title: MPP cells extracted from mouse at steady state, biological replicate 4 of WT control group

city: Lund

first: Sarah

last: Warsi

address: BMC, Sölvegatan 17

country: Sweden

institute: Lund University

description: Gene expression data from hematopoietic multipotent progenitor cells extracted from bone marrow from a wildtype mouse with a C57Bl/6 background, used as control data for comparison with elektra homozygous cells (from littermates). Cells extracted at steady state i.e. no specific treatments given to mice prior to cell extraction.

hyb_protocol: 6.5 µg of fragmented and terminal labeled sense-strand single-stranded cDNA were hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays for 16 h at 45 °C and 60 rpm in an Affymetrix GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing:
Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P-values (t-test) were calculated. Additionally, an in-house analysis was done, please see details in associated publication.
log2 gene level RMA signal intensity, generated by the Affymetrix GeneChip Expression Console v1.4 software. Additionally, an in-house analysis was done, please see details in associated publication.

label: biotin

source_name: bone marrow

label_protocol: The Affymetrix GeneChip WT Pico Kit protocol was used for the preparation of biotinylated sense-strand single-stranded cDNA from approximately 100 to 200 pg of total RNA, including a pre- in vitro transcription amplification by a 12 cycle PCR. Finally the purified single-stranded cDNA was enzymatically fragmented and terminal labeled with biotin.

growth_protocol: The elektra strain was purchased from the MMRRC Repository (strain ID C57BL/6J-Slfn2m1Btlr/Mmucd) and bred at the Lund University animal facility. Mice were housed and bred in ventilated cages with food and water ad libitum. Breedings generated both elektra (Slfn2 mutant) homozygous mice and wildtype homozygous control mice. All experiments involving animals were approved by the regional Animal Ethical Committee.

extract_protocol: Please see associated publication. In brief, elektra (Slfn2 mutant) homozygous mice were sacrificed, as were littermates homozygous for the wildtype Slfn2 allele (used as controls for comparison of elektra expression data to that of wildtype mice). Post-mortem dissection was done to retrieve femur, tibia and iliac. For sufficient cell numbers, bones from two mice of the same genotype (Slfn2 elektra/elektra or wildtype/wildtype) were pooled within each sample. Bone marrow was extracted by crushing bones in PBS with 2% FCS. C-kit enrichment using microbeads and MACS columns (Miltenyi biotec). Cells were stained with fluorescently labeled antibodies and sorted on a FACS Aria, and dead cells excluded using 7AAD. Cells were sorted into RLT buffer and frozen at -80 prior to shipment to KFB (Regensburg, Germany) for further processing. RNA isolation was done using the RNeasy Micro Kit (Qiagen) according to manufacturer’s protocol. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent).

treatment_protocol: No treatments were given to the mice prior to euthanization and cell extraction.

value: purified hematopoietic multipotent progenitor cells

tag: group

value: Wildtype control

tag: genotypes

value: Slfn2 wt/wt


title: MPP cells extracted from mouse at steady state, biological replicate 4 of Elektra (Slfn2 mutant) group

status: Public on Feb 09 2023

type: RNA

description: Gene expression data from hematopoietic multipotent progenitor cells extracted from bone marrow from an elektra homozygous mouse with a C57Bl/6 background. Cells extracted at steady state i.e. no specific treatments given to mice prior to cell extraction.

molecule: total RNA

organism: Mus musculus

tag: tissue

value: Elektra (Slfn2 mutant)

value: Slfn2 elektra/elektra


title: MPP cells extracted from mouse at steady state, biological replicate 3 of WT control group


title: MPP cells extracted from mouse at steady state, biological replicate 2 of Elektra (Slfn2 mutant) group


title: gfp::spt-2 C. elegans, GFP, replicate 1

type: SRA

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Reads were preprocessed using trim-galore (version 0.6.7) and then mapped on the C. elegans genome (wormbase release WS285) using bwa-mem (version 0.7.17).
Reads with mapping quality (MAPQ) higher than 10 were extracted using Samtools, and bigwig tracks generated using bamCoverage (from DeepTools, version 3.5.1) with parameters: "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 100286401 --extendReads".
Assembly: WS285
Supplementary files format and content: BigWig tracks, RPGC-normalized, 1bp resolution

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: gfp::spt-2 synchronised adults

growth_protocol: Worms were grown at 20C on 1xNGM plates with HB101 bacteria.

extract_protocol:
Worms were ground and fixed with EGS solution (final 1.5mM concentration) for 8 minutes, followed by crosslinking with 1% methanol-free formaldehyde for 8 minutes. Chromatin was sonicated to 100-300bp length with a Bioruptor sonicator. 20ug of chromatin was used per IP reaction.
The library preparation was performed as previously described (Janes et al. 2018 eLife) using a modified Illumina TruSeq protocol. Briefly, TruSeq adaptors were ligated using NB Quick Ligase (M2200) and libraries were amplified with a KAPA HiFi Hot Start polymerase mix. Aftr PCR amplification, size selection was performed with AMPure beads (Beckman Coulter) to obtain fragments between 250-370bp, and size distribution was validated with a Agilent Tapestation.

treatment_protocol: Synchronised worms were collected as gravid adults.

tag: evelopmental stage

value: gfp::spt-2 synchronised adults

tag: cell type

value: whole woms

tag: chip antibody

value: GFP (Abcam, ab290)


title: RNAPII_AngII_siGβ1_1

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description:
Sheared chromain
Cardiac fibroblasts were treated 72 h after transfection with 50 nM siRNA. S. pombe chromatin was combined with the rat chromatin and immunoprecipitated with an anti-Rpb1 (8WG16) antibody
RNAPII_AngII_siGβ1.bw

data_processing:
Fastq files were trimmed with TrimGalore (v0.6.0)  with the settings --phred33 --length 36 -q 5 --stringency 1 -e 0.1
Processed reads were aligned to the custom combined rat and S. pombe genome with Bowtie2 (v2.3.5)
Low-quality mapped reads (MAPQ < 10) and reads mapped to non-standard chromosomes were removed wtih SAMtools (v1.9)
Duplicate reads were removed with Picard tools (v2.20.6, Broad Institute)
Aligned reads were separated into individual files for the rat or S. pombe genome respectively
Input reads subtracted with the deepTools (v3.3.1) function bamCompare (--scaleFactorsMethod SES) and negative values set to 0
Values were converted to RPM with library size adjusted by the total number of reads aligned to the S. pombe genome
Genome_build: Rattus_norvegicus.Rnor_6.0.94 and Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: bigwig file of merged biological replicates

organism: Rattus norvegicus

source_name: cardiac fibroblasts

growth_protocol: Cardiac fibroblasts were isolated from 1-3 day old Sprague-Dawley rats.

extract_protocol:
Cardiac fibroblasts were fixed with 1% formaldehyde and the fixed chromatin sonicated for 18 cycles (30 seconds on/30 seconds off) in a Diagenode BioRuptor UCD-200
Libraries were prepared with the NEBNext® UltraTM II DNA Library Prep kit for Illumina

treatment_protocol: Cardiac fibroblasts were treated for 75 min with 1 μM Ang II

tag: age

value: Neonatal

tag: treatment

value: 1 uM AngII/50 nM siGβ1


title: MPP cells extracted from mouse at steady state, biological replicate 1 of WT control group


title: MPP cells extracted from mouse at steady state, biological replicate 2 of WT control group


title: MPP cells extracted from mouse at steady state, biological replicate 3 of Elektra (Slfn2 mutant) group


title: RNAPII_AngII_siCtrl_3

description:
Sheared chromain
Cardiac fibroblasts were treated 72 h after transfection with 50 nM siRNA. S. pombe chromatin was combined with the rat chromatin and immunoprecipitated with an anti-Rpb1 (8WG16) antibody
RNAPII_AngII_siCtrl.bw

value: 1 uM AngII/50 nM siCtrl


title: OD_0.3_r3

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

library_source: transcriptomic

data_processing:
Read trimming and quality control of was executed using BBDuk using the the default adapter sequence database
Read alignment and counting was performed with Bowtie2 (Langmead & Salzberg 2012) and featureCounts (Liao et al. 2014)
Assembly: NC_016810.1
Supplementary files format and content: Unprocessed count matrix from all samples
Supplementary files format and content: bulk_counts.tsv

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial cell

extract_protocol:
Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer’s recommendation using 100ng total RNA as input per sample.
DNA libraries suitable for sequencing were prepared using CORALL Total RNA-Seq Library Prep protocol (Lexogen) according to the manufacturer's recommendation with 13 PCR cycles. Library quality was checked using a 2100 Bioanalyzer DNA High Sensitivity kit.

value: bacterial cell

tag: media

value: Lennox broth media

tag: od

tag: condition

value: MEP


title: RNAPII_AngII_siCtrl_2


title: OD_0.3_r2


title: spt-2 M627A, replicate 2

data_processing:
Reads were trimmed using trim_galore (version 0.6.7), and aligned using bwa mem (version 0.7.17)
Low-quality (q<10) reads and reads mapping to non-assembled contigs mtDNA were discarded.
Normalised coverage was calculated using MACS2: --nomodel –extsize 150 –shift -75 --keep-dup all –SPMR --nolambda
Assembly: WS285
Supplementary files format and content: BigWig tracks, SPMR normalised, 1bp resolution

source_name: synchronised adults

extract_protocol:
The ATAC-seq protocol was performed as previously described (Janes et  al. 2018 eLife). Briefly, worms were ground in Egg buffer (25mM HEPES pH 7.3, 118mM NaCl, 48mM KCl, 2mM CaCl2, 2mM MgCl2) and dounced to obtain cell nuclei. Nuclei were then resuspended in Tagmentation buffer and treated with the Tn5 enzyme (Illumina Nextera kit).
Tagmented DNA was amplified using the Nextera kit protocol, and the amplified libraries were size selected using AMPure beads to recover fragments between 150 and 500pb and sequenced.

value: synchronised adults

value: whole worms

tag: genotype

value: spt-2 M627A

value: growth at 20C


title: OD_0.3_r1


title: OD_0.1_r3

value: EEP


title: RNAPII_DMEM_siCtrl_3

description:
Sheared chromain
Cardiac fibroblasts were treated 72 h after transfection with 50 nM siRNA. S. pombe chromatin was combined with the rat chromatin and immunoprecipitated with an anti-Rpb1 (8WG16) antibody
RNAPII_DMEM_siCtrl.bw

value: DMEM/50 nM siCtrl


title: spt-2 KO-A, replicate 2

value: spt-2 KO-A


title: RNAPII_AngII_siCtrl_1


title: spt-2 M627A, replicate 1


title: cells extracted from mouse at steady state, biological replicate 3 of WT control group

description: Gene expression data from hematopoietic stem cells extracted from bone marrow from a wildtype mouse with a C57Bl/6 background, used as control data for comparison with elektra homozygous cells (from littermates). Cells extracted at steady state i.e. no specific treatments given to mice prior to cell extraction.

hyb_protocol: 3.8 µg of fragmented and terminal labeled sense-strand single-stranded cDNA were hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays for 16 h at 45 °C and 60 rpm in an Affymetrix GeneChip hybridization oven 640.

data_processing:
Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P-values (t-test) were calculated.  Additionally, an in-house analysis was done, please see details in associated publication.
log2 gene level RMA signal intensity, generated by the Affymetrix GeneChip Expression Console v1.4 software. Additionally, an in-house analysis was done, please see details in associated publication.

