title: SUM149PT_shEN1-2_Day-5_Dox-plus_2

description: RNA-seq of SUM149 cells after 5 days with TET-inducible shEN1 with doxycycline


title: Cell_334

status: Public on Aug 22 2019

type: SRA

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

country: USA

institute: ucla

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-87_S277_L005_R1_001.fastq.gz

library_source: transcriptomic

data_processing:
The raw fastq files were trimmed using TrimGalore! In pair-end mode with default parameters.
The trimmed fastq data were aligned to human reference genome Hg38 using STAR in pair-end mode with default parameters.
The alignment results were inputted to featureCounts to compute the number of reads mapped back to each gene in each sample.
Genome_build: hg38
Supplementary_files_format_and_content: Read count table for each gene in each sample generated by featureCounts software.

molecule: total RNA

organism: Homo sapiens

source_name: single cell isolated from hESC derived 3D-retinal ordanoid

growth_protocol: H9 hESCs were maintained in Essential-8 (E8) medium (Invitrogen) on Vitronectin (VTN-N)-coated plates and passaged twice weekly. Medium was changed every day.

extract_protocol: Retinal organoids were dissociated in Accutase (StemPro) for 30 min to create a single-cell suspension. Cells were collected by centrifugation at 300 × g for 5 min and resuspended in 500 μL RDM. we used a mouth pipette to immediately transfer single cells into prepared lysis buffer. scRNA-seq library was constructed following modified Smart-seq2 protocol[6]. In detail, samples were incubated at 72°C for 3 min. The first-strand cDNA was reverse-synthesized using oligo(dT) and template-switching oligonucleotides (TSO). The synthesized first-strand cDNAs were amplified by 18 cycles. After purification, 0.1 ng cDNA were used for Nextera tagmentation (illumina) and library construction. Sequencing was performed on Illumina HiSeq 4000.

treatment_protocol: hESC were enzymatically lifted with dispase (2 mg/mL) and grown as aggregates in suspension. Medium was switched from E8 to neural induction medium (NIM: DMEM/F12 1:1, 1% N2 supplement, MEM nonessential amino acids, penicillin-streptomycin and 2 µg/ml heparin sulfate) gradually over the course of four days. On D7, cell aggregates were attached to the plate with 10% fetal bovine serum (FBS) to facilitate attachment. On D16 cultures were switched to retinal differentiation medium (RDM: DMEM/F12 (3:1), 2% B27 supplement, MEM nonessential amino acids and penicillin-streptomycin). On D18, neural retina structures were manually dissected from the plate and allowed to form free-floating organoids in RDM. From D30, RDM was supplemented with 10% FBS, 100 µM Taurine, 2mM GlutaMAX and 0.5 µM retinoic acid for long-term differentiation.

tag: cell type

value: cell from hESC derived 3D-retinal ordanoid

tag: cell line


title: Cell_333

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-86_S276_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-2_Day-5_Dox-minus_1

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: RNA-seq of SUM149 cells after 5 days with TET-inducible shEN1 without doxycycline (control)

data_processing:
RNA-Seq, ChIP-Seq: Illumina Casava1.7 software used for basecalling.
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
RNA-Seq: Datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the hg19 refGene annotation file available at the UCSC Genome Browser.
ChIP-Seq: QC, alignment and peak calling was performed using ChiLin pipeline 2.0.0 (https://www.ncbi.nlm.nih.gov/m/pubmed/27716038/?i=6&from=chilin). Briefly, reads were aligned to GRCh37/hg19 using BWA, and peak calling was performed using MACS2, in chilin.
Genome_build: RNA-Seq and ChIP-Seq: hg19
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: bed file (BED6+4) of factor peaks from MACS2 peakcaller.

growth_protocol: SUM149 and SUM159: DMEM/F12, 5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin, 50 U/mL penicillin and 50 μg/ml streptomycin. MCF7: 4.5mg/l glucose DMEM, 10% FBS, 10 μg/ml insulin, 50 U/mL penicillin and 50 μg/ml streptomycin

extract_protocol:
ChIP-seq: cell monolayers were fixed with 1% formaldehyde for 10 min, at room temperature for H3K27ac and FOXA1 ChIP-seq, or 37C for V5-EN1 and TLE3 ChIP-seq. Cells were fixet with 1.5mM EGS during 30 min and adding 1% paraformaldehyde during the last 10 min for b-catenin ChIP-seq. All cell fixations were wuenched by adding 125mM glycine during 5 min. After 2 ice-cold PBS washes, cells were scrapped off in PBS, pelleted and snap-frozen. RNA-seq: cells were washed 3 times with ice-cold PBS, scrapped off the plates, pelleted and snap frozen into liquid nitrogen. For RNA-extraction, the RNeasy Mini Kit (Qiagen, #74106) was used, with in-column DNA digestion.
ChIP-seq: the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) was used following manufacturer's instructions. RNA-seq: libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol

treatment_protocol: SUM149 and SUM159: 5x10exp5 cells were seeded in 150mm tissue culture plates, allowed to attach and grow for 24h and then treated or not with 0.1ug/mL doxycycline hyclate for 5 days, with one media change at day 3. MCF7: 2x10exp6 cells were seeded in 150mm tissue culture plate. After 24h, media were change and allow to grow for 5 days, with one media change at day 3.

tag: hairpin

tag: days

tag: treatment

value: No Dox


title: SUM149PT_shEN1-2_Day-5_Dox-minus_2


title: Cell_332

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-85_S275_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-2_Day-5_Dox-plus_1

value: Dox


title: SUM159PT_shEN1-1_Day-5_Dox-minus_2

description: RNA-seq of SUM159 cells after 5 days with TET-inducible shEN1 without doxycycline (control)


title: SUM149PT_shEN1-1_Day-5_Dox-plus_2


title: Cell_331

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-84_S274_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-1_Day-5_Dox-plus_1


title: Cell_330

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-83_S273_L005_R1_001.fastq.gz


title: Cell_329

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-82_S272_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-1_Day-5_Dox-minus_2


title: Cell_328

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-81_S271_L005_R1_001.fastq.gz


title: Cell_327

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-80_S270_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-1_Day-5_Dox-minus_1


title: SUM149PT_shEN1-2_Day-3_Dox-plus_2

description: RNA-seq of SUM149 cells after 3 days with TET-inducible shEN1 with doxycycline


title: Cell_326

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-7_S197_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-2_Day-3_Dox-plus_1


title: SUM159PT_shEN1-1_Day-3_Dox-minus_2

description: RNA-seq of SUM159 cells after 3 days with TET-inducible shEN1 without doxycycline (control)


title: SUM159PT_shEN1-1_Day-3_Dox-plus_1

description: RNA-seq of SUM159 cells after 3 days with TET-inducible shEN1 with doxycycline


title: Cell_325

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-79_S269_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-2_Day-3_Dox-minus_2

description: RNA-seq of SUM149 cells after 3 days with TET-inducible shEN1 without doxycycline (control)


title: SUM149PT_shEN1-2_Day-3_Dox-minus_1


title: Cell_323

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-77_S267_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-1_Day-3_Dox-plus_2


title: Cell_322

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-76_S266_L005_R1_001.fastq.gz


title: Cell_321

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-75_S265_L005_R1_001.fastq.gz


title: SUM149PT_shEN1-1_Day-3_Dox-minus_2


title: SUM149PT_shEN1-1_Day-3_Dox-minus_1


title: Cell_318

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-72_S262_L005_R1_001.fastq.gz


title: Cell_319

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-73_S263_L005_R1_001.fastq.gz


title: 835-1-NoIns-72hrs

city: Stanford

first: Joshua

last: Knowles

state: California

address: 300 Pasteur Dr.

institute: Stanford University

description: Patient cell line 835-1 without insulin for 72 hours

data_processing:
Sequencing reads were first quality checked by FastQC (v 0.11.8) and reads above Q30 are retained.
Retained reads were further mapped and reads per gene were counted by STAR (v2.7)
Read count normalization and differential analyses were performed using Deseq2 R package (v1.22.2) with custom codes
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample.

source_name: Human Induced Pluripotent Stem Cells

extract_protocol:
RNA was extracted as described earlier. [DOI:https://doi.org/10.1016/j.stem.2016.11.005]  Briefly:  Cells were washed once with PBS and RNA was extracted using Purelink RNA mini kit (Thermo Fisher Scientific). RNA integrity was evaluated using 2100 Bioanalyzer via the RNA 6000 Nano assay (Agilent) or Fragment Analyzer (Advanced Analytical). Only samples with RQN/RIN values equal or greater than 7.0 were used.
library was constructed as described earlier. [DOI:https://doi.org/10.1016/j.stem.2016.11.005]  Briefly:  Library preparation was done using standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina). mRNA was isolated and fragmented. cDNA was generated using random hexamers, end-repaired and ligated with respctive adaptors for sequencing.  AMPure XP beads (Beckman Coulter) was used size selection and purification of the library. During PCR amplification step the illumine recommended  6 bp barcode bases were introduced at one end of the adaptors. Before load onto the sequencer,  the size and concentration of the RNA-seq libraries were measured by Qubit fluorometry (Thermo Fisher Scientific) and Bioanalyzer. Illumina HiSeq 2500 System  was used for sequencing of the mRNA libraries with 100 nucleotide single-end reads, according to the Illumina’s standard protocol.

treatment_protocol: hiPSCs were adapted to TeSR-E8 medium (StemCell Technologies). Cultures were washed 4 times prior to experiments.  Insulin free medium was prepared by supplementing mTeSR-E5 medium (StemCell Technologies) with TGFB1(2 µg/l) and bFGF(100 µg/l). For insulin control groups, medium was further supplemented with insulin (insulin, human recombinant, zinc solution; Life Technologies) to the final concentration of 19.4 mg/l. The cultures were fed double medium from day 4 of culture onwards during maintenance in TeSR-E8 and experiments.

