title: H3K27ac+KrasG12D_ChIP

value: anti-H3K27ac (Abcam ab4729)


title: Cl5 rep3

status: Public on Jul 11 2020

type: SRA

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
Processed data file: deseq2_counts.txt
Processed data file: rnaseq_C15vsHTERT_R2R3R4.deseq2.refseq.results_INVITRO.xlsx

library_source: transcriptomic

data_processing:
Reads were aligned using Tophat2 and counted using featureCounts.
Only reversely-stranded fragments (instead of individual paired end reads) that have both ends successfully aligned were counted, grouped by gene id and ignoring chimeric fragments (on separate chromosomes).
Count data was filtered to remove lowly expressed transcripts (quantile of rowsums at 0.3), and normalised and analysed for differential expression using DESeq2. Data was annotated to hg19 using biomaRt.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: deseq2_counts.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: rnaseq_C15vsHTERT_R2R3R4.deseq2.refseq.results_INVITRO.xlsx: Excel file includes DESeq2 differential gene expression.

molecule: total RNA

organism: Homo sapiens

source_name: in vitro transformed human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen).
Stranded total RNA sequencing was performed on rRNA-depleted samples (Ribozero Gold, Epigentre Madison). RNA library quality was assessed on a Picochip BioAnalyser 2100 chip (Agilent), and sequenced on an Illumina HiSeq2500 sequencer with 101bp paired-end reads.

treatment_protocol: SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibroblasts derived from hTERT-immortalized skin fibroblasts.

tag: tissue

tag: phenotype

value: Tumourigenic

tag: treatment

value: No treatment


title: H3K4me-KrasG12D_ChIP

city: Beijing

first: Yi

last: He

address: 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China

country: China

institute: Tsinghua university

library_source: genomic

data_processing:
The adapters of paired-end reads were trimmed and quality control checks were carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”. Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with parameter is “samtools view –b –h –F 1028 –f 3”. Peaks of ChIP-seq were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 1e-3 -f BEDPE”. Analysis of differential peaks intensity was processed using MAnorm (version 1.1.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools

molecule: genomic DNA

organism: Mus musculus

source_name: pancreatic adenocarcinoma

growth_protocol: To KrasG12D cell line: DMEM+10%FBS+1%P/S+1ug/ml Doxycycline; PDA cell line:DMEM+10%FBS+1%P/S

extract_protocol:
Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde,  washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140  mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease  inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six  times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton  X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer  and reverse-crosslinked for 6 h at 65 ºC
DNA samples were treated sequentially with  RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5  (Zymo Research, D4014)

treatment_protocol: To KrasG12D cell line: +KrasG12D means treatment with Dox;-KrasG12D  means No Dox add.PDA cell line:+KrasG12D means endogenous KrasG12D expression.

tag: cell type

value: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line

tag: strain

tag: chip antibody

value: anti-H3K4me1 (ab8895)


title: Cl5 rep4

value: in vitro transformed human skin fibroblasts


title: Cl5 rep2


title: RN_SMA_wt_p5_M34_LCM71

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

description:
LCM71
rpkms_SMA_LCMseq.txt

data_processing:
RNAseq reads were mapped simultaneously to the mm10 mouse genome assembly and the genomic sequence of human SMN2 (including introns) from the hg19 assembly using STAR (version 2.4.1c)
Expression levels were determined using the rpkmforgenes.py software (available at http://sandberg.cmb.ki.se/rnaseq).
Genome_build: mm10 + human SMN2 sequence (hg19 assembly)
Supplementary_files_format_and_content: text file with RPKM

molecule: polyA RNA

source_name: Red nucleus neurons

extract_protocol:
Brains and spinal cords were quickly dissected and snap frozen in 2-Methylbutane on dry ice. Tissues were sectioned in a cryostat and mounted onto PEN membrane glass slides (Zeiss). Quick staining with Histogene (Arcturus/LifeTechnologies) followed by dehydration in rising EtOH concentrations was performed immediately prior to LCM. Individual cells were isolated using a Leica LMD7000 system. Approximately 150 cells were collected into one tube and lysis buffer was added (0.2% triton-X 100 with 2U/ul RNase inhibitor, Clontech) before snap freezing the samples on dry ice. (Nichterwitz et al. 2016)
Smart-seq2 combined with Tn5 tagmentation

value: Red nucleus neurons

tag: genotype

value: control

tag: age (days)

tag: group

tag: mouse id


title: RN_SMA_wt_p5_M75_LCM61

description:
LCM61
rpkms_SMA_LCMseq.txt


title: H3K27ac-KrasG12D_ChIP


title: RN_SMA_wt_p5_M30_LCM82

description:
LCM82
rpkms_SMA_LCMseq.txt


title: Cl5 rep1


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_16h_2

city: Melbourne

first: Shivani

last: Pasricha

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: Peter Doherty Institute

data_processing:
raw fastq files were aligned to the Acanthamoeba castellanii (Neff) genome using Hisat2
reads mapping to genes were counted using featureCounts
differential gene expression analysis was performed using DESeq2
Genome_build: Acanthamoeba castellanii (Neff)
Supplementary_files_format_and_content: raw counts table from featureCounts

organism: Acanthamoeba castellanii

source_name: A. castellanii cells

growth_protocol: 2 × 105 A. castellanii were seeded in technical and biological triplicate in PYG medium in 24-well plates (4 × 105 cells per ml) and incubated for 24 h at RT. A. castellanii was then washed with minimal medium to remove non-adherent cells followed by L. pneumophila infection with MOI of 50 (Coil et al., 2008). After 1 h incubation at 37 ℃ with 5% CO2, cells were washed with minimal medium and incubated in fresh PYG medium at 37 ℃ with 5% CO2.

extract_protocol:
For RNA-sequencing analysis RNA was isolated from A. castellanii using TRIsure™ (Bioline) according to manufacturer’s instructions at 3 h, 8 h, 16 h and 24 h post infection.
cDNA library preparation and sequencing was carried out as described previously (Tanaka et al., 2013). Briefly, 1µg RNA was used for poly(A) selection and cDNA libraries were prepared using the Illumina sample preparation kit. 100 base pair paired-end sequencing was performed on the HiSeq 2500 (Illumina) platform, with the use of TruSeq Stranded mRNA LT sample Prep Kit (IIIumina) according to manufacturer’s instructions

treatment_protocol: A. castellanii trophozoites were left uninfected or infected with wild type L. pneumophila or the isogenic DdotA mutant for 3 h, 8 h (early infection), 16 h (mid infection) or 24 h (late infection).

value: Acanthamoeba castellanii (Neff)

tag: l.pn infection

value: WT 130b L.pnuemophila

tag: hours of infection


title: Foxa2+KrasG12D_input_ChIP


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_16h_1


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_24h_3


title: RN_SMA_ko_p2_M211_LCM188

description:
LCM188
rpkms_SMA_LCMseq.txt

value: SMA


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_8h_3


title: RN_SMA_ko_p2_M209_LCM187

description:
LCM187
rpkms_SMA_LCMseq.txt


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_8h_2


title: RN_SMA_ko_p5_M31_LCM38

description:
LCM38
rpkms_SMA_LCMseq.txt


title: hTert-3-H3K4me1

description: ChIP-seq

data_processing:
Alignments were performed using BWA in paired-end mode, allowing three mismatches across a seed length of the full 101bp sequence
Reads were filtered for proper-pairing and non-PCR duplication using Samtools, and non-overlap of ENCODE blacklisted regions using Bamutils
Peaks of histone enrichment were identified using SICER in broad peak mode
Genome_build: hg19
Supplementary_files_format_and_content: SICER broad peak files

source_name: hTERT immortalised human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing  15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
ChIP was performed as detailed by Burney et al Stem Cells 2013 31(9):1868-80
Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification. Sequenced was performed on an Illumina HiSeq 2500 at The Crick Institute, London.

treatment_protocol: SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibrobalsts derived from hTERT-immortalized skin fribroblasts.

value: Non-tumourigenic


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_8h_1


title: hTert-2-H3K27ac

description: ChIP-seq

value: hTERT immortalised human skin fibroblasts


title: Foxa2-KrasG12D_ChIP

value: anti-Foxa2 (Cell Signaling, #8186)


title: Foxa2-KrasG12D_input_ChIP


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_3h_2


title: 130b Legionella pneumophila infectedAcanthamoeba castellanii_3h_3


title: RN_SMA_ko_p2_M206_LCM168

description:
LCM168
rpkms_SMA_LCMseq.txt


title: RN_SMA_wt_p2_M28_LCM106

description:
LCM106
rpkms_SMA_LCMseq.txt


title: Fosl1+KrasG12D_ChIP

value: pancreatic adenocarcinoma cancer cell line

value: anti-Fosl1 (Thermo Fisher, PA5-76185)


title: hTert-2-H3K4me1

description: ChIP-seq


title: hTert-1-ChIP-Input

description: ChIP-seq

value: Input


title: 130b Legionella pneumophila infected Acanthamoeba castellanii_3h_1


title: Fosl1_input_ChIP


title: RN_SMA_wt_p2_M26_LCM102

description:
LCM102
rpkms_SMA_LCMseq.txt


title: Foxa2+KrasG12D_ChIP


title: WT_D7_R1_ATAC-seq

data_processing:
The adapters of paired-end reads were trimmed and a quality control check was carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”. Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with the parameter “samtools view –b –h –F 1028 –f 3”. ATAC-seq peaks were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 0.01 -f BAMPE --nolambda”. Raw counts of peaks in each sample were counted by featureCounts (version 1.6.3). Analysis of differential peak intensity and size factor for29  each sample were both obtained using DESeq2 (version 1.22.1). Normalized bigwig files were generated with 1/size factor using bamCoverage (version 3.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedtools

source_name: pancreatic "normal' duct cell

extract_protocol:
Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
Libraries were prepared according to TruePrepTM DNA Library Prep Kit V2 for Illumina(Vazyme,TD502). ATAC-seq was performed using 3000 cells isolated from each mouse as described (Wu et al., 2016)

treatment_protocol: Caerulein injections were performed on 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection

tag: days after injection

value: day 7


title: hTert-1-H3K27ac

description: ChIP-seq


title: dotA mutant infected Acanthamoeba castellanii_24h_3

value: dotA mutant strain


title: hTert-1-H3K4me1

description: ChIP-seq

value: No treatment


title: hTert-3-H3K27ac

description: ChIP-seq


title: RN_SMA_wt_p2_M244_LCM211

description:
LCM211
rpkms_SMA_LCMseq.txt


title: WT_D7_R2_ATAC-seq


title: RN_SMA_ko_p2_M207_LCM173

description:
LCM173
rpkms_SMA_LCMseq.txt


title: RN_SMA_wt_p2_M14_LCM110

description:
LCM110
rpkms_SMA_LCMseq.txt


title: dotA mutant infected Acanthamoeba castellanii_24h_2


title: WT_D2_R2_ATAC-seq

source_name: ADM

value: day 2


title: dotA mutant infected Acanthamoeba castellanii_24h_1


title: WT_D2_R1_ATAC-seq


title: Cl5-3-H3K27ac

description: ChIP-seq

value: Tumourigenic


title: Cl5-3-H3K4me1

description: ChIP-seq

value: in vitro transformed human skin fibroblasts


title: WT_D0_R2_ATAC-seq

source_name: pancreatic normal duct cell

value: day 0


title: ASC Microglia ASC Astrocyte HSV 4

type: RNA

city: Chicago

first: Richard

last: Longnecker

state: IL

address: 303 E Chicago Ave

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Test

data_processing:
All data processing was performed using the GeneGlobe online software included with the array: https://geneglobe.qiagen.com/us/analyze/
Normalization was performed using the housekeeping gene GAPDH. The average GAPDH Ct value for each group was used for normalization. Normalized values are 2^-deltaCt, where deltaCt = (Ct_Target − AvgCt_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., test group/WT microglia + WT astrocytes control group) ratios.