label_protocol: The Affymetrix GeneChip WT Pico Kit protocol was used for the preparation of biotinylated sense-strand single-stranded cDNA from approximately 200 pg of total RNA, including a pre- in vitro transcription amplification by a 12 cycle PCR. Finally the purified single-stranded cDNA was enzymatically fragmented and terminal labeled with biotin.

value: purified hematopoietic stem cells

value: Wildtype control

value: Slfn2 wt/wt


title: spt-2 KO-A, replicate 1


title: MPP cells extracted from mouse at steady state, biological replicate 1 of Elektra (Slfn2 mutant) group

value: purified hematopoietic multipotent progenitor cells

value: Elektra (Slfn2 mutant)

value: Slfn2 elektra/elektra


title: cells extracted from mouse at steady state, biological replicate 4 of WT control group


title: RNAPII_DMEM_siCtrl_2

value: Neonatal


title: WT, replicate 2

value: WT N2


title: OD_0.1_r2

value: bacterial cell

value: Lennox broth media


title: OD_0.1_r1


title: WT, replicate 1

value: synchronised adults


title: RNAPII_DMEM_siCtrl_1


title: HFD-fed placebo ApoE-/- 15 mg/kg/day ponatinib rep2

status: Public on Feb 08 2023

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

country: USA

institute: University of Pittsburgh

description: HFD-fed placebo ApoE-/-

data_processing:
Partek Flow
Raw reads (fastq files) were uploaded to the Partek Flow server and pre-alignment quality assessment was performed
Mean base-call quality scores were above Phred-like values of 36 in all positions of all samples, and no hard trimming of the reads was necessary.
Sequences were aligned to the mm10 assembly of the mouse genome using STAR 2.5.3a.
The resulting summary of reads quantified at the gene level to Ensemble transcripts 83 using Partek’s expectation-maximization (E/M) annotation model.
Gene counts were normalized to the total read count per sample and then log-transformed (with an offset of 0.0001)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: left ventricular cardiac

extract_protocol:
RNA was harvested using Rneasy mini kit (74104, Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using the Illumina TruSeq Stranded Total RNA kit.

value: APOE -/-

value: High fat diet (HFD)

value: 15 mg/kg/day ponatinib

value: left ventricular cardiac

tag: time

value: HFD for 8 wks, then HFD + treatment for 2wks


title: HFD-fed placebo ApoE-/- 15 mg/kg/day ponatinib rep4

description: HFD-fed placebo ApoE-/-


title: HFD-fed placebo ApoE-/- 15 mg/kg/day ponatinib rep1

description: HFD-fed placebo ApoE-/-


title: HFD-fed placebo ApoE-/- 15 mg/kg/day ponatinib rep3

description: HFD-fed placebo ApoE-/-


title: cells extracted from mouse at steady state, biological replicate 4 of Elektra (Slfn2 mutant) group

description: Gene expression data from hematopoietic stem cells extracted from bone marrow from an elektra homozygous mouse with a C57Bl/6 background. Cells extracted at steady state i.e. no specific treatments given to mice prior to cell extraction.


title: HFD-fed placebo ApoE-/- placebo rep5

description: HFD-fed placebo ApoE-/-

value: placebo


title: HFD-fed placebo ApoE-/- placebo rep3

description: HFD-fed placebo ApoE-/-


title: HFD-fed placebo ApoE-/- placebo rep2

description: HFD-fed placebo ApoE-/-


title: cells extracted from mouse at steady state, biological replicate 3 of Elektra (Slfn2 mutant) group

value: purified hematopoietic stem cells


title: HFD-fed placebo ApoE-/- placebo rep4

description: HFD-fed placebo ApoE-/-


title: HFD-fed placebo ApoE-/- placebo rep1

description: HFD-fed placebo ApoE-/-


title: cells extracted from mouse at steady state, biological replicate 1 of Elektra (Slfn2 mutant) group


title: cells extracted from mouse at steady state, biological replicate 1 of WT control group

value: Wildtype control


title: cells extracted from mouse at steady state, biological replicate 2 of Elektra (Slfn2 mutant) group


title: cells extracted from mouse at steady state, biological replicate 2 of WT control group

value: Slfn2 wt/wt


title: Wilms3_rep4_reanalyzed

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer HI- RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (4x 44K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) and air dried.

scan_protocol: Slides were scanned with an Agilent Technologies Scanner G2505B using a scan area of 61x21.6 mm, scan resolution of 5µm, dye channel set to green and green PMT set to 100%.

data_processing: Scans were quantified using Agilent Feature Extraction Software V10.7.1.1 or V10.1.1.1 (only Wilms6_rep1 and Wilms6_rep2). Control spots are removed, replicate oligos are averaged. Arrays were quantile normalized between chips using R-software (Limma).

organism: Homo sapiens

source_name: Wilms tumor cell line 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultivated in MCSG-medium (Lonza) at 37 degree and 5% CO2. Medium was changed every third day.

extract_protocol: RNA was prepared using the RNAeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations, with an included on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: kidney

tag: gender

value: male


title: Wilms5_rep2_reanalyzed

source_name: Wilms tumor cell line 5


title: Wilms5_rep3_reanalyzed


title: Wilms3_rep3_reanalyzed


title: Wilms10_P3_reanalyzed

source_name: Wilms10 tumor cell line

value: female


title: Wilms10_P7_reanalyzed


title: Wilms5_rep1_reanalyzed


title: Wilms4_rep1_reanalyzed

source_name: Wilms tumor cell line 4


title: Wilms1_rep2_reanalyzed

source_name: Wilms tumor cell line 1


title: Wilms1_rep4_reanalyzed


title: Wilms2_rep2_reanalyzed

source_name: Wilms tumor cell line 2


title: Wilms2_rep1_reanalyzed


title: Wilms3_rep2_reanalyzed


title: Wilms2_rep4_reanalyzed


title: Wilms2_rep3_reanalyzed


title: Wilms1_rep5_reanalyzed


title: Wilms2_rep5_reanalyzed


title: Wilms1_rep3_reanalyzed


title: CLS1_rep2_reanalyzed

source_name: Wilms tumor cell line CLS1

growth_protocol: For CLS1 samples: Cells were cultivated in Iscoves medium supplemented with 2mM L-Glutamine and 15% FCS. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.


title: Wilms10-M_rep2

source_name: Wilms tumor lung metastasis cell line 10 replicate 2


title: Wilms4_rep3_reanalyzed


title: Wilms1_rep1_reanalyzed


title: Wilms10-M_rep1

source_name: Wilms tumor lung metastasis cell line 10 replicate 1


title: CLS1_rep3_reanalyzed


title: Wilms8_rep2

source_name: Wilms tumor cell line 8 replicate 2


title: Wilms4_rep2_reanalyzed


title: CLS1_rep4_reanalyzed


title: CLS1_rep1_reanalyzed


title: Wilms3_rep1_reanalyzed


title: S18_VEH

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

data_processing:
Sequenced reads were mapped to mm9 using TopHat v2.0.10
Reads counts and differential expressed genes were calculated using Cufflinks and CuffDiff
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: mCG-PML-RAR transgenic mice

growth_protocol: For APL development, leukemic cells derived from two APL C57BL/6-Ly5.2 mice (2x106 cells in the case of CD45.2+ APL#1, or 2x105 cells in the case of CD45.2+ APL#2) were intravenously transplanted into non-irradiated CD45.1+ (C57BL/6-Ly5.1) recipient mice. CD45.2+ APL cells were harvested from spleens and purified using immunomagnetic column selection.

extract_protocol:
RNAs from APL#1 and APL#2 were isolated using an RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: CD45.2+ acute promyelocytic leukemic cells

value: 10 weeks

value: PML-RAR KI APL

tag: cell line

value: Primary murine APL

value: Untreated


title: S12_VEH


title: INPUT_NLP2-T30

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

data_processing:
Read mapping: Paired-end 41 bp reads aligned to tair10 genome assembly using Bowtie2 v2.3.4.1 with --very-sensitive -p 10 parameters. One mismatch allowed.
Duplicate flagging and filtering out genomic regions with aberrant coverage or low sequence complexity (Quadrana et al., 2016; DOI: 10.7554/eLife.15716) using PicardTools MarkDuplicates v2.8.1 and samtools v1.7 to remove sequencing biases.
Peak calling : Peak-calling using MACS2 v2.1.1 in narrow mode, format BAMPE, genome size set to 10e7, --keep-dup parameter set to 5, qvalue threshold set to 2 and -B option.
Irreproducibility Discovery Rate (IDR) was used to measure consistency between biological replicates by statistically determining the reproducibility in score ranking between peaks in each replicate. IDR analysis code available at https://github.com/mlin/encode2/tree/master/chip-seq2/idr/resources/opt/idrCode.
Genome_build: tair10
Supplementary_files_format_and_content: peaks = table of IDR-selected peaks in narrowpeak format (Chromosome_name Start_position_of_peak End_position_of peak Name_of_peak Score Average_signalValue Strand pValue_(-log10) qValue_FDR_ (-log10) peak);bed = table of artefactual peaks (Chromosome_Name Start_position_of_peak End_position_of peak Name_of_peak Enrichment qValue_(-log10)) defined from control sample using MACS2 (INPUT)

organism: Arabidopsis thaliana

source_name: 14-d-old seedlings

growth_protocol: Seedlings were grown for 10 days on a 3 mM KNO3 liquid medium (3 mM KNO3, 1 mM KH2PO4/K2HPO4, pH 5.8, 0.5 mM CaSO4, 0.5 mM MgCl2, 3 mM MES, pH 5.8, 0.25% (w/v) Sucrose, supplemented with microelements) in long-day photoperiod (16/8h at 25°C/18°C). Plants were then nitrogen-starved for three days by changing the culture medium with a nitrogen free medium in which KNO3 was replaced by KCl. A 30 min-nitrate induction was performed by changing the culture medium for the 3 mM nitrate solution (T30 sample). For control samples (T0), the nitrogen-free solution was changed for a fresh one.

extract_protocol:
Chromatin extraction and immunoprecipitation was performed essentially as described in (Bouyer et al., 2018; https://doi.org/10.1371/journal.pgen.1007797) with minor modifications. Briefly, 800 mg of liquid nitrogen-ground seedlings were subject to double crosslinking (2.5mM Di(N-succinimidyl) glutarate 60 min followed by 1% formaldehyde 7 min). Chromatin fragmentation was done using a Covaris S220 ultra-sonicator with the following parameters: 12 min with 5% duty cycle, 105W peak power and 200 cycles per burst. Chromatin immunoprecipitation was done using 3 ug of anti-GFP antibodies (ab290,Abcam) pre-bound to proteinA/G-coupled magnetic beads.
For each replicate, 250 pg of immunoprecipitated (IP) and genomic (INPUT) DNA were used to prepare libraries with the MicroPlex Library Preparation kit (Diagenode). Quality of libraries was validated using Agilent / Advanced Analytical fragment analyzer. Multiplexed libraries were sequenced using a NextSeq 500  system (Illumina) with paired-ends 41 bp reads.