tag: age of donor

tag: sex of donor

value: Female

tag: race of donor

value: White

tag: insulin treatment condition

value: Without insulin

tag: rna harvest time point


title: Cell_317

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-71_S261_L005_R1_001.fastq.gz


title: 835-1-Ins-72hrs

description: Patient cell line 835-1 treated with insulin for 72 hours

value: With insulin


title: Cell_316

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-70_S260_L005_R1_001.fastq.gz


title: Cell_315

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-6_S196_L005_R1_001.fastq.gz


title: 835-1-NoIns-24hrs

description: Patient cell line 835-1 without insulin for 24 hours


title: 334-1-NoIns-72hrs

description: Patient cell line 334-1 without insulin for 72 hours


title: 835-1-Ins-24hrs

description: Patient cell line 835-1 treated with insulin for 24 hours


title: 334-1-Ins-72hrs

description: Patient cell line 334-1 treated with insulin for 72 hours


title: Cell_313

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-68_S258_L005_R1_001.fastq.gz


title: Cell_324

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-78_S268_L005_R1_001.fastq.gz


title: 334-1-Ins-24hrs

description: Patient cell line 334-1 treated with insulin for 24 hours


title: SUM149PT_shEN1-1_Day-3_Dox-plus_1

description: RNA-seq of SUM149 cells after 3 days with TET-inducible shEN1 with doxycycline


title: Cell_312

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-67_S257_L005_R1_001.fastq.gz


title: 334-1-NoIns-24hrs

description: Patient cell line 334-1 without insulin for 24 hours


title: Cell_311

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-66_S256_L005_R1_001.fastq.gz


title: Cell_309

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-64_S254_L005_R1_001.fastq.gz


title: 071-2-NoIns-72hrs

description: Patient cell line 071-2 without insulin for 72 hours


title: Cell_320

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-74_S264_L005_R1_001.fastq.gz


title: Cell_310

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-65_S255_L005_R1_001.fastq.gz


title: 071-2-Ins-72hrs

description: Patient cell line 071-2 treated with insulin for 72 hours


title: Cell_308

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-63_S253_L005_R1_001.fastq.gz


title: Cell_307

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-62_S252_L005_R1_001.fastq.gz


title: 071-2-Ins-24hrs

description: Patient cell line 071-2 treated with insulin for 24 hours


title: Cell_306

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-61_S251_L005_R1_001.fastq.gz


title: Cell_314

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-69_S259_L005_R1_001.fastq.gz


title: Cell_305

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-60_S250_L005_R1_001.fastq.gz


title: Cell_304

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-5_S195_L005_R1_001.fastq.gz


title: Cell_303

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-59_S249_L005_R1_001.fastq.gz


title: M_46.8_negativeControl_BS

city: Shanghai

first: Jing-Dong

middle: Jackie

last: Han

address: 320 Yue Yang Road

country: China

institute: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Human PFC WGBS data were uniquely mapped to the revised Cambridge human mtDNA Reference Genome (rCRS, NC_012920.1) using BSMAP (Xi and Li, 2009) allowing two mismatches with methylation called using “methyratio.py”. All duplicated reads with the same base composition and mapping position are removed.
Genome_build: NC_012920.1
Supplementary_files_format_and_content: tab-delimited text files include methylation ratio for each strand and sample

molecule: genomic DNA

source_name: Caucasian American_Frontal cortex

extract_protocol:
Extraction was performed using roughly 10-20 mg of pooled mitochondrial sample. Extraction of mtDNA was similar to the Clayton and Shadel purification method, performed using the mtDNA isolation kit (Abcam) with modifications to the manufacturers' protocol: dounce homogenization was performed for 25 strokes at 4oC, an additional low speed spin at 700g was performed to improve the removal of cell debris and nuclei, 1 µl of proteinase K (Fermentas) was added to the enzyme mix to degrade DNAase, and a phenol-chloroform extraction was included prior to ethanol precipitation to increase the purity of the final DNA solution.
To further assess the accuracy of our mtDNA BS-seq technique, we checked the apparent background of our technique using unmethylated mtDNA prepared from 4 samples (M_25.6, W_27.7, M_46.8, W_50.5) using long range PCR (LATaq, TaKara) to amplify the complete mtDNA genome in two overlapping fragments, A and B (see below). 50 µl PCR reactions were prepared according to the manufacturers’ recommendations and reaction conditions were 5 min at 98oC, 40 cycles of denaturation for 30 s at 98oC, annealing for 30 s at 58oC, and extension for 10 min at 72oC, with a final extension for 5 mins at 72oC. Products were agarose gel purified on a 0.7% gel at 120V for 2 hours in 1x TBE and gel extracted (Gel extraction kit, QIAgen). Equimolar amounts of each fragment were mixed, and then BS-seq was performed as for purified mtDNA.  mtfullAF: AACCAAACCCCAAAGACACC  mtfullAR: GCCAATAATGACGTGAAGTCC  mtfullBF: TCCCACTCCTAAACACATCC  mtfullBR: TTTATGGGGTGATGTGAGCC

tag: population

value: Caucasian American

tag: mean age (years)

tag: number of individuals

tag: tissue

value: Frontal cortex

tag: molecule subtype

value: mitochondrial DNA


title: W_50.5_negativeControl_BS

source_name: Han Chinese_Frontal cortex

value: Han Chinese


title: M_25.6_negativeControl_BS


title: C_90.2

data_processing:
Basecalls performed using CASAVA
Human PFC WGBS data were uniquely mapped to the revised Cambridge human mtDNA Reference Genome (rCRS, NC_012920.1) using BSMAP (Xi and Li, 2009) allowing two mismatches with methylation called using “methyratio.py”. All duplicated reads with the same base composition and mapping position are removed.
C or G sites were excluded if the ratio of reads at that site showed a difference from the reference greater than 5% to exclude the effect of a common C/T SNPs.
ComBat (Johnson et al., 2007) was used to remove batch effects.
Genome_build: NC_012920.1
Supplementary_files_format_and_content: tab-delimited text files include methylation ratio for each strand and sample

extract_protocol:
Extraction was performed using roughly 10-20 mg of pooled mitochondrial sample. Extraction of mtDNA was similar to the Clayton and Shadel purification method, performed using the mtDNA isolation kit (Abcam) with modifications to the manufacturers' protocol: dounce homogenization was performed for 25 strokes at 4oC, an additional low speed spin at 700g was performed to improve the removal of cell debris and nuclei, 1 µl of proteinase K (Fermentas) was added to the enzyme mix to degrade DNAase, and a phenol-chloroform extraction was included prior to ethanol precipitation to increase the purity of the final DNA solution.
Bisulfite treatment of mtDNA was performed using the EpiTect Bisulfite Kit (QIAgen). 200 ng (PFC samples) or 1 µg (cell line samples) of DNA was first converted using the “Bisulfite DNA conversion” steps of the manufacturers protocol “Sodium Bisulfite Conversion of Unmethylated Cytosines in DNA”, with the optional additional cycle added to the conversion program (a final denaturation step for 5 min at 95oC, followed by 2 h at 60oC, and then hold at 20oC). To ensure the maximum recovery of DNA, cleanup was performed using the “Cleanup of bisulfite converted DNA” steps of the manufacturers’ protocol “Sodium Bisulfite Conversion of Unmethylated Cytosines in Small Amounts of Fragmented DNA” and using the optional carrier RNA during spin column cleanup. Contaminating RNA for PFC samples was removed with 1 µl RNase A (QIAgen) for 10 min at 70oC with shaking in a total volume adjusted to 200 µl with ddH2O. RNase was subsequently removed by phenol-chloroform extraction and DNA was isolated by isopropanol precipitation.


title: C_87.1


title: Cell_301

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-56_S246_L005_R1_001.fastq.gz


title: Cell_300

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-55_S245_L005_R1_001.fastq.gz


title: C_76.7


title: Cell_299

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-54_S244_L005_R1_001.fastq.gz


title: M_62.2


title: 071-2-NoIns-24hrs

description: Patient cell line 071-2 without insulin for 24 hours


title: W_59.2


title: Cell_297

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-52_S242_L005_R1_001.fastq.gz


title: Cell_298

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-53_S243_L005_R1_001.fastq.gz


title: Cell_295

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-50_S240_L005_R1_001.fastq.gz


title: W_53.9


title: W_50.5


title: Cell_294

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-4_S194_L005_R1_001.fastq.gz


title: Cell_296

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-51_S241_L005_R1_001.fastq.gz


title: W_27.7_negativeControl_BS


title: M_46.8


title: Cell_293

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-49_S239_L005_R1_001.fastq.gz


title: Cell_302

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-58_S248_L005_R1_001.fastq.gz


title: W_37.3


title: M_34.0


title: W_40.7


title: Cell_292

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-48_S238_L005_R1_001.fastq.gz


title: W_27.7


title: Cell_291

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-47_S237_L005_R1_001.fastq.gz


title: Cell_290

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-46_S236_L005_R1_001.fastq.gz


title: Cell_289

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-45_S235_L005_R1_001.fastq.gz


title: W_27.2


title: M_25.6


title: DNMT3A_KO_HEK293T [WGBS]

data_processing:
Basecalls performed using CASAVA version 1.4
WGBS data were uniquely mapped to the revised Cambridge human mtDNA Reference Genome (rCRS, NC_012920.1) using BSMAP (Xi and Li, 2009) allowing two mismatches with methylation called using “methyratio.py”.
Genome_build: NC_012920.1
Supplementary_files_format_and_content: tab-delimited text files include methylation ratio for each strand and sample

extract_protocol:
Mitochondrial isolation followed the protocol of Clayton and Shadel (Clayton and Shadel, 2014), with additional purification steps such that low-speed centrifugation is repeated one-step beyond the last time there was a visible pellet of nucleus
DNA Libraries were constructed using Illumina TruSeq DNA sample prep kit V2 by the Shanghai Institute for Biological Sciences core facility.

tag: genotype/variation

value: DNMT3A knockout


title: Cell_287

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-43_S233_L005_R1_001.fastq.gz


title: DNMT3A_WT_HEK293T [WGBS]

value: wild-type


title: Cell_288

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-44_S234_L005_R1_001.fastq.gz


title: DNMT3A_OE [WGBS]

data_processing:
Basecalls performed using CASAVA
WGBS data were uniquely mapped to the revised Cambridge human mtDNA Reference Genome (rCRS, NC_012920.1) using BSMAP (Xi and Li, 2009) allowing two mismatches with methylation called using “methyratio.py”.
Genome_build: NC_012920.1
Supplementary_files_format_and_content: tab-delimited text files include methylation ratio for each strand and sample

value: DNMT3A over expression


title: Cell_286

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-42_S232_L005_R1_001.fastq.gz


title: DNMT3A_Control [WGBS]

value: control


title: Cell_285

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-40_S230_L005_R1_001.fastq.gz


title: DNMT3A_KO_HEK293T [RNA-seq]

data_processing:
Basecalls performed using CASAVA
Reads were uniquely mapped to hg19 using Tophat with '--library-type fr-firststrand'
Gene expression was calucated using Cufflinks with default paramters.
Genome_build: hg19
Supplementary_files_format_and_content: bam files were generated using tophat

extract_protocol:
Total RNA was extracted with TRIzol followed by ethanol precipitation.
RNA-seq library construction  was performed by Berry Genomics, Beijing, China.


