocol:
Immunoprecipitated DNA was extracted using the phenol–chloroform–isoamyl alcohol method.
Library was prepared starting with 5 ng of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications

value: breast

tag: cell type

value: Breast carcinoma cell line

value: 2 µg/ml doxycyline

value: ZEB1 expression

tag: chip antibody

value: ZEB1, Proteintech, catalog 21544-1-AP


title: S_100102

value: LY3009806 + Docetaxel

value: Bladder


title: Tumor cells, Early stage, Ick:IRF4 fish 3_scRNA-Seq

value: Early stage


title: ZEB1 ChIP-seq, ZEB1R2

description: stable cell line (with doxycycline)


title: Tumor cells, Early stage, Ick:IRF4 fish 2_scRNA-Seq

value: tumors driven by overexpression of human IRF4


title: Tumor cells, Early stage, Ick:IRF4 fish 1_scRNA-Seq

value: mCherry sorted cells


title: 2h BMH21 rep1


title: S_100100

value: Placebo + Docetaxel

value: Non-Bladder


title: ZEB1 ChIP-seq, IgGR3

description: stable cell line (with doxycycline)

value: IgG, Sigma Aldrich, catalog 12-370


title: ZEB1 ChIP-seq, ZEB1R1

description: stable cell line (with doxycycline)


title: Normal cells, Control_scRNA-Seq

source_name: Zebrafish cells, control

value: normal cells

value: Control


title: S_100095


title: S_100094


title: S_100098


title: S_100097


title: ZEB1 ChIP-seq, IgGR1

description: stable cell line (with doxycycline)


title: scRNA-seq, Epcam low

data_processing:
The basecalling was performed using Cell Ranger v.3.1.0 for the single cell RNAseq samples.
For the sc-RNA-seq, FASTQ reads were aligned to the reference genome GRCh38-2020-A downloaded from 10X genomics website. All analyses were then carried out in R with the Seurat 3.0 package. QC metrics per cells were calculated with the function PercentageFeatureSet. Only cells with less than 25% mitochondrial RNA and feature counts between 200 and 7000 were kept. Epcam high and Epcam low cells were merged with the function FindIntegrationAnchors, which takes a list of Seurat objects as input and uses these anchors to integrate the two datasets together with IntegrateData. Data were normalized and scaled with the Sctransform function. Dimensional reduction was performed by PCA and UMAP and selection of markers specific to clusters of interest were done with the FindConservedMarkers function.
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: Hdf5 matrix read count matrices.

growth_protocol: Cells were cultured in DMEM complemented with 10% FBS and 1% penicillin/streptomycin. Medium was supplemented with 2 µg/ml doxycycline every 2 days.

extract_protocol: 6000 single cells were captured with the Chromium controller from 10x Genomics. Library was prepared with 3' Library and Gel Bead v3 kit

value: no treatment


title: LL9

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

data_processing:
Base calling was done using Instrument and manufacturer proprietary software.
QC was done using FastQC v.0.11.8, RSeQC v4.0.0, MultiQC v.1.10, and Fastp v.0.21.0.
Pre-processed reads were quantified against the human transcriptome from GRCh38p.12 using Salmon v.1.4. Transcript quantification was summarized into ENSEMBL genes with tximport v.1.12.0 and biomaRt v.2.40.5.
Assembly: GRCh38p.12
Supplementary files format and content: Salmon quantification including pseudo-counts, abundance (length scaled TPM), and observed gene length (RDS file bzip2 compressed).
Supplementary files format and content: Counts were normalized with DESEq2 median ratio method and then transformed with log2(x+1).

source_name: peripheral blood

extract_protocol:
Whole blood was collected in PAXgene tubes (Qiagen, Germany) and RNA was extracted using PAXgene blood RNA kit (Qiagen, Germany) as instructed by the manufacturer.
Poly-A libraries were obtained using NEBNext Poly(A) mRNA magnetic isolation module (New England Bioscience, USA) and NEBNext Ultra II Directional RNA for Illumina kit (New England Bioscience).

value: peripheral blood

value: LAT

tag: group

value: LL

value: M


title: ZEB1 ChIP-seq, IgGR2

description: stable cell line (with doxycycline)

value: breast

value: Breast carcinoma cell line

value: 2 µg/ml doxycyline

value: ZEB1 expression


title: S_100088

value: Bladder


title: scRNA-seq, Epcam high


title: LL7

value: MCF

value: F


title: LL6

value: MSF


title: S_100090

value: Placebo + Docetaxel


title: S_100093


title: LL8

value: GAS


title: S_100092

value: Non-Bladder


title: LL5

value: CAGJ


title: S_100089

value: LY3009806 + Docetaxel


title: LL4

value: peripheral blood

value: JCL


title: S_100096


title: S_100083


title: S_100084


title: S_100080


title: S_100082


title: RNA-seq, +DOX(E2)_rep2

description: stable cell line (with doxycycline)

data_processing:
The basecalling was performed using bcl2fastq v.2.20.0 for the RNAseq samples.
For the RNA-seq, the quality of reads was checked with the fastqc tool. Sequences were mapped against the Human Reference Genome (assembly hg19, NCBI build 37, February 2009) with the STAR, and count tables were produced with the featureCounts function  in R, containing the number of mapped reads per gene. Differential Expression was performed and fold changes were calculated with the edgeR Bioconductor package in R.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including counts scaled to 10 million.

growth_protocol: Cells were deprived of steroids by culturing for at least five days in DMEM without phenol red complemented with 5% charcoal-stripped FBS, 2 mM L-glutamine and 1% penicillin/streptomycin, and treated as indicated. To express ZEB1 medium was suplemented with 2 µg/ml of doxycycline every 2 days. nDOX stands for no doxycycline.

extract_protocol:
Library was prepared starting with 300 ng of total RNA and processed with the Illumina TruSeq stranded mRNA library prep kit according to manufacturer specifications
The RNeasy Mini Kit and columns (QIAGEN) were used according to the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO, 17-beta estradiol (E2), and Forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI) for 6 hours.