value: nlp2-2 complemented with pNLP2::NLP2-GFP construct (in Col-0)

value: 3 mM NO3- for 30 min

tag: antibody


title: KO_2_IP22

city: beijing

first: zhenxi

last: zhang

address: Dongdan Santiao No. 5

country: China

institute: PUMC

description: repeat 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA and clean reads were aligned to the reference genome using BWA mem.
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis. s-Wheeler transform.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Liver

extract_protocol:
For ChIP–seq analysis, mouse liver tissues were cross-linked with 1% formaldehyde for 10 min at room temperature and were stopped by the addition of glycine with gentle shaking for 5 min. Cell lysates were digested and sonicated to generate DNA fragments with an average size between 200-1,000 bp and immunoprecipitated with H3K9/H3K27 acetylation antibodies. The DNA sample of chromatin immunoprecipitation is obtained after de crosslinking and purification of DNA for sequencing. DNA samples were deeply sequenced [1].
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: H3K9 Acetylation antibod

value: P53 KO

value: Ethanol treatment


title: KO_1_Input


title: WT_1_IP1

description: repeat 1

value: P53 WT


title: WT_2_IP11

description: repeat 1


title: WT_2_IP22

description: repeat 2


title: WT_4_IP11

description: repeat 1

value: H3K27 Acetylation antibod


title: WT_3_IP2

description: repeat 2


title: KO_2_IP11

description: repeat 1


title: KO_3_IP2

description: repeat 2


title: KO_1_IP1

description: repeat 1


title: KO_3_IP1

description: repeat 1


title: KO_4_IP22

description: repeat 2


title: WT_2_Input


title: WT_1_IP2

description: repeat 2


title: KO_4_IP11

description: repeat 1


title: KO_2_Input


title: WT_1_Input


title: WT_3_IP1

description: repeat 1


title: WT_4_IP22

description: repeat 2


title: KO_1_IP2

description: repeat 2


title: INPUT_NLP2-T0

value: no


title: Wilms8_rep1

source_name: Wilms tumor cell line 8 replicate 1

value: kidney


title: Wilms6_rep2

source_name: Wilms tumor cell line 6 replicate 2

value: male


title: Wilms6_rep4

source_name: Wilms tumor cell line 6 replicate 4


title: Wilms6_rep3

source_name: Wilms tumor cell line 6 replicate 3


title: NLP2-T30_rep2

value: anti-GFP antibodies (ab290,Abcam)


title: NLP2-T30_rep1


title: Wilms6_rep1

source_name: Wilms tumor cell line 6 replicate 1


title: NLP2-T0_rep2


title: naïve-18-rN18_L2_GGAGAA_L002

city: Stanford

first: Ricardo

middle: Luiz

last: De Azevedo Pereira

state: CA

address: 1201 Welch Road

department: Neurosurgery

institute: Stanford

description:
diffgene_DESeq2_rSC_vs_rN
rN_18

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastqc (version 0.11.4) was used for sequencing quality assessment and fastx toolkit (version 0.0.14) was used to trim the first 10 bp from both reads
The trimmed reads were then aligned to the pooled transcriptome of the human (hg19) and rat (rn5) using Bowtie (version 2.2.7) with splice junctions being defined in GTF file for both genome (obtained from UCSC)
Gene level expression was determined by calculating reads per kilo base per million aligned reads (FPKM) as well as raw count using RNA-Seq by Expectation Maximization (RSEM; version 1.2.30) with a human-rat pooled reference transcriptome.
Genome_build: hg19; rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Host-naïve

extract_protocol:
Transplantation sites were removed for TRAP method and RNA isolated using RNeasy Micro Kit (Qiagen) for graft and RNeasy Mini Kit (Qiagen) for host tissue. RNA from TRAP samples and TRAPnf samples were converted to cDNA using the Ovation RNA-seq v2 (Nugen) and cDNA libraries we prepared by Ovation Ultralow System V2 (Nugen) was used with 2 ng of total RNA for the construction of sequencing libraries.
RNA sequencing was performed on an Illumina HiSeq 2500 system , with TRAP samples from engrafted tissue as single lane 125 bp paired-end read, and TRAPnf and TRAP from in vitro samples as multiplexed (4 samples per lane), 50 bp paired-end reads.

value: cortex

value: host nude rat cortex

value: 12 weeks old

tag: sample type

value: TRAP negative fraction (TRAPnf)


title: naïve-17-rN17_L2_AAGAGG_L002

description:
diffgene_DESeq2_rSC_vs_rN
rN_17


title: rSB_13-rSB13_L1_GTCGTA_L001

source_name: Host-stroke+vehicle

extract_protocol:
In vitro and transplantation sites were removed for TRAP method and RNA isolated using RNeasy Micro Kit (Qiagen) for graft and RNeasy Mini Kit (Qiagen) for host tissue. RNA from TRAP samples and TRAPnf samples were converted to cDNA using the Ovation RNA-seq v2 (Nugen) and cDNA libraries we prepared by Ovation Ultralow System V2 (Nugen) was used with 2 ng of total RNA for the construction of sequencing libraries.
RNA sequencing was performed on an Illumina HiSeq 2500 system , with TRAP samples from engrafted tissue as single lane 125 bp paired-end read, and TRAPnf and TRAP from in vitro samples as multiplexed (4 samples per lane), 50 bp paired-end reads.

value: Nude rat cortex

value: Ischemic-stroke+vehicle


title: stroke-9-rSC9_L2_AGTGAG_L002

description:
diffgene_DESeq2_rSC_vs_rN
rSC_9

source_name: Host-stroke

value: Ischemic-stroke


title: GSL44_LParietalCortex

city: Bethesda

first: Cynthia

middle: J

last: Tifft

state: MD

address: 10 Center Dr

department: MGB

institute: NIH/NHGRI

data_processing:
Alignment performed using STAR v2.7.8 with 149 bp junction gaps.
Aligned files were quantified using RSEM v1.3.2, where the transcriptome reference was generated using the GRCh38.104.gtf file.
Assembly: GRCh38.104
Supplementary files format and content: Raw gene counts, obtained using RSEM

source_name: Left parietal cortex

extract_protocol:
Total RNA was extracted from tissue samples using the Maxwell® RSC simplyRNA Tissue Kit (Promega, Madison, WI, Cat #AS1340) according to manufacturer's protocol. RNA quality was assessed using a Bioanalyzer (Agilent Technologies, Santa Clara, CA) and samples with RNA Integrity Numbers below 7 were discarded.
Library preps for next-generation sequencing were performed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, San Diego, CA, Cat # 20020613) and sequenced on a Novaseq 6000 with 150 bp paired-end reads at an average depth of 1.3E8 reads per sample.

tag: name of_sample

value: Left parietal cortex

tag: donor

value: 17 gw

tag: disease status

value: affected

tag: Sex

value: female


title: GSL44_RMidbrain1

source_name: Right midbrain1

tag: tissue

value: Right midbrain1


title: stroke-8-rSC8_L2_TGGTGA_L002

description:
diffgene_DESeq2_rSC_vs_rN
rSC_8

tag: cell type

tag: age


title: MEL cells, NFIA-ETO2, input

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

country: Switzerland

institute: UKBB-DBM

data_processing:
Reads were mapped to the mouse genome assembly, version mm10, with bowtie2 (version 2. 4.2) using the option '--wrapper basic-0 --maxins 2000 --no-mixed --no-discordant --local'.
The output was sorted and indexed with samtools (version 1.11). Picard markDuplicates (version 2.23.4) was used to collapse samples run on different sequencing lanes.
Coverage tracks per sample were generated by tiling the genome in 20bp windows, counting overlapping reads per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Regions of accessible chromatin were called with macs2 (version 2.2.7.1) using the option '--nomodel --format=BAM --keep-dup=all --bdg --SPMR -g 2652783500 --extsize 155 --qvalue 0.05'. The peak-calling was performed for the HA tag in NFIA-ETO2 MEL sample without using the input as control.
Assembly: mm10
Supplementary files format and content: bigWig, bed

source_name: murine erythroleukemia

growth_protocol: Murine erythroleukemia (MEL) cells were obtained from DSMZ (cultured in suspension in DMEM (Dulbecco's Modified Eagle Medium) (Gibco, Lubio, Thermo Fisher Scientific, Reinach, Switzerland), 5% FCS (Fetal Calf Serum), 1% P/S  (Penicillin-Streptomycin) (Reddy and Shen 1992).

extract_protocol:
MEL cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes, followed by lysis in SDS lysis buffer. Precipitation for all samples was performed with ChIP grade protein A/G coupled magnetic beads. After the overnight incubation, washing steps were performed, followed by the elution in fresh elution buffer.
Libraries were prepared following the manufacturer protocols for Chipseq sequencing with Illumina NextSeq 550DX sequencer (ILLUMINA).

treatment_protocol: Cells were transduced with viral supernatants, containing the vector to express NFIA-ETO2 gene fusion, in presence of 5ug/ml polybrene (Sigma Aldrich, Buchs, Switzerland) 90min, 1800 rpm at 30°C. Cells were incubated overnight with the cells, and washed with PBS and plated in DMEM.

value: murine erythroleukemia

tag: chip antibody


title: stroke-16-rSC16_L2_GCACTA_L002

description:
diffgene_DESeq2_rSC_vs_rN
rSC_16

tag: treatment


title: GSL44_LCerebellum

source_name: Left cerebellum

value: Left cerebellum


title: rSB_6-rSB6_L1_ACCTCA_L001


title: naïve-19-rN19_L2_AGCATG_L002

description:
diffgene_DESeq2_rSC_vs_rN
rN_19


title: rSB_2-rSB2_L1_GTGCTT_L001


title: GSL52_FrontalCortex

source_name: Frontal cortex

value: Frontal cortex


title: GSL52_WhiteMatter

source_name: White matter

value: White matter

value: male


title: GSL52_ParietalCortex

source_name: Parietal cortex

value: Parietal cortex


title: rSB_12-rSB12_L1_AAGCCT_L001

value: cortex


title: G1

city: Toronto

first: Michael

last: Fehlings

state: ON

address: 60 Leonard Avenue, 7KD-430

department: Genetics and Development

institute: University Health Network

data_processing:
Trim Galore (v0.6.5, paired-end, automatic adapter trimming)
RNA STAR (v2.7.8a, paired-end, single-sample 2-pass mapping for novel splice junctions)
Aligned bam files merged between lanes using samtools merge
featureCount (v2.0.1, paired-end)
Assembly: rn6
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: rat epNSPCs, glutamate day 2

extract_protocol:
Total mRNA was isolated from epNSPCs using the mirVana PARIS RNA and Native Protein Purification Kit (Invitrogen).
NEBNext Ultra II Directional RNA Kit was used for library construction following the manufacturer's protocols.