label: SYBR Green

source_name: Primary microglia and astrocytes

label_protocol: Reverse transcription was performed using the RT2 First Strand Kit (QIAGEN) with 400 ng RNA per sample. PCR assay was performed using the RT2 Profiler PCR Array Mouse Inflammatory Cytokines and Receptors kits (QIAGEN, PAMM-011Z). Quantitative real-time PCR was performed (ABI StepOnePlus) wtih 40 cycles at

growth_protocol: Cells were maintained in DMEM containing 10% FBS, 1% L-glutamate, and penicillin/streptomycin for 1 week prior to infection

extract_protocol: Total RNA was isolated using TRIzol according to the protocol

treatment_protocol: Infected with HSV-1 KOS at an MOI of 5 for 12 hours prior to extraction

value: Brain

tag: Sex

value: Male and Female


title: Cl5-2-H3K27ac

description: ChIP-seq


title: dotA mutant infected Acanthamoeba castellanii_16h_3

value: Acanthamoeba castellanii (Neff)


title: WT_D0_R1_ATAC-seq


title: Cl5-2-H3K4me1

description: ChIP-seq


title: ASC Microglia ASC Astrocyte HSV 2

description: Test


title: KrasG12D_D7_R2_ATAC-seq

source_name: Kras maintained ADM and panIN


title: Cl5-1-ChIP-Input

description: ChIP-seq


title: dotA mutant infected Acanthamoeba castellanii_16h_1


title: dotA mutant infected Acanthamoeba castellanii_8h_3


title: KrasG12D_D7_R1_ATAC-seq


title: ASC Microglia ASC Astrocyte HSV 3

description: Test


title: Cl5-1-H3K4me1

description: ChIP-seq


title: ASC Microglia ASC Astrocyte HSV 1

description: Test


title: WT Microglia ASC Astrocyte HSV 3

description: Test


title: dotA mutant infected Acanthamoeba castellanii_8h_1


title: KrasG12D_D2_R1_ATAC-seq


title: BY4742_Rbg2Slh1Rbg1_Control_rep2

city: Urbana

first: Hong

last: Jin

state: Illinois

address: 600 S Mathews Ave

department: Biochemistry

institute: University of Illinois at Urbana-Champaign

description: Rbg1 was depleted by indibiting the trascription and ehancing the degradation using mAID tag.

data_processing:
Library strategy: 5Pseq
The 3' adaptor sequence was identified and removed using the cutadapt package.
The adaptor-removed reads were deduplicated by bbmap based upon random barcode sequences.
The 5' UMI were trimmed by fastx_trimmer.
Non-coding RNAs were filtered by mapping to annotated S.cerevisiae rRNAs, tRNAs, snRNAs, and snoRNAs using Bowtie1.
Unaligned reads were then mapped to the sacCer3 genome using Bowtie2 with the arguments: --local --D 15 -R2 -N 1 -L 20 -i S,1,0,0.75 -S
Reads with multiple alignments, mapping quality values <30, or those containing soft-clipped bases on the 5' end were excluded.
The 5' ends of reads were extracted and the total numbers of reads per genome location were calculated. Reads per million (RPM) values for each genomic locus were calculated using the number of unique reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: csv files. Each line contains the RPM values at every nucleotide for each gene.  5'UTR and 3'UTR were extract from genome as 100nt long for all genes. First column is gene name, second column is the length of the gene. The rest columns are the RPM values.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Wild type and mutant cells were grown to an OD600 of 0.6 in YPGR (2% galactose + 0.2% raffinose) medium at 30℃, harvested by centrifugation, then washed and resuspended in the same volume of YEPD (2% glucose) medium containing 1 mM auxin. These cells were grown in the presence of auxin for another 20 minutes at 30℃ to deplete Rbg1 completely.

extract_protocol:
Total RNA was extracted and DNA was removed by incubation with TURBO Dnase.
50μg of DNA-free total RNA was directly ligated to the rP5_RND oligo at 16℃ overnight. The polyadenylated mRNAs were enriched using Dynabeads (dT)25, followed by fragmentation for 5 minutes at 80℃ in RNA fragmentation buffer. Then the samples were primed with random hexamers and reverse transcribed with Superscript II. Second strand cDNA synthesis was performed using a single PCR cycle. Double-stranded cDNA was purified using HighPrep beads, then was bound to Dynabeads M-280 Streptavidin beads. Bound DNA molecules were subjected to end repair, adenine addition, and adaptor ligation, and a final PCR amplification. 300-500bp regions of the samples was seperated by agarose gel electrophoresis and extracted using single-end, 100bp-read NovaSeq6000 Illumina sequencing.

treatment_protocol: NO treatment with cycloheximide. Cells were harvested quickly by centrifugation.

value: Rbg2-KO, Slh1-KO, Rbg1 depletion

tag: molecule subtype

value: mRNA degradation intermediate


title: WT Microglia ASC Astrocyte HSV 2

description: Test


title: dotA mutant infected Acanthamoeba castellanii_16h_2


title: WT Microglia ASC Astrocyte HSV 1

description: Test


title: dotA mutant infected Acanthamoeba castellanii_8h_2


title: BY4742_Rbg2Slh1Rbg1_Control_rep1


title: KrasG12D_D0_R2_ATAC-seq


title: ASC Microglia WT Astrocyte HSV 4

description: Test


title: dotA mutant infected Acanthamoeba castellanii_3h_2


title: KrasG12D_D0_R1_ATAC-seq


title: dotA mutant infected Acanthamoeba castellanii_3h_3


title: ASC Microglia WT Astrocyte HSV 3

description: Test


title: Cl5-1-H3K27ac

description: ChIP-seq


title: BY4742_Rbg2Slh1Rbg1_5Pseq_rep1


title: Uninfected Acanthamoeba castellanii_24h_3

value: Uninfected


title: ASC Microglia WT Astrocyte HSV 2

description: Test


title: dotA mutant infected Acanthamoeba castellanii_3h_1


title: BY4742_Rbg2Slh1_Control_rep2

description: Rbg2 and Slh1 was knocked out by established homologous recombination techniques.

value: Rbg2-KO, Slh1-KO


title: Uninfected Acanthamoeba castellanii_24h_2


title: BY4742_Rbg2Slh1_Control_rep1


title: WT Microglia WT Astrocyte HSV 3

description: Control


title: WT Microglia WT Astrocyte HSV 2

description: Control


title: Uninfected Acanthamoeba castellanii_24h_1


title: Uninfected Acanthamoeba castellanii_16h_3


title: BY4742_Rbg2Slh1_5Pseq_rep2


title: PtrMYB092-3

city: Harbin

first: Baoguang

last: Liu

state: Heilongjiang Province

address: No.51 Hexing Road

department: forestry

institute: northeast forestry university

data_processing:
Nine libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for Illumina HiSeq 2500 sequencing
150 bp average read lengths were obtained after removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: P. trichocarpa genome release V3.0 (Phytozome V10.0)
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3.0) and the read counts

organism: Populus trichocarpa

source_name: SDX protoplasts

growth_protocol: P. trichocarpa  trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 6 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation.

extract_protocol:
SDX protoplasts (5000000–8000000cells) were collected by centrifugation at 600 × g for 5 min at room temperature. SDX protoplasts were immediately frozen in liquid nitrogen for RNA isolation. Total RNA was isolated from the SDX protoplasts using the RNeasy Mini kit (Invitrogen) for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SDX protoplasts from 6 months old P. trichocarpa  were isolated and transfeted with GFP, PtrHSFB3-1 and PtrMYB092 genes by PEG mediated transfection method.  Protoplasts incubated for 12h  were collected for transcriptomic analysis.

tag: transfected genes


title: HWW

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: control of overexpression_in Multiple Myeloma

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Mutiple Myeloma cell line

value: control of overexpression


title: WT Microglia WT Astrocyte HSV 1

description: Control

tag: tissue


title: BY4742_Rbg2Slh1Rbg1_5Pseq_rep2


title: BY4742_Rbg2Slh1_5Pseq_rep1


title: HKWW

source_name: control of knockdown_in Multiple Myeloma

value: control of knockdown


title: TGF-b treatment

city: Chiba

first: Yoshitoshi

last: Kasuya

address: 1-8-1 Inohana Chuo-ku

department: Grad. Sch. Med

country: Japan

institute: Chiba Univ.

description: miRNA expression data for TGF-b treatment

hyb_protocol: After fragmentation, total RNAs were hybridized for 18 hr at 48°C in a rotating (60 rpm) hybridization oven using GeneChipTM Hybridization Oven 645. GeneChips were washed and stained in the GeneChipTMFluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChipTM Scanner 3000 7G (Thermo Fisher Scientific, Inc.).

data_processing: The expression data was normalized using the Robust Multi-array Average (RMA)

label: biotin

source_name: Human myofibroblast

label_protocol: Biotinylated RNAs were prepared according to the standard FlashTagTM Biotin HSR RNA Labeling Kit protocol from 1000 ng of total RNA.

growth_protocol: Lung tissue from a 46-y old male patient who underwent lung transplantation by reason of severe IPF (usual interstitial pneumonia pattern) was obtained after surgery. The patient provided informed consent, and the study was approved by the Ethics Committee of Chiba University, Graduate School of Medicine and Hospital, Japan. Lung tissue was minced into small pieces, and then were incubated in DMEM supplemented with 1 mg/ml collagenase type I, 0.5 mg/ml dispase, 2 U/ml DNase, 0.1 mg/ml streptomycin, and 100 U/ml penicillin at 37°C for 15 min with gentle shaking. After washing twice with DMEM, the resulting pieces were transferred to a 90 mm-culture dish and were dipped with culture medium (10% FBS in DMEM supplemented with streptomycin and penicillin) and cultured at 37°C and 5% CO2. Outgrowth of cells was monitored daily with changing the culture medium every 4 d. When the dish reached confluence (about 14 days in vitro), outgrown cells were harvested as cells at passage 0. Expanded cells at passage 3 were subjected to the immunofluorescent study to verify population of α-SMAhighED-A-FN+S100A4- cells as myofibroblasts. More than 90% of the cells were myofibroblasts.

extract_protocol: Total RNA of the cells was extracted using ISOGEN plus (Nippon Gene, Toyama, Japan) according to manufacturer instructions.

treatment_protocol: Expanded myofibroblasts at passage 5 were used for the following experiments. After 24 h of serum deprivation in DMEM containing 0.2% fat-free bovine serum albumin, myofibroblasts were treated with/without JQ1 (1 µM) and/or TGF- (10 ng/ml) for a further 48 h.