title: Cell_283

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-39_S229_L005_R1_001.fastq.gz


title: DNMT3A_WT_HEK293T [RNA-seq]


title: DNMT3A_OE_A549 [RNA-seq]

data_processing:
Basecalls performed using CASAVA
Reads were uniquely mapped to hg19 using Tophat with '--library-type fr-firststrand'
Gene expression was calucated using Cufflinks with default paramters.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression files were generated using cufflinks; Scores represent fpkm

tag: genotype


title: Cell_282

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-38_S228_L005_R1_001.fastq.gz

tag: cell type


title: DNMT3A_Control_A549 [RNA-seq]

tag: cell line


title: Input_r3_MeDIP

description:
P13C016_ATGTCA_L008
processed data file: Input_MeDIP.ucsc.bedGraph.gz

data_processing:
Basecalls performed using CASAVA
MeDIP-seq data was uniquely mapped to the chrM (hg19) using Bowtie (Langmead, 2010) (v0.12.8)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

extract_protocol:
Whole cell DNA was extracted from HEK293T cells using the QIAamp DNA mini kit (QIAgen), according to the manufacturers protocol.The MeDIP protocol was based on Weber et al, 2005 (Weber et al., 2005). Contaminating RNA was removed from both mtDNA and whole DNA with 1 µl RNase A (QIAgen) for 30 min at 60oC with shaking in a total volume made up to 200 µl with ddH2O. RNase was subsequently removed by phenol-chloroform extraction and DNA was precipitated with isopropanol. 2 µg of DNA per MeDIP was sheared on a Covaris S220 focused-ultrasonicator using the Illumina 200 protocol (to yield 200 bp fragments) provided by the manufacturer. Shearing size was confirmed using an Agilent 2100 BioAnalyser and the DNA 7500 LabChipTM. Sheared DNA was diluted to 455 µl in TE buffer and denatured at 95oC for 10 min, followed by ice cooling for 10 min. Then, 51 µl of 10x IP buffer (100 mM Na-Phosphate pH 7.0, 1.4 M NaCl, 0.5 % Triton X-100) and 5 µl of either anti-5mC (Abcam, ab10805) or anti-5hmC (Abcam, ab106918) antibodies were added to the DNA and preincubated with overhead shaking for 2 h at 4oC. 20 µl Protein G Dynabeads (Life Technologies) were prewashed 2x with 800 µl 0.1% BSA in PBS for 5 min at RT with shaking. Beads were collected, resuspended in 40 µl of 1x IP buffer (10 mM Na-Phosphate pH 7.0, 0.14 M NaCl, 0.05 % Triton X-100), and then added to the preincubated antibody-DNA mix. Tubes were incubated at 4oC overnight with overhead shaking, and then beads were washed 3x with 800 µl 1x IP buffer. Beads were resuspended in 250 µl of Proteinase K digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5 % SDS) with 7 µl of Proteinase K (Fermentas) and incubated at 50oC for 3 h with shaking. DNA was then extracted using phenol-chloroform extraction followed by isopropanol precipitation (Weber et al., 2005).
DNA Libraries were constructed using Illumina TruSeq DNA sample prep kit V2 by the Shanghai Institute for Biological Sciences core facility.

tag: antibody

tag: replicates


title: Input_r2_MeDIP

description:
P13C013_CTTGTA_L008
processed data file: Input_MeDIP.ucsc.bedGraph.gz


title: Cell_280

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-36_S226_L005_R1_001.fastq.gz


title: 5hmC_r3_MeDIP

description:
P13C015_AGTTCC_L008
processed data file: 5hmC_MeDIP.ucsc.bedGraph.gz

value: anti-5hmC (Abcam, ab106918)


title: Cell_279

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-35_S225_L005_R1_001.fastq.gz


title: Cell_277

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-33_S223_L005_R1_001.fastq.gz


title: 5hmC_r2_MeDIP

description:
P13C012_CAGATC_L008
processed data file: 5hmC_MeDIP.ucsc.bedGraph.gz


title: Cell_276

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-32_S222_L005_R1_001.fastq.gz


title: 5mC_r3_MeDIP

description:
P13C014_AGTCAA_L008
processed data file: 5mC_MeDIP.ucsc.bedGraph.gz

value: anti-5mC (Abcam, ab10805)


title: Cell_275

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-31_S221_L005_R1_001.fastq.gz

value: cell from hESC derived 3D-retinal ordanoid


title: 5hmC_r1_MeDIP

description:
P13C009_TGACCA_L008
processed data file: 5hmC_MeDIP.ucsc.bedGraph.gz


title: Cell_274

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-30_S220_L005_R1_001.fastq.gz


title: Cell_273

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-2_S192_L005_R1_001.fastq.gz


title: 5mC_r2_MeDIP

description:
P13C011_GCCAAT_L008
processed data file: 5mC_MeDIP.ucsc.bedGraph.gz


title: Cell_272

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-29_S219_L005_R1_001.fastq.gz


title: 5mC_r1_MeDIP

description:
P13C008_CGATGT_L008
processed data file: 5mC_MeDIP.ucsc.bedGraph.gz


title: Cell_284

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-3_S193_L005_R1_001.fastq.gz


title: HeLa: PRMT5_ChIPSeq

city: Beijing

first: Jie

last: Gao

address: No. 10, Xitoutiao, You An Men, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: School of Basic Medical Sciences, Capital Medical University

data_processing:
Basecalls performed using CASAVA.
The high quality reads were mapped to the Human genome of Ensembl by using bowtie1 (Langmead, Trapnell, Pop, & Salzberg, 2009) with the default parameter.
Data were filtered using NGS QC Toolkit (Patel & Jain, 2012)
The expression peaks were detected by MACS14 (Zhang et al., 2008).
Genome_build: GRCh37

source_name: HeLa cell

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS and with 5% CO2.

extract_protocol:
Approximately 1 x 107 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibodies against Snail, MTA1, or PRMT5. The DNA was purified with a Qiagen PCR purification kit
Libraries were prepared according to Illumina's instructions. The NEBNext Ultra DNA Library Prep Kit for Illumina was used for DNA library construction.  After adapter ligation DNA PCR was amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from the agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced  following the manufacturer protocols.

value: HeLa

tag: chip antibody


title: HeLa: MTA1_ChIPSeq


title: Cell_281

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-37_S227_L005_R1_001.fastq.gz


title: Cell_270

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-27_S217_L005_R1_001.fastq.gz


title: HeLa: input DNA


title: HeLa: Snail_ChIPSeq

value: Snail


title: Cell_278

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-34_S224_L005_R1_001.fastq.gz


title: Cell_268

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-24_S214_L005_R1_001.fastq.gz


title: Cell_269

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-26_S216_L005_R1_001.fastq.gz


title: Input_r1_MeDIP

description:
P13C010_ACAGTG_L008
processed data file: Input_MeDIP.ucsc.bedGraph.gz


title: Cell_267

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-23_S213_L005_R1_001.fastq.gz


title: Cell_266

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-22_S212_L005_R1_001.fastq.gz


title: Cell_265

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-21_S211_L005_R1_001.fastq.gz


title: Cell_264

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-20_S210_L005_R1_001.fastq.gz


title: Cell_271

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-28_S218_L005_R1_001.fastq.gz


title: ILC_ST2_neg_CD127_neg_Rep2

city: La Jolla

first: Taylor

last: Doherty

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
004_TaDo_ReDo_RNA_15_D5
5 ng totRNA > SmartSeq2 RNA-seq

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

organism: Mus musculus

source_name: Alternaria alternata extract challenged murine lung

growth_protocol: Mice were challenged with PBS or 50μg of Alternaria alternata (Alternaria) extract (Greer, NC) daily for 4 times over 10 days and euthanized 24 hours after the last challenge for lung tissue harvest. lung single-cell suspensions were counted on a Novocyte flow cytometer (Acea Biosciences) and prepared for staining by washing with a solution of 2% FBS and 0.01% sodium azide in PBS.  Cells were incubated with a monoclonal antibody to CD16/CD32 for 10 minutes at 4oC to block Fc receptors and then stained for 30 minutes at 4oC with various combinations of antibodies to surface markers.  All antibodies were purchased from BioLegend unless otherwise noted.  In order to identify eosinophils (defined as CD45+Siglec-F+CD11c−), BAL and lung cells were stained with PerCP conjugated anti-CD45.2, PE conjugated anti–Siglec-F (BD), and FITC conjugated anti-CD11c.

extract_protocol:
ILC RNA was extracted using RNA Easy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.  Prior to RNA seq library preparation, Samples were quantified as described previously (Rosales et al, 2018) and quality of RNA assessed by Fragment Analyzer (Advance Analytical). All samples had a RNA integrity number (RIN)  > 7.5.
Purified total RNA (≈5 ng) was amplified following the Smart-seq2 protocol (Picelli et al, 2013, Rosales et al, 2018). Briefly, mRNA was captured using poly-dT oligos and directly reverse-transcribed into full-length cDNA using the described template-switching oligo. cDNA was amplified by PCR for 15 cycles and purified using AMPure XP magnetic bead (0.9:1 (vol:vol) ratio, Beckman Coulter).  From this step, for each sample, 1 ng of cDNA was used to prepare a standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina).  Barcoded Illumina sequencing libraries (NextEra; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter).  Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability.  Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR preamplification cycles, and fragment library size.  None of the samples failed quality controls.
libraries were pooled at equimolar concentration, loaded and sequenced on the Illumina Sequencing platform (HiSeq2500, or NovaSeq6000).  Libraries were sequenced to obtain more than 10 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina) mapping uniquely to mRNA reference.

treatment_protocol: Lungs were digested using Mouse Lung Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s protocol and subsequently filtered with a 40um cell strainer. Lung single-cell suspensions were counted on a Novocyte flow cytometer (Acea Biosciences) and prepared for staining by washing with a solution of 2% FBS and 0.01% sodium azide in PBS.  Cells were incubated with a monoclonal antibody to CD16/CD32 for 10 minutes at 4˚C to block Fc receptors and then stained for 30 minutes at 4˚C with various combinations of antibodies to surface markers.  All antibodies were purchased from BioLegend unless otherwise noted. In order to identify ILCs (defined as CD45.2+lineage−Thy1.2+ lymphocyte-sized cells) and conventional ILC2s (defined as CD45.2+lineage−Thy1.2+ST2+CD127+ lymphocyte-sized cells), lung cells were stained with: FITC conjugated Lineage Cocktail (anti-CD3e, anti-GR-1, anti-CD11b, anti-B220, anti-Ter119), anti-CD11c, anti-NK1.1, anti-CD5, anti-FcεR1, anti-TCR, and anti-TCRγδ; PerCP conjugated anti-CD45.2; eFluor 450 conjugated anti-Thy1.2 (ThermoFisher); APC conjugated anti-ST2; and PE-Cy7 conjugated anti-CD127.

tag: cell subtype

tag: background

value: Lung

value: Innate lymphoid cells (ILC)


title: ILC_ST2_neg_CD127_pos_Rep2

description:
003_TaDo_ReDo_RNA_14_C5
5 ng totRNA > SmartSeq2 RNA-seq


title: Cell_262

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-19_S209_L005_R1_001.fastq.gz


title: Cell_261

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-18_S208_L005_R1_001.fastq.gz


title: ILC_ST2_pos_CD127_pos_Rep2

description:
001_TaDo_ReDo_RNA_7_A5
5 ng totRNA > SmartSeq2 RNA-seq


title: Cell_260

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-17_S207_L005_R1_001.fastq.gz


title: ILC_ST2_pos_CD127_neg_Rep2

description:
002_TaDo_ReDo_RNA_13_B5
5 ng totRNA > SmartSeq2 RNA-seq


title: Cell_259

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-16_S206_L005_R1_001.fastq.gz


title: Cell_258

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-15_S205_L005_R1_001.fastq.gz


title: NIC_mammarytumour_GSK-rep1

type: RNA

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

country: Canada

institute: McGill University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Biotin-labelled target for the microarray experiment were prepared using 1µg of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix)

