title: KD_3-rep4

city: PUNE

first: Girish

middle: S

last: Ratnaparkhi

state: MH

address: Dr. Homi Bhabha Road Pashan Pune 411008

department: Biology

country: India

institute: Indian Institute of Science Education & Research

description: HEK293T cells transduced with ABHD14B targeting shRNA2 containing lentivirus

data_processing:
Bcl2fastq for base calling and adapter trimming
On an average 9 million reads per sample were mapped to Human genome using Bluebee Genomics Platform
Gene expression counts were generated and DE analysis was performed using Bluebee Genomics Platform
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in complete medium [RPMI1640 supplemented with 10% (v/v) FBS and 1% penicillin-streptomycin] at 37 oC and 5% (v/v) CO2. Lentivirus transduced cells were cultured in the presence of 6 µg/mL of puromycin in the culture medium.

extract_protocol:
Cells were washed with DPBS, harvested by scraping, lysed in QIAzol, and RNA was extracted.
Lexogen (Quantseq 3'mRNA-seq library prep kit for Illumina)


title: WT CD4 replicate 2

status: Public on Jun 10 2022

type: SRA

city: Bethesda

first: Yayi

last: Gao

state: MD

address: 3016 Convert Drive

country: USA

institute: National Cancer Institute

description:
Mature CD4 thymocyte from C57Bl/6 mice
WTCD4_2

library_source: transcriptomic

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: count of RNA reads were performed with Htseq; FPM normalization was performed with the FPM function of the DEseq2 package

molecule: total RNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina) were used for library.   Libraries were pooled and sequenced with paired-end reads of 75bp on a Nexseq to reach 70 million read pairs per sample

tag: strain

tag: cell population

tag: genotype

value: WT


title: Gulotm1Mae VitC+ rep1 hMeDIP-seq

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

library_source: genomic

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with BWA (version 0.7.15.1), PCR duplicates were removed with RmDup (version 2.0) and filtered to remove mitochondrial DNA and not properly aligned sequnces.
Peaks were called with MACS2 callpeak (version 2.1.1.20160309.6) and Bigwig files were created with multiBigwigSummary (version 3.1.2.0.0)
5hmC coverage over defined regions was analyzed with the CEAS package (version 1.0.2)
Genome_build: mm10

molecule: genomic DNA

source_name: Bone

growth_protocol: Gulotm1Mae mice were kept on 3.3g/L vitamin C in drinking water (ad libitum), refreshed twice a week. MC3T3-E1 cells were grown in vitamin C free aMEM at 37ºC in a 5% CO2 humidified atmosphere and splitted around 70% confluence.

extract_protocol:
RNA and DNA was extraced with commercially available extraction kits (Zymo and Qiagen, respectively), chromatin for ChIP-Seq was extracted using standard protocols
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols; hMeDIP-seq: the libraries were prepared by the ACCEL-NGS® 1S Plus DNA library kit (Swift Bioscience, MI, Ann Arbor) following manufacturer’s instructions and sequenced to 51 base pairs from both ends. ChIP-Seq libraries were prepared using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) following the manufacturers instructions. All deep-sequncing runs were perfomed using the Illumina HiSeq 4000 instrument at the Mayo Clinic Medical Genome Facility Sequencing Core.

treatment_protocol: Gulotm1Mae mice were treated with vitamin C for 15 or 20 weeks at a concentration of 3.3g/L in drinking water ad libitum, refreshed twice a week; all mice were sacrificed at 20 weeks of age. MC3T3-E1 cells were cultured for 28 days in aMEM including 4 mM β-glycerophosphate and plus or minus 50 µg/ml vitamin C at 37ºC in a 5% CO2 humidified atmosphere.

tag: tissue

value: Femur

tag: passages

tag: medip antibody

value: 5hmC (Active Motif, 39791)


title: Gulotm1Mae VitC+ rep2 hMeDIP-seq


title: Gulotm1Mae VitC+- rep3 RNA-seq

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with RNA STAR (version 2.6.0b-1)
Gene expression was qantified with featureCounts (version 1.6.3)
Differentially expressed genes were defined with DESeq2 (version 2.11.40.2)
Genome_build: mm10


title: WT CD4 replicate 1

description:
Mature CD4 thymocyte from C57Bl/6 mice
WTCD4_1


title: si5mTe_C

city: Shanghai

first: Ran

last: Tong

address: 227 South Chongqing Road, Huangpu District

country: China

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p13 whole genome using hisat2(Version 2.1.0).
Transcripts Per Million were calculated by RSEM(Version 1.3.3) by default parameters.
Assembly: GRCh38.p13
Supplementary files format and content: gene.count.matrix.annot
Supplementary files format and content: gene.TPM.matrix.annot

molecule: polyA RNA

organism: Homo sapiens

source_name: Human embryonic stem cells

growth_protocol: SHhES8 were grown in mTeSR1 medium.

extract_protocol:
Cells were collected and total RNA was extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SHhES8 cells were dissociated using Accutase (STEMCELL Technologies, Canada), and subsequently seeded at a density of around 4 × 105 cells per well in six-well plates in mTeSR1 medium. Transfection mixture that contains NT siRNA or HESX1 siRNAs was added to the well. After 24 hours of culture, the medium of siNT ME cells, siHESX1#1 ME cells and siHESX1#2 ME cells were changed to ME induction medium [E8 medium (STEMCELL Technologies, Canada) supplemented with 5 ng/mL BMP4 (PeproTech, America) and 25 ng/mL Activin A (PeproTech, America)] . 72 hours of culture after plating, cells were collected for further analysis.

tag: cell lines

value: SHhES8 hESC line

tag: culture medium


title: MSC_Aged_Control

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

description: processed data file: msc_sokm.h5ad

data_processing:
library demultiplexing: bcl2fastq
alignment: kallisto
cellular demultiplexing: bustools
normalization: scVI 0.8.1
feature barcode demultiplexing: kite
Genome_build: mm10
Supplementary_files_format_and_content: h5ad, cells-by-genes count matrices

source_name: Muscle-derived mesenchymal stem cells

growth_protocol: Adipogenic cells and MSCs were cultured in DMEM + 10%FBS, 1% Pen/Strep. Cells were passaged once after isolation prior to transduction with reprogramming factors. Myogenic cells were grown in F10 + 20% FBS, 1% Pen/Strep, 5 ng/mL FGF2 for a week prior to passaging and transduction.

extract_protocol: 10x Chromiums v3.1 NextGEM gene expression assay

treatment_protocol: SOKM experiments transduced cells with a polycistronic TetOn>SOKM casette, induced for three days, and chased for three days with doxycycline. Msx1 experiments followed the same protocol using a TetOn>Msx1 lentivirus. Pooled screening experiments transduced cells with pools of S, O, K, M lentiviruses carrying constituitively expressed barcodes to enable in silico demultiplexing. Pooled screens likewise performed a 3 day pulse, 3 day chase.

tag: age

value: Aged

tag: cellt ype

value: Muscle-derived mesenchymal stem cells

tag: treatment

value: Control


title: NT_mTe_C


title: MSC_Young_0_Screen

description: processed data file: msc_screen.h5ad

value: Young

value: TetO-S-BC; TetO-O-BC; TetO-K-BC; TetO-M-BC


title: KD_3-rep3

value: HEK293T cells transduced with ABHD14B targeting shRNA2 containing lentivirus


title: KD_3-rep2


title: WT CD8 replicate 1

description:
Mature CD8 thymocyte from C57Bl/6 mice
WTCD8_1


title: MSC_Aged_SOKM

description: processed data file: msc_sokm.h5ad

value: TetO-SOKM


title: Gulotm1Mae VitC+- rep2 RNA-seq


title: si5mTe_B


title: WT CD4 replicate 3

description:
Mature CD4 thymocyte from C57Bl/6 mice
WTCD4_3


title: Gulotm1Mae VitC+- rep1 RNA-seq


title: KD_3-rep1


title: MSC_Young_Control

description: processed data file: msc_sokm.h5ad


title: NT_mTe_B


title: si8mTe_B


title: MSC_Young_SOKM

description: processed data file: msc_sokm.h5ad


title: Gulotm1Mae VitC+ rep3 RNA-seq


title: Cancer_HGSOC7

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38Ensembl91
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: High-grade serous ovarian cancer tissue

extract_protocol:
The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. Tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 125 U/mL collagenase IV (Sigma), 25 U/mL collagenase I (Sigma) and 25 U/mL DNase I (Worthington) for 30 min at 37°C, with agitation. After digestion, samples were sieved through a 40µm cell strainer, and then centrifuged at 300g for 5 min. The supernatant was removed and the pelleted cells were suspended in red blood cell lysis buffer (Solarbio) to lyse red blood cells. The cells were re-suspended in RPMI-1640 medium containing 10% FBS and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

tag: tissue type

value: High-grade serous ovarian cancer tissue

tag: pathology

value: HGSOC

tag: tumor stage


title: KD_2-rep3

description: HEK293T cells transduced with ABHD14B targeting shRNA1 containing lentivirus


title: Gulotm1Mae VitC+ rep2 RNA-seq


title: Cancer_HGSOC6

value: IIIC


title: Adipo_Aged_Control

description: processed data file: adipo_sokm.h5ad

source_name: Adipogenic cells

value: Adipogenic cells


title: Adipo_Aged_SOKM

description: processed data file: adipo_sokm.h5ad


title: Adipo_Young_Control

description: processed data file: adipo_sokm.h5ad


title: Cancer_HGSOC4


title: WT rep3 RNA-seq


title: WT rep2 RNA-seq


title: Gulotm1Mae VitC+ rep1 RNA-seq


title: Cancer_HGSOC5

value: IIB


title: Cancer_HGSOC3


title: Adipo_Young_SOKM

description: processed data file: adipo_sokm.h5ad


title: KD_2-rep1

value: HEK293T cells transduced with ABHD14B targeting shRNA1 containing lentivirus


title: ZmMYB73 DAP-seq

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

data_processing:
Library strategy: DAP-seq
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence, then mapped to ZmB73v3 whole genome using bowtie2 v2.2.8 with default parameters. Reads were filtered to remove reads mapping to multiple loci.
Peaks were called using GEM v2.5 with the following parameters: --d Read_Distribution_default.txt --k_min 6 --k_max 20 --outNP --q 5. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Genome_build: ZmB73v3.31
Supplementary_files_format_and_content: bigwig files were generated using deeptools with a bin size of 10bp and RPKM normalization. NarrowPeak files were generated by GEM v2.5.