tag: gender and age

value: Male, 46-year-old

value: Lung

value: myofibroblast

tag: diagnosis

value: Idiopathic pulmonary fibrosis (IPF)


title: 10x scATAC-seq of tumor 2 from P2

data_processing:
Raw data was processed by cellranger-atac  (1.1.0) from 10X genomics website.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak

source_name: PDAC

extract_protocol:
Fresh specimens of control pancreases and PDAC were collected at the time of surgical resection under the supervision of a qualified pathologist. Tissues were transported in RPMI 1640 with 1 mM protease inhibitor on ice to preserve viability, washed 2–3 times with phosphate buffered saline , then minced on ice. We used dissociation enzyme cocktail 1 mg/ml Type VIII Collagenase 2 mg/ml Dispase II, 1 mg/ml Trypsin Inhibitor and 1 unit/ml DNase I dissolved in PBS with 5% Fetal Bovine Serum to digest the tissues. Neoplastic tissues were dissociated at 37 °C with a shaking speed of 50 r.p.m for about 40 min. We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. As for control pancreases, minced tissues were incubated with the same digestion buffer at 37 °C without shaking for about 40 min. We repeatedly collected the dissociated cells at interval of 10 min. Cell suspensions were fifiltered using a 40 μm nylon cell strainer and red blood cells (RBC) were removed by RBC. Dissociated cells were washed with PBS containing 0.04% Bovine Serum Albumin with step by step descending centrifuging speed and increasing time. Cells were stained with 0.4% Trypan blue to check the viability, and then diluted with PBS containing 0.04% BSA to about 5 × 106 cells/ml for single cell ATAC sequencing.Nuclei Isolation is totally followed by demonstrated protocol Nuclei Isolation for Single Cell ATAC Sequencing from 10xgenomics official website.Targeted Nuclei Recovery number is 1 × 104 performed by CG000168_Chromium Single Cell ATAC_Reagent Kits User Guide from 10xgenomics official website.
CG000168_Chromium Single Cell ATAC_Reagent Kits

tag: tissue/cell type

value: PDAC tumor tissue


title: PtrMYB092-2


title: JQ-1 treatment

description: miRNA expression data for JQ-1 treatment

tag: cell type


title: BY4742_Rbg1_Control_rep2

description: Rbg1 was knocked out by established homologous recombination techniques.

tag: strain


title: TGF-b and JQ-1 treatment

description: miRNA expression data for TGF-b and JQ-1 treatment


title: PtrMYB092-1


title: Non-treatment (control)

description: miRNA expression data for control


title: Uninfected Acanthamoeba castellanii_16h_1


title: ASC Microglia WT Astrocyte HSV 1

description: Test


title: Uninfected Acanthamoeba castellanii_8h_3


title: Uninfected Acanthamoeba castellanii_16h_2


title: BY4742_Rbg1_5Pseq_rep2

tag: genotype


title: PtrHSFB3-1-3


title: HK_DWW

source_name: CHEK1 knockdown_in Multiple Myeloma

value: CHEK1 knockdown


title: Uninfected Acanthamoeba castellanii_8h_2


title: PtrHSFB3-1-2


title: BY4742_Rbg1_Control_rep1


title: BY4742_Rbg1_5Pseq_rep1


title: AWW


title: Uninfected Acanthamoeba castellanii_8h_1


title: PtrHSFB3-1-1


title: AKWW


title: BY4742_WT_Control_rep2

value: WT


title: Uninfected Acanthamoeba castellanii_3h_3


title: GFP-3

value: GFP


title: BY4742_WT_Control_rep1


title: GFP-2


title: Uninfected Acanthamoeba castellanii_3h_2


title: AK_DWW


title: ACWW

source_name: CHEK1 overexpression_in Multiple Myeloma

value: CHEK1 overexpression


title: BY4742_WT_5Pseq_rep2


title: LAM uterus

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: snRNA-seq

data_processing:
Read alignment and gene-expression quantification of human single-cell RNA-seq (scRNA-seq) and single-nuclear RNA-seq (snRNA-seq) data were performed using Cell Ranger version 2.0.0/3.0.2 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built human (hg19) reference package was used. For snRNA-seq alignment and quantification, a Cell Ranger compatible human (hg19) "pre-mRNA" reference package was generated according to Cell Ranger’s instructions
Genome_build: hg19
Supplementary_files_format_and_content: tar file containing  barcodes.tsv, genes.tsv,  matrix.mtx

source_name: LAM patient_uterus

extract_protocol:
Single-cell and single-nuclei suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol
single-cell RNA-seq, single-nuclear RNA-seq

tag: subject status

value: Lymphangioleiomyomatosis (LAM) patient

value: Uterus


title: GFP-1


title: HCWW


title: Uninfected Acanthamoeba castellanii_3h_1

value: Acanthamoeba castellanii (Neff)


title: BY4742_WT_5Pseq_rep1

value: mRNA degradation intermediate


title: Exp. 2 L_3

status: Public on Jul 10 2020

city: Calgary

first: Hena

middle: Rehman

last: Ramay

state: AB

address: 6 Erlton Terrace SW

department: International microbiome centre

country: Canada

institute: University of Calgary

data_processing: raw counts

source_name: T82 Human Colonic Epithelial Cells

growth_protocol: T84 colonic epithelial cells were maintained in 10% FBS 1:1 DMEM/F12 Ham medium (Sigma) containing HEPES (2mM), L-glutamine (2.68mM), sodium pyruvate (0.6mM), sodium bicarbonate (0.015%), and pen/strep (120units/mL pen, 0.12mg/mL strep). Cells were seeded on 12W plates and treated at 70% confluency. Bacteria were grown on agar plates (LB for F18 and HB101, Sheep Blood for LF82) 2 days prior to experiment, and in broth 1 day prior to experiment overnight at 37 degrees celcius (LB for F18 and HB101, penassay broth for LF82)

extract_protocol:
RNA was isolated from T84 cells using the Aurum Total RNA Mini Kit (Bio-Rad)
Illumina TruSeq Stranded mRNA LT library preparation kit

treatment_protocol: Bacteria were diluted in antibiotic free T84 medium (described in growth protocol) at 10^4 CFU/mL, cells were washed 1x with antibiotic free medium, and cells were incubated with bacteria for 16h.

tag: treatment

value: E. coli LF82, 16h, 10^4 CFU/mL


title: Exp. 2 L_2


title: Exp. 2 C_2

value: Untreated (control)


title: Exp. 2 L_1


title: Exp. 2 F_2

value: E. coli F18, 16h, 10^4 CFU/mL


title: Exp. 2 H_3

value: E. coli HB101, 16h, 10^4 CFU/mL


title: Exp. 2 F_1


title: Exp. 2 F_3


title: Exp. 2 H_2


title: Exp. 2 C_1


title: Exp. 2 H_1


title: Exp. 1 LF82_4_2

growth_protocol: T84 colonic epithelial cells were maintained in 10% FBS 1:1 DMEM/F12 Ham medium (Sigma) containing HEPES (2mM), L-glutamine (2.68mM), sodium pyruvate (0.6mM), sodium bicarbonate (0.015%), and pen/strep (120units/mL pen, 0.12mg/mL strep). Cells were seeded on 12W plates and treated at 70% confluency. Bacteria were grown on agar plates (LB for F18, Sheep Blood for LF82) 2 days prior to experiment, and in broth 1 day prior to experiment overnight at 37 degrees celcius (LB for F18, penassay broth for LF82)

treatment_protocol: Bacteria were diluted in antibiotic free T84 medium (described in growth protocol) at 10^4 CFU/mL or 10^8 CFU/mL, cells were washed 1x with antibiotic free medium, and cells were incubated with bacteria for 4h or 16h.

value: E. coli LF82, 4h, 10^8 CFU/mL


title: Exp. 1 LF82_4_3


title: Exp. 1 F18_4_1

value: E. coli F18, 4h, 10^8 CFU/mL


title: Exp. 1 F18_4_3


title: Exp. 1 F18_4_2


title: Exp. 1 LF82_16h_3


title: Plate4_Well_H9, SR, ACFs

city: Oxford

first: Svetlana

last: Reilly

state: Oxfordshire

address: JOhn Radcliffe Hospita, Headley Way

department: Cardiovascular Medicine, Radcliffe Dept of Medicine

institute: University of Oxford

data_processing:
Adapter and quality trimming with cutadapt
Reads aligned to hg38 using STAR aligner
Raw read counts obtained using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: raw_reads_counts_matrix.txt

source_name: cardiac right atria

growth_protocol: Cells were cultured in FBM-3 media (#CC-3131, Lonza, USA) containing 10% FBS and a supplement pack (#CC-4525, Lonza, USA)

extract_protocol:
On the morning of the experiment, cells were quickly trypsinised, resuspended in ice-cold PBS containing 3% BSA, stained with DAPI and only viable singlets were sorted on a BD FACS Aria Fusion III sorter into 96-well plates containing 4ul SMART-seq2 lysis buffer; cells were kept on ice through the whole procedure. The released RNA was converted to cDNA and then sequence ready libraries essentially as described (https://www.nature.com/articles/nprot. 2014.006), with minor modifications. ThermoFisher Superscript II reverse transcriptase and Roche Kapa PCR enzyme were substituted for Takara Smartscribe reverse transcriptase and SeqAmp PCR enzyme respectively. Twenty PCR cycles were used to amplify cDNA and Illumina Nextera XT kit was used to generate the sequence ready libraries.
75bp single end

treatment_protocol: Cells were initially cultured in FBM-3 media (#CC-3131, Lonza, USA) containing 10% FBS and a supplement pack (#CC-4525, Lonza, USA); then starved for ~16 hours  and treated with CT in serum-free media for 24 hours.