value: 17-beta estradiol (E2)


title: S_100079


title: S_100085


title: S_100077


title: S_100086


title: S_100075


title: RNA-seq, +DOX(FI)_rep1

description: stable cell line (with doxycycline)

value: Forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI)


title: RNA-seq, +DOX(E2)_rep1

description: stable cell line (with doxycycline)


title: S_100076


title: RNA-seq, +DOX(FI)_rep2

description: stable cell line (with doxycycline)


title: LL2

value: MR

value: LL

value: M


title: LL3

value: LCG


title: RNA-seq, +DOX(ctl)_rep2

description: stable cell line (with doxycycline)

value: Breast carcinoma cell line

value: DMSO


title: S_100073

value: Bladder


title: LL1

value: LPS


title: RNA-seq, +DOX(ctl)_rep1

description: stable cell line (with doxycycline)


title: ENL9

value: ASR

value: ENL


title: S_100078


title: S_100070

value: Placebo + Docetaxel


title: ENL8

value: GPS


title: RNA-seq, -DOX(FI)_rep1

description: stable cell line (no doxycycline)


title: S_100072

value: LY3009806 + Docetaxel


title: ENL7

value: peripheral blood

value: CPS

value: F


title: RNA-seq, -DOX(E2)_rep2

description: stable cell line (no doxycycline)

value: 17-beta estradiol (E2)


title: S_100069


title: S_100074


title: S_100066


title: S_100065


title: S_100068


title: ENL5

value: MJSS


title: ENL6

value: JFAS


title: RNA-seq, -DOX(E2)_rep1

description: stable cell line (no doxycycline)


title: RNA-seq, -DOX(FI)_rep2

description: stable cell line (no doxycycline)

value: Forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI)


title: S_100064

value: Non-Bladder


title: RNA-seq, -DOX(ctl)_rep2

description: stable cell line (no doxycycline)

value: Breast carcinoma cell line


title: S_100060


title: ENL4

value: FSRM

value: M


title: RNA-seq, -DOX(ctl)_rep1

description: stable cell line (no doxycycline)

value: DMSO


title: S_100099

value: Bladder


title: ER ChIP-seq, +DOX(FI)_rep4

description:
stable cell line (with doxycycline)
ChIPseq_FI_counts.txt

data_processing:
The basecalling was performed using bcl2fastq v.2.20.0 for the ChIPSeq.
For the ChIP-seq of samples in wild-type MCF7-V cells, sequences were aligned to the Human Reference Genome (assembly hg19, NCBI build 37, February 2009) with BWA-MEM. Peak calling was carried out using the MACS2 tool of the Galaxy tool suite.
For the ChIP-seq of MCF7-V-ZEB1 cells, FASTQ reads were aligned to the human genome hg19 using BWA-MEM. MACS2 with default parameters was used to call peaks. These peaks were then used to build a reference dataset of binding regions. For each treatment (E2, FI), peaks were added in the reference dataset when they were found in all four replicates for each treatment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including counts scaled to 10 million.

growth_protocol: Cells were deprived of steroids by culturing for at least five days in DMEM without phenol red complemented with 5% charcoal-stripped FBS, 2 mM L-glutamine and 1% penicillin/streptomycin, and treated as indicated. Cells stably expressing a doxycycline-inducible construct to express ZEB1 were induced for ZEB1 expression with 2 µg/ml of doxycycline (DOX) supplemented every 2 days in the medium.

extract_protocol:
Library was prepared starting with 5 ng of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications
Immunoprecipitated DNA was extracted using the phenol–chloroform–isoamyl alcohol method.

treatment_protocol: Cells were treated with DMSO, 17-beta estradiol (E2), and Forskolin + 3-isobutyl-1-methylxanthine (IBMX) (FI) for 90 minutes.


title: ENL3

value: DFI

value: ENL


title: S_100057

value: Placebo + Docetaxel


title: S_100059

value: LY3009806 + Docetaxel


title: S_100058


title: S_100062


title: S_100063


title: S_100056


title: S_100051


title: S_100054


title: ENL2

value: peripheral blood

value: WCN


title: ER ChIP-seq, +DOX(FI)_rep3


title: S_100048


title: ER ChIP-seq, +DOX(E2)_rep4

description:
stable cell line (with doxycycline)
ChIPseq_E2_counts.txt


title: ER ChIP-seq, +DOX(FI)_rep2


title: ENL14

value: GAS


title: ENL13

value: MAD

value: F


title: S_100050


title: ER ChIP-seq, +DOX(FI)_rep1

extract_protocol:
Library was prepared starting with 2.4 ng of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications
Immunoprecipitated DNA was extracted using the phenol–chloroform–isoamyl alcohol method.


title: ENL12

value: RCM


title: S_100047


title: S_100049


title: ENL15

value: JPSA


title: S_100045

value: Non-Bladder


title: S_100046


title: S_100052


title: S_100043


title: S_100041


title: S_100040


title: ENL10

value: WGP


title: ENL11

value: ISM


title: ER ChIP-seq, +DOX(E2)_rep3

value: Breast carcinoma cell line

value: 17-beta estradiol (E2)


title: S_100039

value: Bladder


title: S_100035


title: S_100042


title: ENL1

value: ACS

value: M


title: ER ChIP-seq, +DOX(E2)_rep2

extract_protocol:
Library was prepared starting with 3 ng of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications
Immunoprecipitated DNA was extracted using the phenol–chloroform–isoamyl alcohol method.