organism: Zea mays

source_name: 1-3cm maize ear

extract_protocol:
genomic DNA was extracted from 1-3cm field grown ears
genomic DNA was purified using a standard phenol:chloroform extraction protocol. HALO-MYB73 fusion protein was expressed using Promega's TNT rabbit reticulocyte expression system.
sequencing libraries were constructed as described in Bartlett et al., 2017

tag: background

tag: notes

value: 1-3cm maize ear


title: WT rep1 RNA-seq

value: Femur


title: NT-rep4

description: HEK293T cells transduced with non-targeting shRNA containing lentivirus


title: Cancer_HGSOC2


title: NT-rep2

value: HEK293T cells transduced with non-targeting shRNA containing lentivirus


title: KD_2-rep4


title: Aechmea_fasciata, IP494-1C-EIN3, biol rep3

city: Danzhou

first: Jiabin

last: Wang

state: Hainan

address: Baodaoxincun

institute: Chinese Academy of Tropical Agricultural Sciences

data_processing:
Basecalls were performed using bcl2fastq2 (v2.20).
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.36, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the genome of Aechmea fasciata. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v 2.1.1.20160309 with the significance cut-off q-value <=0.01.
Assembly: The genome of Aechmea fasciata.
Supplementary files format and content: bedGraph files

organism: Aechmea fasciata

source_name: leaf

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
Libraries were prepared using a library preparation kit (New England Biolabs) according to the manufacturer’s instructions.

value: leaf

tag: chip antibody


title: NT-rep3


title: Aechmea_fasciata, IN494-1C, biol rep3


title: Normal ovarian tissue5

source_name: Normal ovarian tissue

value: Normal ovarian tissue

value: Uterine leiomyomas, ovarian cysts


title: KD_2-rep2


title: Control-rep4

description: HEK293T wild-type cells

value: HEK293T wild-type cells


title: Aechmea_fasciata, IP494-1B-EIN3, biol rep2


title: Normal ovarian tissue4

value: Adenomyosis


title: Aechmea_fasciata, IN494-1A, biol rep1


title: Aechmea_fasciata, IP494-1A-EIN3, biol rep1


title: Normal ovarian tissue1

value: Mucinous cystadenoma of ovary


title: Control-rep2

description: HEK293T wild-type cells


title: Normal ovarian tissue3

value: Ovarian endometrotic cyst


title: Normal ovarian tissue2


title: 2.5 M NaCl, LL34, rep2

status: Public on Jun 09 2022

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

country: Japan

institute: Meijo University

data_processing:
After removing the adapter sequence with Cutadapt (ver. 1.9.1), we used Sickle (ver 1.33) to remove bases with a quality score of less than 20 and paired reads with a quality score of less than 40 bases.
Hisat 2 (ver. 2.1.1) to map high quality reads to the reference sequence and sam-format data was output.
After converting sam format to bam format using Samtools (ver. 1.11), the data was sorted and indexed.
Using featureCounts (ver. 2.0.0), the reads mapped to the gene region of the reference sequence were counted. After that, the total number of reads and gene length between samples were corrected by Reads Per Kilobase Million (RPKM) normalization and Transcripts Per Million (TPM) normalization.
Assembly: Halothece sp. PCC7418 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000317635.1/)
Supplementary files format and content: Tab-delimited text files include RPKM and TPM values for each Sample

organism: Halothece sp. PCC 7418

source_name: cyanobacterium

growth_protocol: Halothece sp. PCC7418 was grown photoautotrophically in BG11 medium plus Turk Island salt solution, containing 0.5 M or 2.5 M NaCl, under continuous light (LL) conditions.

extract_protocol:
Total RNA was extracted utilizing TRIzol LS Reagent (Thermo Fisher Scientific), according to the manufacturer’s protocol.
For the preparation of libraries, MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) was utilized, according to the manufacturer’s protocol, following the removal of ribosomal RNA by using riboPool (siTOOLs Biotech).

treatment_protocol: To synchronize the circadian clock, the cultures acclimated to each NaCl condition were treated with two LD cycles.

tag: cell type

value: cyanobacterium

value: WT

value: 2.5 M NaCl


title: NT-rep1


title: 2.5 M NaCl, LL16, rep2


title: 2.5 M NaCl, LL4, rep2


title: Control-rep3

description: HEK293T wild-type cells


title: Control-rep1

description: HEK293T wild-type cells


title: 0.5 M NaCl, LL28, rep2

value: 0.5 M NaCl


title: 2.5 M NaCl, LL10, rep2


title: 2.5 M NaCl, LL22, rep2


title: Cancer_HGSOC1

value: High-grade serous ovarian cancer tissue

value: HGSOC

value: IIIB


title: 0.5 M NaCl, LL22, rep2


title: 0.5 M NaCl, LL34, rep2


title: 0.5 M NaCl, LL16, rep2


title: 0.5 M NaCl, LL10, rep2


title: 2.5 M NaCl, LL28, rep1


title: 2.5 M NaCl, LL34, rep1


title: 2.5 M NaCl, LL16, rep1


title: 2.5 M NaCl, LL10, rep1


title: Aechmea_fasciata, IN_494_1B, biol_rep2


title: 0.5 M NaCl, LL28, rep1


title: 0.5 M NaCl, LL22, rep1


title: 2.5 M NaCl, LL28, rep2


title: 0.5 M NaCl, LL16, rep1


title: 0.5 M NaCl, LL10, rep1


title: 0.5 M NaCl, LL4, rep2


title: 0.5 M NaCl, LL34, rep1


title: Brain, tert-, 9months, rep2

city: Sheffield

first: Catarina

middle: Martins

last: Henriques

address: Bateson Centre, Firth Court, The University of Sheffield, Western Bank

department: Oncology & Metabolism

country: United Kingdom

institute: The University of Sheffield

data_processing:
Quality control was performed using MultiQC version 1.9.
Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads.
Read alignment: Single-end reads were aligned against the reference genome Danio_rerio.GRCz11.dna. primary_assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio_rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht-seq count was run in non-stranded mode to obtain per gene read counts.
Assembly: Danio_rerio.GRCz11.dna.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: brain

growth_protocol: Zebrafish were maintained at the standard conditions of 27-28ºC, in a 14:10 hour light-dark cycle, and fed twice a day with Artemia (live rotifers) and Sparus (dry food).

extract_protocol:
Whole tissues were dissected in cold PBS (Sigma-Aldrich), transferred to a microcentrifuge tube containing 100 μl of Trizol (Thermo Fisher Scientific), snap-frozen in dry ice and stored at -80°. To isolate the RNA, extra 50 μl of Trizol was added to each sample, and the tissue was homogenized with a mechanical homogenizer (VWR International) and a 1.5 pestle (Kimble Chase, Vineland, NJ, USA). After 5 min incubation at room temperature (RT), 30 μl of chloroform (1:5, VWR International) was added and the samples were incubated for further 3 min at RT before centrifuged at 13,000g, for 30 min, at 4°C. Isopropanol (Thermo Fisher Scientific) was then added to the aqueous phase of the solution, and the resultant mix was incubated for 10 min at RT, before centrifuged (13,000g for 15 min at 4°C). Finally, the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air-dry, before resuspended in 14 μl of nuclease-free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). All the samples had a RNA integrity number (RIN) ≥9.
Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo-dT beads, capturing poly(A) tails, using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc). cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following the manufacturer’s instructions (New England Biolabs Inc).

value: brain

tag: strain

value: AB background

value: tert-

value: 9 months


title: 0.5 M NaCl, LL4, rep1

tag: genotype


title: Brain, tert-, 22months, rep2

tag: tissue

value: 22 months


title: Brain, tert-, 2months, rep3

value: 2 months


title: Brain, tert-, 2months, rep1


title: Brain, tert-, 9months, rep3


title: Brain, tert-, 22months, rep1


title: 2.5 M NaCl, LL4, rep1


title: Brain, tert-, 9months, rep1


title: Brain, WT, >30months, rep1

value: > 30 months


title: Brain, tert-, 2months, rep2


title: Brain, WT, >30months, rep2


title: Brain, WT, 22months, rep3


title: Brain, tert-, 22months, rep3


title: Brain, WT, 22months, rep1


title: Brain, WT, >30months, rep3


title: 2.5 M NaCl, LL22, rep1


title: Brain, WT, 22months, rep2


title: Brain, WT, 9months, rep3


title: Brain, WT, 9months, rep2


title: Brain, WT, 2months, rep1


title: Brain, WT, 9months, rep1


title: Brain, WT, 2months, rep3


title: Bristol_wild_Littoral_2_WGBS

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

description:
Total DNA from homogenized tissue
Littoral_wild_n2_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)

data_processing:
RNAseq reads were mapped to MZ_UMD2a and transcript expression values (tpm) were calculated using kallisto (see methods)
WGBS and RRBS reads were mapped to MZ_UMD2a and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see Methods).
Genome_build: GCF_000238955.4_M_zebra_UMD2a_genomic.fa
Supplementary_files_format_and_content: bw files containing mean mCG/CG levels averaged over 50bp non-overlapping bins and across samples for each group. Only CG with ≥4x coverage were used.
Supplementary_files_format_and_content: GeneQuant_tpm_Masoko_wild_liver.txt contains gene expression values (tpm) for all RNAseq samples.
Supplementary_files_format_and_content: Common_mCG_RRBS.txt file contains methylation values at common CG sites across all RRBS samples (min. 4x coverage in all CGs of all samples)

organism: Astatotilapia calliptera

source_name: homogenized adult liver

extract_protocol:
Genomic DNA extracted using silica column based approach (see methods)
DNA strand-specific library using methylated adaptor (NEB) followed by bisulfite conversion (Imprint, Sigma), according to manusfacturer's instructions. WGBS libraries contain lambda genome spike-in control (0.2% w/w).