value: primary atrial fibroblasts

tag: cell culture

value: No

tag: condition

value: SR


title: Exp. 1 LF82_16h_1


title: Exp. 1 C_1


title: Plate4_Well_H8, SR, ACFs


title: Exp. 1 C_2


title: Exp. 2 C_3


title: Plate4_Well_H7, SR, ACFs


title: Plate4_Well_H5, AF, ACFs

value: AF


title: KrasG12D_D2_R2_ATAC-seq

value: day 2


title: Plate4_Well_H4, AF, ACFs


title: Plate4_Well_H1, AF, ACFs


title: Plate4_Well_H3, AF, ACFs


title: Plate4_Well_H10, SR, ACFs


title: Plate4_Well_G9, SR, ACFs


title: Plate4_Well_G8, SR, ACFs


title: Plate4_Well_H11, SR, ACFs


title: Exp. 1 LF82_4_1


title: Plate4_Well_H2, AF, ACFs


title: Plate4_Well_G7, SR, ACFs


title: Plate4_Well_G5, AF, ACFs


title: Plate4_Well_G6, AF, ACFs


title: Plate4_Well_H12, SR, ACFs


title: Plate4_Well_G2, AF, ACFs


title: Plate4_Well_G12, SR, ACFs


title: Exp. 1 C_3


title: Plate4_Well_G4, AF, ACFs


title: Plate4_Well_G11, SR, ACFs


title: Exp. 1 LF82_16h_2


title: Plate4_Well_G3, AF, ACFs


title: Plate4_Well_G10, SR, ACFs


title: Plate4_Well_F8, SR, ACFs


title: Plate4_Well_F9, SR, ACFs


title: Plate4_Well_F6, AF, ACFs


title: Plate4_Well_F5, AF, ACFs


title: Plate4_Well_F4, AF, ACFs


title: Plate4_Well_H6, AF, ACFs


title: Plate4_Well_F3, AF, ACFs


title: Plate4_Well_F11, SR, ACFs


title: Plate4_Well_E8, SR, ACFs


title: Plate4_Well_F1, AF, ACFs


title: Plate4_Well_F12, SR, ACFs


title: Plate4_Well_E9, SR, ACFs


title: Plate4_Well_E5, AF, ACFs


title: Plate4_Well_E6, AF, ACFs


title: Plate4_Well_E7, SR, ACFs


title: Plate4_Well_E4, AF, ACFs


title: Plate4_Well_E11, SR, ACFs


title: Plate4_Well_E2, AF, ACFs


title: Plate4_Well_E12, SR, ACFs


title: Plate4_Well_E10, SR, ACFs


title: Plate4_Well_D8, SR, ACFs


title: Plate4_Well_E1, AF, ACFs


title: Plate4_Well_D7, SR, ACFs


title: Plate4_Well_F7, SR, ACFs


title: Plate4_Well_D5, AF, ACFs


title: Plate4_Well_D4, AF, ACFs


title: Plate4_Well_D2, AF, ACFs


title: Plate4_Well_D6, AF, ACFs


title: Plate4_Well_D12, SR, ACFs


title: Plate4_Well_F2, AF, ACFs


title: Plate4_Well_F10, SR, ACFs


title: Plate4_Well_D3, AF, ACFs


title: Plate4_Well_D11, SR, ACFs


title: Plate4_Well_C9, SR, ACFs


title: Plate4_Well_D10, SR, ACFs


title: Plate4_Well_C7, SR, ACFs


title: Plate4_Well_C6, AF, ACFs


title: Plate4_Well_C5, AF, ACFs


title: Plate4_Well_C3, AF, ACFs


title: Plate4_Well_D9, SR, ACFs


title: Plate4_Well_C8, SR, ACFs


title: Plate4_Well_D1, AF, ACFs


title: Plate4_Well_C2, AF, ACFs


title: Plate4_Well_B8, SR, ACFs


title: Plate4_Well_C11, SR, ACFs


title: Plate4_Well_B9, SR, ACFs


title: Plate4_Well_B4, AF, ACFs


title: Plate4_Well_C1, AF, ACFs


title: Plate4_Well_B7, SR, ACFs


title: Plate4_Well_C10, SR, ACFs


title: Plate4_Well_C12, SR, ACFs


title: Plate4_Well_B3, AF, ACFs


title: Plate4_Well_B5, AF, ACFs


title: Plate4_Well_B6, AF, ACFs


title: Plate4_Well_B2, AF, ACFs


title: Plate4_Well_B12, SR, ACFs


title: Plate4_Well_B11, SR, ACFs


title: Plate4_Well_C4, AF, ACFs


title: Plate4_Well_B10, SR, ACFs


title: Plate4_Well_B1, AF, ACFs


title: Plate4_Well_A9, SR, ACFs


title: Plate4_Well_A2, AF, ACFs


title: Plate4_Well_A12, SR, ACFs


title: Plate4_Well_A6, AF, ACFs


title: Plate4_Well_A11, SR, ACFs


title: Plate4_Well_A3, AF, ACFs


title: Plate4_Well_A5, AF, ACFs


title: Plate3_Well_H6, AF, ACFs


title: Plate3_Well_H4, AF, ACFs


title: Plate3_Well_H8, SR, ACFs


title: Plate3_Well_H7, SR, ACFs


title: Plate3_Well_H5, AF, ACFs


title: Plate4_Well_A10, SR, ACFs


title: Plate3_Well_H2, AF, ACFs


title: Plate3_Well_H3, AF, ACFs


title: Plate4_Well_A1, AF, ACFs


title: Plate3_Well_H1, AF, ACFs


title: Plate3_Well_H11, SR, ACFs


title: Plate3_Well_G9, SR, ACFs


title: Plate3_Well_G8, SR, ACFs


title: Plate4_Well_A8, SR, ACFs


title: Plate4_Well_A4, AF, ACFs


title: Plate3_Well_G7, SR, ACFs


title: Plate4_Well_A7, SR, ACFs


title: Plate3_Well_G6, AF, ACFs


title: Plate3_Well_G5, AF, ACFs


title: Plate3_Well_G11, SR, ACFs


title: Plate3_Well_G12, SR, ACFs


title: Plate4_Well_E3, AF, ACFs


title: Plate3_Well_G10, SR, ACFs


title: Plate3_Well_H9, SR, ACFs


title: Plate3_Well_G1, AF, ACFs


title: Plate3_Well_H12, SR, ACFs


title: Plate3_Well_G4, AF, ACFs


title: Plate3_Well_H10, SR, ACFs


title: Plate3_Well_F9, SR, ACFs


title: Plate3_Well_F8, SR, ACFs


title: Plate3_Well_E9, SR, ACFs


title: Plate3_Well_F4, AF, ACFs


title: Plate3_Well_F2, AF, ACFs


title: Plate3_Well_F7, SR, ACFs


title: Plate3_Well_F11, SR, ACFs


title: Plate3_Well_F10, SR, ACFs


title: Plate3_Well_F5, AF, ACFs


title: Plate3_Well_F6, AF, ACFs


title: Plate3_Well_E7, SR, ACFs


title: Plate3_Well_E5, AF, ACFs


title: Plate3_Well_F3, AF, ACFs


title: Plate3_Well_F1, AF, ACFs


title: Plate3_Well_G2, AF, ACFs


title: Plate3_Well_F12, SR, ACFs


title: Plate3_Well_E6, AF, ACFs


title: Plate3_Well_E8, SR, ACFs


title: Plate3_Well_E3, AF, ACFs


title: Plate3_Well_E10, SR, ACFs


title: Plate3_Well_E12, SR, ACFs


title: Plate3_Well_G3, AF, ACFs


title: Plate3_Well_E2, AF, ACFs


title: Plate3_Well_E11, SR, ACFs


title: Plate3_Well_E1, AF, ACFs


title: Plate3_Well_D8, SR, ACFs


title: Plate3_Well_D9, SR, ACFs


title: Plate4_Well_G1, AF, ACFs


title: Plate3_Well_D7, SR, ACFs


title: Plate3_Well_D6, AF, ACFs


title: Plate3_Well_D5, AF, ACFs


title: Plate3_Well_D3, AF, ACFs


title: Plate3_Well_C7, SR, ACFs


title: Plate3_Well_C9, SR, ACFs


title: Plate3_Well_D2, AF, ACFs


title: Plate3_Well_D11, SR, ACFs


title: Plate3_Well_D10, SR, ACFs


title: Plate3_Well_E4, AF, ACFs


title: Plate3_Well_D4, AF, ACFs


title: Plate3_Well_C3, AF, ACFs


title: Plate3_Well_C4, AF, ACFs


title: Plate3_Well_C8, SR, ACFs


title: Plate3_Well_C6, AF, ACFs


title: Plate3_Well_C12, SR, ACFs


title: Plate3_Well_C5, AF, ACFs


title: Plate3_Well_C2, AF, ACFs


title: Plate3_Well_C11, SR, ACFs


title: Plate3_Well_C10, SR, ACFs


title: Plate3_Well_B9, SR, ACFs


title: Plate3_Well_B8, SR, ACFs


title: Plate3_Well_B4, AF, ACFs


title: Plate3_Well_B2, AF, ACFs


title: Plate3_Well_B5, AF, ACFs


title: Plate3_Well_B6, AF, ACFs


title: Plate3_Well_B3, AF, ACFs


title: Plate3_Well_D12, SR, ACFs


title: Plate3_Well_D1, AF, ACFs


title: Plate3_Well_B11, SR, ACFs


title: Plate3_Well_A9, SR, ACFs


title: Plate3_Well_A6, AF, ACFs


title: Plate3_Well_A5, AF, ACFs


title: Plate3_Well_A7, SR, ACFs


title: Plate3_Well_B1, AF, ACFs


title: Plate3_Well_A11, SR, ACFs


title: Plate3_Well_A3, AF, ACFs


title: Plate3_Well_A10, SR, ACFs


title: Plate3_Well_A12, SR, ACFs


title: Plate3_Well_C1, AF, ACFs


title: Plate3_Well_A4, AF, ACFs


title: Plate3_Well_A2, AF, ACFs


title: Plate3_Well_B7, SR, ACFs


title: Plate3_Well_A1, AF, ACFs


title: Plate2_Well_H9, SR, ACFs


title: Plate2_Well_H7, SR, ACFs


title: Plate2_Well_H5, AF, ACFs


title: Plate2_Well_H8, SR, ACFs


title: Plate2_Well_H6, AF, ACFs


title: Plate3_Well_B12, SR, ACFs


title: Plate2_Well_H4, AF, ACFs


title: Plate2_Well_H3, AF, ACFs


title: Plate2_Well_H12, SR, ACFs


title: Plate2_Well_H2, AF, ACFs


title: Plate2_Well_H11, SR, ACFs


title: Plate3_Well_A8, SR, ACFs


title: Plate2_Well_H1, AF, ACFs


title: Plate2_Well_H10, SR, ACFs


title: Plate2_Well_G8, SR, ACFs


title: Plate2_Well_G9, SR, ACFs


title: Plate2_Well_G7, SR, ACFs


title: Plate2_Well_G6, AF, ACFs


title: Plate2_Well_G5, AF, ACFs


title: Plate2_Well_G11, SR, ACFs


title: Plate2_Well_G12, SR, ACFs


title: Plate2_Well_G4, AF, ACFs


title: Plate2_Well_F9, SR, ACFs


title: Plate2_Well_G10, SR, ACFs


title: Plate2_Well_G1, AF, ACFs


title: Plate2_Well_F8, SR, ACFs


title: Plate2_Well_F7, SR, ACFs


title: Plate2_Well_F6, AF, ACFs


title: Plate2_Well_F5, AF, ACFs


title: Plate2_Well_F4, AF, ACFs


title: Plate2_Well_F2, AF, ACFs


title: Plate2_Well_F12, SR, ACFs


title: Plate3_Well_B10, SR, ACFs


title: Plate2_Well_F3, AF, ACFs


title: Plate2_Well_F11, SR, ACFs


title: Plate2_Well_F1, AF, ACFs


title: Plate2_Well_F10, SR, ACFs


title: Plate2_Well_E9, SR, ACFs


title: Plate2_Well_E8, SR, ACFs


title: Plate2_Well_E5, AF, ACFs


title: Plate2_Well_E6, AF, ACFs


title: Plate2_Well_E7, SR, ACFs


title: Plate2_Well_G3, AF, ACFs


title: Plate2_Well_G2, AF, ACFs


title: Plate2_Well_E12, SR, ACFs


title: Plate2_Well_E2, AF, ACFs


title: Plate2_Well_E11, SR, ACFs


title: Plate2_Well_D9, SR, ACFs


title: Plate2_Well_D5, AF, ACFs


title: Plate2_Well_D7, SR, ACFs