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: The Affymetrix Power Tools software package (Affymetrix) was used to quantile normalize the probe fluorescence intensities and to summarize the probe set (representing exon expression) and meta-probe set (representing gene expression) intensities.

label: Biotin

source_name: ErbB2 driven mouse mammary tumour

label_protocol: Biotin

growth_protocol: Breast cancer cell lines were established from the MMTV-NIC (ErbB2-IRES-Cre) model (PMID: 18273058, Ursini-Siegel et al.) and routinely cultured in DMEM supplemented with 5% FBS, EGF (5 ng/ml), Hydrocortisone (1 μg/ml), Insulin (5 μg/ml) and Bovine Pituitary Extract (BPE) (35μg/ml)). Cells were grown in a humidified, 5% CO2, 37°C incubator

extract_protocol: Total RNA was purified using RNeasy Mini Kit Columns following the manufacturers instructions. We assessed The RNA quality using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Tumors were hybridized independently at the functional genomics facility of McGill University and Genome Quebec Innovation Centre (Montreal, Quebec, Canada).

treatment_protocol: Cells were treated with 2uM GSK-126 or DMSO for 96 hours prior to harvesting

tag: gender

value: Female

tag: strain

value: FVB

value: mammary tumour

tag: treatment

value: H3K27me3 inhibitor GSK-126


title: Cell_257

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-14_S204_L005_R1_001.fastq.gz


title: Cell_256

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-13_S203_L005_R1_001.fastq.gz


title: Cell_255

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-12_S202_L005_R1_001.fastq.gz


title: NIC_mammarytumour_GSK-rep2


title: Cell_254

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-11_S201_L005_R1_001.fastq.gz


title: NIC_mammarytumour_DMSO-rep1

value: DMSO


title: Cell_263

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-1_S191_L005_R1_001.fastq.gz


title: Cell_253

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-10_S200_L005_R1_001.fastq.gz


title: TGFβ #2 ATAC-seq

city: Philadelphia

first: Andrew

last: Gibb

state: PA

address: 3500 N. Broad St.

institute: Temple University

data_processing:
Reads were trimmed of adaptor sequences and low quality bases removed before mapping to the mm10 genome using Illumina sequencing hub
Peaks were called using MACS2 analysis
BigWig files were generated and scores represent the number of reads associated with each base
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated

source_name: Primary Cardiac Fibroblasts

growth_protocol: Cardiac Fibroblasts were isolated from the adult heart. Cells were cultured in 25mM glucose DMEM supplemented with 10% FBS and 1% Penicilin/Streptomycin.

extract_protocol:
Genomic DNA was isolated from cells and incubated with Tn5 transposase
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: At 80% confluence, media was changed to reduce FBS to 1%. After 16h, cells were treated ± TGFβ 10 (ng/mL) for 24h.

value: Primary Cardiac Fibroblasts

tag: passage


title: Veh #2 ATAC-seq


title: Veh #1 ATAC-seq


title: Veh #3 ATAC-seq


title: TGFβ #3 ATAC-seq


title: TGFβ #3 RNA-seq

data_processing:
Illumina used for basecalling
Reads were trimmed of adaptor sequences and low quality bases removed before mapping to the mm10 genome using Illumina sequencing hub
RPKM calculated for each transcript
DEseq2 was used to perform differnetial expressing analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab separated values include RPKMs for each sample

extract_protocol:
Total RNA was harvested from cells using a Qiagen RNA Isolation kit. Illumina TruSeq stranded mRNA Library Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: TGFβ #2 RNA-seq


title: TGFβ #1 ATAC-seq


title: Cell_252

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-102_S292_L005_R1_001.fastq.gz


title: Veh #3 RNA-seq


title: Cell_251

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-101_S291_L005_R1_001.fastq.gz


title: TGFβ #1 RNA-seq


title: Cell_249

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-9_S114_L004_R1_001.fastq.gz


title: Cell_250

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-100_S290_L005_R1_001.fastq.gz


title: NIC_mammarytumour_DMSO-rep2


title: Veh #2 RNA-seq


title: Veh #1 RNA-seq


title: Cell_248

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-8_S113_L004_R1_001.fastq.gz


title: Cell_247

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-85_S190_L004_R1_001.fastq.gz


title: Cell_246

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-84_S189_L004_R1_001.fastq.gz


title: 6h.R1

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15).
The sequencing reads were mapped to the reference genome (mm10 and VSV) using Bowtie2 (v2.3.4.3).
Redundant reads were removed if having the same barcode and genomic location
A pesudoread was generated by extending 15bp each side from the most 5' nucleotide of each read.
Peaks were called based on previously described pipeline [L. J. Ma et al., Genome Res. 27, 385-392 (2017)],  with 30bp sliding window size and using the whole gene as background.
Genome_build: mm10 and VSV
Supplementary_files_format_and_content: bed

source_name: RAW264.7 cells

growth_protocol: ALKBH5 stable overexpression RAW264.7 cells were cultured in endotoxin-free DMEM medium with 10% (v/v) fetal bovine serum (FBS, Gibco).

extract_protocol:
Cells were cross-linked at 254â€‰nm once for 400â€‰mJ/cm2 and then again for 200 mJ/cm2 in the UV cross-linker. Then harvested and lysed cells in NP-40 lysis buffer. Cell lysates were treated with RNase T1 at 10 U/microL for 15 min at 22 °C, and then added Anti-c-Myc Magnetic Beads (88843, Thermo Fisher Scientific)  to the supernatant and incubated overnight at 4C . IgG were used as isotype control. After immunoprecipitation, beads were washed three times by washing buffer (50 mM Tris-HCl, pH 7.5; 100 mM NaCl; 0.5% NP40) and dephosphorylated by T4 PNK. After linker ligation, samples were separated on a 4-12% NuPAGE gel (NP0321B0X, Invitrogen), then the protein-RNA complexes were transferred to nitrocellulose filter membrane and treated by protease K.
The RNA libraries were prepared mainly as previous protocol [B. Zarnegar et al., Nat Methods 13, 489-492 (2016).] except with the use of SuperScriptâ„¢ III Reverse Transcriptase for cDNA synthesis.

treatment_protocol: Cells were uninfected or infected with VSV (MOI=1) for 6 hours.

value: RAW264.7 cells

value: ALKBH5 stable overexpression

value: VSV infection for 6h


title: Cell_245

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-83_S188_L004_R1_001.fastq.gz


title: 0h.R1

extract_protocol:
Cells were cross-linked at 254 nm once for 400 mJ/cm2 and then again for 200 mJ/cm2 in the UV cross-linker. Then harvested and lysed cells in NP-40 lysis buffer. Cell lysates were treated with RNase T1 at 10 U/microL for 15 min at 22 C, and then added Anti-c-Myc Magnetic Beads (88843, Thermo Fisher Scientific)  to the supernatant and incubated overnight at 4C . IgG were used as isotype control. After immunoprecipitation, beads were washed three times by washing buffer (50 mM Tris-HCl, pH 7.5; 100 mM NaCl; 0.5% NP40) and dephosphorylated by T4 PNK. After linker ligation, samples were separated on a 4-12% NuPAGE gel (NP0321B0X, Invitrogen), then the protein-RNA complexes were transferred to nitrocellulose filter membrane and treated by protease K.
The RNA libraries were prepared mainly as previous protocol [B. Zarnegar et al., Nat Methods 13, 489-492 (2016).] except with the use of SuperScript™ III Reverse Transcriptase for cDNA synthesis.

value: No treatment


title: 0h.R2


title: 6h.R2


title: Cell_239

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-78_S183_L004_R1_001.fastq.gz


title: murine CD8+ T cells 1 d activated by aCD3/CD28+ co-culture with Keratinocytes for 1 d

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v7.5.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38

source_name: CD8+ T cells

extract_protocol:
Cells were lysed in RLT-buffer supplemented with beta-Mercaptoethanol and total RNA was isolated according to the manual (Rneasy plus mini kit; Qiagen)
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 20 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.


title: murine CD8+ T cells 1 d activated by aCD3/CD28 rep2

value: CD8+ T cells 1 d activated by aCD3/CD28


title: Cell_243

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-81_S186_L004_R1_001.fastq.gz

data_processing:
The raw fastq files were trimmed using TrimGalore! In pair-end mode with default parameters.
The trimmed fastq data were aligned to human reference genome Hg38 using STAR in pair-end mode with default parameters.
The alignment results were inputted to featureCounts to compute the number of reads mapped back to each gene in each sample.
Genome_build: hg38
Supplementary_files_format_and_content: Read count table for each gene in each sample generated by featureCounts software.


title: murine CD8+ T cells 1 d activatred+ 1 d in co-culture with Ker


title: Cell_238

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-77_S182_L004_R1_001.fastq.gz


title: murine CD8+ T cells 1 d activated by aCD3/CD28 rep1


title: murine CD8+ T cells 1 d activated+ 1 d culture in Kera-Med.