title: ER ChIP-seq, +DOX(E2)_rep1


title: S_100038


title: ER ChIP-seq, +DOX(Ctl)_rep4

description: stable cell line (with doxycycline)

value: DMSO


title: ENL.THAL.9

value: ASR

value: THAL


title: ER ChIP-seq, +DOX(Ctl)_rep3

description: stable cell line (with doxycycline)


title: ENL.THAL.8

value: peripheral blood

value: GPS


title: S_100033

value: Placebo + Docetaxel


title: S_100034

value: LY3009806 + Docetaxel


title: ER ChIP-seq, +DOX(Ctl)_rep2

description: stable cell line (with doxycycline)


title: S_100028


title: S_100027


title: S_100031


title: S_100032


title: ER ChIP-seq, +DOX(Ctl)_rep1

description: stable cell line (with doxycycline)


title: S_100030


title: ENL.THAL.6

value: JFAS


title: S_100026


title: S_100025


title: ENL.THAL.4

value: FSRM


title: X351 RNA-seq

city: Durham

first: Deepak

last: Voora

state: NC

address: 101 Science Dr

institute: Duke

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
351_S44_L007_R1_001

data_processing:
DEEPAK: base calling
raw single-end sequencing reads were first trimmed to remove adapter sequences and low-quality bases using a sliding window approach with Trimmomatic v0.32 (SE, ILLUMINACLIP:adapters.fasta:2:20:7:1:true, LEADING:5, TRAILING:5, SLIDINGWINDOW:4:10, MINLEN:21).
Sequence reads were aligned with Bowtie2 v2.1.0 ( --local, -U) against a custom ribosomal RNA (rRNA) database created by searching the NCBI non-redundant nucleotide database (NR) for Homo Sapiens ribosomal rRNA sequences. Unmapped reads which did not align to the rRNA database were then aligned with TopHat2 v2.0.9 to the hg19 transcriptome (Ensemble v74).
Expression quantification was done using Cuffquant v2.2.0 and Cuffnorm v2.2.0 (cuffquant -u -b)
Cuffnorm counts were denomralized using cuffnorm reported scale factors, outlier samples identified and removed, lowley expressed genes removed
TMM normalization and then voom normalization of the Qced counts. R code: # Normalization steps  dge <- DGEList(counts=QCed_counts, samples = Metadata)  dge <- calcNormFactors(dge, method = "TMM")  design = model.matrix(~0+treatment_drug + sex.x + Qubitconc.ng.ul + Order_Flowcell, data = dge$samples)  v <- voom(dge, design)  cor <- duplicateCorrelation(v , design, block=dge$samples$StudyID)  print(cor$consensus.correlation)  # repeat both voom and correlation estimate, per gordan smyth https://support.bioconductor.org/p/59700/  v2 <- voom(dge, design, plot=TRUE,correlation=cor$consensus.correlation)  #v2$E is log2 normalized expresion, v2$weights are the gene-sample weights used in duplicate correlation and lmFit results  cor <- duplicateCorrelation(v2 , design, block=dge$samples$StudyID)    # Analysis steps    cor <- duplicateCorrelation(v2 , design, block=dge$samples$StudyID)  fit <- lmFit(v2 , design, block=dge$samples$StudyID, correlation = cor$consensus.correlation)  fit <- eBayes(fit)    contrastM = makeContrasts("LowDoseVsNone" = treatment_drug1-treatment_drug0,      "HighDoseVsNone" = treatment_drug2-treatment_drug0,      "TicagrelorVsNone"=treatment_drug3-treatment_drug0,      "AspirinVsNone" = .5*(treatment_drug1 + treatment_drug2) - treatment_drug0,      "ASAvsTicagrelorResponse" = .5*(treatment_drug1 + treatment_drug2) - treatment_drug3,      "ASAHighvsLow" = treatment_drug2-treatment_drug1,  levels = design  )    fit2 = contrasts.fit(fit, contrastM)  fit2 <- eBayes(fit2)
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited plain text file with denormalized cuffnorm gene counts for all samples and genes passing QC
Supplementary_files_format_and_content: tab-delimited text file with the numeric matrix of normalized expression values on the log2 scale. Obtained from the "$E" argument of the limma::voom object. To be used with file "voom_weights.txt" when testing in limma::lmFit
Supplementary_files_format_and_content: tab-delimited text file with numeric matrix of inverse variance weights from voom. Obtained from the "$weights" argument of the limma::voom object. To be used with file "Voom_normalized_expression.txt" when using limma::lmFit

source_name: mRNA extracted from purified platelets

extract_protocol:
Platelet RNA samples from the same participant were batched together at every stage from platelet RNA extraction through sequencing in order to minimize introducing technical artifacts between visits.RNA Isolation from purified platelets using a phenol-chloroform method.  Platelet lysates thawed on wet ice. Molecular grade Chloroform [200ul m, EMD #CZ1057-6] was added to each 1 ml sample, shaken vigorously by hand for 15 seconds, and allowed to rest for 3 minutes at ambient temperature before centrifugation at 12,000 x g for 10 minutes at 4 degrees. The upper aqueous phase, 500ul 100% isopropanol [Sigma #19516], and 1ul glycogen [Invitrogen #10814-010], were mixed and incubated at ambient temperature for 10 minutes and centrifuged [12,000 x g for 10 minutes at 4 degrees]. After removing the supernatant, the pellet was resuspended with 1ml 75% ethanol [Sigma E-7023], pelleted [8000 x g for 8 minutes at 4 degrees], and eluted in 20ul molecular grade nuclease-free water.   DNase treatment was with 2ul (10% volume) 10X DNase Buffer, and 1ul DNase [Invitrogen DNA-free kit #AM1907] for 25 minutes at 37 degrees C. The purified RNA was then precipitated by adding 11.5ul 5M ammonium acetate [USB Ultrapure# 75901], 103.5ul 100% isopropanol and 1ul glycogen at -20 degrees overnight.
Samples with sufficient quantity and quality RNA went on to poly(A) mRNA capture and construction of stranded mRNA-seq libraries from total RNA was achieved using the commercially available KAPA Stranded mRNA-Seq Kit (catalog #KK8421). The manufacturer’s protocol was followed. In brief, mRNA transcripts were first captured from 100ng-200ng of total RNA using magnetic oligo-dT beads. Captured mRNA transcripts were then fragmented using heat and magnesium and reverse transcribed to produce dscDNA. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. Libraries were indexed using molecular indexes allowing for multiple libraries to be pooled and sequenced on the same sequencing lane on a HiSeq 4000 Illumina sequencing platform.  Each lane consisted of 8-10 samples and yielded about 43 million single-end 50bp sequences per sample.