title: Plate2_Well_E1, AF, ACFs


title: Plate2_Well_D4, AF, ACFs


title: Plate2_Well_D8, SR, ACFs


title: Plate2_Well_D6, AF, ACFs


title: Plate2_Well_E10, SR, ACFs


title: Plate2_Well_D3, AF, ACFs


title: Plate2_Well_D1, AF, ACFs


title: Plate2_Well_D2, AF, ACFs


title: Plate2_Well_C9, SR, ACFs


title: Plate2_Well_C7, SR, ACFs


title: Plate2_Well_D11, SR, ACFs


title: Plate2_Well_C8, SR, ACFs


title: Plate2_Well_D10, SR, ACFs


title: Plate2_Well_C5, AF, ACFs


title: Plate2_Well_C3, AF, ACFs


title: Plate2_Well_E4, AF, ACFs


title: Plate2_Well_C6, AF, ACFs


title: Plate2_Well_C4, AF, ACFs


title: Plate2_Well_C2, AF, ACFs


title: Plate2_Well_C12, SR, ACFs


title: Plate2_Well_C1, AF, ACFs


title: Plate2_Well_C11, SR, ACFs


title: Plate2_Well_C10, SR, ACFs


title: Plate2_Well_B9, SR, ACFs


title: Plate2_Well_B8, SR, ACFs


title: Plate2_Well_D12, SR, ACFs


title: Plate2_Well_B4, AF, ACFs


title: Plate2_Well_B7, SR, ACFs


title: Plate2_Well_B5, AF, ACFs


title: Plate2_Well_B3, AF, ACFs


title: Plate2_Well_B2, AF, ACFs


title: Plate2_Well_B12, SR, ACFs


title: Plate2_Well_B10, SR, ACFs


title: Plate2_Well_B6, AF, ACFs


title: Plate2_Well_B11, SR, ACFs


title: Plate2_Well_A8, SR, ACFs


title: Plate2_Well_A3, AF, ACFs


title: Plate2_Well_A4, AF, ACFs


title: Plate2_Well_B1, AF, ACFs


title: Plate2_Well_A7, SR, ACFs


title: Plate2_Well_A6, AF, ACFs


title: Plate2_Well_E3, AF, ACFs


title: Plate2_Well_A9, SR, ACFs


title: Plate2_Well_A5, AF, ACFs


title: Plate2_Well_A12, SR, ACFs


title: Plate2_Well_A11, SR, ACFs


title: Plate2_Well_A10, SR, ACFs


title: Plate1_Well_H9, SR, ACFs


title: Plate1_Well_H8, SR, ACFs


title: Plate1_Well_H7, SR, ACFs


title: Plate2_Well_A2, AF, ACFs


title: Plate2_Well_A1, AF, ACFs


title: Plate1_Well_H6, AF, ACFs


title: Plate1_Well_H5, AF, ACFs


title: Plate1_Well_H3, AF, ACFs


title: Plate1_Well_H4, AF, ACFs


title: Plate1_Well_H11, SR, ACFs


title: Plate1_Well_H10, SR, ACFs


title: Plate1_Well_G9, SR, ACFs


title: Plate1_Well_H1, AF, ACFs


title: Plate1_Well_G7, SR, ACFs


title: Plate1_Well_H2, AF, ACFs


title: Plate1_Well_G8, SR, ACFs


title: Plate1_Well_G6, AF, ACFs


title: Plate1_Well_F9, SR, ACFs


title: Plate1_Well_G4, AF, ACFs


title: Plate1_Well_G3, AF, ACFs


title: Plate1_Well_F7, SR, ACFs


title: Plate1_Well_F8, SR, ACFs


title: Plate1_Well_G11, SR, ACFs


title: Plate1_Well_G10, SR, ACFs


title: Plate1_Well_G1, AF, ACFs


title: Plate1_Well_F4, AF, ACFs


title: Plate1_Well_F6, AF, ACFs


title: Plate1_Well_F11, SR, ACFs


title: Plate1_Well_F12, SR, ACFs


title: Plate1_Well_F5, AF, ACFs


title: Plate1_Well_F2, AF, ACFs


title: Plate1_Well_F10, SR, ACFs


title: Plate1_Well_F1, AF, ACFs


title: Plate1_Well_F3, AF, ACFs


title: Plate1_Well_H12, SR, ACFs


title: Plate1_Well_E6, AF, ACFs


title: Plate1_Well_E9, SR, ACFs


title: Plate1_Well_E5, AF, ACFs


title: Plate1_Well_G5, AF, ACFs


title: Plate1_Well_E3, AF, ACFs


title: Plate1_Well_E8, SR, ACFs


title: Plate1_Well_E4, AF, ACFs


title: Plate1_Well_E7, SR, ACFs


title: Plate1_Well_E12, SR, ACFs


title: Plate1_Well_G12, SR, ACFs


title: Plate1_Well_G2, AF, ACFs


title: Plate1_Well_E2, AF, ACFs


title: Plate1_Well_E11, SR, ACFs


title: Plate1_Well_D8, SR, ACFs


title: Plate1_Well_D7, SR, ACFs


title: Plate1_Well_D5, AF, ACFs


title: Plate1_Well_E1, AF, ACFs


title: Plate1_Well_D9, SR, ACFs


title: Plate1_Well_E10, SR, ACFs


title: Plate1_Well_D6, AF, ACFs


title: Plate1_Well_D11, SR, ACFs


title: Plate1_Well_D12, SR, ACFs


title: Plate1_Well_D4, AF, ACFs


title: Plate1_Well_D2, AF, ACFs


title: Plate1_Well_D3, AF, ACFs


title: Plate1_Well_C9, SR, ACFs


title: Plate1_Well_C3, AF, ACFs


title: Plate1_Well_D10, SR, ACFs


title: Plate1_Well_C7, SR, ACFs


title: Plate1_Well_C4, AF, ACFs


title: Plate1_Well_C6, AF, ACFs


title: Plate1_Well_C8, SR, ACFs


title: Plate1_Well_C2, AF, ACFs


title: Plate1_Well_C12, SR, ACFs


title: Plate1_Well_C11, SR, ACFs


title: Plate1_Well_B9, SR, ACFs


title: Plate1_Well_C10, SR, ACFs


title: Plate1_Well_B8, SR, ACFs


title: Plate1_Well_B7, SR, ACFs


title: Plate1_Well_B6, AF, ACFs


title: Plate1_Well_B4, AF, ACFs


title: Plate1_Well_B5, AF, ACFs


title: Plate1_Well_B2, AF, ACFs


title: Plate1_Well_B3, AF, ACFs


title: Plate1_Well_D1, AF, ACFs


title: Plate1_Well_B12, SR, ACFs


title: Plate1_Well_B1, AF, ACFs


title: Plate1_Well_A9, SR, ACFs


title: Plate1_Well_A8, SR, ACFs


title: Plate1_Well_C5, AF, ACFs


title: Plate1_Well_A7, SR, ACFs


title: Plate1_Well_A6, AF, ACFs


title: Plate1_Well_C1, AF, ACFs


title: Plate1_Well_A5, AF, ACFs


title: Plate1_Well_A2, AF, ACFs


title: Plate1_Well_A4, AF, ACFs


title: Plate1_Well_A3, AF, ACFs


title: Plate1_Well_A11, SR, ACFs


title: Plate1_Well_A1, AF, ACFs


title: Plate1_Well_A12, SR, ACFs


title: Plate1_Well_A10, SR, ACFs


title: Plate1_Well_B11, SR, ACFs


title: bulk MM087 EGR3-KD 72h

city: Leuven

first: k

last: spanier

address: Herestraat 49

country: Belgium

institute: KU Leuven

description:
S10__197669__RNA_MM087_EGR3-KD_S10
processed data file:
bulkRNASeq_EGR3_KD_raw_counts.tsv
bulkRNASeq_EGR3_KD_normalized_counts.tsv

data_processing:
The 10x samples were processed (alignment, barcode assignment and UMI counting) with the CellRanger count pipeline; pools with samples from different cell lines were demultiplexed using demuxlet (Kang et al. 2018); cells expressing less than 1000 genes and cells with more than 20% mitochondrial reads were removed
The Drop-seq samples were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011) and processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools pipeline (v1.12) developed by James Nemesh from the McCarroll lab (Macosko et al. 2015), using Picard tools (v1.140; Broad Institute) and the STAR aligner (v2.5.1b; Dobin 2013); cells expressing less than 1000 genes, more than 50000 and/or more than 10% mitochondrial reads were removed.
bulk RNA-Seq reads were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011), mapped using STAR (v2.5.1b; Dobin 2013) and counted with HTSeq (v0.6.1p1; Anders 2014); normalized count matrices were made with DESeq2 (v1.18.1; Love et al. 2014)
Omni-ATAC-Seq raw reads were mapped using Bowtie (v2.2.6; Langmead and Salzberg 2012); Duplicate reads were removed with Picard (v1.134; Broad Institute 2019) and low quality reads were removed with SAMtools (Q30) (v1.8; Li et al. 2009). bigWig files were created with deepTools (Ramírez et al. 2016).
Genome_build: hg19
Supplementary_files_format_and_content: raw and normalized count matrices

source_name: MM_siEGR3 72h

extract_protocol: not provided; requested

treatment_protocol: The MM lines were cultured in Ham’s F10 nutrient mix (ThermoFisher Scientific) supplemented with 10% fetal bovine serum (Invitrogen) and 100 µg ml-1 penicillin/streptomycin (ThermoFisher Scientific). The A375 cell line was maintained in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Invitrogen) and penicillin-streptomycin (ThermoFisher Scientific). Cell cultures were kept at 37°C, with 5% CO2, regular tests for mycoplasma contamination were negative. Knockdowns of SOX10, EGR3 and NFATC2 were performed using a SMARTpool (Dharmacon) of four siRNAs, respectively (ON-TARGETplus SOX10 siRNA (L017192-00); ON-TARGETplus EGR3 siRNA (L006528-00); ON-TARGETplus NFATC2 siRNA (L003606-00)). SMARTpool was applied at final concentrations of 20nM (SOX10) and 40 nM (EGR3 and NFATC2) in Opti-MEM medium (Thermo Fisher Scientific), after which cells were sampled at the indicated time points. To control for transfection artefacts, we used a pool of non-targeting siRNAs (SMARTpool: ON-TARGETplus Non-targeting Pool, number D001810-10-05, Dharmacon). Inhibition of CDK7-dependent transcription was achieved by treatment with THZ2 (HY-12280, MedChemExpress). For each treated melanoma culture, IC50 concentrations were calculated for 48 hours of treatment. As a control, DMSO treatment was used. Treatment with TGFbeta (10ng/ml; 100-21C, peprotech) and TNFalpha (1000 U/ml;  300-01A, peprotech) was performed in serum-free medium. As a control, also serum-free medium was used. For bulk RNA-seq, RNA was extracted from attached cells using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions. For scRNA-seq and Omni-ATAC-seq, cells were detached by trypsinization, counted and processed according to downstream protocols.