tag: ecomoprh

value: Littoral

tag: Sex

value: male

tag: type

value: wild caught

value: liver


title: G10H05_Littoral_33958_1#92_RNAseq

description:
Total RNAs from homogenized tissue
GeneQuant_tpm_Masoko_wild_liver.txt.gz

extract_protocol:
total RNA extracted using phenol/chlorophorm approach (see methods)
ribosomal RNA depletion (RiboZero Illumina) followed by Illumina RNAseq stranded library kit, according to manusfacturer's instructions


title: Bristol_wild_Benthic_3_WGBS

description:
Total DNA from homogenized tissue
Benthic_wild_n3_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)

value: Benthic


title: G10G02_Benthic_33958_1#83_RNAseq


title: G10H04_Littoral_33958_1#91_RNAseq


title: G10G05_Littoral_33958_1#84_RNAseq


title: G10E09_Benthic_33958_1#74_RNAseq


title: G09D10_Riverine_33750_1#86_RNAseq

value: Riverine


title: G10F07_Benthic_33958_1#79_RNAseq


title: G10G01_Benthic_33958_1#82_RNAseq


title: G10E03_Benthic_33958_1#72_RNAseq


title: G08H10_Littoral_33750_1#60_RNAseq


title: G08F07_Riverine_33750_1#83_RNAseq


title: G10H04_Littoral_RRBS

description:
Total DNA from homogenized tissue
Common_mCG_RRBS.txt.gz

extract_protocol:
Genomic DNA extracted using silica column based approach (see methods)
RRBS protocol (including MSPI step) using the Diagenode Premium RRBS kit following manufacturer's intructions, followed by single-end 75bp stranded sequencing (see Methods)


title: G09D07_Riverine_33750_1#85_RNAseq


title: G10G10_Littoral_RRBS


title: G10H05_Littoral_RRBS


title: G10G06_Littoral_RRBS


title: G10G09_Littoral_RRBS


title: G10G02_Benthic_RRBS


title: G10F09_Benthic_RRBS


title: G10H02_Littoral_RRBS


title: G10G05_Littoral_RRBS


title: G10F10_Benthic_RRBS


title: G10F04_Benthic_RRBS


title: G10G01_Benthic_RRBS


title: G10F02_Benthic_RRBS


title: G10E09_Benthic_RRBS


title: G10E07_Benthic_RRBS


title: G10E05_Benthic_RRBS


title: G09D04_Riverine_33750_1#84_RNAseq


title: G10E04_Benthic_RRBS


title: G10D07_Riverine_RRBS


title: G10E03_Benthic_RRBS


title: G10C07_Riverine_RRBS


title: G09D08_Riverine_RRBS


title: G10F07_Benthic_RRBS


title: G09E01_Riverine_RRBS


title: G10D06_Riverine_RRBS


title: G09D10_Riverine_RRBS


title: G09D07_Riverine_RRBS


title: G09D05_Riverine_RRBS


title: G08H10_Littoral_RRBS


title: G09D04_Riverine_RRBS


title: G09D02_Riverine_RRBS


title: G08G02_Littoral_RRBS


title: G08F07_Riverine_RRBS


title: G08I06_Littoral_RRBS


title: G08G03_Littoral_RRBS


title: KO DMSO 2

city: Madrid

first: Orlando

last: Domínguez

address: Melchor F. Almagro 3

country: Spain

institute: CNIO

description: KO generated by CRISPR/Cas9

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Sequencing read alignment and quantification and differential gene expression analysis was performed in the Bluebee Genomics Platform, a cloud-based service provider (www.bluebee.com.)
Reads were first trimmed with bbduk from BBTools (Bushnell B., BBMap, https://sourceforge.net/projects/bbmap/) to remove adapter sequences and polyA tails.  Trimmed reads were aligned with STAR v 2.5 (Dobin A et al. Bioinformatics 29:15, 2013.) Read counting was performed with HTSeq (Anders S et al. Bioinformatics 31:166, 2015.)
Differential gene expression analysis was performed with DESeq2 (Love MI et al. Genome Biol 15:550, 2014)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Normalized counts and result table from results() function, both from DESeq2.

source_name: colorectal adenocarcinoma (DLD1)

growth_protocol: Cells were cultured at 37ºC in a humidified air atmosphere with 5% CO2. Cells were grown using high glucose Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma, D5796) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from cell pellets using the Agilent Absolutely RNA Miniprep Kit following the manufacturer’s instructions
Total RNA samples, 250ng with RQS=10 in a labchip analysis, were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.  {This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

treatment_protocol: Tigecycline was dissolved in DMSO to 10mM. 1µl of this was added to 10ml of culture media to a final concentration of 10 µM. 1µl of DMSO was added to 10 ml of culture media in the control group. After 24h cells were collected for RNA extraction.

value: FBXW7 -/-

value: DMSO for 24h


title: WT DMSO 2

value: Wild Type


title: G08H08_Littoral_RRBS


title: KO DMSO 1

description: KO generated by CRISPR/Cas9


title: WT DMSO 1


title: KO TIG 1

description: KO generated by CRISPR/Cas9

value: Tigecycline 10uM for 24h


title: WT TIG 1


title: KO TIG 2

description: KO generated by CRISPR/Cas9


title: WT TIG 2


title: EGFRF+ 4692#3 Caudal

city: Raleigh

first: Troy

last: Ghashghaei

state: North Carolina

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: North Carolina State University

data_processing:
Sequenced reads were adapter trimmed with BBDuk v. 38.94 (parameters> ref=adapters.fa t=10 ktrim=r minlength=60 entropy=0.01 maq=10 tpe tbo)
Trimmed reads were aligned to the GENCODE GRCm39 primary genome using STAR v. 2.7.8a (parameters> --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outSAMmultNmax 1 --sjdbOverhang 75
Reads were quantified with featureCounts v. 2.0.3 (parameters> -s 2 -M -O --fraction --countReadPairs)
Assembly: GRCm39
Supplementary files format and content: tab-deliminated files include read counts per sample

source_name: Cerebral cortex

extract_protocol:
E17.5 Nestin-EgfrF/F and control (EgfrF/+) embryos were obtained from time-pregnant females.  The day of vaginal plug detection was considered E0.5.  Embryos were collected in fresh ice cold HBSS and brains were taken out of the skull, and forebrains were separated from the rest of the brain using fine microforceps in ice cold HBSS.  The cortices and the hippocampal formation were dissected away from the ventral forebrain using microforceps and split into rostral and caudal halves.  Samples were collected and Total RNA was extracted using the RNeasy Mini kit (Qiagen, catalog no. 74104).
1 µg of total RNA per sample underwent mRNA capture and was then fragmented at 94 °C for 6 min. Sequencing libraries were prepared according to the manufacturer’s protocol using ten cycles of final amplification (KAPA mRNA HyperPrep Kit, catalog no. KK8580 and KAPA UDI Adapter Kit, catalog no. KK8727)
Next-generation sequencing was performed on an Illumina NextSeq500 (75-bp paired end) to a targeted depth of ~20 million reads per sample.

value: Cerebral cortex

tag: cortex region

value: caudal

tag: developmental stage

value: EGFRF+


title: EGFRF+ 4692#9 Caudal


title: EGFRF+ 4858#1 Caudal


title: EGFRF+ 4692#9 Rostral

value: rostral


title: EGFRF+ 4858#1 Rostral


title: NcreEGFRFF 4692#2 Caudal

value: NcreEGFRFF


title: NcreEGFRFF 4858#5 Caudal


title: EGFRF+ 4692#3 Rostral


title: NcreEGFRFF 4692#7 Rostral


title: MEF_hypoxia_10h

city: Boston

first: Xu

last: Zhou

state: MA

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

description: Mouse embryonic fibroblasts (MEFs) were harvested from E13.5-E14.4 embryos. Staged embryos were removed from a pregnant female by removing the uterus and separating each embryo from its amniotic sac. The head and “red tissue,” including fetal liver, were removed and discarded. The remaining portion of each embryo was minced using razor blades in 0.05% trypsin + EDTA and placed in a 37° C incubator for 30 min. After digestion, the tissue was transferred into a conical tube, washed with complete DMEM (DMEM + 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, 200U/mL penicillin/streptomycin, 10% FBS; Gibco) and resuspended in complete DMEM in 15cm tissue culture plates overnight. The following day, cells and undigested tissue debris were lifted from the plates using 0.05% trypsin + EDTA, spun down, resuspended, and filtered over a 70 um filter. These cells were expanded for 1-2 passages and used for experiments at p3-p7.