treatment_protocol: Participants were exposed to either no drug, 81mg/day aspirin, 325mg/day aspirin, or 90mg twice a day ticagrelor

value: Pass

value: 325 mg Aspirin

tag: flowcell

value: Female

tag: age

tag: plateletfunctionscore

tag: logscaledsalicylatelevel


title: X349 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
349_S43_L007_R1_001

tag: Sex


title: X352 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
352_S45_L007_R1_001


title: ENL.THAL.5

value: MJSS

value: F


title: ENL.THAL.3

value: DFI


title: X348 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
348_S42_L007_R1_001

value: 180 mg Ticagrelor


title: ENL.THAL.2

value: WCN

value: M


title: S_100021

value: Bladder


title: S_100020


title: ENL.THAL.13

value: APS

value: THAL


title: X347 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
347_S41_L007_R1_001


title: ENL.THAL.12

value: peripheral blood

value: SMSF


title: S_100018

value: Placebo + Docetaxel


title: S_100015

value: LY3009806 + Docetaxel

value: Non-Bladder


title: S_100014


title: X346 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
346_S40_L007_R1_001

value: Pass

value: 81 mg Aspirin


title: S_100016


title: S_100013


title: S_100022


title: S_100012


title: X345 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
345_S39_L006_R1_001

value: 325 mg Aspirin

value: Female


title: S_100011


title: S_100010


title: ENL.THAL.11

value: ISM


title: S_100009


title: ENL.THAL.10

value: WGP


title: S_100019


title: X343 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
343_S37_L006_R1_001

value: 180 mg Ticagrelor


title: X344 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
344_S38_L006_R1_001


title: ENL.THAL.1

value: ACS


title: S_100024


title: S_100023


title: X342 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
342_S36_L006_R1_001


title: S_100008


title: S_100007


title: S_100004


title: S_100005


title: X341 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
341_S35_L006_R1_001


title: Y27-E6D7_16

city: Rockville

first: Ilyas

last: Singec

state: MD

address: 9800 Medical Center Dr

department: NCATS

institute: NIH

data_processing:
library strategy: RASL-Seq
RASL-seq data processing and counting was performed using the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov). RASL-seq libraries were 8 bases-dual indexed at PCR amplification step. Each well has a unique pair of sequence barcodes to identify the corresponding treatment. Sequencing runs were demultiplexed using the bcl2fasq from Illumina to produce 384 FASTQ sequence files.
A custom python script took demultiplexed fastqs from Illumina Basespace, aligned to an oligonucleotide probe sequence list, using Hamming Distance of <+ 3, allowing up to 3 base misses. The script outputs the number of reads that map to each probe. QC information was also output that describes the number input sequence reads per sample (well) and the number mapping to probe sequences.
Negative controls (no template control) were removed, and gene count data were normalized across samples using DESeq2. Probes of which the maximum responding read count less than 20 (maxBM: average normalized count between treatment and basal condition) across all conditions were removed from analysis to minimize the noise.
Assembly: hg38 custom subset
Supplementary files format and content: counts per oligo (3 per gene); tab delimited csv files with genes and counts

source_name: Y-27632 and E6 medium

growth_protocol: For EB formation, WA09 hESCs were single-cell dissociated using Accutase (Thermo Fisher Scientific) and plated into 96-well ULA round-bottom plates (Corning) at a density of 20,000 cells per well in Essential 6 (E6) Medium (Thermo Fisher Scientific) for 7 days. Three different protocols were used to differentiate hESCs into ectoderm, mesoderm, and endoderm, which served as positive controls for lineage-specific gene expression. For neural induction, hESCs were treated with LDN-193189 (100 nM; Sigma Aldrich) and A83-01 (2 µM; Tocris) in E6 Medium for 6 days. For either mesoderm or endoderm induction, commercially available kits were used for 5 days following the instructions of the manufacturer (STEMdiff™ Mesoderm Induction Medium and STEMdiff™ Definitive Endoderm Kit, STEMCELL Technologies).

extract_protocol:
oligo-dt primers; Samples were harvested and lysed in TCL lysis buffer (Qiagen).
Lysates were transferred to TurboCapture 384 format plates (Qiagen) and incubated at RT 1 hr at 100 rpm for polyA RNA capture. Cell lysate then washed with a binding buffer (20 mM Tris-HCl, pH 7.5 at 25 ⁰C, 500 mM NaCl, 1 mM EDTA, 0.1% SDS) twice and 20 µL probes mixture was added into each well with 0.05 pmol/oligo in binding buffer. The binding mixture was incubated at 65 ⁰C for 10 minutes and gradually the temperature was lowered to 45 ⁰C by every 3 degree/per minute rate before 1 hr incubation at 45 ⁰C in the thermocycler. The ligation step was performed after three times wash with wash buffer (20 mM Tris-HCl, pH7.5 at 25⁰C, 100 mM NaCl, 1 mM EDTA, 0.1% Tween 80) and one time wash with ligation buffer (40 mM Tris-HCl, pH7.5 at 25⁰C, 10 mM MgCl2, 10 mM DTT, 10 µM ATP). A 20 µL ligation mixture containing 5U (Weiss unit) of T4 DNA ligase in ligation buffer was added into each well. After ligation at 37 ⁰C for 1 hr, the wells were washed three times with wash buffer. The final products were eluted with 25 µl elution buffer. Final products of 5 µL/sample were used for PCR amplification with 0.05 µM barcoded primers and AmpliTaqGold DNA polymerase (0.06 U/reaction, Thermo Fisher Scientific) in buffer I supplied by the manufacturer. The dual indexed PCR products were then pooled as one single sample and purified using size-selected column to remove primer dimers (Zymo research). The purified samples were quantified and sequenced on NextSeq 550 using custom sequencing primers.

treatment_protocol: During the first 24 hour of EB formation, single-cell dissociated cells were treated with either Y-27632 (named as Y27 group) or CEPT (named as CEPT group).