title: murine Keratinocytes only rep2

source_name: Keratinocytes

value: Keratinocytes only


title: murine Keratinocytes after co-culture with CD8+ T cells rep1


title: Cell_235

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-74_S179_L004_R1_001.fastq.gz

value: cell from hESC derived 3D-retinal ordanoid


title: murine Keratinocytes after co-culture with CD8+ T cells rep2


title: Cell_236

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-75_S180_L004_R1_001.fastq.gz


title: murine CD8+ T cells 1 d activated by aCD3/CD28, then 1 day in Kera-medium


title: Cell_234

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-73_S178_L004_R1_001.fastq.gz


title: Cell_240

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-79_S184_L004_R1_001.fastq.gz


title: O5_TA_Hi_9 [scBS-seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
BS-Seq sequences were trimmed with Trim Galore (v0.5.0; Cutadapt v1.15) in single-end mode with the options --clip_r1 6. Trimmed sequences were mapped to the mouse GRCm38 genome in single-end, --non_direcional mode using Bismark (Krueger and Andrews, 2011) (v0.20.0); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.cov: Bismark coverage files: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

source_name: Tibialis anterior muscles

extract_protocol:
We prepared scM&T-seq libraries by isolating mRNA on magnetic beads and separating from the single-cell lysate prior to reverse transcription and amplification using Smartseq2 but with 25 PCR cycles.
scM&T-seq (C. Angermueller et al., 2016)

treatment_protocol: Mice were sacrificed by cervical dislocation. Tibialis anterior muscles were dissected and placed into cold DMEM (ThermoFisher, 31966). Muscles were then chopped and put into a 15 ml Falcon tube containing 10 ml of DMEM, 0.08% collagenase D (Sigma, 11 088 882 001), 0.1% trypsin (ThermoFisher, 15090), 10 µg/ml DNaseI (Sigma, 11284932) at 37°C under gentle agitation for 25 min. Digests were allowed to stand for 5 min at room temperature and the supernatants were collected on 5 ml of foetal bovine serum (FBS; Gibco) on ice. The digestion was repeated 3 times until complete digestion of the muscle. The supernatants were filtered through a 70-µm cell strainer (Miltenyi, 130-098-462). Cells were spun for 15 min at 515g at 4°C and the pellets were resuspended in 1 ml freezing medium (10% DMSO (Sigma, D2438) in foetal calf serum (FCS, Invitrogen)) for long term storage in liquid nitrogen. Before FACS isolation, samples were thawed in 50 ml of cold DMEM, spun for 15 min at 515g at 4°C. Pellets were resuspended in 300 µl of DMEM 2% FCS 1 µg/mL propidium iodide (Calbiochem, 537060) and filtered through a 40-µm cell strainer (BD Falcon, 352235). Viable cells were isolated based on size, granulosity and GFP expression level (top 10% nGFPHi cells) using a MoFlo Astrios cell sorter (Beckmann Coulter). Single cells were collected in 2.5 µL cold RLT Plus buffer (Qiagen, 1053393) containing 1U/µL RNase inhibitor (Ambion, AM2694) in 96 well-plates (LoBind Eppendorf, 0030129504), flash-frozen on dry ice and stored at -80°C.

value: Muscle stem cells

tag: age

value: 2 months

tag: mouse id


title: Cell_242

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-80_S185_L004_R1_001.fastq.gz

extract_protocol: Retinal organoids were dissociated in Accutase (StemPro) for 30 min to create a single-cell suspension. Cells were collected by centrifugation at 300 × g for 5 min and resuspended in 500 μL RDM. we used a mouth pipette to immediately transfer single cells into prepared lysis buffer. scRNA-seq library was constructed following modified Smart-seq2 protocol[6]. In detail, samples were incubated at 72°C for 3 min. The first-strand cDNA was reverse-synthesized using oligo(dT) and template-switching oligonucleotides (TSO). The synthesized first-strand cDNAs were amplified by 18 cycles. After purification, 0.1 ng cDNA were used for Nextera tagmentation (illumina) and library construction. Sequencing was performed on Illumina HiSeq 4000.


title: murine Keratinocytes only rep1


title: Cell_237

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-76_S181_L004_R1_001.fastq.gz


title: O5_TA_Hi_8 [scBS-seq]


title: Cell_233

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-72_S177_L004_R1_001.fastq.gz


title: O5_TA_Hi_7 [scBS-seq]


title: Cell_231

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-70_S175_L004_R1_001.fastq.gz


title: Cell_232

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-71_S176_L004_R1_001.fastq.gz


title: O5_TA_Hi_6 [scBS-seq]


title: Cell_244

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-82_S187_L004_R1_001.fastq.gz


title: Cell_241

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-7_S112_L004_R1_001.fastq.gz


title: Cell_230

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-6_S111_L004_R1_001.fastq.gz


title: Cell_229

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-69_S174_L004_R1_001.fastq.gz


title: Cell_228

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-68_S173_L004_R1_001.fastq.gz


title: O5_TA_Hi_4 [scBS-seq]


title: O5_TA_Hi_5 [scBS-seq]


title: Cell_225

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-65_S170_L004_R1_001.fastq.gz


title: Cell_226

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-66_S171_L004_R1_001.fastq.gz


title: O5_TA_Hi_46 [scBS-seq]


title: Cell_227

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-67_S172_L004_R1_001.fastq.gz


title: O5_TA_Hi_47 [scBS-seq]


title: O5_TA_Hi_48 [scBS-seq]


title: O5_TA_Hi_44 [scBS-seq]


title: O5_TA_Hi_42 [scBS-seq]


title: Cell_224

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-64_S169_L004_R1_001.fastq.gz


title: Cell_221

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-61_S166_L004_R1_001.fastq.gz


title: Cell_222

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-62_S167_L004_R1_001.fastq.gz


title: O5_TA_Hi_3 [scBS-seq]


title: Cell_223

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-63_S168_L004_R1_001.fastq.gz


title: O5_TA_Hi_40 [scBS-seq]


title: Cell_218

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-59_S164_L004_R1_001.fastq.gz


title: Cell_217

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-58_S163_L004_R1_001.fastq.gz


title: O5_TA_Hi_39 [scBS-seq]


title: O5_TA_Hi_38 [scBS-seq]


title: Cell_216

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-57_S162_L004_R1_001.fastq.gz


title: O5_TA_Hi_45 [scBS-seq]


title: O5_TA_Hi_43 [scBS-seq]


title: Cell_215

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-56_S161_L004_R1_001.fastq.gz


title: O5_TA_Hi_36 [scBS-seq]


title: Cell_219

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-5_S110_L004_R1_001.fastq.gz


title: O5_TA_Hi_41 [scBS-seq]


title: O5_TA_Hi_35 [scBS-seq]


title: O5_TA_Hi_37 [scBS-seq]


title: Cell_220

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-60_S165_L004_R1_001.fastq.gz


title: O5_TA_Hi_34 [scBS-seq]


title: Cell_213

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-54_S159_L004_R1_001.fastq.gz


title: Cell_210

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-51_S156_L004_R1_001.fastq.gz


title: Cell_212

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-53_S158_L004_R1_001.fastq.gz


title: Cell_209

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-50_S155_L004_R1_001.fastq.gz


title: Cell_211

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-52_S157_L004_R1_001.fastq.gz


title: Cell_206

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-48_S153_L004_R1_001.fastq.gz


title: Cell_207

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-49_S154_L004_R1_001.fastq.gz


title: O5_TA_Hi_30 [scBS-seq]


title: O5_TA_Hi_32 [scBS-seq]


title: O5_TA_Hi_29 [scBS-seq]


title: O5_TA_Hi_2 [scBS-seq]


title: O5_TA_Hi_31 [scBS-seq]


title: Cell_205

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-47_S152_L004_R1_001.fastq.gz


title: O5_TA_Hi_28 [scBS-seq]


title: O5_TA_Hi_27 [scBS-seq]


title: Cell_204

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-46_S151_L004_R1_001.fastq.gz


title: Cell_214

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-55_S160_L004_R1_001.fastq.gz


title: Cell_203

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-45_S150_L004_R1_001.fastq.gz


title: O5_TA_Hi_26 [scBS-seq]


title: O5_TA_Hi_33 [scBS-seq]


title: O5_TA_Hi_25 [scBS-seq]


title: O5_TA_Hi_24 [scBS-seq]


title: O5_TA_Hi_23 [scBS-seq]


title: Cell_200

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-42_S147_L004_R1_001.fastq.gz


title: Cell_208

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-4_S109_L004_R1_001.fastq.gz


title: Cell_202

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-44_S149_L004_R1_001.fastq.gz


title: O5_TA_Hi_22 [scBS-seq]


title: Cell_201

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-43_S148_L004_R1_001.fastq.gz


title: O5_TA_Hi_21 [scBS-seq]


title: Cell_199

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-41_S146_L004_R1_001.fastq.gz


title: Cell_198

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-40_S145_L004_R1_001.fastq.gz


title: O5_TA_Hi_1 [scBS-seq]


title: Cell_196

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-39_S144_L004_R1_001.fastq.gz


title: Cell_195

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-38_S143_L004_R1_001.fastq.gz


title: O5_TA_Hi_18 [scBS-seq]


title: O5_TA_Hi_20 [scBS-seq]


title: O5_TA_Hi_19 [scBS-seq]


title: Cell_197

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-3_S108_L004_R1_001.fastq.gz


title: Cell_193

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-36_S141_L004_R1_001.fastq.gz


title: O5_TA_Hi_17 [scBS-seq]


title: Cell_192

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-35_S140_L004_R1_001.fastq.gz


title: Cell_191

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-34_S139_L004_R1_001.fastq.gz


title: O5_TA_Hi_15 [scBS-seq]


title: O5_TA_Hi_14 [scBS-seq]


title: O5_TA_Hi_16 [scBS-seq]


title: O5_TA_Hi_12 [scBS-seq]


title: Cell_190

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-33_S138_L004_R1_001.fastq.gz


title: O5_TA_Hi_13 [scBS-seq]


title: Cell_188

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-31_S136_L004_R1_001.fastq.gz


title: O5_TA_Hi_11 [scBS-seq]


title: Cell_186

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-2_S107_L004_R1_001.fastq.gz


title: O5_TA_Hi_10 [scBS-seq]


title: Cell_194

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-37_S142_L004_R1_001.fastq.gz


title: Cell_187

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-30_S135_L004_R1_001.fastq.gz


title: Y8_TA_Hi_9 [scBS-seq]


title: Cell_185

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-29_S134_L004_R1_001.fastq.gz


title: Y8_TA_Hi_7 [scBS-seq]


title: Cell_183

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-27_S132_L004_R1_001.fastq.gz


title: Y8_TA_Hi_8 [scBS-seq]


title: Cell_182

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-26_S131_L004_R1_001.fastq.gz


title: Cell_184

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-28_S133_L004_R1_001.fastq.gz


title: Cell_179

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-23_S128_L004_R1_001.fastq.gz


title: Cell_180

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-24_S129_L004_R1_001.fastq.gz


title: Cell_189

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-32_S137_L004_R1_001.fastq.gz


title: Y8_TA_Hi_6 [scBS-seq]


title: Cell_181

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-25_S130_L004_R1_001.fastq.gz


title: Y8_TA_Hi_47 [scBS-seq]


title: Y8_TA_Hi_46 [scBS-seq]


title: Cell_178

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-22_S127_L004_R1_001.fastq.gz


title: Cell_177

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-21_S126_L004_R1_001.fastq.gz


title: Y8_TA_Hi_48 [scBS-seq]


title: Y8_TA_Hi_45 [scBS-seq]


title: Cell_175

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-1_S106_L004_R1_001.fastq.gz


title: Y8_TA_Hi_44 [scBS-seq]


title: Cell_176

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-20_S125_L004_R1_001.fastq.gz


title: Y8_TA_Hi_43 [scBS-seq]


title: Cell_174

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-19_S124_L004_R1_001.fastq.gz


title: Cell_173

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-18_S123_L004_R1_001.fastq.gz


title: Y8_TA_Hi_42 [scBS-seq]


title: Y8_TA_Hi_41 [scBS-seq]


title: Y8_TA_Hi_5 [scBS-seq]


title: Cell_172

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-17_S122_L004_R1_001.fastq.gz