value: melanoma cell line

value: siEGR3 72h

tag: sequencing method

value: bulk RNA-Seq


title: bulk MM087 NTC 72h (EGR3-KD negative control)

description:
S10__4503d2__RNA_MM087_NTC-KD_S9
processed data file:
bulkRNASeq_EGR3_KD_raw_counts.tsv
bulkRNASeq_EGR3_KD_normalized_counts.tsv

source_name: MM_siNTC 72h

value: siNTC 72h


title: bulk MM057 NTC 72h (EGR3-KD negative control)

description:
S10__a07230__RNA_MM057_NTC-KD_S1
processed data file:
bulkRNASeq_EGR3_KD_raw_counts.tsv
bulkRNASeq_EGR3_KD_normalized_counts.tsv


title: bulk MM057 NTC 72h (NFATC2-KD negative control)

description:
RNA-seq_TruSeq_MM057_NTC_KD_S16
processed data file:
bulkRNASeq_NFATC2_KD_raw_counts.tsv
bulkRNASeq_NFATC2_KD_normalized_counts.tsv


title: bulk MM087 NTC 72h (NFATC2-KD negative control)

description:
S10__99278e__MM087_NTC_R1.fastq.gz
processed data file:
bulkRNASeq_NFATC2_KD_raw_counts.tsv
bulkRNASeq_NFATC2_KD_normalized_counts.tsv


title: bulk MM057 NFATC2-KD 72h

description:
RNA-seq_TruSeq_MM057_NFATC2_KD_S17
processed data file:
bulkRNASeq_NFATC2_KD_raw_counts.tsv
bulkRNASeq_NFATC2_KD_normalized_counts.tsv

source_name: MM_siNFATC2 72h

value: siNFATC2 72h


title: bulk MM087 NFATC2-KD 72h

description:
S10__d052e0__MM087_NFATC2_KD_R1.fastq.gz
processed data file:
bulkRNASeq_NFATC2_KD_raw_counts.tsv
bulkRNASeq_NFATC2_KD_normalized_counts.tsv


title: Plate1_Well_B10, SR, ACFs


title: OmniATAC MM029 untreated

data_processing:
The 10x samples were processed (alignment, barcode assignment and UMI counting) with the CellRanger count pipeline; pools with samples from different cell lines were demultiplexed using demuxlet (Kang et al. 2018); cells expressing less than 1000 genes and cells with more than 20% mitochondrial reads were removed
The Drop-seq samples were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011) and processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools pipeline (v1.12) developed by James Nemesh from the McCarroll lab (Macosko et al. 2015), using Picard tools (v1.140; Broad Institute) and the STAR aligner (v2.5.1b; Dobin 2013); cells expressing less than 1000 genes, more than 50000 and/or more than 10% mitochondrial reads were removed.
bulk RNA-Seq reads were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011), mapped using STAR (v2.5.1b; Dobin 2013) and counted with HTSeq (v0.6.1p1; Anders 2014); normalized count matrices were made with DESeq2 (v1.18.1; Love et al. 2014)
Omni-ATAC-Seq raw reads were mapped using Bowtie (v2.2.6; Langmead and Salzberg 2012); Duplicate reads were removed with Picard (v1.134; Broad Institute 2019) and low quality reads were removed with SAMtools (Q30) (v1.8; Li et al. 2009). bigWig files were created with deepTools (Ramírez et al. 2016).
Genome_build: hg19

source_name: melanoma cell line

extract_protocol: Not Provided

treatment_protocol: The MM lines were cultured in Ham's F10 nutrient mix (ThermoFisher Scientific) supplemented with 10% fetal bovine serum (Invitrogen) and 100 µg ml-1 penicillin/streptomycin (ThermoFisher Scientific). The A375 cell line was maintained in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Invitrogen) and penicillin-streptomycin (ThermoFisher Scientific). Cell cultures were kept at 37°C, with 5% CO2 and were regularly tested for mycoplasma contamination, and were found negative. Knockdown of SOX10 was performed using a SMARTpool of four siRNAs (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00, Dharmacon) at a final concentration of 20nM in Opti-MEM medium (Thermo Fisher Scientific) after which cells were sampled at the indicated time points. To control for transfection artefacts, we used a pool of non-targeting siRNAs (SMARTpool: ON-TARGETplus Non-targeting Pool, number D001810-10-05, Dharmacon). Inhibition of CDK7-dependent transcription was achieved by treatment with THZ2 (HY-12280, MedChemExpress). For each treated melanoma culture, IC50 concentrations were calculated for 48 hours of treatment. As a control, DMSO treatment was used. For bulk RNA-seq, RNA was extracted from attached cells using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions. For scRNA-seq and Omni-ATAC-seq, cells were detached by trypsinization, counted and processed according to downstream protocols.

value: no treatment

value: Omni-ATAC-Seq


title: OmniATAC MM047 untreated


title: OmniATAC MM087 untreated


title: OmniATAC MM057 untreated


title: OmniATAC MM074 untreated rep1


title: OmniATAC MM011 untreated


title: OmniATAC MM031 untreated


title: OmniATAC MM001 untreated


title: OmniATAC MM074 untreated rep2


title: bulk MM057 NTC 72h


title: bulk MM057 SOX10-KD 72h

value: siSOX10 72h


title: bulk MM074 SOX10-KD 72h


title: bulk MM057 EGR3-KD 72h

description:
S10__d2ef12__RNA_MM057_EGR3-KD_S2
processed data file:
bulkRNASeq_EGR3_KD_raw_counts.tsv
bulkRNASeq_EGR3_KD_normalized_counts.tsv


title: bulk MM031 NTC 72h


title: bulk MM011 SOX10-KD 72h


title: bulk MM031 SOX10-KD 72h


title: bulk MM074 NTC 72h


title: bulk MM001 NTC 72h


title: Drop-seq MM057 NTC

value: single cell RNA-Seq Drop-seq


title: 10x MM087 NTC

description: CellRanger v1.3.1

value: single cell RNA-Seq 10x


title: Unrestricted feeding 15:00 Participant: 11

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
Sample ID: RF894.U.T9
RESTRICT.txt
URF T9 Participant: 11

data_processing:
Quality was estimaed using v0.11.2 FASTQC
Reads were mapped using v2.5.3a STAR --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate
Mapped reads were counted with v1.6.0 featureCounts -p -B -C -T -t exon -g gene_id -a
Genome_build: hg38 release 92
Supplementary_files_format_and_content: Tab-delimited text files include cpm values for each sample.

source_name: Skeletal muscle

extract_protocol:
Skeletal muscle (~25-30 mg) tissue RNA extraction was performed with the All Prep kit (Qiagen, Hilden, Germany) according to the manufacturer’s directions.
RNA quality was assed using the Bioanalyzer instrument (Agilent Technologies) and RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina). Libraries were sequenced on a NextSeq500 instrument (Illumina) with 38- bp paired end