tag: molecule type

value: mRNA selected by oligo-dts with RASL-Seq

tag: cell line/type

value: WiCell WA09 hESC

tag: genotype/variation

value: normal


title: H9_ISRL010_Meso_3

source_name: hESC differentiated into mesoderm

value: STEMdiff™ Mesoderm Induction Medium (STEMCELL Technologies)


title: H9_ISRL010_Meso_4


title: X338 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
338_S32_L005_R1_001


title: X339 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
339_S33_L006_R1_001


title: S_100002

tag: primary site

value: Bladder


title: S_100003


title: H9_ISRL010_Meso_2


title: CEPT-E6D7_16

source_name: CEPT and E6 medium

value: CEPT cocktail, E6 media


title: X340 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
340_S34_L006_R1_001


title: S_100001

value: Placebo + Docetaxel


title: X337 RNA-seq

value: Fail


title: X336 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
336_S30_L005_R1_001


title: H9_ISRL010_Meso_1


title: Y27-E6D7_15


title: S_100461

value: LY3009806 + Docetaxel


title: S_100454


title: H9_ISRL010_Endo_4

source_name: hESC differentiated into endoderm

value: STEMdiff™ Definitive Endoderm Kit (STEMCELL Technologies)


title: X333 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
333_S27_L005_R1_001

value: Pass

value: Male


title: X331 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
331_S52_L008_R1_001

value: 81 mg Aspirin


title: CEPT-E6D7_15


title: H9_ISRL010_Endo_3


title: S_100460


title: S_100456


title: S_100452


title: X330 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
330_S51_L008_R1_001

value: 325 mg Aspirin


title: X332 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
332_S26_L005_R1_001


title: ENL.THAL.7

tag: tissue

value: peripheral blood

value: CPS

value: THAL

value: F


title: S_100453


title: X329 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
329_S50_L008_R1_001


title: S_100446


title: S_100439


title: S_100451


title: S_100457


title: S_100435


title: S_100431


title: S_100434


title: S_100438


title: H9_ISRL010_Endo_1

value: mRNA selected by oligo-dts with RASL-Seq

value: WiCell WA09 hESC


title: S_100430


title: S_100428


title: S_100450

value: Non-Bladder


title: H9_ISRL010_Endo_2

value: normal


title: S_100445

value: Bladder


title: S_100441

value: Placebo + Docetaxel


title: X326 RNA-seq

value: Fail

value: Female


title: Y27-E6D7_14


title: S_100437

value: LY3009806 + Docetaxel


title: S_100433


title: S_100427


title: X325 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
325_S48_L008_R1_001

value: Pass


title: S_100429


title: S_100426


title: CEPT-E6D7_14

value: CEPT cocktail, E6 media


title: X324 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
324_S47_L008_R1_001


title: H9_ISRL010_Ecto_4

source_name: hESC differentiated into ectoderm


title: X322 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
322_S45_L007_R1_001

value: Male


title: H9_ISRL010_Ecto_3


title: H9_ISRL010_Ecto_2


title: X321 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
321_S44_L007_R1_001

value: 325 mg Aspirin


title: H9_ISRL010_Ecto_1


title: X320 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
320_S43_L007_R1_001

value: 81 mg Aspirin


title: Y27-E6D7_13


title: X319 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
319_S42_L007_R1_001


title: S_100420


title: CEPT-E6D7_13


title: S_100425


title: S_100419


title: S_100416


title: S_100418


title: S_100421


title: X318 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
318_S41_L007_R1_001

value: 180 mg Ticagrelor


title: S_100415


title: S_100409


title: S_100413


title: X317 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
317_S40_L007_R1_001


title: S_100424


title: CEPT-E6D7_12


title: S_100414


title: S_100411


title: S_100408


title: S_100417


title: S_100410


title: S_100407


title: X314 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
314_S37_L006_R1_001


title: X316 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
316_S39_L007_R1_001


title: Y27-E6D7_11


title: CEPT-E6D7_11


title: Y27-E6D7_12


title: S_100406


title: X311 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
311_S36_L006_R1_001


title: Y27-E6D7_10


title: S_100405


title: S_100422


title: CEPT-E6D7_10


title: X310 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
310_S35_L006_R1_001


title: X308 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
308_S33_L006_R1_001


title: S_100396


title: S_100400


title: S_100398


title: X309 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
309_S34_L006_R1_001


title: Y27-E6D7_9


title: X307 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
307_S32_L006_R1_001


title: S_100394


title: CEPT-E6D7_9


title: S_100395


title: Y27-E6D7_8


title: S_100392


title: X306 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
306_S31_L005_R1_001


title: X304 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
304_S29_L005_R1_001


title: S_100403


title: X323 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
323_S46_L008_R1_001


title: CEPT-E6D7_8


title: S_100388


title: Y27-E6D7_7


title: S_100390


title: S_100387


title: S_100385


title: DVS96 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS96_S5_L001_R1_001


title: S_100382


title: DVS95 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS95_S4_L001_R1_001


title: S_100379


title: S_100402


title: S_100386


title: S_100389


title: Y27-E6D7_6


title: S_100377


title: S_100376


title: S_100380


title: S_100378


title: DVS93 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS93_S2_L001_R1_001


title: S_100393


title: S_100375


title: DVS94 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS94_S3_L001_R1_001


title: CEPT-E6D7_7


title: H9_ISRL010_1

source_name: hESC without treatment


title: H9_ISRL010_3


title: DVS335R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS335R_S29_L005_R1_001


title: CEPT-E6D7_6


title: DVS50 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS50_S47_L007_R1_001


title: DVS353R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS353R_S46_L007_R1_001


title: Y27-E6D7_5


title: CEPT-E6D7_5


title: H9_ISRL010_4


title: S_100373


title: DVS315R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS315R_S38_L006_R1_001


title: DVS92 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS92_S1_L001_R1_001


title: S_100369


title: Y27-E6D7_4


title: H9_ISRL010_2


title: DVS305R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS305R_S30_L005_R1_001


title: S_100362


title: S_100358


title: S_100370


title: DVS334R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS334R_S28_L005_R1_001


title: S_100367


title: S_100364


title: S_100361


title: S_100357


title: S_100366


title: S_100359


title: S_100363


title: S_100371


title: S_100368


title: S_100365


title: S_100356


title: Y27-E6D7_3


title: DVS303R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS303R_S28_L005_R1_001


title: CEPT-E6D7_4


title: S_100355


title: DVS302 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS302_S27_L005_R1_001


title: CEPT-E6D7_3


title: Y27-E6D7_2


title: DVS299 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS299_S25_L005_R1_001


title: S_100353


title: CEPT-E6D7_2


title: DVS298 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS298_S24_L004_R1_001


title: CEPT-E6D7_1


title: DVS297 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS297_S23_L004_R1_001


title: Y27-E6D7_1


title: S_100352


title: S_100350


title: S_100348


title: S_100347


title: DVS296 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS296_S22_L004_R1_001


title: DVS295 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS295_S21_L004_R1_001


title: ∆PDS5B G1 Replicate 2 HiC

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: ∆PDS5B G1 Replicate 2

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions).