title: Cell_171

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-16_S121_L004_R1_001.fastq.gz


title: Y8_TA_Hi_39 [scBS-seq]


title: Y8_TA_Hi_4 [scBS-seq]


title: Y8_TA_Hi_40 [scBS-seq]


title: Y8_TA_Hi_3 [scBS-seq]


title: Cell_168

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-13_S118_L004_R1_001.fastq.gz


title: Cell_167

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-12_S117_L004_R1_001.fastq.gz


title: Cell_169

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-14_S119_L004_R1_001.fastq.gz


title: Y8_TA_Hi_36 [scBS-seq]


title: Y8_TA_Hi_37 [scBS-seq]


title: Cell_166

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-11_S116_L004_R1_001.fastq.gz


title: Cell_165

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-10_S115_L004_R1_001.fastq.gz


title: Y8_TA_Hi_35 [scBS-seq]


title: Y8_TA_Hi_34 [scBS-seq]


title: Y8_TA_Hi_33 [scBS-seq]


title: Cell_163

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-99_S99_L003_R1_001.fastq.gz


title: Y8_TA_Hi_32 [scBS-seq]


title: Cell_162

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-98_S98_L003_R1_001.fastq.gz


title: Cell_161

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-97_S97_L003_R1_001.fastq.gz


title: Cell_170

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-2-15_S120_L004_R1_001.fastq.gz


title: Y8_TA_Hi_31 [scBS-seq]


title: Y8_TA_Hi_30 [scBS-seq]


title: Cell_160

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-96_S96_L003_R1_001.fastq.gz


title: Cell_158

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-94_S94_L003_R1_001.fastq.gz


title: Cell_159

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-95_S95_L003_R1_001.fastq.gz


title: Y8_TA_Hi_2 [scBS-seq]


title: Y8_TA_Hi_38 [scBS-seq]


title: Cell_157

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-93_S93_L003_R1_001.fastq.gz


title: Y8_TA_Hi_27 [scBS-seq]


title: Cell_156

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-92_S92_L003_R1_001.fastq.gz


title: Cell_154

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-90_S90_L003_R1_001.fastq.gz


title: Cell_155

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-91_S91_L003_R1_001.fastq.gz


title: Cell_153

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-8_S8_L003_R1_001.fastq.gz


title: Y8_TA_Hi_24 [scBS-seq]


title: Y8_TA_Hi_26 [scBS-seq]


title: Cell_164

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-9_S9_L003_R1_001.fastq.gz


title: Y8_TA_Hi_25 [scBS-seq]


title: Y8_TA_Hi_23 [scBS-seq]


title: Y8_TA_Hi_21 [scBS-seq]


title: Cell_150

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-87_S87_L003_R1_001.fastq.gz


title: Cell_151

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-88_S88_L003_R1_001.fastq.gz


title: Y8_TA_Hi_20 [scBS-seq]


title: Cell_152

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-89_S89_L003_R1_001.fastq.gz


title: Y8_TA_Hi_22 [scBS-seq]


title: Cell_149

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-86_S86_L003_R1_001.fastq.gz


title: Cell_148

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-85_S85_L003_R1_001.fastq.gz


title: Y8_TA_Hi_1 [scBS-seq]


title: Y8_TA_Hi_28 [scBS-seq]


title: Y8_TA_Hi_19 [scBS-seq]


title: Y8_TA_Hi_29 [scBS-seq]


title: Y8_TA_Hi_18 [scBS-seq]


title: Cell_145

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-82_S82_L003_R1_001.fastq.gz


title: Y8_TA_Hi_17 [scBS-seq]


title: Y8_TA_Hi_16 [scBS-seq]


title: Y8_TA_Hi_15 [scBS-seq]


title: Cell_147

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-84_S84_L003_R1_001.fastq.gz


title: Y8_TA_Hi_14 [scBS-seq]


title: Cell_141

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-79_S79_L003_R1_001.fastq.gz


title: Cell_142

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-7_S7_L003_R1_001.fastq.gz


title: Y8_TA_Hi_12 [scBS-seq]


title: Y8_TA_Hi_13 [scBS-seq]


title: Cell_140

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-78_S78_L003_R1_001.fastq.gz


title: Cell_138

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-76_S76_L003_R1_001.fastq.gz


title: Cell_139

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-77_S77_L003_R1_001.fastq.gz


title: Y8_TA_Hi_11 [scBS-seq]


title: Y8_TA_Hi_10 [scBS-seq]


title: Cell_137

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-75_S75_L003_R1_001.fastq.gz


title: Y7_TA_Hi_7 [scBS-seq]


title: Y7_TA_Hi_8 [scBS-seq]


title: Cell_136

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-74_S74_L003_R1_001.fastq.gz


title: Cell_135

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-73_S73_L003_R1_001.fastq.gz


title: Y7_TA_Hi_9 [scBS-seq]


title: Y7_TA_Hi_6 [scBS-seq]


title: Cell_144

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-81_S81_L003_R1_001.fastq.gz


title: Y7_TA_Hi_5 [scBS-seq]


title: Cell_134

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-72_S72_L003_R1_001.fastq.gz


title: Y7_TA_Hi_4 [scBS-seq]


title: Cell_133

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-71_S71_L003_R1_001.fastq.gz


title: Cell_143

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-80_S80_L003_R1_001.fastq.gz


title: Y7_TA_Hi_48 [scBS-seq]


title: Cell_132

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-70_S70_L003_R1_001.fastq.gz


title: Y7_TA_Hi_47 [scBS-seq]


title: Cell_130

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-69_S69_L003_R1_001.fastq.gz


title: Cell_129

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-68_S68_L003_R1_001.fastq.gz


title: Y7_TA_Hi_46 [scBS-seq]


title: Y7_TA_Hi_45 [scBS-seq]


title: Y7_TA_Hi_44 [scBS-seq]


title: Cell_128

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-67_S67_L003_R1_001.fastq.gz


title: Cell_127

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-66_S66_L003_R1_001.fastq.gz


title: Y7_TA_Hi_43 [scBS-seq]


title: Cell_126

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-65_S65_L003_R1_001.fastq.gz


title: Y7_TA_Hi_42 [scBS-seq]


title: Y7_TA_Hi_41 [scBS-seq]


title: Y7_TA_Hi_3 [scBS-seq]


title: Cell_123

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-62_S62_L003_R1_001.fastq.gz


title: Cell_378

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-34_S326_L006_R1_001.fastq.gz


title: Y7_TA_Hi_40 [scBS-seq]


title: Cell_146

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-83_S83_L003_R1_001.fastq.gz


title: Cell_131

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-6_S6_L003_R1_001.fastq.gz


title: Cell_122

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-61_S61_L003_R1_001.fastq.gz


title: Y7_TA_Hi_38 [scBS-seq]


title: Cell_121

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-60_S60_L003_R1_001.fastq.gz


title: Cell_120

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-5_S5_L003_R1_001.fastq.gz


title: Cell_119

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-59_S59_L003_R1_001.fastq.gz


title: Y7_TA_Hi_36 [scBS-seq]


title: Cell_118

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-58_S58_L003_R1_001.fastq.gz


title: Y7_TA_Hi_39 [scBS-seq]


title: Y7_TA_Hi_37 [scBS-seq]


title: Y7_TA_Hi_35 [scBS-seq]


title: Y7_TA_Hi_34 [scBS-seq]


title: Cell_125

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-64_S64_L003_R1_001.fastq.gz


title: Y7_TA_Hi_33 [scBS-seq]


title: Cell_116

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-56_S56_L003_R1_001.fastq.gz


title: Y7_TA_Hi_32 [scBS-seq]


title: Cell_114

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-54_S54_L003_R1_001.fastq.gz


title: Cell_124

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-63_S63_L003_R1_001.fastq.gz


title: Cell_113

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-53_S53_L003_R1_001.fastq.gz


title: Y7_TA_Hi_30 [scBS-seq]


title: Y7_TA_Hi_2 [scBS-seq]


title: Cell_112

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-52_S52_L003_R1_001.fastq.gz


title: Y7_TA_Hi_29 [scBS-seq]


title: Cell_111

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-51_S51_L003_R1_001.fastq.gz


title: Cell_109

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-4_S4_L003_R1_001.fastq.gz


title: Y7_TA_Hi_27 [scBS-seq]


title: Y7_TA_Hi_28 [scBS-seq]


title: Cell_117

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-57_S57_L003_R1_001.fastq.gz


title: Cell_108

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-49_S49_L003_R1_001.fastq.gz


title: Cell_107

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-48_S48_L003_R1_001.fastq.gz


title: Cell_106

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-47_S47_L003_R1_001.fastq.gz


title: Y7_TA_Hi_25 [scBS-seq]


title: Y7_TA_Hi_24 [scBS-seq]


title: Cell_115

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-55_S55_L003_R1_001.fastq.gz


title: Y7_TA_Hi_26 [scBS-seq]


title: Y7_TA_Hi_23 [scBS-seq]


title: Cell_105

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-46_S46_L003_R1_001.fastq.gz


title: Cell_104

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-45_S45_L003_R1_001.fastq.gz


title: Y7_TA_Hi_22 [scBS-seq]


title: Y7_TA_Hi_21 [scBS-seq]


title: Y7_TA_Hi_31 [scBS-seq]


title: Cell_103

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-44_S44_L003_R1_001.fastq.gz


title: Cell_101

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-42_S42_L003_R1_001.fastq.gz


title: Cell_102

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-43_S43_L003_R1_001.fastq.gz


title: SUM149_Control_Input_EGS

description: input for sample S149_shEN1_C_bcat_R. Input of SUM149 cells in control condition.

data_processing:
RNA-Seq, ChIP-Seq: Illumina Casava1.7 software used for basecalling.
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
RNA-Seq: Datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the hg19 refGene annotation file available at the UCSC Genome Browser.
ChIP-Seq: QC, alignment and peak calling was performed using ChiLin pipeline 2.0.0 (https://www.ncbi.nlm.nih.gov/m/pubmed/27716038/?i=6&from=chilin). Briefly, reads were aligned to GRCh37/hg19 using BWA, and peak calling was performed using MACS2, in chilin.
Genome_build: RNA-Seq and ChIP-Seq: hg19
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: bed file (BED6+4) of factor peaks from MACS2 peakcaller.