data_processing:
RNA-seq library was sequenced with Next-seq 500
Fastq files were downloaded from Basespace and were aligned with Kallisto v0.43.1 against all cDNA transcripts from mouse genome assembly GRCm38, with 100 rounds of boostrap method.
ESEMBL id of each aligned transrpt was matched to the offical gene symbols through BioaRt in R
The expression of a gene is calculated by summing the TPM of all ESEMBL transcripts matching that gene.
Assembly: GRCm38
Supplementary files format and content: The processed csv file contain the final processed gene expresion in TPM. The first column is the ESEMBL gene ID, the second column is the official gene symbol, the third to the ninth columns are the TPM expression values in murine embyronic fibroblasts of the indicated RNAseq samples.

source_name: Embryo

growth_protocol: All cell cultures were in their growth medium as descrbied in a 37° C incubator at 5% CO2.

extract_protocol:
RNA was purified from cells using Qiagen RNeasy columns with on-column DNAse digestion according to the manufacturer’s instructions.
Sequencing libraries were constructed following Illumina Tru-seq stranded mRNA protocol. Paired-end sequencing was performed with Next-seq 500 with 76 bp from each end.

treatment_protocol: After overnight culture, cells were treated as indidcated for each sample. The adherent cells were washed twice with ice-cold PBS and collected with RLT buffer (Qiagen RNeasy kit).

value: Embryo

tag: cell line

value: embryonoic fibroblast

value: Fibroblast

value: wild type

value: 0.1% oxygen for 10h


title: NcreEGFRFF 4692#2 Rostral


title: MEF_Oxidative_3h

tag: treatment

value: 10 uM NaAsO2 for 3h


title: MEF_noglutamine_10h

value: No glutamine for 10h


title: MEF_Nacl_3h

value: 100 mM NaCl for 3h


title: MEF_ER_10h

value: 1 uM thapsigargin for 10h


title: MEF_ctr

value: control


title: MEF_noglucose_10h

value: No glucose for 10h


title: SE+LEV6h rep2

city: Sanuki

first: Rie

last: Komori

department: Kagawa School of Pharmaceutical Sciences

institute: Tokushima Bunri University

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina).
Obtained reads (CAGE tags) were mapped to the mouse mm9 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5).
CAGE tag clustering, detection of differential expressed genes and motif discovery were performed by pipeline RECLU (Ohmiya et al., BMC Genetics 2014, 15:269). Tag count data were clustered using the modified Paraclu program. Clusters with count per million (CPM) < 0.1 were discarded. Regions that have 90% overlap between replicates were extracted by BEDtools (version 2.12.0). The clusters with irreproducible discovery rate (IDR) ≥ 0.1 and clusters longer than 200 bp were discarded.
Differentially expressed genes were detected using the edgeR package (version 3.22.5).
For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2016 vertebrates were evaluated by Tomtom.
The list of differentially expressed genes detected by RECLU with false discovery rate (FDR) ≤ 0.05 were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: hippocampus

extract_protocol:
Hippocampi were removed and RNA was extracted using High Pure RNA Isolation Kit (Roche).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: hippocampus

value: 6 h after PILO-SE+LEV


title: SE+LEV6h rep1


title: SE2d rep1

value: 2 d after PILO-SE


title: SE6h rep2

value: 6 h after PILO-SE


title: SE2d rep2


title: SE+LEV2d rep1

value: 2 d after PILO-SE+LEV


title: SE+LEV2d rep2


title: pre rep2

value: untreated


title: SE6h rep1


title: pre rep1


title: NcreEGFRFF 4692#7 Caudal

value: Cerebral cortex

value: caudal

value: NcreEGFRFF


title: NcreEGFRFF 4858#5 Rostral

value: rostral


title: RNAseq-shPcgf6-R2

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

description: R1 and R2 are duplicate samples

data_processing:
RNA-seq data is applied quality and adapter trimming by Trim Galore (v0.6.4_dev) and mapped to the mm9 reference genome using STAR (v2.7.1a).
And we performed reads summarization for genomic features via featureCounts (v2.0.0).
The raw read counts normalization and differential expression were determined by DESeq2 (for duplicate samples) and edgeR (for single sample).
Assembly: mm9
Supplementary files format and content: raw count

growth_protocol: E14 mouse embryonic stem cells (mESCs) using high-glucose Dulbecco’s modified Eagle’s medium supplemented with 15% ESC-qualified fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× non-essential amino acids, and 1000 U/mL of LIF.

extract_protocol:
Total RNA was isolated from cells using the GeneJet RNA purification kit, and 1 μg total RNA was reverse transcribed to generate cDNA using the PrimeScript RT reagent Kit.
For RNA-seq, libraries were prepared from two biological replicates using the TruSeq RNA Sample Prep Kit.

treatment_protocol: Rif1 conditional deletion (CKO) ESCs which were treated with 4-OHT (0.2μM) for 2 days and control ESCs which were treated with DMSO for 2 days, cultured for another 2 days without treatment.

value: Embryonic stem cells

value: Pcgf6 KD


title: RNAseq-WT-R2

description: R1 and R2 are duplicate samples

value: WT


title: RNAseq-shPcgf6-R1

description: R1 and R2 are duplicate samples


title: RNAseq-shMax-R2

description: R1 and R2 are duplicate samples

value: Max KD


title: RNAseq-WT-R1

description: R1 and R2 are duplicate samples


title: RNAseq-shRNF2-R1

description: R1 and R2 are duplicate samples

value: RNF2 KD


title: RNAseq-shMax-R1

description: R1 and R2 are duplicate samples


title: RNAseq-Rif1-CKO-R2

description: R1 and R2 are duplicate samples


title: ChIPseq-Rif1-WT-RNF2

data_processing:
Adapters and low-quality bases were removed using Trim Galore (v0.6.4_dev).
ChIP-seq reads were mapped to the mm9 genome using Bowtie2 (v2.3.5.1).
To remove PCR duplicate reads, which might occur false positive results, MarkDuplicates (v4.1.4.1, Picard) was used to locate and tag duplicate reads. And duplicates were removed using the REMOVE_SEQUENCING_DUPLICATES options.
ChIP-seq peaks were called using MACS2 (v2.2.6).
Assembly: mm9
Supplementary files format and content: bigwig

extract_protocol:
Briefly, mESCs of 80–90% confluency were crosslinked with a final concentration of 1% formaldehyde for 10 min at room temperature, and then quenched by the addition of 125 mM glycine. The cells were then rinsed twice with ice-cold DPBS, and harvested by scraping using silicon scraper. The supernatant was discarded after spinning at 1350 g for 5 min at 4 ℃, and the pellet was lysed with lysis buffer A (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.25% Triton X-100, 10% glycerol and protease inhibitor cocktail), incubated at 4℃ for 10 min with rotating, and collected by spinning at 1350 g for 5 min at 4℃. Cells were then resuspended in lysis buffer B (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and protease inhibitor cocktail), and incubated at room temperature for 10 min. The nuclei were then pelleted by spinning at 1350 g for 5 min at 4℃. The pellet was resuspended with lysis buffer C (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, and protease inhibitor cocktail), incubated for 15 min on ice, and transferred into Covaris microTUBEs. The DNA was sonicated to 200 bp fragments using Covaris S220 (duty cycle: 10%; intensity: 5; cycles/burst: 200; duration: 195s). After sonication, a final concentration of 1% Triton X-100 was added and gently mixed by pipetting. The chromatin solution was clarified by spinning at 12000 rpm at 4℃ for 10 min. 50 μL of supernatant from each sample was reserved as input and the rest chromatin solution was incubated with the indicated primary antibodies overnight at 4℃. The magnetic beads (Thermo, 88803) were added after blocking in the block buffer (0.5% (w/v) RNase/DNase-free BSA in 1 × PBS), and incubated with chromatin solution and antibodies for 4 h at 4℃. The immunoprecipitant was then washed 5 times with wash buffer (50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate). The DNA was then eluted with Elution Buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS). To reverse the crosslinks, samples were incubated at 65℃ overnight. The RNA was digested with a final concentration of 1 mg/mL RNases A at 37℃ for 1 h, and the proteins were degraded subsequently with a final concentration of 0.5 mg/mL Proteinase K at 55℃ for 2 h. The immunoprecipitated DNA was then extracted with AMPure beads according to the manufacturer’s instructions (Beckman, A63881).
For ChIP-seq, 1 ng precipitated DNA or input was used to generate the DNA library using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

treatment_protocol: For ChIP-seq of Pcgf6, we first introduce HA tag at N-terminal endogenous Pcgf6 using CRISPR/Cas9 system. Rif1 conditional deletion (CKO) ESCs which were treated with 4-OHT (0.2μM) for 2 days and control ESCs which were treated with DMSO for 2 days, cultured for another 2 days without treatment.Cells were infected with lenti-viral based shNT (control) or shRif1(Rif1 KD), cells were harvested 4 days after infection.