tag: sample type

value: Unrestricted feeding

tag: time point


title: 10x MM087 SOX10-KD 72h

description: CellRanger v1.3.1


title: Unrestricted feeding 07:00 Participant: 11

description:
Sample ID: RF894.U.T1
RESTRICT.txt
URF T1 Participant: 11


title: Drop-seq MM057 Baseline


title: Unrestricted feeding 23:00 Participant: 11

description:
Sample ID: RF894.U.T17
RESTRICT.txt
URF T17 Participant: 11


title: Time restricted feeding 11:00 Participant: 11

description:
Sample ID: RF894.R.T5
RESTRICT.txt
TRF T5 Participant: 11

value: Time restricted feeding


title: Time restricted feeding 03:00 Participant: 11

description:
Sample ID: RF894.R.T19
RESTRICT.txt
TRF T19 Participant: 11


title: Time restricted feeding 23:00 Participant: 11

description:
Sample ID: RF894.R.T17
RESTRICT.txt
TRF T17 Participant: 11


title: Drop-seq MM057 SOX10-KD 72h


title: Time restricted feeding 15:00 Participant: 10

description:
Sample ID: RF789.R.T9
RESTRICT.txt
TRF T9 Participant: 10


title: Time restricted feeding 19:00 Participant: 11

description:
Sample ID: RF894.R.T13
RESTRICT.txt
TRF T13 Participant: 11


title: Unrestricted feeding 19:00 Participant: 11

description:
Sample ID: RF894.U.T13
RESTRICT.txt
URF T13 Participant: 11


title: Time restricted feeding 07:00 Participant: 11

description:
Sample ID: RF894.R.T1
RESTRICT.txt
TRF T1 Participant: 11


title: bulk MM011 NTC 72h


title: Time restricted feeding 07:00 Participant: 10

description:
Sample ID: RF789.R.T1
RESTRICT.txt
TRF T1 Participant: 10


title: bulk MM001 SOX10-KD 72h


title: Time restricted feeding 19:00 Participant: 10

description:
Sample ID: RF789.R.T13
RESTRICT.txt
TRF T13 Participant: 10


title: Time restricted feeding 15:00 Participant: 11

description:
Sample ID: RF894.R.T9
RESTRICT.txt
TRF T9 Participant: 11


title: Unrestricted feeding 11:00 Participant: 10

description:
Sample ID: RF789.U.T5
RESTRICT.txt
URF T5 Participant: 10


title: Time restricted feeding 23:00 Participant: 10

description:
Sample ID: RF789.R.T17
RESTRICT.txt
TRF T17 Participant: 10


title: Time restricted feeding 03:00 Participant: 10

description:
Sample ID: RF789.R.T19
RESTRICT.txt
TRF T19 Participant: 10


title: Unrestricted feeding 07:00 Participant: 10

description:
Sample ID: RF789.U.T1
RESTRICT.txt
URF T1 Participant: 10


title: Unrestricted feeding 03:00 Participant: 11

description:
Sample ID: RF894.U.T19
RESTRICT.txt
URF T19 Participant: 11


title: Unrestricted feeding 03:00 Participant: 10

description:
Sample ID: RF789.U.T19
RESTRICT.txt
URF T19 Participant: 10


title: Unrestricted feeding 11:00 Participant: 11

description:
Sample ID: RF894.U.T5
RESTRICT.txt
URF T5 Participant: 11


title: Unrestricted feeding 19:00 Participant: 10

description:
Sample ID: RF789.U.T13
RESTRICT.txt
URF T13 Participant: 10


title: Unrestricted feeding 23:00 Participant: 9

description:
Sample ID: RF614.U.T17
RESTRICT.txt
URF T17 Participant: 9


title: Time restricted feeding 03:00 Participant: 9

description:
Sample ID: RF614.R.T19
RESTRICT.txt
TRF T19 Participant: 9


title: Time restricted feeding 15:00 Participant: 9

description:
Sample ID: RF614.R.T9
RESTRICT.txt
TRF T9 Participant: 9


title: Unrestricted feeding 23:00 Participant: 10

description:
Sample ID: RF789.U.T17
RESTRICT.txt
URF T17 Participant: 10


title: Unrestricted feeding 03:00 Participant: 9

description:
Sample ID: RF614.U.T19
RESTRICT.txt
URF T19 Participant: 9


title: Unrestricted feeding 19:00 Participant: 9

description:
Sample ID: RF614.U.T13
RESTRICT.txt
URF T13 Participant: 9


title: 10x 10 cell lines Baselines

description: CellRanger v1.3.1; Demultiplexed with demuxlet

source_name: melanoma cell lines

value: melanoma cell lines


title: Time restricted feeding 11:00 Participant: 10

description:
Sample ID: RF789.R.T5
RESTRICT.txt
TRF T5 Participant: 10


title: Unrestricted feeding 11:00 Participant: 9

description:
Sample ID: RF614.U.T5
RESTRICT.txt
URF T5 Participant: 9


title: Unrestricted feeding 15:00 Participant: 9

description:
Sample ID: RF614.U.T9
RESTRICT.txt
URF T9 Participant: 9


title: Time restricted feeding 07:00 Participant: 9

description:
Sample ID: RF614.R.T1
RESTRICT.txt
TRF T1 Participant: 9


title: Time restricted feeding 07:00 Participant: 8

description:
Sample ID: RF536.R.T1
RESTRICT.txt
TRF T1 Participant: 8


title: Unrestricted feeding 19:00 Participant: 8

description:
Sample ID: RF536.U.T13
RESTRICT.txt
URF T13 Participant: 8


title: Time restricted feeding 19:00 Participant: 8

description:
Sample ID: RF536.R.T13
RESTRICT.txt
TRF T13 Participant: 8


title: Time restricted feeding 23:00 Participant: 8

description:
Sample ID: RF536.R.T17
RESTRICT.txt
TRF T17 Participant: 8


title: Unrestricted feeding 19:00 Participant: 7

description:
Sample ID: RF508.U.T13
RESTRICT.txt
URF T13 Participant: 7


title: Unrestricted feeding 15:00 Participant: 8

description:
Sample ID: RF536.U.T9
RESTRICT.txt
URF T9 Participant: 8


title: Unrestricted feeding 15:00 Participant: 10

description:
Sample ID: RF789.U.T9
RESTRICT.txt
URF T9 Participant: 10


title: Time restricted feeding 15:00 Participant: 8

description:
Sample ID: RF536.R.T9
RESTRICT.txt
TRF T9 Participant: 8


title: Unrestricted feeding 07:00 Participant: 9

description:
Sample ID: RF614.U.T1
RESTRICT.txt
URF T1 Participant: 9


title: Time restricted feeding 11:00 Participant: 8

description:
Sample ID: RF536.R.T5
RESTRICT.txt
TRF T5 Participant: 8


title: Unrestricted feeding 07:00 Participant: 8

description:
Sample ID: RF536.U.T1
RESTRICT.txt
URF T1 Participant: 8


title: Unrestricted feeding 11:00 Participant: 8

description:
Sample ID: RF536.U.T5
RESTRICT.txt
URF T5 Participant: 8


title: Unrestricted feeding 23:00 Participant: 8

description:
Sample ID: RF536.U.T17
RESTRICT.txt
URF T17 Participant: 8


title: Time restricted feeding 03:00 Participant: 8

description:
Sample ID: RF536.R.T19
RESTRICT.txt
TRF T19 Participant: 8


title: Time restricted feeding 15:00 Participant: 7

description:
Sample ID: RF508.R.T9
RESTRICT.txt
TRF T9 Participant: 7


title: Unrestricted feeding 03:00 Participant: 7

description:
Sample ID: RF508.U.T19
RESTRICT.txt
URF T19 Participant: 7


title: Unrestricted feeding 07:00 Participant: 7

description:
Sample ID: RF508.U.T1
RESTRICT.txt
URF T1 Participant: 7


title: Unrestricted feeding 15:00 Participant: 7

description:
Sample ID: RF508.U.T9
RESTRICT.txt
URF T9 Participant: 7


title: Time restricted feeding 03:00 Participant: 7

description:
Sample ID: RF508.R.T19
RESTRICT.txt
TRF T19 Participant: 7


title: Time restricted feeding 11:00 Participant: 7

description:
Sample ID: RF508.R.T5
RESTRICT.txt
TRF T5 Participant: 7


title: Unrestricted feeding 11:00 Participant: 7

description:
Sample ID: RF508.U.T5
RESTRICT.txt
URF T5 Participant: 7


title: Time restricted feeding 23:00 Participant: 7

description:
Sample ID: RF508.R.T17
RESTRICT.txt
TRF T17 Participant: 7


title: Unrestricted feeding 23:00 Participant: 7

description:
Sample ID: RF508.U.T17
RESTRICT.txt
URF T17 Participant: 7


title: Time restricted feeding 07:00 Participant: 7

description:
Sample ID: RF508.R.T1
RESTRICT.txt
TRF T1 Participant: 7


title: Time restricted feeding 19:00 Participant: 7

description:
Sample ID: RF508.R.T13
RESTRICT.txt
TRF T13 Participant: 7


title: Unrestricted feeding 11:00 Participant: 6

description:
Sample ID: RF477.U.T5
RESTRICT.txt
URF T5 Participant: 6


title: Time restricted feeding 07:00 Participant: 6

description:
Sample ID: RF477.R.T1
RESTRICT.txt
TRF T1 Participant: 6


title: Time restricted feeding 19:00 Participant: 6

description:
Sample ID: RF477.R.T13
RESTRICT.txt
TRF T13 Participant: 6


title: Time restricted feeding 11:00 Participant: 9

description:
Sample ID: RF614.R.T5
RESTRICT.txt
TRF T5 Participant: 9


title: Unrestricted feeding 03:00 Participant: 8

description:
Sample ID: RF536.U.T19
RESTRICT.txt
URF T19 Participant: 8


title: Unrestricted feeding 03:00 Participant: 6

description:
Sample ID: RF477.U.T19
RESTRICT.txt
URF T19 Participant: 6


title: Time restricted feeding 15:00 Participant: 6

description:
Sample ID: RF477.R.T9
RESTRICT.txt
TRF T9 Participant: 6


title: Unrestricted feeding 23:00 Participant: 6

description:
Sample ID: RF477.U.T17
RESTRICT.txt
URF T17 Participant: 6


title: Time restricted feeding 03:00 Participant: 6

description:
Sample ID: RF477.R.T19
RESTRICT.txt
TRF T19 Participant: 6


title: Unrestricted feeding 15:00 Participant: 6

description:
Sample ID: RF477.U.T9
RESTRICT.txt
URF T9 Participant: 6


title: Unrestricted feeding 15:00 Participant: 5

description:
Sample ID: RF312.U.T9
RESTRICT.txt
URF T9 Participant: 5


title: Time restricted feeding 11:00 Participant: 6

description:
Sample ID: RF477.R.T5
RESTRICT.txt
TRF T5 Participant: 6


title: Unrestricted feeding 07:00 Participant: 6

description:
Sample ID: RF477.U.T1
RESTRICT.txt
URF T1 Participant: 6


title: Unrestricted feeding 11:00 Participant: 5

description:
Sample ID: RF312.U.T5
RESTRICT.txt
URF T5 Participant: 5


title: Time restricted feeding 07:00 Participant: 5

description:
Sample ID: RF312.R.T1
RESTRICT.txt
TRF T1 Participant: 5


title: Unrestricted feeding 23:00 Participant: 5

description:
Sample ID: RF312.U.T17
RESTRICT.txt
URF T17 Participant: 5


title: Time restricted feeding 15:00 Participant: 5

description:
Sample ID: RF312.R.T9
RESTRICT.txt
TRF T9 Participant: 5


title: Time restricted feeding 23:00 Participant: 5

description:
Sample ID: RF312.R.T17
RESTRICT.txt
TRF T17 Participant: 5


title: Time restricted feeding 19:00 Participant: 5

description:
Sample ID: RF312.R.T13
RESTRICT.txt
TRF T13 Participant: 5


title: Unrestricted feeding 07:00 Participant: 5

description:
Sample ID: RF312.U.T1
RESTRICT.txt
URF T1 Participant: 5


title: Unrestricted feeding 03:00 Participant: 5

description:
Sample ID: RF312.U.T19
RESTRICT.txt
URF T19 Participant: 5


title: Time restricted feeding 11:00 Participant: 5

description:
Sample ID: RF312.R.T5
RESTRICT.txt
TRF T5 Participant: 5


title: Unrestricted feeding 19:00 Participant: 5

description:
Sample ID: RF312.U.T13
RESTRICT.txt
URF T13 Participant: 5


title: Unrestricted feeding 03:00 Participant: 4

description:
Sample ID: RF287.U.T19
RESTRICT.txt
URF T19 Participant: 4


title: Unrestricted feeding 15:00 Participant: 4

description:
Sample ID: RF287.U.T9
RESTRICT.txt
URF T9 Participant: 4


title: Unrestricted feeding 07:00 Participant: 4

description:
Sample ID: RF287.U.T1
RESTRICT.txt
URF T1 Participant: 4


title: Time restricted feeding 15:00 Participant: 4

description:
Sample ID: RF287.R.T9
RESTRICT.txt
TRF T9 Participant: 4


title: HCC1428-LTED-9_Untreated (DMSO)

city: Cambridge

first: Joon Sang

last: Lee

state: MA

address: 270 Albany Street

department: Oncology

institute: Sanofi

description:
no treatment
HCC1428-LTED-9_ATACGCAG

data_processing:
STAR aligner
Cufflink
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw TPM values for every gene and every sample

source_name: HCC1428-LTED_Untreated (DMSO)

growth_protocol: Cells were grown and plated in improved modified eagle's medium (IMEM, Corning) supplemented with 5% charcoal stripped fetal bovine calf serum

extract_protocol:
Qiagen total RNA extraction with DNase treatment
RNA libraries were prepared for sequencing using stranded NuGEN protocols

treatment_protocol: Cells were treated for 24h with the ligands

value: breast cancer cell line

tag: cell line status

value: long term estrogen deprived (LTED)

value: Untreated (DMSO)


title: HCC1428-LTED-7_Untreated (DMSO)

description:
no treatment
HCC1428-LTED-7_GGTGTACA


title: HCC1428-LTED-105_AZD-SAR (300nM)

description:
Hybrid molecule with the scaffold of AZD9496 and the side chain of SAR439859
HCC1428-LTED-105_ATACGCAG

source_name: HCC1428-LTED_AZD-SAR (300nM)

value: AZD-SAR (300nM)


title: Time restricted feeding 23:00 Participant: 6

description:
Sample ID: RF477.R.T17
RESTRICT.txt
TRF T17 Participant: 6


title: Time restricted feeding 11:00 Participant: 4

description:
Sample ID: RF287.R.T5
RESTRICT.txt
TRF T5 Participant: 4


title: HCC1428-LTED-104_AZD-SAR (300nM)

description:
Hybrid molecule with the scaffold of AZD9496 and the side chain of SAR439859
HCC1428-LTED-104_CATACGGA


title: Time restricted feeding 03:00 Participant: 5

description:
Sample ID: RF312.R.T19
RESTRICT.txt
TRF T19 Participant: 5


title: HCC1428-LTED-103_AZD-SAR (300nM)

description:
Hybrid molecule with the scaffold of AZD9496 and the side chain of SAR439859
HCC1428-LTED-103_ACTCCTAC


title: HCC1428-LTED-102_AZD-SAR (30nM)

description:
Hybrid molecule with the scaffold of AZD9496 and the side chain of SAR439859
HCC1428-LTED-102_GACTACGA

source_name: HCC1428-LTED_AZD-SAR (30nM)

value: AZD-SAR (30nM)


title: Time restricted feeding 19:00 Participant: 4

description:
Sample ID: RF287.R.T13
RESTRICT.txt
TRF T13 Participant: 4


title: HCC1428-LTED-101_AZD-SAR (30nM)

description:
Hybrid molecule with the scaffold of AZD9496 and the side chain of SAR439859
HCC1428-LTED-101_AACACCAC


title: Time restricted feeding 03:00 Participant: 4

description:
Sample ID: RF287.R.T19
RESTRICT.txt
TRF T19 Participant: 4


title: HCC1428-LTED-100_AZD-SAR (30nM)

description:
Hybrid molecule with the scaffold of AZD9496 and the side chain of SAR439859
HCC1428-LTED-100_TCACTCGA


title: Unrestricted feeding 19:00 Participant: 4

description:
Sample ID: RF287.U.T13
RESTRICT.txt
URF T13 Participant: 4


title: Time restricted feeding 15:00 Participant: 3

description:
Sample ID: RF272.R.T9
RESTRICT.txt
TRF T9 Participant: 3


title: HCC1428-LTED-99_GDC-SAR (300nM)