extract_protocol:
ChIP-seq: cell monolayers were fixed with 1% formaldehyde for 10 min, at room temperature for H3K27ac and FOXA1 ChIP-seq, or 37C for V5-EN1 and TLE3 ChIP-seq. Cells were fixet with 1.5mM EGS during 30 min and adding 1% paraformaldehyde during the last 10 min for b-catenin ChIP-seq. All cell fixations were wuenched by adding 125mM glycine during 5 min. After 2 ice-cold PBS washes, cells were scrapped off in PBS, pelleted and snap-frozen. RNA-seq: cells were washed 3 times with ice-cold PBS, scrapped off the plates, pelleted and snap frozen into liquid nitrogen. For RNA-extraction, the RNeasy Mini Kit (Qiagen, #74106) was used, with in-column DNA digestion.
ChIP-seq: the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) was used following manufacturer's instructions. RNA-seq: libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol

value: input


title: Cell_110

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-50_S50_L003_R1_001.fastq.gz


title: Y7_TA_Hi_20 [scBS-seq]


title: Y7_TA_Hi_1 [scBS-seq]


title: Cell_100

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-41_S41_L003_R1_001.fastq.gz


title: Cell_99

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-40_S40_L003_R1_001.fastq.gz


title: Y7_TA_Hi_18 [scBS-seq]


title: Cell_98

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-3_S3_L003_R1_001.fastq.gz


title: Y7_TA_Hi_19 [scBS-seq]


title: Cell_97

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-39_S39_L003_R1_001.fastq.gz


title: Cell_96

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-38_S38_L003_R1_001.fastq.gz


title: Cell_95

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-37_S37_L003_R1_001.fastq.gz


title: Y7_TA_Hi_16 [scBS-seq]


title: Y7_TA_Hi_14 [scBS-seq]


title: Y7_TA_Hi_15 [scBS-seq]


title: Y7_TA_Hi_17 [scBS-seq]


title: Cell_94

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-36_S36_L003_R1_001.fastq.gz


title: Cell_92

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-34_S34_L003_R1_001.fastq.gz


title: Y7_TA_Hi_13 [scBS-seq]


title: Y7_TA_Hi_12 [scBS-seq]


title: Cell_91

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-33_S33_L003_R1_001.fastq.gz


title: Y7_TA_Hi_10 [scBS-seq]


title: Cell_90

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-32_S32_L003_R1_001.fastq.gz


title: Cell_88

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-30_S30_L003_R1_001.fastq.gz


title: Cell_89

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-31_S31_L003_R1_001.fastq.gz


title: Y2_TA_Hi_9 [scBS-seq]


title: Y2_TA_Hi_7 [scBS-seq]


title: Y2_TA_Hi_5 [scBS-seq]


title: Cell_87

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-2_S2_L003_R1_001.fastq.gz


title: Cell_85

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-28_S28_L003_R1_001.fastq.gz


title: Cell_86

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-29_S29_L003_R1_001.fastq.gz


title: Cell_84

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-27_S27_L003_R1_001.fastq.gz


title: Y2_TA_Hi_4 [scBS-seq]


title: Y2_TA_Hi_48 [scBS-seq]


title: Y2_TA_Hi_45 [scBS-seq]


title: Cell_83

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-26_S26_L003_R1_001.fastq.gz


title: Y7_TA_Hi_11 [scBS-seq]


title: Y2_TA_Hi_47 [scBS-seq]


title: Cell_81

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-24_S24_L003_R1_001.fastq.gz


title: Cell_82

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-25_S25_L003_R1_001.fastq.gz


title: Y2_TA_Hi_44 [scBS-seq]


title: Y2_TA_Hi_42 [scBS-seq]


title: Cell_93

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-35_S35_L003_R1_001.fastq.gz


title: Cell_80

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-23_S23_L003_R1_001.fastq.gz


title: Cell_78

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-21_S21_L003_R1_001.fastq.gz


title: Cell_79

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-22_S22_L003_R1_001.fastq.gz


title: Y2_TA_Hi_3 [scBS-seq]


title: Cell_77

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-20_S20_L003_R1_001.fastq.gz


title: Y2_TA_Hi_43 [scBS-seq]


title: Y2_TA_Hi_6 [scBS-seq]


title: Y2_TA_Hi_41 [scBS-seq]


title: Cell_75

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-19_S19_L003_R1_001.fastq.gz


title: Y2_TA_Hi_39 [scBS-seq]


title: Cell_76

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-1_S1_L003_R1_001.fastq.gz


title: Y2_TA_Hi_37 [scBS-seq]


title: Cell_74

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-18_S18_L003_R1_001.fastq.gz


title: Cell_73

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-17_S17_L003_R1_001.fastq.gz


title: Y2_TA_Hi_36 [scBS-seq]


title: Cell_71

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-15_S15_L003_R1_001.fastq.gz


title: Cell_72

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-16_S16_L003_R1_001.fastq.gz


title: Y2_TA_Hi_30 [scBS-seq]


title: Cell_69

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-13_S13_L003_R1_001.fastq.gz


title: Cell_70

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-14_S14_L003_R1_001.fastq.gz


title: Y2_TA_Hi_2 [scBS-seq]


title: Cell_68

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-12_S12_L003_R1_001.fastq.gz


title: Y2_TA_Hi_29 [scBS-seq]


title: Cell_66

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-10_S10_L003_R1_001.fastq.gz


title: Cell_67

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-11_S11_L003_R1_001.fastq.gz


title: Y2_TA_Hi_28 [scBS-seq]


title: Y2_TA_Hi_26 [scBS-seq]


title: Cell_65

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-105_S105_L003_R1_001.fastq.gz


title: Y2_TA_Hi_27 [scBS-seq]


title: Y2_TA_Hi_25 [scBS-seq]


title: Y2_TA_Hi_38 [scBS-seq]


title: Y2_TA_Hi_23 [scBS-seq]


title: Y2_TA_Hi_22 [scBS-seq]


title: Cell_63

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-103_S103_L003_R1_001.fastq.gz


title: Cell_64

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-104_S104_L003_R1_001.fastq.gz


title: Cell_62

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-102_S102_L003_R1_001.fastq.gz


title: Y2_TA_Hi_20 [scBS-seq]


title: Y2_TA_Hi_33 [scBS-seq]


title: Y2_TA_Hi_32 [scBS-seq]


title: Cell_60

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-100_S100_L003_R1_001.fastq.gz


title: Y2_TA_Hi_31 [scBS-seq]


title: Cell_59

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-9_S31_L008_R1_001.fastq.gz


title: Y2_TA_Hi_1 [scBS-seq]


title: Cell_58

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-8_S30_L008_R1_001.fastq.gz


title: Y2_TA_Hi_19 [scBS-seq]


title: Y2_TA_Hi_15 [scBS-seq]


title: Y2_TA_Hi_17 [scBS-seq]


title: Cell_56

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-6_S28_L008_R1_001.fastq.gz


title: Cell_55

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-64_S81_L008_R1_001.fastq.gz


title: Y2_TA_Hi_14 [scBS-seq]


title: Cell_54

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-63_S80_L008_R1_001.fastq.gz


title: Y2_TA_Hi_13 [scBS-seq]


title: Y2_TA_Hi_12 [scBS-seq]


title: Cell_52

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-61_S78_L008_R1_001.fastq.gz


title: Cell_51

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-60_S77_L008_R1_001.fastq.gz


title: Y2_TA_Hi_21 [scBS-seq]


title: Cell_53

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-62_S79_L008_R1_001.fastq.gz


title: Y2_TA_Hi_10 [scBS-seq]


title: Cell_50

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-5_S27_L008_R1_001.fastq.gz


title: Y2_TA_Hi_11 [scBS-seq]


title: Cell_61

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-1-101_S101_L003_R1_001.fastq.gz


title: O8_TA_Hi_9 [scBS-seq]

value: 24 months


title: Cell_49

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-59_S76_L008_R1_001.fastq.gz


title: Cell_48

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-58_S75_L008_R1_001.fastq.gz


title: Cell_47

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-57_S74_L008_R1_001.fastq.gz


title: Cell_46

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-56_S73_L008_R1_001.fastq.gz


title: O8_TA_Hi_8 [scBS-seq]


title: O8_TA_Hi_7 [scBS-seq]


title: Cell_45

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-55_S72_L008_R1_001.fastq.gz


title: O8_TA_Hi_6 [scBS-seq]


title: Cell_57

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-7_S29_L008_R1_001.fastq.gz


title: Cell_44

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-54_S71_L008_R1_001.fastq.gz


title: O8_TA_Hi_5 [scBS-seq]


title: O8_TA_Hi_4 [scBS-seq]


title: O8_TA_Hi_48 [scBS-seq]


title: Cell_43

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-53_S70_L008_R1_001.fastq.gz


title: Cell_42

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-52_S69_L008_R1_001.fastq.gz


title: O8_TA_Hi_47 [scBS-seq]


title: O8_TA_Hi_46 [scBS-seq]


title: Cell_41

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-51_S68_L008_R1_001.fastq.gz


title: O8_TA_Hi_44 [scBS-seq]


title: Cell_39

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-4_S26_L008_R1_001.fastq.gz


title: O8_TA_Hi_43 [scBS-seq]


title: Cell_38

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-49_S66_L008_R1_001.fastq.gz


title: O8_TA_Hi_42 [scBS-seq]


title: Cell_37

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-48_S65_L008_R1_001.fastq.gz


title: Cell_36

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-47_S64_L008_R1_001.fastq.gz


title: Cell_35

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-46_S63_L008_R1_001.fastq.gz


title: O8_TA_Hi_3 [scBS-seq]


title: Cell_32

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-39_S61_L008_R1_001.fastq.gz


title: Cell_34

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-45_S62_L008_R1_001.fastq.gz


title: O8_TA_Hi_40 [scBS-seq]


title: Cell_31

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-38_S60_L008_R1_001.fastq.gz


title: O8_TA_Hi_41 [scBS-seq]


title: O8_TA_Hi_37 [scBS-seq]


title: O8_TA_Hi_38 [scBS-seq]


title: O8_TA_Hi_39 [scBS-seq]


title: O8_TA_Hi_36 [scBS-seq]


title: O8_TA_Hi_35 [scBS-seq]


title: Cell_33

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-3_S25_L008_R1_001.fastq.gz


title: Cell_29

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-36_S58_L008_R1_001.fastq.gz


title: Cell_30

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-37_S59_L008_R1_001.fastq.gz


title: O8_TA_Hi_45 [scBS-seq]


title: Cell_40

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-50_S67_L008_R1_001.fastq.gz


title: Cell_28

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-35_S57_L008_R1_001.fastq.gz


title: O8_TA_Hi_33 [scBS-seq]


title: Cell_27

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-34_S56_L008_R1_001.fastq.gz


title: O8_TA_Hi_32 [scBS-seq]


title: Cell_26

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-33_S55_L008_R1_001.fastq.gz


title: O8_TA_Hi_30 [scBS-seq]


title: Cell_25

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-32_S54_L008_R1_001.fastq.gz


title: Cell_23

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-30_S52_L008_R1_001.fastq.gz


title: O8_TA_Hi_2 [scBS-seq]


title: Cell_24

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-31_S53_L008_R1_001.fastq.gz


title: O8_TA_Hi_29 [scBS-seq]


title: O8_TA_Hi_28 [scBS-seq]


title: Cell_22

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-2_S24_L008_R1_001.fastq.gz


title: O8_TA_Hi_27 [scBS-seq]


title: Cell_20

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-28_S50_L008_R1_001.fastq.gz