value: anti-RNF2 (Active Motif, 39663)


title: ChIPseq-Rif1_WT_Input_forPcgf6


title: ChIPseq-Rif1_WT_Pcgf6

value: anti-HA (CST, 3724S)


title: ChIPseq-Rif1_KD_Pcgf6


title: ChIPseq-Rif1_KD_Input_forPcgf6


title: ChIPseq-Rif1-CKO-RNF2


title: RNAseq-shRNF2-R2

description: R1 and R2 are duplicate samples


title: ChIPseq Foxa2 in EB+48hr(iAscl1.Lmx1b.Foxa2.V5) rep2

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description:
Foxa2_iALF_48hr.events.txt
Foxa2_iALF_48hr.bed

data_processing:
Fastq files were aligned to the mouse genome (mm10) using Bowtie (v1.3.0) with options “-q --best --strata -m 1 --chunkmbs 1024”.
MultiGPS (v.0.75) was used to call peaks after alignment on all transcription factors, with a cutoff of q-value < 0.01 (using binomial tests and Benjamini-Hochberg multiple hypothesis correction) for designating statistically significant events.  Differential binding analysis between different conditions was also performed with MultiGPS, which uses EdgeR internally.
Assembly: mm10
Supplementary files format and content: MultiGPS: MultiGPS output files (text format)
Supplementary files format and content: BED: MultiGPS peak positions

source_name: ES-derived embryoid bodies with induced transcription factors

growth_protocol: Inducible cell lines were generated using a previously described inducible cassette exchange (ICE) method [Iacovino, et al. Stem Cells 2011]. Resulting transgenic lines contain a single-copy insertion of the transgenes into the HPRT locus that is expression competent. p2Lox-Ascl1 (iAscl1) plasmid was generated by cloning mouse Ascl1 cDNA into p2Lox-V5 plasmid. Likewise, the additional transcription factors were cloned by amplifying open reading frames with p2a or t2a linker peptides as shown in Figure 1. Lmx1b sequence was V5-tagged in iAL and FLAG-tagged at the C-terminal in iALF, iALP, and iALFP, and iALFiP combinations to facilitate immunoprecipitation for ChIP experiments and asses induction efficiency by antibody staining. Pet1 was also V5-tagged for ChIP experiments. Second tetracycline response element (TRE) containing inducible line was generated by inserting TRE-Pet1-HA construct into p2Lox-ALF plasmid which allows two separate TRE elements to control expression of ALF vs Pet1 constructs. HA-tag was added to second TRE Pet1 construct to facilitate ChIP experiments. The inducible mESCs were grown in 2i (2-inhibitors) based medium (Advanced DMEM/F12: Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% mESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM beta-mercaptoethanol (Gibco), 1,000 U ml–1 leukemia inhibitory factor (Millipore), 3 mM CHIR (BioVision) and 1 mM PD0325901 (Sigma) on 0.1% gelatin (Milipore) coated plates at 37 °C, 8% CO2. To generate embryoid bodies (EBs), mESCs were dissociated using TrpLE (Gibco) and plated in AK medium (Advanced DMEM/F12: Neurobasal (1:1) Medium, 10% Knockout SR (vol/vol) (Gibco), penicillin–streptomycin (Gibco), 2 mM L-glutamine and 0.1 mM beta-mercaptoethanol) on untreated plates for 2 days (day −2) at 37 °C, 8% CO2.

extract_protocol:
Cells were collected and fixed with 1 mM DSG (ProtoChem) followed by 1% FA (vol/vol) each for 15 min at room temperature. Pellets containing 25–30 × 10^6 cells were aliquoted and flash-frozen at −80 °C. Cells were lysed in lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1× protease inhibitors (Roche, 11697498001) at 4 °C for 10 minutes. Cells were resuspended in 50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol), and incubated 10 minutes at 4 °C. Nuclear extracts were resuspended in cold sonication buffer (50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (wt/vol)). Sonication was performed with Bioruptor Pico sonicator device (Diagenode) with 30 sec ON/ 30 sec OFF, 18 cycles, with Bioruptor sonication beads (0.45 mg beads per 1 ml sample). Immunoprecipitation was done overnight at 4 °C on a rotator with Dynabeads protein-G (Thermo Fisher) conjugated antibodies. 5 µg of the following antibodies were used for immunoprecipitation: anti-Ascl1 (Abcam, ab74065); anti-HA (Abcam, ab9110); anti-V5 (Abcam, ab15828). Subsequent washes were done in 1X sonication buffer (cold) first, sonication buffer with 500 nM NaCl (cold), LiCl wash buffer (20 mM Tris-HCl (pH 8.0)) (cold), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) (cold), and TE buffer (10 mM Tris, 1 mM EDTA, (pH 8)) (cold). Samples were eluted in elution buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) by incubating for 45 min at 65 °C. Eluted sample and input (sonicated only) were incubated overnight at 65 °C to reverse the crosslink. RNA was digested by the addition of 0.2 mg ml–1 RNase A (Sigma) and incubating for 2 h at 37 °C. Protein digestion was performed by adding 0.2 mg ml–1 Proteinase K (Invitrogen) for 30 min at 55 °C. DNA extraction was done with Phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) followed by ethanol precipitation.
1/3 of ChIP DNA (1:100 dilution of input DNA) was used to prepare lllumina DNA sequencing libraries. Bioo Scientific multiplexed adapters were ligated after end repair and A-tailing, and unligated adapters were removed with Agencourt AmpureXP beads (Beckman Coulter) purification. Adapter-ligated DNA was amplified by PCR using TruSeq primers (Sigma). DNA libraries between 300 and 500 bp in size were purified from agarose gel using a Qiagen minElute column, and the final quantification of the library before pooling was done using a KAPA library amplification kit (Roche Lightcycler 480). The libraries were sequenced on an Illumina NextSeq 500 using V2 chemistry for 50 cycles (single-end) at NYU Genomics Core facility.

treatment_protocol: After 2 days, the expression of the transgenes was induced by adding 3 µg ml–1 doxycycline (Sigma, D9891) to the AK medium. For differentiating mESC (EB) antibody stainings, RNA-seq, sc-RNAseq, and ATAC-seq experiments, 2–3 × 10^5 cells were plated in each 100-mm untreated dishes (Corning). For ChIP-seq experiments, the same conditions were used, but the seeded cell number was scaled up to 3–3.5 × 10^6 cells in 245 mm × 245 mm square dishes (Corning). For day 9 attached neuron antibody stainings, bulk RNA-seq, ATAC-seq experiments, EBs induced with doxycycline for 2 days (48 h + doxycycline) were dissociated with 0.05% Trypsin-EDTA (Gibco) and plated on poly-D-lysine (Sigma, P0899) on coated 4-well plates. The dissociated neurons were grown in neuronal medium with supplements (Neurobasal Medium supplemented with 2% fetal bovine serum, B27, 0.5 mM L-glutamine, 0.01 mM β-mercaptoethanol, 3 µg ml–1 doxycycline, 10 ng ml–1 GDNF (PeproTech, 450–10), 10 ng ml–1 BDNF (PeproTech, 450–02), 10 ng ml–1 CNTF (PeproTech 450–13), 10 µM Forskolin (Fisher, BP2520–5), and 100 µM IBMX (Tocris, 2845)) at 37 Co, 5% CO2. Antimitotic reagents (4 µM 5-fluoro-2′-deoxyuridine (Sigma, F0503) and 4 µM uridine (Sigma, U3003)) were added to eliminate residual proliferating cells.

tag: chip target

value: anti-V5 (Abcam, ab15828)

value: Dox induction + 48 hours

value: Embryoid bodies


title: ChIPseq Pet1 in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep2

description:
Pet1_iALFiP_48hr.events.txt
Pet1_iALFiP_48hr.bed

value: anti HA (Abcam, ab9110)


title: Input DNA in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA)

value: Input


title: ChIPseq Foxa2 in EB+48hr(iAscl1.Lmx1b.Foxa2.V5) rep1


title: Input DNA in EB+48hr(iAscl1.Lmx1b.Pet1.V5)


title: ChIPseq Pet1 in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep1


title: Input DNA in EB+48hr(iAscl1.Lmx1b.Foxa2.V5)


title: ChIPseq Pet1 in EB+48hr(iAscl1.Lmx1b.Pet1.V5) rep1

description:
Pet1_iALP_48hr.events.txt
Pet1_iALP_48hr.bed


title: ChIPseq Pet1 in EB+48hr(iAscl1.Lmx1b.Pet1.V5) rep2


title: ChIPseq-Rif1-CKO-H2A119ub

value: anti-H2AK119ub (CST, 8240S)


title: RNAseq-Rif1-CKO-R1

description: R1 and R2 are duplicate samples

value: Rif1 CKO


title: Input DNA in EB+48hrDox(iAscl1.v5.TRE.Lmx1b.HA)


title: ChIPseq-Rif1-WT-H2A119ub


title: ChIPseq Lmx1b in EB+48hrDox(iAscl1.v5.TRE.Lmx1b.HA) rep2

description:
Lmx1b_iAL.events.txt
Lmx1b_iAL.bed


title: ATACseq in EB+d9Dox(iAscl1.V5) rep2

data_processing:
Alignment: ATAC-seq data was mapped to the mouse genome (version mm10) using bowtie2-2.4.2 (Robinson et al., 2009) using “-q --very-sensitive” options.
Domain-finding: Enriched domains were identified using the DomainFinder module in SeqCode: (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java). Briefly, contiguous 50bp genomic bins with significantly higher read enrichment compared to normalized input were identified (binomial test, p-value < 0.05). Further, contiguous blocks within 200bp were joined together to call enriched domains.
Assembly: mm10
Supplementary files format and content: BED: Domains displaying significant enrichment of ATAC-seq reads

extract_protocol:
50,000 cells were harvested and washed twice in cold 1X PBS. Cells were resuspended in 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40, and centrifuged immediately at 4 °C for 10 minutes. Day 9 attached neuron samples were lyzed in 0.01% NP-40 instead. The pellet was resuspended in 25 µl of 2× TD buffer, 2.5 µl TDE1 (Nextera DNA sample preparation kit, FC-121– 1030) followed by incubation for 30 min at 37 °C. The reaction was cleaned up with Min-elute PCR purification kit (Qiagen, 28004). The optimal number of PCR cycles were determined to be the one-third of the maximum fluorescence measured by quantitative PCR reaction with 1× SYBR Green (Invitrogen), custom-designed primers [45].) and 2× NEB MasterMix (New England Labs, M0541). The library was cleaned up with Min-elute PCR kit and quantified using Qubit (Life Technologies, Q32854).
Nextera DNA sample preparation kit, FC-121-1030 was used for ATAC-seq. The fragment length distribution of the library was determined by Agilent High Sensitivity DNA D1000 Screentape (5067- 5585) system and the final quantification of the library before pooling was done with KAPA library amplification kit (Roche Lightcycler 480).