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in Iscove’s modified Dulbecco’s medium (Invitrogen), supplemented with 10% FCS (Clontech), 1% UltraGlutamin (Lonza) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol:
Hi-C libraries were prepared as previously described (Rao et al., 2014). The protocol was adapted slightly for G1 analyses. An asynchronous pool of cells was first crosslinked using 2% formaldehyde. Then the 10% smallest cells were sorted based on Forward Scatter and Side Scatter. 5 million cells were collected for Hi-C analysis and then processed according to protocol following crosslinking.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: CRISPRs targeting ESCO1 (5’-CATGAGTACAAGGTCATCAA-3’ and 5’-AGCTTAACCGGAGATCACAA-3’), HDAC8 (5’-CAGTGGGCAGTCGCTGGTCC-3’ and 5’-CGGGACTATAGATATAAACC-3’), PDS5A (5’-GTGGCGTCGTGAGTGCCGACGGG-3’ and 5’-GGAAGATCGCTTACCCTCCG-3’), and PDS5B (5’-TCTGATATTTCCTTGACCCC-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL cells were generated before (Haarhuis et al., 2017), and used as a parental cell line to generate double knockout cells for WAPL and ESCO1. Either blasticidine or puromycin resistance cassettes were used, as described previously (Blomen et al., 2015). Knockout cell lines were confirmed by PCR genotyping and Western Blotting Analysis.

tag: cell line


title: DVS301 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS301_S26_L005_R1_001


title: ∆ESCO1/∆HDAC8 G1 Replicate 2 HiC

description: ∆ESCO1/∆HDAC8 G1 Replicate 2

tag: genotype


title: DVS293 RNA-seq


title: S_100346


title: S_100349


title: ∆PDS5A/∆HDAC8 G1 Replicate 2 HiC

description: ∆PDS5A/∆HDAC8 G1 Replicate 2


title: S_100344


title: S_100335


title: S_100339


title: S_100336


title: S_100338


title: S_100331


title: DVS292 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS292_S9_L002_R1_001


title: S_100333


title: S_100330


title: ∆WAPL G1 Replicate 2 HiC

description: ∆WAPL G1 Replicate 2

value: {delta}WAPL


title: S_100337


title: DVS291 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS291_S20_L004_R1_001


title: DVS289 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS289_S30_L004_R1_001


title: S_100341


title: ∆WAPL/∆ESCO1 G1 Replicate 2 HiC

description: ∆WAPL/∆ESCO1 G1 Replicate 2


title: Wild Type G1 Replicate 5 HiC

description: Wild Type G1 Replicate 5

value: Wild Type


title: S_100328


title: DVS288 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS288_S18_L003_R1_001


title: S_100334


title: S_100325


title: S_100327


title: S_100326


title: S_100323


title: S_100322


title: Wild Type G1 Replicate 4 HiC

description: Wild Type G1 Replicate 4


title: S_100320


title: S_100321


title: DVS287 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS287_S17_L003_R1_001


title: S_100329


title: Wild Type G1 Replicate 3 HiC

description: Wild Type G1 Replicate 3


title: ∆PDS5A G1 Replicate 2 HiC

description: ∆PDS5A G1 Replicate 2


title: DVS286 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS286_S16_L003_R1_001


title: DVS290 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS290_S19_L003_R1_001


title: ∆PDS5A/∆HDAC8 G1 Replicate 1 HiC

description: ∆PDS5A/∆HDAC8 G1


title: DVS285 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS285_S13_L002_R1_001


title: ∆PDS5A G1 Replicate 1 HiC

description: ∆PDS5A G1


title: DVS284 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS284_S15_L003_R1_001


title: S_100324


title: S_100318


title: ∆WAPL/∆ESCO1 G1 Replicate 1 HiC

description: ∆WAPL/∆ESCO1 G1


title: S_100316


title: S_100313


title: S_100311


title: S_100315


title: S_100314


title: S_100319


title: ∆WAPL G1 Replicate 1 HiC

description: ∆WAPL G1


title: DVS282 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS282_S13_L002_R1_001


title: ∆ESCO1/∆HDAC8 G1 Replicate 1 HiC

description: ∆ESCO1/∆HDAC8 G1


title: DVS280 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS280_S11_L002_R1_001


title: ∆HDAC8 G1 Replicate 2 HiC

description: ∆HDAC8 G1 Replicate 2


title: S_100309


title: S_100308


title: ∆HDAC8 G1 Replicate 1 HiC

description: ∆HDAC8 G1 Replicate 1


title: DVS279 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS279_S10_L002_R1_001


title: S_100304


title: ∆ESCO1 G1 Replicate 2 HiC

description: ∆ESCO1 G1 Replicate 2


title: DVS278 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS278_S9_L002_R1_001


title: S_100317


title: DVS274 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS274_S8_L002_R1_001


title: DVS283 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS283_S14_L002_R1_001


title: ∆ESCO1 G1 Replicate 1 HiC

description: ∆ESCO1 G1 Replicate 1


title: Wild Type G1 Replicate 2 HiC

description: Wild Type G1 Replicate 2


title: S_100301


title: DVS272 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS272_S7_L001_R1_001


title: S_100312


title: DVS281R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS281R_S12_L002_R1_001


title: S_100302


title: S_100298


title: S_100297


title: S_100300


title: S_100299


title: Wild Type G1 Replicate 1 HiC

description: Wild Type G1 Replicate 1


title: S_100296


title: S_100306


title: DVS270 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS270_S6_L001_R1_001


title: Tumor4_Input_ChIP-seq

data_processing:
ChIP-seq reads were mapped to zebrafish (Danio rerio GRCz11) reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were processed with samtools rmdup package to remove duplicates.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the braodpeaks called is P-value < 1E-3 and broadPeak cutoff is P-value < 1e-3
Assembly: GRCz11
Supplementary files format and content: broadPeak files of zv11 H3K27ac called with MACS2 --broad-cutoff 1e-3 -p 1e-3 --broad --keep-dup 1 -f BAM --SPMR

source_name: Zebrafish cells

growth_protocol: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  After the development of lymphoma phenotype, tumor cells were harvested.