title: Cell_19

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-27_S49_L008_R1_001.fastq.gz


title: Cell_21

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-29_S51_L008_R1_001.fastq.gz


title: O8_TA_Hi_26 [scBS-seq]


title: Cell_18

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-26_S48_L008_R1_001.fastq.gz


title: O8_TA_Hi_25 [scBS-seq]


title: O8_TA_Hi_34 [scBS-seq]


title: Cell_17

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-25_S47_L008_R1_001.fastq.gz


title: Cell_16

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-24_S46_L008_R1_001.fastq.gz


title: Cell_14

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-22_S44_L008_R1_001.fastq.gz


title: O8_TA_Hi_23 [scBS-seq]


title: O8_TA_Hi_22 [scBS-seq]


title: O8_TA_Hi_21 [scBS-seq]


title: Cell_15

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-23_S45_L008_R1_001.fastq.gz


title: Cell_13

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-21_S43_L008_R1_001.fastq.gz


title: O8_TA_Hi_24 [scBS-seq]


title: O8_TA_Hi_31 [scBS-seq]


title: Cell_12

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-20_S42_L008_R1_001.fastq.gz


title: O8_TA_Hi_1 [scBS-seq]


title: O8_TA_Hi_20 [scBS-seq]


title: O8_TA_Hi_19 [scBS-seq]


title: Cell_11

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-1_S23_L008_R1_001.fastq.gz


title: Art_shBCLAF1_RNAseq2

city: St. Louis

first: Jeffery

middle: J

last: Bednarski

state: Missouri

address: 660 S. Euclid Ave., Campus Box 8208

department: Department of Pediatrics

institute: Washington University School of Medicine

description:
sample.asb_2_sti
ART Vs ART_shBCLAF1.xls

data_processing:
Gene counts by Subread-featureCount version 1.4.5.
R/Bioconductor package EdgeR and TMM to adjust for differences in library size.
Differential expression analysis using the R/Bioconductor package limma-voom
DAVID (Database for Annotation, Visualization and Integrated Discovery, v6.8) was used to display annotated pathways
Genome_build: mm9
Supplementary_files_format_and_content: Tab delilmited files

source_name: pre-B cells

extract_protocol:
RNA was extracted using RNeasy Kit (Qiagen).
DNA  libraries were prepared using Illumina TruSeq

value: Art -/- Abelson cells

tag: shRNA


title: Art_shBCLAF1_RNAseq3

description:
sample.asb_3_sti
ART Vs ART_shBCLAF1.xls


title: Art_shBCLAF1_RNAseq1

description:
sample.asb_1_sti
ART Vs ART_shBCLAF1.xls


title: Cell_10

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-19_S41_L008_R1_001.fastq.gz


title: Art_RNAseq2

description:
sample.art_sti2
Rag_SPIC_tet_NoDOX Vs Art.xls


title: Cell_9

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-18_S40_L008_R1_001.fastq.gz


title: O8_TA_Hi_17 [scBS-seq]


title: Art_RNAseq1

description:
sample.art_sti1
Rag_SPIC_tet_NoDOX Vs Art.xls


title: O8_TA_Hi_16 [scBS-seq]


title: Rag_SPIC_tet_DOX_shBCLAF1_RNAseq2

description:
sample.rsb_2_sd
Rag_SPIC_tet_DOX Vs Rag_SPIC_tet_DOX_shBCLAF1.xls

value: Rag -/- Abelson cells

tag: agent

value: DOX


title: Cell_8

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-17_S39_L008_R1_001.fastq.gz


title: O8_TA_Hi_15 [scBS-seq]


title: Rag_SPIC_tet_DOX_shBCLAF1_RNAseq3

description:
sample.rsb_3_sd
Rag_SPIC_tet_DOX Vs Rag_SPIC_tet_DOX_shBCLAF1.xls


title: Rag_SPIC_tet_DOX_shBCLAF1_RNAseq1

description:
sample.rsb_1_sd
Rag_SPIC_tet_DOX Vs Rag_SPIC_tet_DOX_shBCLAF1.xls


title: O8_TA_Hi_14 [scBS-seq]


title: Rag_SPIC_tet_DOX_RNAseq3

description:
sample.rssd3
Rag_SPIC_tet_NoDOX Vs Rag_SPIC_tet_DOX.xls


title: Cell_6

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-15_S37_L008_R1_001.fastq.gz


title: O8_TA_Hi_13 [scBS-seq]


title: Rag_SPIC_tet_DOX_RNAseq1

description:
sample.rssd1
Rag_SPIC_tet_NoDOX Vs Rag_SPIC_tet_DOX.xls


title: Rag_SPIC_tet_NoDOX_RNAseq3

description:
sample.rss3
Rag_SPIC_tet_NoDOX Vs Rag_SPIC_tet_DOX.xls


title: Rag_SPIC_tet_DOX_RNAseq2

description:
sample.rssd2
Rag_SPIC_tet_NoDOX Vs Rag_SPIC_tet_DOX.xls


title: O8_TA_Hi_18 [scBS-seq]


title: O8_TA_Hi_12 [scBS-seq]


title: Rag_SPIC_tet_NoDOX_RNAseq1

description:
sample.rss1
Rag_SPIC_tet_NoDOX Vs Rag_SPIC_tet_DOX.xls


title: Cell_5

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-14_S36_L008_R1_001.fastq.gz


title: Cell_3

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-12_S34_L008_R1_001.fastq.gz


title: O8_TA_Hi_11 [scBS-seq]


title: Art_RNAseq3

description:
sample.art_sti3
Rag_SPIC_tet_NoDOX Vs Art.xls


title: Input_Rag SPIC_tet

data_processing:
MACS version 2 for peak calling
bigwig to BED tool v0.1.0 in Galaxy V18.09.
Overlapping ChIP peaks by R package (GenomicRanges) and Bedtools V2.25.0
Motif discovery using HOMER2 and MEME-ChIP
ETS enrichment by rtfbs_db from CisBP for mouse.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig  files for ChiP seq samples

extract_protocol:
For ChiP Seq: All cells were treated with imatinib for 48 hours. ChIP was performed using anti-PU.1, anti-FLAG anti-HA anti-BCLAF1, control rabbit IgG and control mouse IgG antibodies DNA was cross-linked with 2% formaldehyde for 10 min at room temp (1 x 106 cells/ml). Reaction was stopped with 125 M Glycine. Cells were lysed with NP-40 and nuclei were frozen in liquid nitrogen then lysed with SDS. DNA was fragmented by sonicating with 30-second pulses for 60 cycles using a Bioruptor.DNA fragmentation was in the range of 200-500 bp and was monitored by agarose gel electrophoresis. Immunoprecipitation was performed with anti-PU.1 anti-HA anti-BCLAF1 or control rabbit IgG and Protein A Dynabeads DNA was eluted, reverse cross-linked and then purified with QIAquick PCR purification kit. For ChIP-PCR analysis, PCR was performed. For ChIP-seq analysis, fragmented DNA was quantified using 2100 Bioanalyzer and DNA libraries were prepared using Illumina TruSeq. Sequencing was performed using an Illumina HiSeq 3000 by the Washington University Genome Technology Access Center.
DNA  libraries were prepared using Illumina TruSeq


title: Input_Art


title: Input_Art SPIC_tet


title: Input_Rag


title: Rag_SPIC_tet_DOX_BCLAF1_07

value: anti-BCLAF1 (A300-608A, Bethyl Laboratories)


title: Cell_2

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-11_S33_L008_R1_001.fastq.gz


title: O1_TA_Hi_9 [scBS-seq]


title: O1_TA_Hi_8 [scBS-seq]


title: Cell_1

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-10_S32_L008_R1_001.fastq.gz


title: Art_SPIC_tet_NoDOX_PU.1_05

value: anti-PU.1 (PA5-17505, Thermo Fisher Scientific)


title: Rag_SPIC_tet_DOX_SPIC_06

value: anti-HA (ab9110, Abcam)


title: Rag_SPIC_tet_DOX_PU.1_04


title: Rag_SPIC_tet_NoDOX_RNAseq2

description:
sample.rss2
Rag_SPIC_tet_NoDOX Vs Rag_SPIC_tet_DOX.xls


title: O1_TA_Hi_7 [scBS-seq]


title: Cell_7

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-16_S38_L008_R1_001.fastq.gz


title: O1_TA_Hi_6 [scBS-seq]


title: O1_TA_Hi_5 [scBS-seq]


title: Art_PU.1_02


title: Cell_4

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
17F-6-13_S35_L008_R1_001.fastq.gz


title: Rag_PU.1_01


title: Rag_SPIC_tet_NoDOX_PU.1_03


title: O1_TA_Hi_48 [scBS-seq]


title: O8_TA_Hi_10 [scBS-seq]


title: O1_TA_Hi_47 [scBS-seq]


title: O1_TA_Hi_44 [scBS-seq]


title: O1_TA_Hi_43 [scBS-seq]


title: O1_TA_Hi_42 [scBS-seq]


title: O1_TA_Hi_41 [scBS-seq]


title: O1_TA_Hi_40 [scBS-seq]


title: O1_TA_Hi_3 [scBS-seq]


title: O1_TA_Hi_46 [scBS-seq]


title: O1_TA_Hi_39 [scBS-seq]


title: O1_TA_Hi_35 [scBS-seq]


title: O1_TA_Hi_38 [scBS-seq]


title: O1_TA_Hi_34 [scBS-seq]


title: 9114097

type: genomic

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

hyb_protocol: One fraction was bisulfite converted and analyzed by hybridization to the Illumina Epic Array. The second fraction was first glucosylated to protect the 5hmC using the TAB-array kit (WiseGene, Lnc.,Chicago, IL), followed by bisulfite treatment and hybridization to the EPIC arrays

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

tag: sample id

tag: tissue type

value: Adjacent

tag: subject id

tag: organism

value: Homo sapiens

value: Female

tag: tab


title: 8146533

value: Male


title: O1_TA_Hi_33 [scBS-seq]

tag: cell type


title: 8019257


title: 9106618


title: 8018743

value: Tumor


title: 9096584


title: 7016896


title: 8018391


title: 9113914


title: O1_TA_Hi_32 [scBS-seq]


title: 9005912


title: 8019260


title: 8018388


title: 8017336


title: 9005915


title: 8017531


title: 8146529


title: 9114094


title: 8018740


title: 9107420


title: 9057296


title: 9106615


title: 8017535


title: 9096587


title: O1_TA_Hi_2 [scBS-seq]


title: 9107424


title: 9057300


title: 7044676


title: O1_TA_Hi_28 [scBS-seq]


title: O1_TA_Hi_29 [scBS-seq]


title: O1_TA_Hi_26 [scBS-seq]


title: O1_TA_Hi_27 [scBS-seq]


title: O1_TA_Hi_30 [scBS-seq]


title: O1_TA_Hi_25 [scBS-seq]