value: Dox induction + 9 days


title: ATACseq in EB+d9Dox(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep2


title: ATACseq in EB+d9Dox(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep1


title: ChIPseq Foxa2 in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep2

description:
Foxa2_iALFiP_48hr.events.txt
Foxa2_iALFiP_48hr.bed


title: ATACseq in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep2


title: ChIPseq Foxa2 in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep1


title: ChIPseq Lmx1b in EB+48hrDox(iAscl1.v5.TRE.Lmx1b.HA) rep1

description:
Lmx1b_iAL.events.txt
Lmx1b_iAL.bed


title: ATACseq in EB+48hr(iAscl1.Lmx1b.Foxa2.V5.TRE.Pet1.HA) rep1


title: ATACseq in EB+48hr(iAscl1.Lmx1b.Foxa2.V5) rep2


title: ATACseq in EB+48hr(iAscl1.Lmx1b.Foxa2.V5) rep1


title: ATACseq in EB+48hrDox(iAscl1.V5) rep2


title: ATACseq in EB+48hrDox(iAscl1.V5) rep1


title: aff1-2 10uM IAA-3

city: Saint Louis

first: Ryan

middle: Joseph

last: Emenecker

state: MO

address: 660 S Euclid Ave

department: Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

description: file identifier is ACCATAC

data_processing:
The samples were sequenced across three (1x50bp) lanes using an Illumina HiSeq 3000.
The reads were then demultiplexed and aligned to the TAIR 10 Ensemble Release 23 assembly using STAR.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount.
All gene counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in any sample greater than one count-per-million were excluded from further analysis. In addition, genes not expressed in at least 2 out of the 3 samples were not considered for downstream analysis. The TMM size factors and the matrix of counts were then imported into R/Bioconductor package Limma.
Performance of the samples was assessed with a Spearman correlation matrix and Multi-Dimensional Scaling plot. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and gene performance was assessed with plots of residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
A generalized linear model was then created to test for gene level differential expression and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Genome_build: TAIR 10 Ensemble Release 23 assembly
Supplementary_files_format_and_content: The all_gene_counts_aff1.txt file contains the raw gene counts from the RNAseq experiment. The file is a plain text file.

organism: Arabidopsis thaliana

source_name: Whole Seedling

growth_protocol: Seedlings were surface sterilized with 20% bleach having 0.01% Triton X-100 for 15 min, then rinsed four times with sterile water. Sterilized seeds were suspended in 0.1% agar and then stratified for 2 d at 4ºC to promote uniform germination. After stratification, seeds were grown on PNS media (PNS + 0.5% agar) for 4 days at 22 °C under continuous illumination.

extract_protocol:
Total RNA was isolated from whole seedlings using the RNeasy Plant Mini Kit from Qiagen according to manufacturer’s instructions.
Samples were prepared for sequencing using the SMARTer cDNA synthesis kit (Clontech) according to manufacturer’s instructions.

treatment_protocol: For treatment, 4 day old seedlings were transferred from plant nutrient growth medium + 0.5% agar plates to PN liquid medium containing either 10mM IAA or an equivalent amount of ethanol for mock (control) treatment. Seedlings were treated for 2 hours before RNA was isolated from whole seedling tissue.

value: Whole Seedling

value: 10uM IAA


title: aff1-2 10uM IAA-2

description: file identifier is CTCAATG


title: aff1-2 10uM IAA-1

description: file identifier is CTTGGAA


title: aff1-1 CTRL-2

description: file identifier is AGACTGA

value: Mock


title: aff1-1 10uM IAA-2

description: file identifier is AACGGAG


title: aff1-1 10uM IAA-3

description: file identifier is TCCGGGA


title: aff1-2 CTRL-1

description: file identifier is TTTTCGG


title: aff1-1 CTRL-1

description: file identifier is TTCGCTG


title: COL 10uM IAA-1

description: file identifier is CATTTAG


title: aff1-2 CTRL-2

description: file identifier is TTTCAGA


title: aff1-2 CTRL-3

description: file identifier is TATCTTA


title: ATACseq in EB+d9Dox(iAscl1.V5) rep1


title: COL CTRL-3

description: file identifier is TGTGCCA


title: COL 10uM IAA-2

description: file identifier is AGGACCT


title: COL 10uM IAA-3

description: file identifier is CCAGGCA


title: aff1-1 CTRL-3

description: file identifier is ACAGATA


title: COL CTRL-2

description: file identifier is TGCCCAT


title: COL CTRL-1

description: file identifier is GAGTACG


title: hormone intact, scRNA-Seq

city: New York

first: XIANXIAO

last: ZHOU

state: NY

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: LNCaP

extract_protocol:
Total RNA was extracted from LNCaP cells
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: LNCaP

tag: age


title: castrate, scRNAseq

description: 10x Genomics


title: Figue 4E 1x1011 vg mice 3

city: Aarhus

first: Zongliang

last: Gao

address: Høegh-Guldbergs Gade 10, C. F. Møllers Allé 6

country: Denmark

institute: Aarhus University

data_processing:
Analysis of prime editing outcomes was performed by CRISPResso2 using the HDR mode. Only sequencing reads with a minimum homology of 90% and an average quality score ≥30 were included in the analysis. The percentage of ‘HDR’ in the report represented the percentage of correct prime edits, and the indel yields were calculated as: (number of indel containing reads + imperfect HDR)/(total reads).
Supplementary files format and content: Barchart showing the allele assignments

source_name: liver

extract_protocol:
The genomic DNA of liver samples were obtained by treatment with chorion villi buffer followed by isopropanol precipitation
NGS was performed by Eurofins using the INVIEW CRISPR Check - 2nd PCR service with MiSeq Sequencing, 60k read pairs (2x300 bp). Briefly, genomic sites of interest were PCR-amplified using Phusion Hot Start II PCR Master Mix with primers containing forward and reverse adapters. The PCR products were agarose gel-purified and submitted to Eurofins for library construction and sequencing.

value: liver

value: tissue

value: AAV injected

value: 1x1011 vg dual AAV


title: Figue 4E 1x1012 vg mice 2

value: 1x1012 vg dual AAV


title: Figue 4E 1x1011 vg mice 2


title: Figue 4E 1x1011 vg mice 1


title: Figue 4E control mice 1

value: control

value: no


title: Figue 4E 1x1012 vg mice 1


title: Figue 4E control mice 2


title: Figue 4E control mice 3


title: aff1-1 10uM IAA-1

description: file identifier is AAACCTT


title: ChIP_primary_hepatocytes_VC

city: East Lansing

first: Sudin

last: Bhattacharya

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

data_processing:
Sequences (50 nucleotide reads, single end) were aligned to the human genome (hg19) using the BWA algorithm. Aligns were extended in silico at their 3′-ends to a length of 150 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p = 10−7
Signal maps and peak locations were used as input data to Active Motif's proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (TCDD vs. VC)

growth_protocol: Cells were plated on Rat Collagen I-coated plates and Geltrex was added for a final concentration of 0.25 mg/ml approximately 6 h after plating. Cells were maintained at 37 °C in a humidified 5% CO2 atmosphere in William E medium supplemented with cell maintenance cocktail B (Invitrogen)

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 15 min and quenched with 0.125 M glycine and shipped to Active Motif (Carlsbad, CA, U.S.A) for ChIP-seq analysis. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated using a Misonix Sonicator 3000. For each ChIP reaction, 30 μg of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and a rabbit polyclonal antibody against AhR (ENZO Lifesciences, BML-SA210, Lot# 01031447) and incubated overnight at 4 °C. Protein A agarose beads were added and incubation at 4 °C was continued for another 3 h. Immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. Immune complexes were eluted from the beads with SDS buffer and subjected to RNase treatment and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified on a NanoDrop spectrophotometer. .equipped with a microtip in order to shear the DNA to an average length of 300–500 bp. Lysates were cleared by centrifugation and stored at −80 °C.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3′-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200–250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

treatment_protocol: Cells were treated with 1 nM TCDD (dissolved in 0.1% DMSO). and 0.1% DMSO as vehicle control

value: hepatocytes

value: vehicle control (0.1% DMSO) for 24h


title: ChIP_primary_hepatocytes_TCDD

value: 1nM TCDD for 24h

value: AhR (ENZO Lifesciences, BML-SA210, Lot# 01031447)


title: ChIP_primary_hepatocytes_input


title: Seedlings, wt, rep2

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Bowtie2+RSEM+DESeq2 and Limma
Reads were mapped on the reference Arabidopsis thaliana transcriptome (TAIR, version 10) using the bowtie2 program (Langmead and Salzberg, 2012)
Estimation of gene expression levels was performed using RSEM (Li and Dewey, 2011)
Estimation of gene expression levels was performed using RSEM (Li and Dewey, 2011)
Differential expression analysis was performed applying the latest versions of DESeq2 (Love et al., 2014) and Limma (Ritchie et al., 2015) to RSEM estimated reads counts
Assembly: tair10
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Seedlings

growth_protocol: Seedlings were grown for 7 d on B5 media in continuous white light with standard, 32-W linear florescent tubes (GE product number 26668) producing a light intensity of ∼150 μE

extract_protocol:
Total RNA was isolated using the E.Z.N.A. Plant RNA Kit from Omega Biotek. To ensure low levels of contaminating rRNA, two rounds of poly(A) mRNA purification were performed using the µMACS mRNA Isolation Kit (Miltenyi Biotech).
Indexed RNA-seq libraries were prepared from 100 ng of poly(A) RNA starting material using the NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific; catalog no. 5130). Sequencing of 150-bp paired-end reads was performed on an Illumina HiSeq 2500 in rapid output mode at the Texas A&M Agrilife Research Facility (College Station, TX). Sample demultiplexing was performed using CASAVA software v1.8.2, and bcl2fastq was performed using conversion software v1.8.4.