extract_protocol:
Library construction from the ChIP samples and sequencing of single-end 50-bp-long reads by the BGISEQ-500 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single-end ChIP-Seq

treatment_protocol: Tumor cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated by ChIP using a specific antibody.  A sample of whole cell lysate (WCL) was sequenced and used as the background to determine enrichment.

value: None (whole cell lysate)


title: S_100293


title: S_100295


title: S_100303


title: DVS269 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS269_S19_L003_R1_001


title: S_100292


title: S_100294


title: S_100290


title: Tumor4_H3K27ac_ChIP-seq

value: H3K27ac antibody (ab4729)


title: DVS268 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS268_S18_L003_R1_001


title: DVS267 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS267_S17_L003_R1_001


title: Tumor cells, JQ1_day3_rep2_RNA-Seq

data_processing:
RNA-seq datasets of DMSO-treated control samples and JQ1-treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike-in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation.
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1-treated  samples.
Genome_build: danRer11
Supplementary_files_format_and_content: featureCount read count for all sample, DESeq2 files for differentially expressed genes

source_name: Zebrafish tumor cells

growth_protocol: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  After the development of lymphoma phenotype, animals were treated with JQ1.   Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Total RNAs were harvested from each sample and then applied for RNA-seq analysis.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).  ERCC spike-in was added based on the total cell number.
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: JQ1 was dissolved in DMSO.  Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days.  Experiments were done using 3 independent animals.

value: Zebrafish tumor cells

tag: condition

value: treatment


title: DVS266 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS266_S28_L004_R1_001


title: DVS265 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS265_S16_L003_R1_001


title: Tumor cells, JQ1_day3_rep1_RNA-Seq

tag: treatment


title: Tumor cells, DMSO_day3_rep3_RNA-Seq

tag: cell type

value: control

value: DMSO


title: S_100288

value: Placebo + Docetaxel

value: Non-Bladder


title: S_100287

value: LY3009806 + Docetaxel


title: DVS264 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS264_S15_L003_R1_001

value: Pass

value: Female


title: Tumor cells, DMSO_day3_rep2_RNA-Seq


title: S_100286

value: Bladder


title: DVS263 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS263_S14_L002_R1_001


title: Tumor cells, DMSO_day3_rep1_RNA-Seq


title: S_100284


title: S_100285


title: DVS261 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS261_S12_L002_R1_001

value: 325 mg Aspirin


title: S_100283


title: S_100281


title: Tumor cells, JQ1_day1_rep3_RNA-Seq


title: S_100279


title: S_100282


title: S_100278


title: S_100276


title: S_100291


title: Tumor cells, JQ1_day3_rep3_RNA-Seq


title: S_100275


title: S_100277


title: S_100274


title: DVS260 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS260_S11_L002_R1_001


title: Tumor cells, JQ1_day1_rep2_RNA-Seq


title: DVS259 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS259_S10_L002_R1_001

value: Male


title: Tumor cells, JQ1_day1_rep1_RNA-Seq


title: S_100270


title: Tumor cells, DMSO_day1_rep3_RNA-Seq


title: DVS256 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS256_S7_L001_R1_001

value: 81 mg Aspirin


title: S_100271


title: Tumor cells, DMSO_day1_rep2_RNA-Seq


title: S_100268


title: Tumor cells, DMSO_day1_rep1_RNA-Seq


title: S_100269


title: S_100264


title: S_100266


title: DVS255 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS255_S6_L001_R1_001


title: S_100265


title: Thymus5-Input_ChIP-Seq

data_processing:
ChIP-seq reads were mapped to zebrafish (Danio rerio GRCz11) reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were processed with samtools rmdup package to remove duplicates.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the braodpeaks called is P-value < 1E-3 and broadPeak cutoff is P-value < 1e-3
Genome_build: GRCz11
Supplementary_files_format_and_content: broadPeak file of zv11 H3K27ac called with MACS2 --broad-cutoff 1e-3 -p 1e-3 --broad --keep-dup 1 -f BAM --SPMR

growth_protocol: For normal thymus samples (thymus 2, 3 and 5), mCherry fluorescent marker gene was transduced under the zebrafish lck promoter in zebrafish. Thymus were harvested at 3 months and mCherry-positive cells were sorted by flow cytometry. For tumor samples (T0, T1, T2, TA), the human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. After the development of tumor phenotype, tumor cells were harvested.

treatment_protocol: The cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated by ChIP using a specific antibody. A sample of whole cell lysate (WCL) was sequenced and used as the background to determine enrichment.

value: normal thymus

tag: chip antibody


title: DVS254 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS254_S5_L001_R1_001

value: 180 mg Ticagrelor


title: Thymus5-H3K27ac_ChIP-Seq


title: DVS253 RNA-seq

value: Fail


title: Thymus3-Input_ChIP-Seq


title: S_100260


title: S_100257


title: S_100259


title: S_100263


title: S_100254


title: S_100256


title: DVS251R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS251R_S2_L001_R1_001


title: S_100258


title: DVS257 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS257_S8_L002_R1_001


title: Thymus3-H3K27ac_ChIP-Seq

value: H3K27ac antibody (ab4729)


title: DVS250 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS250_S1_L001_R1_001


title: Thymus2-Input_ChIP-Seq


title: DVS249 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS249_S25_L004_R1_001


title: Thymus2-H3K27ac_ChIP-Seq


title: S_100252


title: DVS248 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS248_S24_L004_R1_001