value: spinal cord ependymal stem cell

value: treatment, neurobasal media + glutamate (500 uM)


title: G3


title: C2

source_name: rat epNSPCs, control day 2

value: control, neurobasal media


title: G2


title: C3


title: NLP2-T0_rep1

source_name: 14-d-old seedlings

value: nlp2-2 complemented with pNLP2::NLP2-GFP construct (in Col-0)

value: no

value: anti-GFP antibodies (ab290,Abcam)


title: GSL44_RParietalCortex

source_name: Right parietal cortex

value: Right parietal cortex

value: 17 gw


title: GSL52_Midbrain

source_name: Midbrain

value: Midbrain

value: affected


title: C1


title: CTRL2_RCentrumSemiovale

source_name: Right centrum semiovale

value: Right centrum semiovale

value: CTRL2 (UMBN#4711)

value: 18 gw

value: unaffected


title: GSL44_RMidbrain2

source_name: Right midbrain2

value: Right midbrain2

value: female


title: CTRL2_RParietalCortex

value: male


title: CTRL2_RThalamus

source_name: Right thalamus

value: Right thalamus


title: CTRL2_RVermis

source_name: Right vermis

value: Right vermis


title: CTRL1_LCentrumSemiovale

source_name: Left centrum semiovale

value: Left centrum semiovale

value: CTRL1 (UMBN#1771)


title: Karpas_wt_SETD2i_RNAseq_rep3

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

data_processing:
Adapter contamination, polyA read through, and low quality sequences were removed using bbduk (version 38.23) with the following parameters: ref=polyA.fa.gz,truseq_rna.fa.gz k=13 int=f ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20.
Read mapping was performed with STAR (version 2.7.0e) with the following parameters: --genomeDir Homo_sapiens.GRCh38.dna.primary_assembly.fa --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Reads aligned over annotated genes were quantified using HTSeq (version 0.6.1) using the following command: htseq = count -s yes.
Changes in expression calculated through DEseq2 are detailed in the tab-delimited text file: Karpas_wt_SETD2i_Differential_Genes.txt containing Transcript_ID in the first column and values for expression change as well as statistical significance in the subsequent columns.
Assembly: hg38
Supplementary files format and content: The HTSeq raw count files for each individual sample are provided as well as a summary table, "Karpas_wt_SETD2i_Differential_Genes.txt", describing the expression changes upon SETD2 inhibitor treatment.

molecule: polyA RNA

source_name: Karpas-422 wild-type cells

growth_protocol: Karpas-422 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

treatment_protocol: Karpas-422 cells were seeded at 250,000/mL and then treated with SETD2i (5 µM) or DMSO (0.1% v/v) for 10 days.

value: non-hodgkin's lymphoma

value: Karpas-422 wild-type cells treated with SETD2-IN-1 (5 uM) for 10 days


title: CTRL1_LBrainstem

source_name: Left brainstem

value: Left brainstem


title: Karpas_wt_SETD2i_RNAseq_rep2


title: CTRL1_LParietalCortex

source_name: Left parietal cortex

value: Left parietal cortex


title: Karpas_wt_DMSO_RNAseq_rep3

value: Karpas-422 wild-type cells treated with vehicle (DMSO 0.1% v/v) for 10 days


title: Karpas_wt_DMSO_RNAseq_rep2


title: single-cell_TLE_4

city: Nanjing

first: Dijun

last: Chen

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (v6.0.2,10X Genomics).
Assembly: GRCh38
Supplementary files format and content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary files format and content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed)

source_name: Brain

extract_protocol:
Brain were removed, flash frozen on dry ice, and 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.
Single nuclei were captured in the 10×Genomics Chromium Single Cell 3′ Solution, and RNA-seq libraries were prepared following the manufacturer’s protocol (10×Genomics). The libraries were subjected to high-throughput sequencing on an illumina Novaseq6000 platform, and 150-bp paired-end reads were generated.

value: Brain

value: TLE patients


title: K562_wt_RNAseq_rep2

data_processing:
Adapter contamination, polyA read through, and low quality sequences were removed using bbduk (version 38.23) with the following parameters: ref=polyA.fa.gz,truseq_rna.fa.gz k=13 int=f ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20.
Read mapping was performed with STAR (version 2.7.0e) with the following parameters: --genomeDir Homo_sapiens.GRCh38.dna.primary_assembly.fa --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Reads aligned over annotated genes were quantified using HTSeq (version 0.6.1) using the following command: htseq = count -s yes.
Changes in expression calculated through DEseq2 are detailed in the tab-delimited text file: K562_wt_CXCdel_Differential_Genes.txt containing Transcript_ID in the first column and values for expression change as well as statistical significance in the subsequent columns.
Assembly: hg38
Supplementary files format and content: The HTSeq raw count files for each individual sample are provided as well as a summary table, "K562_wt_CXCdel_Differential_Genes.txt ", describing the expression changes in the CXCdel knock-in versus wild-type cell line.

source_name: K562 wild-type cells

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

value: chronic mylogeneous leukemia

value: K562 wild-type untreated cells


title: K562_wt_RNAseq_rep3


title: K562_CXCdel_RNAseq_rep1

source_name: K562 CXCdel knock-in cells

value: K562 CXCdel knock-in untreated cells


title: CTRL1_LVermis

source_name: Left vermis

value: Left vermis

value: 18 gw

value: unaffected


title: K562_wt_RNAseq_rep1


title: CTRL1_RThalamus

value: Right thalamus

value: male


title: Karpas_wt_DMSO_RNAseq_rep1


title: K562_CXCdel_RNAseq_rep2


title: WF_969530K

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the human genome (hg19) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Gene counts were imported into R and analysis of differential expression between groups was done using the limma-voom pipeline. Raw counts are included as processed data.
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts) and columns include samples. A single file is included for all samples.

source_name: Placenta

extract_protocol:
RNA was extracted from placenta tissue from individual subjects using TRi regaents and cleanup was done using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a sphectrophometrically.
Directional cDNA libraries for mRNA-sequencing were prepared using polyA-mRNA from individual RNA samples using Illumina TruSeq reagents. Briefly, 1 μg of total RNA was utilized for mRNA isolation using poly-A magnetic beads and was fragmented prior to first and second strand cDNA synthesis. Libraries were generated via PCR including dual-indexed barcodes. Following purification with AmpureXP beads libraries were quantitated using Qubit dsDNA reagents. Pooled cDNA libraries were sequenced (150 bp paired reads) using a NovaSeq 6000 instrument.

value: Placenta

tag: arm

value: three

value: Female

value: Yes


title: WF_968940T

value: one


title: WF_970220S

value: two

value: No


title: WF_969220C


title: WF_970310R

value: Male


title: WF_969360J


title: WF_968880L


title: WF_968640I


title: WF_965760N


title: CTRL2_RBrainstem

source_name: Right brainstem

value: Right brainstem

value: CTRL2 (UMBN#4711)


title: WF_965740T


title: K562_CXCdel_RNAseq_rep3

value: chronic mylogeneous leukemia


title: Karpas_wt_SETD2i_RNAseq_rep1

value: non-hodgkin's lymphoma

value: Karpas-422 wild-type cells treated with SETD2-IN-1 (5 uM) for 10 days


title: WF_965270H


title: WF_964710K


title: WF_964960K


title: WF_964740B


title: WF_952820T


title: WF_952220U


title: WF_952170J


title: WF_964490V


title: single-cell_Normal_4

value: Brain

value: Untreated


title: WF_964440N


title: WF_964070U


title: WF_964370I


title: WF_947380C


title: WF_947340O


title: WF_952060Q


title: WF_951890D


title: WF_951630G


title: WF_944070J


title: WF_943960E


title: WF_947240S


title: WF_947190H


title: WF_943470V


title: WF_946990D


title: WF_943710E


title: WF_939410P


title: WF_943060R


title: WF_939310T


title: WF_939220U


title: WF_934580P


title: WF_938640D


title: WF_934230T


title: WF_934270H


title: WF_934220W


title: WF_938990W


title: WF_943580O


title: WF_931650M


title: WF_931710U


title: WF_931560N


title: WF_931240I


title: WF_931270W


title: WF_931720R


title: WF_931450U


title: WF_931230L


title: WF_930580M


title: WF_931110V


title: WF_930830P


title: WF_930870D


title: WF_930380U


title: WF_930310S


title: WF_930180F


title: WF_939050T


title: WF_931830K


title: WF_927290P


title: WF_930120A


title: WF_927140L


title: WF_927040P


title: WF_926810U


title: WF_927130O


title: WF_926370W


title: WF_931190U


title: WF_926020D


title: WF_925840Q


title: WF_926350F


title: WF_926710B


title: WF_926420K


title: WF_921350H


title: WF_918440A


title: WF_918420G


title: WF_918050N


title: WF_925640B


title: WF_926040U


title: WF_921410P


title: WF_917720W


title: WF_918020W


title: WF_909180B


title: WF_927230K


title: WF_908910S


title: WF_917310S


title: WF_908850K


title: WF_926750M


title: WF_917170I


title: WF_926230P


title: WF_925920S


title: WF_908630B


title: WF_908540C


title: WF_908690G


title: WF_905560L


title: WF_905170B


title: WF_905080C


title: WF_904820Q


title: WF_904650P


title: WF_905090W


title: WF_904570N


title: WF_904530C


title: WF_904430G


title: WF_905020U


title: WF_901930B


title: WF_901960P


title: WF_904710A


title: WF_904310Q


title: WF_904450A


title: WF_900990L


title: WF_901070C


title: WF_908760L


title: WF_901020R


title: WF_900950A


title: WF_900980O


title: WF_900720R


title: WF_900630S


title: WF_900830K


title: WF_900590E


title: WF_900460R


title: WF_900570K


title: WF_900420G


title: WF_900350B


title: snRNA-seq_human_NASH_rep3

city: Philadelphia

first: Yang

last: Xiao

state: PA

address: 12-193 Smilow Translational Research Center, 3400 Civic Center Boulevard

institute: UNIVERSITY OF PENNSYLVANIA

description: human study

library_source: transcriptomic single cell

data_processing:
The raw fastq files of snRNA-seq were mapped to Homo sapiens genome assembly GRCh38 (hg38) using CellRanger (3.0.2). Unique molecular identifiers (UMI) count matrices were imported into Seurat (3.2.0) (Stuart et al., 2019) to generate Seurat object to each experiment.
Assembly: hg38
Supplementary files format and content: feature-barcode matrix

source_name: liver

extract_protocol:
human study: liver nuclei were isolated and loaded to 10X Genomics Chromium controller
human study: snRNAseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell 3′ Kit
human study: In addition to the standard 10X Genomic snRNAseq library preparation, targeted sequencing libraries for EPHB2 were prepared using xGen Hybridization and Wash Kit from IDT
snRNA-seq

tag: disease state

value: NASH

tag: race

value: Caucasian

value: liver


title: snRNA-seq_human_healthy_rep2

description: human study

value: healthy


title: snRNA-seq_human_NASH_rep2

description: human study

value: Female


title: WF_901480G

value: Placenta

value: Yes


title: ATAC-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 12 hrs replicate 2

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
sDUX ATAC dox6hr rep2
sDux_B.macsbroad_peaks.narrowPeak

data_processing:
Paired-end Illumina sequencing reads were trimmed with TrimGalore (0.6.0).
Transcript abundance was quantified using the human Gencode annotations (v38) using Salmon (v 1.9) with the GC-bias correction option.
Counts were imported into R (4.2.1) using tximport (v 1.24.0). Differentially expressed genes were identified with DESeq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: Excel table of normalized FPKMs and Raw Counts and rdata object containing annotated DESeq2 dataset.
Supplementary files format and content: NarrowPeak format for called peaks and bigWig files of merged coverage.

source_name: cell line

growth_protocol: LHCN-M2 immortalized human myoblasts were cultured in F10 medium (HyClone) with 20% FBS (Peak Serum), 2-mercaptoethanol 1x (Gibco), 10-9 M dexamethasone (Sigma), 10 ng/mL bFGF (Peprotech), Glutamax (Gibco), and Penicillin/Streptomycin (P/S, Gibco) at 37°C and 5% CO2

extract_protocol:
Illumina ATAC-seq kit
RNA-seq samples were extracted with Zymo RNA extraction kit.

treatment_protocol: Cells were mock treated or treated with doxycycline as indicated.