value: Seedlings

value: wild type


title: Figue 4E 1x1012 vg mice 3


title: B-0028_VP1 [GG1CR2]

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

data_processing:
library strategy: 4C-seq
Demultiplexing : Different samples were demultiplexed using the primer sequences
Mapping: Reads were mapped to the human reference genome (hg19 assembly) using Bowtie (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: Only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located +-10kb from the viewpoint were discarded.
Contact frequency: The number of reads overlapping per restriction fragment was calculated using bedtools intersect. A 30 fragment sliding window was applied in order to smoothen the signal.
Data visualization: Smoothed data were uploaded to UCSC Browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: BEDGRAPH

source_name: B lymphoblastoid cell line

extract_protocol:
B lymphoblastoid cell lines (5 x 10^6 cells) were harvested by centrifugation and resuspended in 5 mL PBS with 10% FBS. To cross-link cells, 5 mL 4% formaldehyde was added and samples incubated for 10 min. Cross-linking was quenched by adding 1 M glycine to 125 mM final concentration and cells collected by centrifugation at 300 x g for 10 min at 4°C.
4C-seq assays and data processing were performed as previously reported (Fernández-Miñán et al. 2016)

value: B lymphoblastoid cell line

tag: viewpoint

value: Intergenic (between CD55 and CR2)


title: Seedlings, co, sail, rep2

value: constans mutant


title: B-0028_VP3 [GG3CR2]

value: CR1 intron 1


title: B-0028_VP4 [GG4CR2]

value: CR1 intron 29


title: B-0056_VP3 [AA3CR2]


title: Seedlings, co, sail, rep1


title: Seedlings, c3c4c9, rep2

value: nfy yc3 yc4 yc9 triple mutant


title: Seedlings, c3c4c9, rep1


title: B-0056_VP2 [AA2CR2]

value: CR2 intron 1


title: Seedlings, wt, rep1


title: B-0056_VP4 [AA4CR2]


title: Seedlings, b2b3, rep2

value: nfy yb2 yb3 double mutant


title: ip2_pol2s5p_1

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Reads were trimmed for a minimum average quality of Q20 in a window of 20 nucleotides using Reaper 13.274 from the EBI Kraken package.
In order to normalize all samples to the same sequencing depth, 17 million reads per sample were randomly selected for further analysis.
These were mapped versus the hg19 version of the human genome with STAR 2.4.2a using only unique alignments to exclude reads with unclear origin.
The reads were further deduplicated using Picard 1.136 to remove PCR artefacts leading to multiple copies of the same original fragment.
The MUSIC peakcaller (version from Dec. 2015) was employed to accommodate for the range of peak widths typically expected for the selected histone modifications.
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Peaks were annotated based on data from GENCODE v19. The annotation was run using two different modes to accommodate for histone modifications centred on the promoter (H3K9K14ac, HDAC1, HDAC2, Pol2, H3K4me3, Pol2S5P) and those covering the gene body (H4K5ac, H3K4me1, H3K27ac, H3K27me3, H3K9me3). Peaks of modifications centred on the promoter were annotated with the promoter (TSS +- 5000 nt) of the gene most closely located to the centre of the peak. Peaks of modifications covering the gene body were annotated with the gene that showed the most complete coverage of the peak (highest overlap).
To permit a recounting of reads on different regions (unified peaks, promoters, genes), a background-correction was performed by subtracting reads of the Input sample from reads of the respective Treatment sample in windows of 50nt length. All windows with negative values (Input > Treatment) were set to zero. Background-corrected counts for regions were calculated using bigWigAverageOverBed (UCSC Tools).
In order to be able to compare peaks in different samples to assess reproducibility, the resulting lists of significant peaks per histone mark were overlapped and unified to represent identical regions.
Background-corrected counts for unified peaks were submitted to DESeq2 for normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of DESeq normalized unified peaks.

source_name: Pulmonary Artery Adventital  Fibroblasts (PAAF)

growth_protocol: PAFBs were maintained ex vivo in fibroblast growth medium (ScienCell Research Laboratories, Catalog: 2301) under normoxic conditions.

extract_protocol:
PAFBs from donor and PAH patients were crosslinked for 10 min with 1% formaldehyde at 37°C and the reaction was stopped by addition of glycine 0.125 M for 5 min at room temperature. Chromatin immunoprecipitation (ChIP) assay was performed on the lysates after sonication.
For ChIP library preparation 10ng of obtained DNA was used as input for Ion Xpress Plus gDNA Fragment Library Preparation Kit (Thermo) starting from the end repair step in the protocol. Insert size and Library quality was checked with BioAnalyzer 2100 instrument (Agilent).

tag: donor status

value: IPAH

tag: histone modification

value: RNA Pol2 Ser5P

tag: antibody


title: ip1_pol2s5p_1

tag: cell type

value: Pulmonary Artery Adventital  Fibroblasts (PAAF)


title: Seedlings, b2b3, rep1


title: d2_pol2s5p_1

value: healthy


title: ip2_h4k5_1


title: ip1_pol2_1

value: RNA Pol2


title: d2_pol2_1


title: ip1_h4k5_1


title: ip2_h3k9k14ac_1


title: d2_h4k5_1


title: B-0028_VP2 [GG2CR2]


title: B-0056_VP1 [AA1CR2]


title: ip1_h3k9k14ac_1


title: ip1_h3k4me3_1

value: Active Motif:39159


title: d1_pol2_1


title: d2_h3k4me3_1


title: d2_h3k9k14ac_1


title: d1_pol2s5p_1


title: ip2_h3k27me3_1

value: Active Motif:39155


title: ip2_pol2_1


title: d1_h3k4me3_1


title: d2_h3k27ac_1

value: Active Motif:39133


title: ip1_h3k27ac_1


title: d1_h3k9k14ac_1


title: d1_h3k27me3_1


title: ip1_h3k4me1_1


title: d1_h3k27ac_1


title: ip2_h3k27ac_1


title: ip2_h3k4me3_1


title: ip1_in_1

value: INPUT


title: d1_h4k5_1


title: d1_in_1


title: ip1_h3k27me3_1


title: d2_in_1


title: ip2_in_1


title: d1_h3k4me1_1


title: Pdgfra-Cre:LmnaF/F-1

city: Houston

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

data_processing:
FASTQC was used for the quality control check.
DESeq2 was used to identify differentially expressed genes.
Assembly: mm10 (Gencode version M25)
Supplementary files format and content: text file with raw gene read counts

source_name: PDGFRA+ cells

extract_protocol:
Total RNA was extracted from  PDGFRA+ cells upon FACS sorting from mouse ventricular tissue from  using the miRNeasy Mini Kit .
RNA extracts with an RNA Integrity Number (RIN) value of >8, determined using an Agilent Bioanalyzer RNA chip, were used to construct sequencing libraries. Strand-specific ribosomal RNA depleted sequencing libraries were generated using TruSeq stranded total RNA library preparation kit . The libraries were sequenced as 150bp paired-end reads on an Illumina HiSeq 2500 instrument.

value: Lmna-KO

tag: strain

value: C57BL/6 (mixed)


title: WT-4

tag: genotype

value: WT


title: Pdgfra-Cre:LmnaF/F-4


title: Pdgfra-Cre:LmnaF/F-2


title: WT-2


title: ip2_h3k4me1_1


title: WT-1


title: WT-3


title: 293FT, gCTSL, rep 1  24h

city: Durham

first: Qianben

last: Wang

address: 905 S. Lasalle Street

institute: Duke University

data_processing:
Raw RNA-seq reads were mapped to human hg19 genome by HISAT2
The expression counts were computed by htseq-count
The Differentially Expressed Genes were identified by DESeq2
Assembly: hg19
Supplementary files format and content: counts

extract_protocol:
RNeasy Mini Kit from Qiagen following manufacturer's instructions
Libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following manufacturer's instructions

value: human embryonal kidney cells

value: CTSL knockdown

value: transfection


title: 293FT, gCTSL, rep 3  24h


title: 293FT, gCtrl, rep 2  24h

value: Control


title: 293FT, gCtrl, rep 1  24h


title: 293FT, gCTSL, rep 2  24h


title: Pdgfra-Cre:LmnaF/F-3


title: TBX5_3

description: IPAH + TBX5 siRNA Control

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for subsequent analyses.
Trimmed and filtered reads were aligned versus Homo sapiens genome version hg38 (GRCh38) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1”.
Duplicate reads were removed with Picard 2.21.7.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Counts were normalized using DESeq2 version 1.30.0.
Genome_build: hg38
Supplementary_files_format_and_content: pul36_rnaseq.txt: Tab-delimited text file contains DESeq normalized counts.

source_name: Pulmonary Artery

growth_protocol: PAAFs were maintained ex vivo in fibroblast growth medium (ScienCell Research Laboratories, Catalog: 2301) under normoxic conditions.

extract_protocol:
RNA was isolated from treated PAH PAAFs using the miRNeasy mini kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
3µg total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacturer’s protocol (Vazyme).