title: S_100250


title: Tumor3_Input_ChIP-seq

value: tumors driven by overexpression of human IRF4


title: DVS247 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS247_S23_L004_R1_001


title: DVS252 RNA-seq


title: DVS246 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS246_S22_L004_R1_001


title: Tumor3_H3K27ac_ChIP-seq


title: Tumor2_Input_ChIP-seq


title: DVS243 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS243_S5_L001_R1_001


title: S_100247


title: Tumor2_H3K27ac_ChIP-seq


title: S_100244


title: S_100253


title: S_100255


title: S_100251


title: S_100246


title: S_100241


title: S_100242


title: S_100248


title: S_100240


title: Tumor1_Input_ChIP-seq


title: DVS242 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS242_S4_L001_R1_001


title: S_100239


title: S_100249


title: S_100238


title: DVS240 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS240_S2_L001_R1_001


title: Tumor1_H3K27ac_ChIP-seq


title: S_100245


title: S_100289


title: S_100235


title: S_100234


title: S_100236


title: S_100272


title: IRF4 overexpression with p53 mutation RNA-seq #2

data_processing:
RNA-seq datasets of two control thymus samples and four tumor samples (two from lck:IRF4 and two from lRF4;p53+/-) were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation (GRCz11 gtf file)
Bioconductor package DESeq2 v1.12.4, with the intersection-strict mode, was used to analyze differential gene expression.
Genome_build: GRCz11
Supplementary_files_format_and_content: txt files for raw counts, differentially expressed genes

growth_protocol: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  After the development of lymphoma phenotype, tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA-seq analysis.

extract_protocol:
Total RNA was harvested using the Qiagen miRNeasy kit.
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

value: IRF4 overexpression and p53 mutation


title: DVS239 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS239_S21_L004_R1_001


title: IRF4 overexpression RNA-seq #2

value: IRF4 overexpression


title: S_100233


title: IRF4 overexpression with p53 mutation RNA-seq #1


title: DVS238 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS238_S20_L004_R1_001


title: IRF4 overexpression RNA-seq #1


title: DVS237 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS237_S19_L003_R1_001


title: DVS236 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS236_S18_L003_R1_001


title: DVS241 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS241_S3_L001_R1_001


title: S_100229


title: S_100230


title: S_100228


title: S_100231


title: S_100225


title: mCherry control RNA-seq #2

source_name: lck-mCherry

value: control


title: DVS235 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS235_S17_L003_R1_001


title: mCherry control RNA-seq #1


title: DVS234 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS234_S16_L003_R1_001


title: DVS233 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS233_S15_L003_R1_001


title: MRPL28_4C

city: Cleveland

first: Shanshan

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

data_processing:
library strategy: 4C-seq
The 4C-Seq data were analyzed using pipe4C to generate bam files(hg19 build) and wig files for visualization
Supplementary files format and content: wig.gz
Assembly: hg19

source_name: GM12878 cell line

growth_protocol: GM12878 cells were maintained in RPMI 1640 medium (Gibco, Cat#11875-085) supplemented with 15% FBS (Gibco, Cat#16000-044) and 1% pen/strep (Gibco, Cat#10378-016).

extract_protocol:
The fixed cells were then lysed with a cell lysis buffer, which contains 50 mM Tris-Cl pH7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and 1x protease inhibitor cocktail (Roche, Cat#11873580001), for 20-30 minutes on ice. After lysing, the nuclei were harvest and washed with 1x restriction enzyme buffer once. The nuclei pellets were then resuspended in 1x restriction enzyme buffer and treated with 0.3% SDS for 1 hour at 37°C under shaking, followed by another hour with 2.5% Triton X-100. Chromatin digestion was then done by incubating the samples with designated restriction enzyme at proper temperature for overnight while rotating in an airbath. The restriction enzymes used for each locus were listed in "VPinfo.txt". After digestion, heat inactivation at 65°C was applied to inactivate the enzymes and the nuclei were then subjected to ligation with 50μl of T4 DNA ligase (Invitrogen, Cat# 15224-090) in a 7ml ligation solution at 16°C for overnight. Reverse-linking was then performed by treating the samples with proteinase K to get the proximity ligated DNA. The purified DNAs were quantified and subjected to the secondary restriction enzyme digestion, roughly 1 unit of restriction enzyme for 1μg DNA, at the suggested temperature for overnight. After inactivation of the restriction enzymes, the samples were then self-ligated with T4 DNA ligase. The ligated DNAs were recovered with Sodium Acetate and ethanol and quantified with Qubit dsDNA HS assay kit (Thermo Fisher, Cat# Q32851).
The 4C-templates were then amplified with designed primers to generate libraries for sequencing. Firstly, the 4C templates were amplified with locus specific primers using 200ng template in each reaction, and we combined 5 reactions for each locus. A 50 μl PCR product aliquots were purified with homemade seramega beads. And one fifth of the purified DNAs were used for the second PCR. The final products were then purified and subjected to sequencing.

value: GM12878 cell line

tag: locus

tag: primer

value: CGGAACCGGAAGCCGATC

tag: 1st enzyme

value: NlaIII

tag: 2nd enzyme

value: DpnII


title: S_100224

value: Placebo + Docetaxel


title: S_100226

value: Bladder


title: MEST_4C

value: MEST

value: GATAGTGGGGCAGGAGTAC


title: DVS232 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS232_S14_L003_R1_001

value: Pass

value: 325 mg Aspirin

tag: flowcell

value: Female

tag: age

tag: plateletfunctionscore

tag: logscaledsalicylatelevel


title: S_100223

value: LY3009806 + Docetaxel


title: S_100221

value: Non-Bladder


title: S_100219


title: S_100222


title: H19_4C

value: CGGCTTGTGGACTCGGTAC


title: DVS231 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS231_S13_L003_R1_001

value: 81 mg Aspirin

tag: Sex


title: GPNMB_4C

value: GPNMB

value: AGATGGGGTTTCCCCAT


title: DVS230 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS230_S12_L002_R1_001


title: S_100218

tag: primary site


title: S_100215


title: S_100214


title: S_100227


title: ACBD7_4C

value: GM12878 cell line

value: TCCCTCAAGCACCTGATC


title: S_100217