value: cell line

value: immortalized human myoblast

tag: lentiviral _transduction

value: FUGW-rtTA and pSAM2-sDUX

value: 200 ng/mL doxycycline for 12 hrs


title: snRNA-seq_human_healthy_rep3

description: human study

value: Male


title: snRNA-seq_human_NASH_rep1

description: human study

value: Asian or Pacific Islander


title: snRNA-seq_human_healthy_rep1

description: human study


title: ATAC-seq of LHCN-M2 cells with inducible sDUX mock treated for 12 hrs replicate 1

description:
sDUX ATAC control rep1
sDux_A.macsbroad_peaks.narrowPeak

value: Mock treatment 12 hrs


title: ATAC-seq of LHCN-M2 cells with inducible DUXB mock treated for 12 hrs replicate 2

description: DUXB ATAC control rep2

value: FUGW-rtTA and pSAM2-DUXB


title: ATAC-seq of LHCN-M2 cells with inducible sDUX mock treated for 12 hrs replicate 2

description:
sDUX ATAC control rep2
sDux_B.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 12 hrs replicate 2

description:
DUXA ATAC dox6hr rep2
DUXA_B.macsbroad_peaks.narrowPeak

value: FUGW-rtTA and pSAM2-DUXA


title: ATAC-seq of LHCN-M2 cells with inducible DUXA-VP64 mock treated for 12 hrs replicate 1

description:
DUXA-VP64 ATAC control rep1
DuxAVP64_A.macsbroad_peaks.narrowPeak

value: FUGW-rtTA and pSAM2-DUXA-VP64


title: ATAC-seq of LHCN-M2 cells with inducible DUXB mock treated for 12 hrs replicate 1

description: DUXB ATAC control rep1


title: ATAC-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 12 hrs replicate 1

description: DUXB ATAC dox6hr rep1


title: ATAC-seq of LHCN-M2 cells with inducible DUXA-VP64 mock treated for 12 hrs replicate 2

description:
DUXA-VP64 ATAC control rep2
DuxAVP64_B.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUX4 treated with doxycycline for 12 hrs replicate 2

description:
DUX4 ATAC dox6hr rep2
DUX4_B.macsbroad_peaks.narrowPeak

value: FUGW-rtTA and pSAM2-DUX4


title: ATAC-seq of LHCN-M2 cells with inducible DUXA mock treated for 12 hrs replicate 2

description:
DUXA ATAC control rep2
DUXA_B.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 12 hrs replicate 1

description:
DUXA ATAC dox6hr rep1
DUXA_A.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUXA mock treated for 12 hrs replicate 1

description:
DUXA ATAC control rep1
DUXA_A.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUX4 treated with doxycycline for 12 hrs replicate 1

description:
DUX4 ATAC dox6hr rep1
DUX4_A.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUX4 mock treated for 12 hrs replicate 1

description:
DUX4 ATAC control rep1
DUX4_A.macsbroad_peaks.narrowPeak


title: ATAC-seq of LHCN-M2 cells with inducible DUX4 mock treated for 12 hrs replicate 2

description:
DUX4 ATAC control rep2
DUX4_B.macsbroad_peaks.narrowPeak


title: DU20-02S0003646

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 310 Trent Drive

department: Medicine

institute: Duke Department of Medicine

data_processing:
Both batches sequenced using an Illumina NovaSeq 6000.
Adapters were automatically detected and trimmed using fastp version 0.19.5.
Reads were aligned to the GRCh38 reference genome and quantified using STAR version 2.7.1a.
Lowly-expressed transcripts were filtered out: For batch 1, transcripts were kept if they exceeded 2.25 counts per million in at least 70% of samples.  For batch 2, transcripts were kept if they exceeded 1 count per million in at least 65% of samples.
Any remaining ribosomal transcripts were filtered out.
Expression data were normalized using the trimmed mean of M-values approach, specifically using the calcNormFactors function in the edgeR package in R.
Assembly: NA
Supplementary files format and content: The processed data file is a .csv that contains the log counts per million.

source_name: whole blood

extract_protocol:
RNA was extracted from PAXgene tubes using the QIAGEN miRNAseq Kit for total RNAs.
Libraries were contstructed using Nugen Universal Plus mRNA-seq kit with Globin AnyDeplete to isolate stranded, poly(A) mRNAs.

tag: studyid

tag: sequencing batch

tag: rna extraction batch

tag: time

value: acute

tag: hcv/control

value: Control

tag: any cmv viremia

tag: clinical cmv viremia

value: No

tag: days to cmv viremia

tag: rejection

tag: days to rejection

value: White


title: ATAC-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 12 hrs replicate 1

description:
sDUX ATAC dox6hr rep1
sDux_A.macsbroad_peaks.narrowPeak

tag: tissue

tag: cell line

tag: cell type


title: ATAC-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 12 hrs replicate 2

description: DUXB ATAC dox6hr rep2

tag: treatment


title: DU20-02S0003647

value: Hepatitis C

tag: age

tag: Sex

value: Female


title: DU20-02S0003643

value: 6 months

tag: race

value: Black


title: ATAC-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 12 hrs replicate 2

description:
DUXA-VP64 ATAC dox6hr rep2
DuxAVP64_B.macsbroad_peaks.narrowPeak

value: cell line

value: immortalized human myoblast

tag: lentiviral _transduction


title: DU20-02S0003641

tag: studyid

tag: sequencing batch

value: Male


title: ATAC-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 12 hrs replicate 1

description:
DUXA-VP64 ATAC dox6hr rep1
DuxAVP64_A.macsbroad_peaks.narrowPeak

value: 200 ng/mL doxycycline for 12 hrs


title: DU20-02S0003637

tag: rna extraction batch

tag: time


title: DU20-02S0003638

tag: hcv/control

tag: any cmv viremia


title: DU20-02S0003635

tag: clinical cmv viremia

tag: days to cmv viremia


title: DU20-02S0003636

tag: rejection

value: Yes

tag: days to rejection


title: DU20-02S0003633


title: DU20-02S0003629

value: 3 months


title: DU20-02S0003632


title: DU20-02S0003648


title: DU20-02S0003627


title: DU20-02S0003623


title: DU20-02S0003624

value: PRN

value: Asian


title: DU20-02S0003625


title: DU20-02S0003622


title: DU20-02S0003626


title: DU20-02S0003645


title: DU20-02S0003642


title: DU20-02S0003621


title: DU20-02S0003619


title: DU20-02S0003620


title: DU20-02S0003616

value: 2+ races


title: DU20-02S0003615


title: DU20-02S0003639

value: acute


title: DU20-02S0003618

value: Control


title: DU20-02S0003630

value: No


title: DU20-02S0003612

value: White


title: DU20-02S0003613


title: DU20-02S0003644


title: DU20-02S0003640

value: Hepatitis C


title: DU20-02S0003610


title: DU20-02S0003611


title: DU20-02S0003605

value: Female


title: DU20-02S0003606


title: DU20-02S0003604


title: DU20-02S0003607

value: 6 months


title: DU20-02S0003603

value: Black


title: DU20-02S0003602


title: DU20-02S0003601

value: Unknown


title: DU20-02S0003598


title: DU20-02S0003600


title: DU20-02S0003597


title: DU20-02S0003595


title: DU20-02S0003596


title: DU20-02S0003594


title: DU20-02S0003592


title: DU20-02S0003593


title: DU20-02S0003591


title: DU20-02S0003590


title: DU20-02S0003608


title: DU20-02S0003589


title: DU20-02S0003586


title: DU20-02S0003584


title: DU20-02S0003609


title: DU20-02S0003583


title: WF_930040V

tag: tissue

value: Placenta

tag: arm

value: one


title: DU20-02S0003581

value: Male


title: DU20-02S0003588

value: Yes


title: DU20-02S0003579


title: DU20-02S0003599


title: DU20-02S0003576


title: DU20-02S0003577


title: DU20-02S0003578


title: DU20-02S0003574


title: DU20-02S0003573


title: DU20-02S0003575


title: DU20-02S0003572


title: DU20-02S0003569


title: DU20-02S0003567


title: DU20-02S0003582


title: DU20-02S0003568


title: DU20-02S0003566

value: 3 months


title: DU20-02S0003564


title: DU20-02S0000783


title: DU20-02S0003565


title: DU20-02S0000761


title: DU20-02S0003563


title: DU20-02S0003580


title: DU20-02S0000772


title: DU20-02S0003562


title: DU20-02S0000733


title: DU20-02S0000724


title: DU20-02S0000751


title: DU20-02S0000735


title: DU20-02S0000667


title: DU20-02S0000657


title: DU20-02S0000648


title: DU20-02S0000614


title: DU20-02S0000592


title: DU20-02S0000565


title: DU20-02S0000545


title: DU20-02S0000581


title: DU20-02S0000612


title: DU20-02S0000527


title: DU20-02S0000494


title: DU20-02S0000492


title: DU20-02S0000478


title: DU20-02S0000490


title: DU20-02S0000413


title: DU20-02S0000685


title: DU20-02S0000467


title: DU20-02S0000436


title: DU20-02S0000438


title: DU20-02S0000368


title: DU20-02S0000401


title: DU20-02S0000335


title: DU20-02S0000348


title: DU20-02S0000309


title: DU20-02S0000286


title: DU20-02S0000319


title: DU20-02S0000275


title: DU20-02S0000204


title: DU20-02S0000185


title: DU20-02S0000183


title: DU20-02S0000155


title: DU20-02S0003617


title: DU20-02S0000141


title: DU20-02S0000153


title: DU20-02S0000488


title: DU20-02S0000106


title: DU20-02S0000082


title: DU20-02S0000102


title: DU20-02S0000104


title: DU20-02S0000039


title: DU20-02S0000062


title: DU20-02S0000288


title: DU20-02S0000050


title: DU20-02S0000027


title: OPM2_polysomes_dBRD9A_Rep3

city: Boston

first: Keiji

last: Kurata

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using RNA-specific STAR aligner.
Read count tables were created using FeatureCounts using UCSC refFlat gene models.
Assembly: hg19 (GRCh37)
Supplementary files format and content: tab-delimited text files include raw read counts and normalized counts for each sample

growth_protocol: OPM2 and H929 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OPM2 and H929 cells were treated with 100 nM dBRD9-A or DMSO for 24h.

tag: cell line

tag: cell type

value: multiple myeloma cell line

tag: treatment


title: DU20-02S0000029

tag: age

tag: Sex

tag: race


title: DU20-02S0000064

tag: studyid

tag: sequencing batch


title: OPM2_polysomes_dBRD9A_Rep1


title: DU20-02S0000244

tag: rna extraction batch

tag: time


title: OPM2_polysomes_DMSO_Rep2

value: DMSO


title: OPM2_polysomes_dBRD9A_Rep2


title: OPM2_polysomes_DMSO_Rep3


title: OPM2_polysomes_DMSO_Rep1


title: H929_shBRD9_Rep2


title: DU20-02S0000129

tag: hcv/control

tag: any cmv viremia


title: DU20-02S0000202

tag: clinical cmv viremia

tag: days to cmv viremia


title: H929_shBRD9_Rep1


title: H929_shLuc_Rep3

value: shLuc


title: OPM2_shBRD9_Rep1


title: H929_shLuc_Rep1


title: H929_shBRD9_Rep3


title: OPM2_shLuc_Rep3


title: OPM2_shBRD9_Rep3


title: OPM2_shBRD9_Rep2


title: OPM2_shLuc_Rep2


title: OPM2_Input_dBRD9A

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 with default parameters.
Duplicate reads were removed.
BAM files were converted to bed files using a custom script, and converted to BigWig using bedtobigwig.
Assembly: hg19 (GRCh37)
Supplementary files format and content: bigWig files containing read normalized read densities.