treatment_protocol: PAAFs were untreated or treated with Scrambled control siRNA or with gene-specific siRNAs.

tag: diagnosis

value: Idiopathic pulmonary arterial hypertension (IPAH)

value: Pulmonary Artery Adventitial  Fibroblasts (PAAF or FBs)

tag: sirna

value: TBX5 siRNA Control


title: TBX5_4

description: IPAH + TBX5 siRNA Control


title: TBX4_3

description: IPAH + TBX4 siRNA Control

value: TBX4 siRNA Control


title: SOX9_1

description: IPAH + SOX9 siRNA Control

value: SOX9 siRNA Control


title: TBX4_2

description: IPAH + TBX4 siRNA Control


title: SOX9_4

description: IPAH + SOX9 siRNA Control


title: TBX4_4

description: IPAH + TBX4 siRNA Control


title: TBX5_2

description: IPAH + TBX5 siRNA Control


title: SOX9_3

description: IPAH + SOX9 siRNA Control


title: TBX4_1

description: IPAH + TBX4 siRNA Control


title: EP300_1

description: IPAH + EP300 siRNA Control

value: EP300 siRNA Control


title: EP300_3

description: IPAH + EP300 siRNA Control


title: Scr_4

description: IPAH + Scrambled siRNA Control

value: Scrambled siRNA Control


title: EP300_4

description: IPAH + EP300 siRNA Control


title: Scr_3

description: IPAH + Scrambled siRNA Control


title: Scr_2

description: IPAH + Scrambled siRNA Control


title: 293FT, gCtrl, rep 3  24h


title: SOX9_2

description: IPAH + SOX9 siRNA Control


title: Mock_4

value: Untreated


title: Scr_1

description: IPAH + Scrambled siRNA Control


title: TBX5_1

description: IPAH + TBX5 siRNA Control


title: Mock_3


title: Mock_1


title: Mock_2


title: IPAH2_SGC-CBP30

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for subsequent analyses.
Trimmed and filtered reads were aligned versus Homo sapiens genome version hg38 (GRCh38) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1”.
Duplicate reads were removed with Picard 2.21.7.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Counts were normalized using DESeq2 version 1.30.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: pul35_rnaseq.txt: Tab-delimited text file contains DESeq normalized counts.

extract_protocol:
RNA was isolated from treated PAH PAAFs using the miRNeasy mini kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
2µg total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacturer’s protocol (Vazyme).

treatment_protocol: PAAFs were treated with 20µM of vehicle (DMSO) or with SGC-CBP30.

value: Pulmonary Artery Adventitial Fibroblasts (PAAF or FBs)


title: IPAH3_DMSO

value: DMSO


title: IPAH2_DMSO


title: IPAH3_SGC-CBP30


title: IPAH1_SGC-CBP30


title: EP300_2

description: IPAH + EP300 siRNA Control


title: IPAH3_Untreated


title: IPAH1_DMSO


title: IPAH1_Untreated


title: IPAH2_Untreated


title: Donor 3

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for subsequent analyses.
Trimmed and filtered reads were aligned versus Homo sapiens genome version hg38 (GRCh38) using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1”.
Duplicate reads were removed with Picard 2.21.7.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Counts were normalized using DESeq2 version 1.26.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: pul28_rnaseq.txt: Tab-delimited text file contains DESeq normalized counts.

extract_protocol:
RNA was isolated from ex vivo isolated donor and PAH PAAFs from early passage using the miRNeasy mini kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
2µg total RNA was used as input for TruSeq Stranded mRNA Library preparation following the low sample protocol (Illumina).

treatment_protocol: No Treatment.

value: Healthy

value: Pulmonary Artery Adventitial Fibroblasts (PAAF)


title: Donor 4


title: Donor 1


title: IPAH 2


title: Donor 2


title: NALM-6_CARTtreated_24h_sc0001 [H9_S72]

first: Birgit

last: Knoechel

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description:
coculture24h_CART_NALM6_5to1_ATACseq_H9_S72
052721_countmatrix_scATACseq.csv

data_processing:
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5'.
Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: scRNA-Seq: 052721_countmatrix_scRNAseq.csv: HTSeq count matrix with raw counts for all individual cells.
Supplementary_files_format_and_content: scATAC-Seq: 052721_countmatrix_scATACseq.csv: Fragments file with fragments for all individual cells; raw counts.

source_name: B-cell precursor leukemia cell line NALM-6

growth_protocol: NALM-6 cells were cultured in RPMI-1640 media with 10% of heat-inactivated fetal bovine serum, 100 μM penicillin/streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 1x NEAA, 20 mM HEPES and 0.5 mM 2-mercaptoethanol.

extract_protocol:
5000 NALM-6 cells were bulk sorted. Following tagmentation, single cells were sorted into 96 well plates containing 4 μl of lysis buffer and Nextera XT indexes.
Libraries were prepared using the plate-based scATAC-seq protocol as described by Chen et al. (2018).

treatment_protocol: Cells were treated for 24h with CAR T-cells/uninfected T-cells.

value: CAR T-cells

tag: library strategy

value: scATAC-seq


title: NALM-6_CARTtreated_24h_sc0001 [H8_S256]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H8_S256
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H8_S64]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H8_S64
052721_countmatrix_scATACseq.csv


title: IPAH 1


title: NALM-6_CARTtreated_24h_sc0001 [H8_S160]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H8_S160
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H9_S168]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H9_S168
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H7_S56]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H7_S56
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H6_S144]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H6_S144
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H5_S232]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H5_S232
052721_countmatrix_scATACseq.csv


title: IPAH 4


title: NALM-6_CARTtreated_24h_sc0001 [H6_S240]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H6_S240
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H7_S152]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H7_S152
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H6_S48]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H6_S48
052721_countmatrix_scATACseq.csv


title: IPAH 3


title: NALM-6_CARTtreated_24h_sc0001 [H7_S248]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H7_S248
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H5_S40]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H5_S40
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H9_S264]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H9_S264
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H2_S208]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H2_S208
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H3_S24]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H3_S24
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H3_S120]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H3_S120
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H3_S216]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H3_S216
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H2_S16]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H2_S16
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H4_S128]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H4_S128
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H2_S112]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H2_S112
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H12_S192]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H12_S192
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H10_S80]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H10_S80
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H10_S176]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H10_S176
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H11_S280]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H11_S280
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H11_S184]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H11_S184
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H5_S136]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H5_S136
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G9_S263]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G9_S263
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G8_S255]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G8_S255
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H4_S32]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H4_S32
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G8_S63]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G8_S63
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G6_S143]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G6_S143
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G7_S151]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G7_S151
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G7_S247]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G7_S247
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G5_S231]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G5_S231
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G5_S39]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G5_S39
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H1_S104]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H1_S104
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G4_S31]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G4_S31
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G6_S47]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G6_S47
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G4_S127]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G4_S127
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G3_S23]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G3_S23
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G1_S199]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G1_S199
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G2_S111]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G2_S111
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G2_S15]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G2_S15
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G11_S87]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G11_S87
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [H11_S88]

description:
coculture24h_CART_NALM6_5to1_ATACseq_H11_S88
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G3_S119]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G3_S119
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G11_S279]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G11_S279
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G11_S183]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G11_S183
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F9_S70]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F9_S70
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G1_S7]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G1_S7
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G12_S287]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G12_S287
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G9_S71]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G9_S71
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G10_S175]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G10_S175
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G10_S271]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G10_S271
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F8_S158]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F8_S158
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F9_S166]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F9_S166
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F9_S262]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F9_S262
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F8_S62]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F8_S62
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [G12_S191]

description:
coculture24h_CART_NALM6_5to1_ATACseq_G12_S191
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F8_S254]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F8_S254
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F7_S150]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F7_S150
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F7_S246]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F7_S246
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F5_S134]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F5_S134
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F6_S46]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F6_S46
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F5_S38]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F5_S38
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F6_S142]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F6_S142
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F7_S54]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F7_S54
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F4_S126]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F4_S126
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F3_S214]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F3_S214
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F5_S230]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F5_S230
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F4_S30]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F4_S30
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F4_S222]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F4_S222
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F3_S118]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F3_S118
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F3_S22]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F3_S22
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F2_S14]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F2_S14
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F1_S102]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F1_S102
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F2_S206]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F2_S206
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F12_S286]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F12_S286
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F12_S190]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F12_S190
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F1_S198]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F1_S198
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F11_S86]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F11_S86
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F10_S174]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F10_S174
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F10_S78]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F10_S78
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F11_S278]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F11_S278
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F11_S182]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F11_S182
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E9_S261]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E9_S261
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E9_S69]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E9_S69
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E7_S149]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E7_S149
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E8_S157]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E8_S157
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E8_S253]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E8_S253
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E8_S61]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E8_S61
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E7_S53]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E7_S53
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E9_S165]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E9_S165
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F1_S6]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F1_S6
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [F12_S94]

description:
coculture24h_CART_NALM6_5to1_ATACseq_F12_S94
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E6_S141]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E6_S141
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E6_S237]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E6_S237
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E5_S37]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E5_S37
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E5_S229]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E5_S229
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E5_S133]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E5_S133
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E4_S221]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E4_S221
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E6_S45]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E6_S45
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E3_S21]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E3_S21
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E4_S29]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E4_S29
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E2_S205]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E2_S205
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E3_S117]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E3_S117
052721_countmatrix_scATACseq.csv


title: NALM-6_CARTtreated_24h_sc0001 [E3_S213]

description:
coculture24h_CART_NALM6_5to1_ATACseq_E3_S213
052721_countmatrix_scATACseq.csv