growth_protocol: OPM2 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
OPM2 cells were crosslinked, lysed and sonicated. For ChIP with reference exogenous genome, spike-in chromatin (Active Motif, 53083) was then added. The protein-bound DNA fragments were then immunoprecipitated with specific antibodies. After reverse-crosslinking, DNA was purified. Libraries were prepared using ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufacturer's instructions.
Libraries were prepared using ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufacturer's instructions.

treatment_protocol: OPM2 cells were treated with 100 nM dBRD9-A or DMSO for 6h or 24h.

tag: chip antibody


title: OPM2_RNAPII_dBRD9A

value: RNAPII (Diagenode, C15100055-100)


title: OPM2_MYC_dBRD9-A

value: MYC (Cell Signaling Technology, 18583)


title: OPM2_BRD4_dBRD9A

value: BRD4 (Cell Signaling Technology, 13440)


title: OPM2_shLuc_Rep1


title: OPM2_Input_DMSO


title: OPM2_RNAPII_DMSO


title: OPM2_MYC_DMSO


title: OPM2_BRD4_DMSO


title: MYCN-amplified retinoblastoma organoid cells treated with sunitinib_02

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed using default parameters of Trimmomatic. Only reads with minimum length of 36 base pairs were retained for further downstream analysis.
Transcript level counts using Ensemble version 82 annotation were generated using Kallisto utility.
Gene level counts were computed from transcript level counts using tximport R package
Assembly: hg38
Supplementary files format and content: CSV file

source_name: xcells derived from retinoblastoma tissue

growth_protocol: Tumor tissue was dissociated, and the resulting cells were cultured in the growth medium developed previously in Saengwimol et al. "A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma." Final concentration of a 1% Matrigel matrix solution was added in suspension culture, while that of 65 % Matrigel matrix (growth factor reduced; Corning Inc., Corning, NY, USA) was used to embed cells for organoid culture. RB170 was manually dissociated and passaged at a 1:2 or 1:4 ratio once a week for suspension culture or every 3 weeks for organoids. Cold freezing medium (culture medium containing 10% dimethyl sulfoxide) was used to freeze cells at −80°C for 24 hours before long-term storage in liquid nitrogen. A human retinoblastoma cell line (Y79) was maintained in RPMI-1640 (Hyclone Laboratories Inc., Logan, UT, USA) containing 15% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA), 100 U/mL penicillin, 100 µg/mL streptomycin, and 0.25 µg/mL amphotericin B. Medium was changed every 3 days for both RB170 and Y79 cells.

extract_protocol:
RNA was extracted from cultures by using TriPure isolation reagent (Roche Applied Science, Penzberg, Germany). The quality and quantity of RNA were determined by RNA6000 assay (Agilent Technologies, Santa Clara, CA, USA). Specimens with an RNA integrity number (RIN) >8.0 were used in this study.
RNA Libraries were constructed by using the TruSeq Stranded mRNA LT Sample Prep Kit

value: retinoblastoma organoid cells

tag: genotype

value: MYCN-amplified

value: Sunitib treatment


title: RB1-/- retinoblastoma organoid cells treated with vehicle_02

value: No drug treatment


title: RB1-/- retinoblastoma organoid cells treated with sunitinib_01


title: RB1-/- retinoblastoma organoid cells treated with sunitinib_02


title: MYCN-amplified retinoblastoma organoid cells treated with vehicle_02


title: MYCN-amplified retinoblastoma organoid cells treated with vehicle_01


title: RB1-/- retinoblastoma organoid cells treated with vehicle_01


title: MYCN-amplified retinoblastoma organoid cells treated with sunitinib_01


title: Karpas_CXCdel_GSK343_RNAseq_rep2

city: Cambridge

data_processing:
Adapter contamination, polyA read through, and low quality sequences were removed using bbduk (version 38.23) with the following parameters: ref=polyA.fa.gz,truseq_rna.fa.gz k=13 int=f ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20.
Read mapping was performed with STAR (version 2.7.0e) with the following parameters: --genomeDir Homo_sapiens.GRCh38.dna.primary_assembly.fa --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Reads aligned over annotated genes were quantified using HTSeq (version 0.6.1) using the following command: htseq = count -s yes.
Changes in expression calculated through DEseq2 are detailed in the tab-delimited text file: CXCdel_72h_Differential_Genes.txt, containing Transcript_ID in the first column and values for expression change as well as statistical significance in the subsequent columns.
Assembly: hg38
Supplementary files format and content: The HTSeq raw count files for each individual sample are provided as well as a summary table, "CXCdel_72h_Differential_Genes.txt", describing the expression changes upon GSK343 withdrawal.

source_name: Karpas-422 CXCdel

treatment_protocol: Cells were seeded at 250,000 cell/mL and then treated with GSK343 (1 µM) or DMSO (0.1% v/v) for 72 hours.

value: non-hodgkin's lymphoma

value: Karpas-422 CXCdel cells grown in 1 μM GSK343 were subject to continued growth in 1 μM GSK343 for 72 hours


title: Karpas_CXCdel_GSK343_RNAseq_rep1


title: Karpas_CXCdel_DMSO_RNAseq_rep2

value: Karpas-422 CXCdel cells grown in 1 μM GSK343 were subjected to drug withdrawal with DMSO (0.1% v/v) for 72 hours


title: K562_CXCdel_EZH2

data_processing:
Reads were aligned to a composite reference genome for dm6 and hg38 utilizing bowtie2 (version 2.3.2) according to the Spiker (version 1.03) analysis framework. For standard ChIP processing, reads were aligned to the hg38 reference genome using bowtie2 (version 2.3.2).
Aligned reads were sorted using samtools (version 0.1.19).
For the quantitative samples, the Spiker split_bam.py script was run to calculate scaling factors and to split reads into an alignment file containing reads specifically aligning to the hg38 genome (Spiker, version 1.0.3).
For quantitative ChIP-seq, the alignment file was then converted into spike-in normalized bigwig file for further analysis and visualization utilizing the deepTools (version 3.4.3) bamCoverage command with the following parameters: -binSize 50 --normalizeUsing RPKM --ignoreDuplicates --ignoreForNormalization chrM --extendReads –scaleFactor. For the standard ChIP-seq protocol, the alignment file was converted to a normalized bigwig file for further analysis and visualization utilizing the deepTools (version 3.4.3) bamCoverage command with the following parameters: -binSize 50 --normalizeUsing RPKM --ignoreDuplicates --ignoreForNormalization chrM --extendReads with blacklisted regions excluded.
Peaks for H3K27me3 and H3K36me3 were called using Sicer2 (version 1.0.3) with the parameters: -e 8000 -s hg38 -g 12000 -w 4000. Individual replicate peaks were subsequently combined utilizing Bedtools2 merge -d 12000 (version 2.26.0).
Assembly: hg38
Supplementary files format and content: BigWig density files were generated by deepTools (version 3.4.3).

source_name: K562 CXCdel

growth_protocol: Karpas-422 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin. K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Sonication of crosslinked cells was calibrated such that DNA was sheared to between 300bp and 2000bp. For the quantitative ChIP-seq samples (histone ChIPs) Drosophila S2 chromatin (Active Motif) and spike-in antibody (Active Motif) were added following lysis and sonication but prior to immunoprecipitation.
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

treatment_protocol: Cells were seeded at 250,000/mL and then treated with GSK343 (1 µM), SETD2i (5 µM) or DMSO (0.1% v/v) for the specified duration of time.

value: chronic myeloid leukemia

tag: antibody

value: K562 CXCdel cells were grown according to standard protocol


title: Karpas_CXCdel_DMSO_RNAseq_rep1


title: Karpas_wt_EZH2

source_name: Karpas-422 wt

value: Karpas-422 wt cells grown in DMSO (0.1% v/v) for 72 hours


title: Karpas_CXCdel_DMSO_RNAseq_rep3


title: Karpas_CXCdel_EZH2


title: Karpas_CXCdel_GSK343_RNAseq_rep3


title: K562_wt_EZH2

source_name: K562 wt

value: K562 wt cells were grown according to standard protocol


title: Karpas_wt_H3K36me3_SETD2i_Rep_2

value: Karpas-422 wt cells were treated with 5 μM SETD2i for 10 days


title: K562_CXCdel_H3K27me3_Rep_1


title: Karpas_wt_H3K36me3_DMSO_Rep_1


title: K562_CXCdel_H3K27me3_Rep_2


title: K562_wt_H3K27me3_Rep_1


title: Karpas_CXCdel_H3K27me3_GSK343_Rep_2


title: Karpas_wt_H3K27me3_SETD2i_Rep_2


title: Karpas_CXCdel_H3K27me3_DMSO_Rep_1


title: Karpas_wt_H3K27me3_SETD2i_Rep_1


title: Karpas_CXCdel_H3K27me3_GSK343_Rep_1


title: K562_wt_H3K27me3_Rep_2


title: Karpas_CXCdel_H3K27me3_DMSO_Rep_2


title: Karpas_wt_H3K27me3_DMSO_Rep_2


title: Submandibular Gland 13 bulk

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: Main Cir

institute: SUNY University at Buffalo

data_processing:
Alignment was performed usiing HiSat2 v2.1.0
Sam files converted to sorted bam files using Samtools v1.3
Reads were counted using subread v1.6.5
Assembly: hg38
Supplementary files format and content: tab-delimited featureCount text files for each bulk RNA-seq sample

source_name: Submandibular Gland

extract_protocol:
SMGs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: M


title: Submandibular Gland 12 bulk


title: Karpas_wt_H3K27me3_DMSO_Rep_1


title: Karpas_wt_H3K36me3_DMSO_Rep_2


title: Submandibular Gland 15 bulk

value: F


title: Submandibular Gland 14 bulk


title: Submandibular Gland 11 bulk


title: Submandibular Gland 09 bulk


title: Submandibular Gland 10 bulk


title: Submandibular Gland 08 bulk


title: Submandibular Gland 07 bulk


title: bulkRNA-seq_D11_IROrganoids_TGFB1_rep2

first: Lei

address: No.2 Sipailou

institute: Southeast University

data_processing:
For RNA-seq, raw sequencing reads (fastq) were first quality checked using fastQC (v0.11.3) and were further aligned to mouse (mm9) genomes using Tophat2 (v2.1.0) to generate bam files. Cuffquant (v2.2.1) was used to generate cxb files from bam files. Cuffnorm (v2.2.1) was performed to calculate FPKM values using quartile normalization. Cuffdiff (v2.2.1) was applied to identify differentially expressed genes between groups using quartile normalization and per-condition dispersion.
For scRNA-seq of organoid samples, prior to processing, a mouse STAR reference was generated using a mouse genome FASTA build from the Ensembl 102 release and GTF annotations from GENCODE (GRCm39 vM29 2022.04) using STAR’s genomeGenerate function. BCLs derived from Illumina sequencing of PIPseq samples were demultiplexed and output in FASTQ format using BCL-convert v4.0.3. Barcode whitelisting and error correction were performed using PIPseeker v0.55. Reads passing this stage were then aligned to the mouse reference genome using STARsolo (STAR v2.7.10a). An aligned, sorted BAM file was generated by STAR, which included required information for RNA velocity analysis. Cell calling was performed using PIPseeker’s transcript-count thresholding approach and sensitivity 3 was chosen for all samples, which most closely targeted the first inflection point after the knee point on the barcode-rank plot. For sorted Ki67-RFP+ DAPI- cells, samples were processed in the same way, but using salmon v1.4 instead of STAR. A reference genome was first built from the same sources as above using the salmon index command with a 19-bp k-mer size.
For ATAC-seq, paired-end ATAC-seq fastq file was quality checked using fastQC. ATAC-seq adapter sequences were removed from each read file using CutAdapt (v1.9.1). Each read file was then aligned to the mouse mm9 genome using bowtie2. Picard (v2.18.27) was used to determine the median alignment size of each alignment bam file. Peak region bed files were called from each alignment bam file using MACS2 (v2.1.0). MACS2 was run with a “shift” distance of -0.5 times the median alignment size and an “extsize” distance equal to the median alignment size for each alignment bed file. The peak files were filtered against ENCODE blacklist, which is known to yield false ChIP-seq signals due to the inaccuracies of a particular genome assembly. BEDtools was used to subtract the sites on the ENCODE blacklist.
Assembly: RNA-seq and ATAC-seq: mm9; scRNA-seq: mm39
Supplementary files format and content: RNA-seq: fpkm_table.txt files.
Supplementary files format and content: scRNA-seq: barcodes.tsv, genes.tsv, and matrix.mtx files.
Supplementary files format and content: ATAC-seq: bigwig, Peaks BED files.

source_name: Primary intestinal organoids

extract_protocol:
For cultured organoids, QIAGEN RNeasy Micro Kit was used to extract RNA according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China).

tag: tissue

value: Primary intestinal organoids

tag: strain

value: WT

value: 4 Gy IR on Day 4, 2 ng/mL TGFB1 on Day 6 for 24h, organoids collected on Day 11


title: bulkRNA-seq_D11_IROrganoids_TGFB1_rep1

tag: treatment


title: bulkRNA-seq_D11_IROrganoids_TGFB1_rep3


title: H929_shLuc_Rep2

tag: cell line

tag: cell type

value: multiple myeloma cell line

value: shLuc


title: Submandibular Gland 05 bulk

tag: Sex

tag: age


title: Submandibular Gland 06 bulk


title: bulkRNA-seq_D11_IROrganoids_Vehicle_rep2

value: 4 Gy IR on Day 4, Vehicle on Day 6 for 24h, organoids collected on Day 11


title: Submandibular Gland 04 bulk


title: bulkRNA-seq_D11_IROrganoids_Vehicle_rep1


title: Submandibular Gland 02 bulk


title: bulkRNA-seq_D7_IROrganoids_Vehicle_rep2

value: 4 Gy IR on Day 4, Vehicle on Day 6 for 24h, organoids collected on Day 7


title: bulkRNA-seq_D7_IROrganoids_TGFB1_rep1

value: 4 Gy IR on Day 4, 2 ng/mL TGFB1 on Day 6 for 24h, organoids collected on Day 7


title: bulkRNA-seq_D7_IROrganoids_TGFB1_rep3


title: bulkRNA-seq_D7_IROrganoids_Vehicle_rep3


title: bulkRNA-seq_D7_IROrganoids_Vehicle_rep1


title: Submandibular Gland 15 scRNA

description: scRNA-seq Data

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 6 mkoutput with Bcl2Fastq 2.20.0.422
Cellranger 6 Count against GRCh38 genome to produce count matrix
Seurat 4.0 used for marker gene analysis and visualization
Assembly: GRCh38
Supplementary files format and content: H5 Matrix Files

extract_protocol:
Chromium Single Cell 3' v2 (10X Genonics)
TruSeq Stranded RNA (illumina)


title: bulkRNA-seq_D7_Non-IROrganoids_TGFB1_rep3

value: 2 ng/mL TGFB1 on Day 6 for 24h


title: bulkRNA-seq_D7_Non-IROrganoids_TGFB1_rep2


title: Fibroblasts  - CHIKV infected+scleroglucan treated rep2

city: Irvine

first: Arunachalam

last: Ramaiah

address: McGaugh Hall

department: Ecology and Evolutionary Biology

institute: University of California, Irvine

data_processing:
Illumina reads from all the samples were mapped to human and CHIKV reference genomes by STAR v2.2.9a and read counts per gene were quantified using human Ensembl GRCh38.98 and CHIKV GTF file to generate raw reads counts . Differential expression analysis was performed using DESeq2 v1.28.1 in R v4.0.3
Genome_build: hg38 & Chikungunya virus NC_004162.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: fibroblasts

growth_protocol: Cells were cultured in DMEM+10%FBS+1% Pen-Strep + 1% HEPES +1%Glutamine

extract_protocol:
Samples were harvested in TriZol and RNA was extracted using the RNeasy Mini Kit (Qiagen)
Libraries for RNA-Seq that were prepared with KAPA Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand.  cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: Human fibroblast cells were either drug treated or vehicle treated; and uninfected (mock) or infected with CHIKV at MOI 0.1 for 24 hrs

value: fibroblasts

tag: infection

value: Chikungunya virus (CHIKV)

value: scleroglycon


title: bulkRNA-seq_D11_IROrganoids_Vehicle_rep3


title: bulkRNA-seq_D7_Non-IROrganoids_TGFB1_rep1


title: bulkRNA-seq_D7_Non-IROrganoids_Vehicle_rep3

value: Vehicle on Day 6 for 24h


title: Fibroblasts  - CHIKV infected+Vehicle treated rep1

value: Vehicle


title: bulkRNA-seq_D7_Non-IROrganoids_Vehicle_rep2


title: bulkRNA-seq_D7_IROrganoids_TGFB1_rep2


title: Submandibular Gland 01 bulk


title: bulkRNA-seq_D7_Non-IROrganoids_Vehicle_rep1


title: Fibroblasts  - Mock+cAIMP treated rep2

value: mock

value: cAIMP


title: Fibroblasts  - Mock+scleroglycon treated rep1


title: Escherichia coli, Day 15, FeCl3 Control, rep 3

city: Newark

first: Mark

last: Blenner

state: DE

department: Chemical and Biomolecular Engineering

institute: University of Delaware

data_processing:
Data processing was performed using the Palmetto Cluster and rStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt commands (v2.8) and fastQC analysis (v0.11.8) within Trim Galore (v0.6.5)
Trimmed sequence reads were aligned to ASM584v2 RefSeq annotation GCF_000005845.2 using HISAT2 (v2.2.1) following instructions for paired-end reads and preparing HISAT2 genome index
Samtools (v1.4) was used for file conversion of aligned reads before transcripts were assembled using StringTie (v1.3.3b) using genome guided mapping
tximport (v1.20.0) was used to estimate counts and transcript lengths for import into DESeq2 (v1.35.0) for differential expression analysis within rStudio
ClusterProfiler (v4.0.2) was used for KEGG pathway and Gene Ontology analyses
Assembly: ASM584v2, GCF_000005845.2
Supplementary files format and content: txt file containing matrix of abundance, counts, and transcript lengths

organism: Escherichia coli

source_name: bacterial

growth_protocol: E. coli DH10β (New England Biolabs) cells were grown in 100 L M9 minimal medium supplemented with 0.5% glucose (Sigma-Aldrich), 1% thiamine hydrochloride (Spectrum), and 1% (w/v) casamino acids (Bacto) at 28°C and shaking at 215 rpm overnight. When appropriate radionuclide sources were spiked into liquid growth medium prior to inoculation of overnight E. coli cultures to acheive an approximate absorbed dose rate of 9 mGy d-1.

extract_protocol:
Total RNA was harvested using Rneasy mini  kit (Qiagen). Ribosomal RNA was removed from total RNA samples using either Ribo-Zero rRNA Removal Kit Bacteria (Illumina) or RiboMinus Bacteria 2.0 Transcriptome Isolation Kit following the manufacturer's instructions. Ethanol precipitation was used to purify depleted RNA. 100 ng of purified mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols for purified mRNA input and Low Sample Protocol.

treatment_protocol:
Radionuclide sources were added to growth flasks prior to inoculation. Final activity concentration of internal sources were as follows (approx): Pu-239 in 0.01 M HCl at 0.12 kBq mL-1; Tritiated water (HTO) at 3 uCi mL-1; Fe-55 in 0.5 M HCl at 4.9 uCi mL-1. Non-irradiated controls either contained no additional chemical addition or an equimolar amount of stable FeCl3 (2.47uM).
Cultures were irradiated continuously for 15 days with samples for RNA extration taken at one and 15-days after inoculation/spike addition. Samples were spun down into cell pellets and flask frozen for storage at -80C.

value: bacterial

tag: time point

value: Day 15

value: Growth with FeCl3


title: Escherichia coli, Day 15, FeCl3 Control, rep 2

value: WT


title: Fibroblasts  - Mock+scleroglycon treated rep2


title: Fibroblasts  - CHIKV infected+scleroglucan treated rep1


title: Fibroblasts  - Mock+Vehicle treated rep2


title: Fibroblasts  - CHIKV infected+cAIMP treated rep2


title: DU20-02S0003570

tag: studyid

tag: sequencing batch

tag: rna extraction batch

tag: time

value: 6 months

value: Control

value: No

tag: rejection

tag: days to rejection

value: Female

tag: race

value: White


title: Fibroblasts  - Mock+cAIMP treated rep1


title: Escherichia coli, Day 15, FeCl3 Control, rep 1

tag: genotype


title: Fibroblasts  - CHIKV infected+cAIMP treated rep1


title: Escherichia coli, Day 1, FeCl3 Control, rep 2

value: Day 1


title: Fibroblasts - Mock+Vehicle treated rep1

value: fibroblasts


title: Fibroblasts  - CHIKV infected+Vehicle treated rep2

value: Chikungunya virus (CHIKV)


title: HFO_FP_b001_98_cbc

first: Scott

last: Jelinsky

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

data_processing:
Processing of the fastq files was performed using the QuickRNAseq (https://doi.org/10.1186/s12864-015-2356-9) (pipeline utilizing Hg38 for the genome and Gencode v24 for annotation). Normalization and differential expression analyses were conducted using limma-voom(https://doi.org/10.1186/gb-2014-15-2-r29).
Genome_build: Hg38
Supplementary_files_format_and_content: Gene-count-table.txt

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

tag: passage

tag: growth conditions

value: organoid

tag: replicate

tag: tissue

value: Ileum

tag: disease state

value: CD (Crohn's disease)

tag: inflamed

value: previously inflamed

tag: gender

tag: medium

value: cCDM

tag: time (in expansion media)

value: 3 days

tag: time (in diff media)

value: 4 days

tag: individual

value: Donor 4


title: HFO_FP_b001_9_cbc

value: (Ascending) Colon

value: WT

value: normal

value: Male

value: Donor 89


title: HFO_FP_b001_99_cbc

value: Female


title: Escherichia coli, Day 15, Fe-55, rep 3

tag: cell type

value: bacterial

tag: strain

tag: time point

value: Day 15

tag: treatment

value: Fe-55 exposure


title: Escherichia coli, Day 15, Fe-55, rep 2


title: Escherichia coli, Day 1, FeCl3 Control, rep 1

value: Day 1

value: Growth with FeCl3


title: Escherichia coli, Day 15, Fe-55, rep 1


title: HFO_FP_b001_97_cbc

value: organoid

value: Ileum

value: CD (Crohn's disease)


title: Escherichia coli, Day 1, Fe-55, rep 3


title: HFO_FP_b001_95_cbc

value: previously inflamed

value: eCDM

value: 3 days


title: HFO_FP_b001_96_cbc

value: 4 days

value: Donor 4


title: Escherichia coli, Day 1, Fe-55, rep 2

value: WT


title: Escherichia coli, Day 1, Fe-55, rep 1


title: Escherichia coli, Day 15, H-3, rep 3

value: H-3 exposure


title: HFO_FP_b001_94_cbc


title: HFO_FP_b001_93_cbc

value: CNM


title: Escherichia coli, Day 1, FeCl3 Control, rep 3


title: Escherichia coli, Day 15, H-3, rep 2


title: HFO_FP_b001_92_cbc

value: Female


title: HFO_FP_b001_91_cbc


title: HFO_FP_b001_90_cbc

value: normal

value: cCDM

value: Donor 3


title: HFO_FP_b001_8_cbc

value: (Ascending) Colon

value: Male

value: Donor 89


title: Escherichia coli, Day 15, H-3, rep 1

value: bacterial

value: Day 15


title: Escherichia coli, Day 1, H-3, rep 2

value: Day 1


title: Escherichia coli, Day 1, H-3, rep 3


title: Escherichia coli, Day 1, H-3, rep 1


title: HFO_FP_b001_89_cbc

value: organoid

value: Ileum

value: CD (Crohn's disease)


title: HFO_FP_b001_88_cbc

value: 3 days

value: 4 days


title: HFO_FP_b001_87_cbc

value: eCDM


title: Escherichia coli, Day 15, Pu-239, rep 3

value: Pu-239 exposure

value: WT


title: Submandibular Gland 03 bulk

tag: Sex

value: M

tag: age


title: HFO_FP_b001_86_cbc

tag: passage

value: normal

value: Female


title: Escherichia coli, Day 15, Pu-239, rep 1

tag: genotype


title: Escherichia coli, Day 15, Pu-239, rep 2


title: Escherichia coli, Day 1, Pu-239, rep 3


title: HFO_FP_b001_84_cbc

tag: growth conditions

tag: replicate

value: CNM

value: Donor 3


title: Escherichia coli, Day 1, Pu-239, rep 2


title: HFO_FP_b001_83_cbc

tag: tissue

tag: disease state


title: HFO_FP_b001_82_cbc

tag: inflamed

tag: gender


title: Escherichia coli, Day 15, Control, rep 1

value: Control


title: HFO_FP_b001_81_cbc

tag: medium

value: cCDM

tag: time (in expansion media)

value: Donor 10


title: HFO_FP_b001_80_cbc

tag: time (in diff media)

tag: individual


title: Escherichia coli, Day 1, Control, rep 3

tag: cell type

value: bacterial

tag: strain

value: Day 1


title: Escherichia coli, Day 15, Control, rep 2

tag: time point

value: Day 15

tag: treatment


title: HFO_FP_b001_7_cbc

value: organoid

value: (Ascending) Colon

value: Male

value: Donor 89


title: Escherichia coli, Day 1, Control, rep 2


title: HFO_FP_b001_79_cbc

value: Ileum

value: CD (Crohn's disease)

value: 3 days

value: 4 days


title: HFO_FP_b001_77_cbc

value: normal

value: Female

value: eCDM


title: Escherichia coli, Day 1, Control, rep 1

value: Control

value: WT


title: HFO_FP_b001_85_cbc

value: Donor 3


title: HFO_FP_b001_76_cbc

value: Donor 10


title: HFO_FP_b001_75_cbc

value: CNM


title: HFO_FP_b001_74_cbc


title: Escherichia coli, Day 1, Pu-239, rep 1

value: bacterial

value: Day 1

value: Pu-239 exposure


title: wild-type, anti-FLAG antibody, 24 hr rep 3

city: Madison

first: Heungyun

middle: Harrison

last: Moon

state: WI

address: 1550 Linden drive

department: Bacteriology

institute: University of Wisconsin-Madison

data_processing:
Read sequences were mapped to the genome using bowties2 and Homer (version 4.11) was utilized to call peaks.
To make peak calls, high sensitivity settings were used in the Homer program: more than two-fold changes and a p-value less than 0.001.
Identification of VeA and LaeA direct targets was done by selecting genes, in which peaks are found in their promoter regions within the 1.5kb upstream range from the translation start site (TSS).
Assembly: GCF_000149205.2
Supplementary files format and content: tab-delimited text files include associated peak information for each sample

organism: Aspergillus nidulans

source_name: Vegetatively grown cells

growth_protocol: The fungal strains were inoculated into liquid or solid 1% glucose minimal medium (GMM) with appropriate supplements and incubated at 37 °C. To collect vegetatively growing cells (Vege), 5×105 conidia/ml were inoculated into 100 ml liquid GMM and incubated for 24 h at 37 °C, 220 rpm in the dark.

extract_protocol:
To collect samples for ChIP-seq analysis, vegetatively grown cells (24 h) of RDIT9.32, RJW324.3, and RJW302.11 were cross-linked with 1% formaldehyde, resuspended in lysis buffer, and homogenized by a mini-beadbeater with 0.5mm zirconia/silica beads. The lysates were then sonicated for five to seven cycles (60 s on, 60 s off) with a sonicator to achieve 150-200 bp size DNA fragments. After centrifugation, the lysates were diluted in the ChIP dilution buffer and applied for ChIP assays using the MAGnify Chromatin Immunoprecipitation System (Invitrogen) follwing the manufacturer’s instruction with a modest modification. The diluted chromatin extracts were incubated with 1 μg of mouse monoclonal Anti-FLAG antibody (Sigma-Aldrich). As negative controls, the chromatin extracts were reacted with 1 μg of Anti-rabbit IgG. Initial input DNAs before immunoprecipitation were used as positive controls. The enriched DNA fragments were retrieved and used as a template for ChIP-seq.
DNA libraries were prepared using TruSeq ChIP library Preparation Kit (Illumina) and sequenced using an Illumina HiSeq2500 platform.

tag: time

value: 24 hours

value: Vegetatively grown cells

value: wild-type

value: mouse monoclonal anti-FLAG antibody


title: Escherichia coli, Day 15, Control, rep 3

value: Day 15


title: wild-type, anti-FLAG antibody, 24 hr rep 2


title: wild-type, anti-FLAG antibody, 24 hr rep 1


title: wild-type, anti-rabbit IgG, 24 hr

value: anti-rabbit IgG antibody


title: LaeA-FLAG strain, anti-FLAG antibody, 24 hr rep 3

value: LaeA::FLAG expressing strain


title: HFO_FP_b001_70_cbc

tag: passage

value: organoid

value: (Ascending) Colon

value: CD (Crohn's disease)

value: normal

value: Female

value: cCDM

value: 3 days

value: 4 days

value: Donor 4


title: HFO_FP_b001_6_cbc

value: WT

value: Male

value: eCDM

value: Donor 89


title: VeA-FLAG strain, anti-rabbit IgG, 24 hr

value: 24 hours

value: Vegetatively grown cells

tag: genotype

value: VeA::FLAG expressing strain


title: LaeA-FLAG strain, anti-FLAG antibody, 24 hr rep 1

value: LaeA::FLAG expressing strain

value: mouse monoclonal anti-FLAG antibody


title: HFO_FP_b001_69_cbc

tag: growth conditions

value: organoid

value: (Ascending) Colon


title: HFO_FP_b001_67_cbc

tag: replicate

value: CD (Crohn's disease)

value: normal


title: HFO_FP_b001_78_cbc

tag: tissue

value: Ileum

value: Female

value: Donor 10


title: HFO_FP_b001_68_cbc

tag: disease state

value: 3 days

value: 4 days

value: Donor 4


title: VeA-FLAG strain, anti-FLAG antibody, 24 hr rep 3


title: HFO_FP_b001_66_cbc

tag: inflamed

value: CNM


title: VeA-FLAG strain, anti-FLAG antibody, 24 hr rep 2


title: HFO_FP_b001_64_cbc

tag: gender


title: LaeA-FLAG strain, anti-rabbit IgG, 24 hr

value: anti-rabbit IgG antibody


title: HFO_FP_b001_71_cbc

tag: medium

value: cCDM


title: HFO_FP_b001_73_cbc

tag: time (in expansion media)


title: M4 muscle cell, segment A2, animal 8, cell d306087

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
NextSeq 500 sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.0 and STAR version 2.5.3a alignment to a transcriptome derived from the human BDGP6 primary assembly and a version 92 annotation.
Assembly: BDGP6 Drosophila melanogaster assembly with version 92 annotation
Supplementary files format and content: 1b1sm_isoform_intCt.txt.gz is a tab delimited text file of isoform counts
Supplementary files format and content: 1b1sm_isoform_l2tpm.txt.gz is a tab delimited text file of isoform l2tpm vaules
Supplementary files format and content: 1b1sm_l2tpm.txt.gz is a tab delimited text file of gene l2tpm vaules
Supplementary files format and content: 1b1sm_intCt.txt.gz is a tab delimited text file of gene counts

organism: Drosophila melanogaster

source_name: muscle cell

growth_protocol: Fly stocks were raised at 25°C on standard molasses food in an incubator with 12 hrs day/night cycle. Actively crawling 3rd instar larvae that are size and age matched were used for all experiments.

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

value: muscle cell

tag: segment

tag: animal

value: M


title: M1 muscle cell, segment A2, animal 8, cell d306088

tag: cell type


title: HFO_FP_b001_62_cbc

value: (Proximal) Colon)

value: UC (ulcerative colitis)

value: Male

tag: time (in diff media)

tag: individual

value: Donor 7


title: M1 muscle cell, segment A1, animal 8, cell d306086

tag: strain


title: HFO_FP_b001_61_cbc

value: organoid


title: LaeA-FLAG strain, anti-FLAG antibody, 24 hr rep 2

tag: time

value: 24 hours

value: Vegetatively grown cells

value: LaeA::FLAG expressing strain

tag: treatment

value: mouse monoclonal anti-FLAG antibody


title: HFO_FP_b001_60_cbc

tag: passage

value: normal

value: eCDM

value: 3 days


title: M4 muscle cell, segment A4, animal 8, cell d306083

tag: genotype


title: M4 muscle cell, segment A4, animal 8, cell d306085


title: M4 muscle cell, segment A2, animal 8, cell d306082


title: VeA-FLAG strain, anti-FLAG antibody, 24 hr rep 1

value: VeA::FLAG expressing strain


title: HFO_FP_b001_58_cbc

tag: growth conditions

tag: replicate

value: 4 days


title: HFO_FP_b001_59_cbc

tag: tissue

tag: disease state


title: HFO_FP_b001_57_cbc

tag: inflamed

tag: gender

value: CNM


title: M4 muscle cell, segment A5, animal 6, cell d306048

value: muscle cell


title: M4 muscle cell, segment A4, animal 6, cell d306047

value: M


title: HFO_FP_b001_65_cbc

value: (Ascending) Colon

value: CD (Crohn's disease)

value: Female

tag: medium

tag: time (in expansion media)

value: Donor 4


title: HFO_FP_b001_56_cbc

value: organoid

value: (Proximal) Colon)

value: UC (ulcerative colitis)

value: Male

value: Donor 7


title: HFO_FP_b001_55_cbc

value: normal


title: HFO_FP_b001_63_cbc

value: cCDM


title: M4 muscle cell, segment A4, animal 6, cell d306046

tag: segment

tag: animal


title: Karpas_wt_H3K36me3_SETD2i_Rep_1

tag: cell type

value: non-hodgkin's lymphoma

tag: antibody

value: Karpas-422 wt cells were treated with 5 μM SETD2i for 10 days