description:
Hybrid molecule with the scaffold of GDC-0810 and the side chain of SAR439859
HCC1428-LTED-99_CTCACCAA

source_name: HCC1428-LTED_GDC-SAR (300nM)

value: GDC-SAR (300nM)


title: Time restricted feeding 07:00 Participant: 4

description:
Sample ID: RF287.R.T1
RESTRICT.txt
TRF T1 Participant: 4


title: HCC1428-LTED-98_GDC-SAR (300nM)

description:
Hybrid molecule with the scaffold of GDC-0810 and the side chain of SAR439859
HCC1428-LTED-98_TGGAAGCA


title: HCC1428-LTED-97_GDC-SAR (300nM)

description:
Hybrid molecule with the scaffold of GDC-0810 and the side chain of SAR439859
HCC1428-LTED-97_CTGTGGTA


title: Time restricted feeding 03:00 Participant: 3

description:
Sample ID: RF272.R.T19
RESTRICT.txt
TRF T19 Participant: 3


title: HCC1428-LTED-8_Untreated (DMSO)

description:
no treatment
HCC1428-LTED-8_AAGCTGGT


title: Unrestricted feeding 23:00 Participant: 4

description:
Sample ID: RF287.U.T17
RESTRICT.txt
URF T17 Participant: 4


title: Unrestricted feeding 19:00 Participant: 3

description:
Sample ID: RF272.U.T13
RESTRICT.txt
URF T13 Participant: 3


title: HCC1428-LTED-95_GDC-SAR (30nM)

description:
Hybrid molecule with the scaffold of GDC-0810 and the side chain of SAR439859
HCC1428-LTED-95_TCTAGGAG

source_name: HCC1428-LTED_GDC-SAR (30nM)

value: GDC-SAR (30nM)


title: Unrestricted feeding 07:00 Participant: 3

description:
Sample ID: RF272.U.T1
RESTRICT.txt
URF T1 Participant: 3


title: HCC1428-LTED-96_GDC-SAR (30nM)

description:
Hybrid molecule with the scaffold of GDC-0810 and the side chain of SAR439859
HCC1428-LTED-96_CATTCGTC


title: HCC1428-LTED-94_GDC-SAR (30nM)

description:
Hybrid molecule with the scaffold of GDC-0810 and the side chain of SAR439859
HCC1428-LTED-94_TGTGGCTT


title: Unrestricted feeding 03:00 Participant: 3

description:
Sample ID: RF272.U.T19
RESTRICT.txt
URF T19 Participant: 3


title: Time restricted feeding 19:00 Participant: 3

description:
Sample ID: RF272.R.T13
RESTRICT.txt
TRF T13 Participant: 3


title: HCC1428-LTED-86_AZD9496 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-86_CCGCTTAA


title: Time restricted feeding 23:00 Participant: 3

description:
Sample ID: RF272.R.T17
RESTRICT.txt
TRF T17 Participant: 3


title: HCC1428-LTED-87_AZD9496 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-87_AAGCTGGT


title: Time restricted feeding 11:00 Participant: 3

description:
Sample ID: RF272.R.T5
RESTRICT.txt
TRF T5 Participant: 3


title: Time restricted feeding 23:00 Participant: 4

description:
Sample ID: RF287.R.T17
RESTRICT.txt
TRF T17 Participant: 4


title: HCC1428-LTED-84_AZD9496 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-84_CTCTCAGA


title: Unrestricted feeding 15:00 Participant: 3

description:
Sample ID: RF272.U.T9
RESTRICT.txt
URF T9 Participant: 3


title: HCC1428-LTED-85_AZD9496 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-85_TTCACGGA


title: Unrestricted feeding 11:00 Participant: 3

description:
Sample ID: RF272.U.T5
RESTRICT.txt
URF T5 Participant: 3


title: HCC1428-LTED-83_AZD9496 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-83_CCACAACA


title: Unrestricted feeding 23:00 Participant: 3

description:
Sample ID: RF272.U.T17
RESTRICT.txt
URF T17 Participant: 3


title: HCC1428-LTED-82_AZD9496 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-82_AACACGCT


title: Time restricted feeding 07:00 Participant: 2

description:
Sample ID: RF141.R.T1
RESTRICT.txt
TRF T1 Participant: 2


title: HCC1428-LTED-80_GDC-0810 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-80_CATGGATC


title: HCC1428-LTED-81_GDC-0810 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-81_GCATAGTC


title: Time restricted feeding 11:00 Participant: 2

description:
Sample ID: RF141.R.T5
RESTRICT.txt
TRF T5 Participant: 2


title: HCC1428-LTED-79_GDC-0810 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-79_CTTCCTTC


title: Time restricted feeding 15:00 Participant: 2

description:
Sample ID: RF141.R.T9
RESTRICT.txt
TRF T9 Participant: 2


title: Unrestricted feeding 15:00 Participant: 2

description:
Sample ID: RF141.U.T9
RESTRICT.txt
URF T9 Participant: 2


title: HCC1428-LTED-77_GDC-0810 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-77_CCAGTTGA


title: HCC1428-LTED-69_SAR439859 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-69_TCGACAAG


title: Time restricted feeding 03:00 Participant: 2

description:
Sample ID: RF141.R.T19
RESTRICT.txt
TRF T19 Participant: 2


title: HCC1428-LTED-68_SAR439859 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-68_CACGATTC


title: Time restricted feeding 23:00 Participant: 2

description:
Sample ID: RF141.R.T17
RESTRICT.txt
TRF T17 Participant: 2


title: HCC1428-LTED-76_GDC-0810 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-76_AGACCTTG


title: HCC1428-LTED-67_SAR439859 (300nM)

description:
novel selective estrogen degrader
HCC1428-LTED-67_TGAGCTGT


title: Unrestricted feeding 23:00 Participant: 2

description:
Sample ID: RF141.U.T17
RESTRICT.txt
URF T17 Participant: 2


title: Unrestricted feeding 07:00 Participant: 2

description:
Sample ID: RF141.U.T1
RESTRICT.txt
URF T1 Participant: 2


title: Time restricted feeding 19:00 Participant: 2

description:
Sample ID: RF141.R.T13
RESTRICT.txt
TRF T13 Participant: 2


title: HCC1428-LTED-65_SAR439859 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-65_GGATTCAC


title: Unrestricted feeding 19:00 Participant: 2

description:
Sample ID: RF141.U.T13
RESTRICT.txt
URF T13 Participant: 2


title: HCC1428-LTED-63_Fulvestrant (300nM)

description:
Standard of care, selective estrogen degrader
HCC1428-LTED-63_CTGATGAG

source_name: HCC1428-LTED_Fulvestrant (300nM)

value: Fulvestrant (300nM)


title: HCC1428-LTED-64_SAR439859 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-64_AGAAGGAC


title: Unrestricted feeding 11:00 Participant: 2

description:
Sample ID: RF141.U.T5
RESTRICT.txt
URF T5 Participant: 2


title: Unrestricted feeding 19:00 Participant: 1

description:
Sample ID: RF029.U.T13
RESTRICT.txt
URF T13 Participant: 1


title: Time restricted feeding 15:00 Participant: 1

description:
Sample ID: RF029.R.T9
RESTRICT.txt
TRF T9 Participant: 1


title: Unrestricted feeding 11:00 Participant: 1

description:
Sample ID: RF029.U.T5
RESTRICT.txt
URF T5 Participant: 1


title: HCC1428-LTED-61_Fulvestrant (300nM)

description:
Standard of care, selective estrogen degrader
HCC1428-LTED-61_TAGCAGGA


title: HCC1428-LTED-62_Fulvestrant (300nM)

description:
Standard of care, selective estrogen degrader
HCC1428-LTED-62_ACTGGTGT


title: Time restricted feeding 11:00 Participant: 1

description:
Sample ID: RF029.R.T5
RESTRICT.txt
TRF T5 Participant: 1


title: Unrestricted feeding 03:00 Participant: 2

description:
Sample ID: RF141.U.T19
RESTRICT.txt
URF T19 Participant: 2


title: Time restricted feeding 23:00 Participant: 1

description:
Sample ID: RF029.R.T17
RESTRICT.txt
TRF T17 Participant: 1


title: HCC1428-LTED-59_Fulvestrant (30nM)

description:
Standard of care, selective estrogen degrader
HCC1428-LTED-59_CAGGTTCA

source_name: HCC1428-LTED_Fulvestrant (30nM)

value: Fulvestrant (30nM)


title: HCC1428-LTED-78_GDC-0810 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-78_GCACACAA


title: Time restricted feeding 03:00 Participant: 1

description:
Sample ID: RF029.R.T19
RESTRICT.txt
TRF T19 Participant: 1


title: Unrestricted feeding 15:00 Participant: 1

description:
Sample ID: RF029.U.T9
RESTRICT.txt
URF T9 Participant: 1


title: HCC1428-LTED-58_Fulvestrant (30nM)

description:
Standard of care, selective estrogen degrader
HCC1428-LTED-58_TATCGCGA


title: RPE_Soy.3

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Cell isolation protocol: iPSC 377E is a human iPSCs line reprogrammed from skin biopsies and were maintained in feeder-free conditions in Essential 8 medium (ThermoFisher Scientific) and on human embryonic stem cell-qualified hESC qualified MatrigelTM (Corning) coated 6-well plates. Cells were passaged every 3-4 days using EDTA-based protocol.

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.44.0 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.8.0 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.28.1.
Genome_build: GRCm38.p6 with Ensembl v94

source_name: Homo sapiens iPSC derived RPE differentiated on Soy

extract_protocol:
RNA isolation using the RNeasy Mini Kit (Qiagen) was performed according to the manufacturer’s protocol. RNA integrity numbers were obtained using an Agilent Technologies, Inc. Bioanalyzer following the manufacturer’s protocol.
Strand-specific mRNA sequencing libraries were constructed from 100 ng of total RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: The protocols to differentiate iPSCs into RPEs were modified as follows. Once iPSC cultures reached 100% confluence, cells were placed in Essential 6 medium (ThermoFisher Scientific). After 48 hours, the cells were placed into neural induction media (NIM: DMEM/F12 (1:1), 1% N2 Supplement, 1x non-essential amino acids, 1% antibiotic-antimycotic (ThermoFisher Scientific), and 20 µg/ml heparin (MilliporeSigma)). The medium was changed every two days for up to 22 weeks. Cell patches with apparent RPE morphology and dark pigmentation were manually picked with tungsten needles, dissociated into single cells with 0.25% Trypsin/EDTA (ThermoFisher Scientific) exposure for five minutes and seeded on laminin (5µg/ml, rhLN521, BioLamina)-coated dishes at 200,000 cells per 1.12 cm2 in Retinal Differentiation Media (RDM: DMEM:F12 3:1, 2% B27 with vitamin A, 2mM Glutamax, 1% Antibiotic-antimycotic (ThermoFisher Scientific), and 10% FBS (Atlanta Biologics)) with 10 µM ROCK Inhibitor (RI), Y-27632 (Tocris), for the first 24 hours. FBS was removed once cell-cell junctions reappeared as assessed by visualization of epithelial-like hexagonal morphology and tight cellular packing under light microscopy (up to 1-1.5 weeks after seeding). After 5-25 weeks RPEs were trypsinized and seeded onto laminin-coated scaffolds at a density of 178,000 cells per cm2 in RDM with RI and 10% FBS. RI was removed after 24 hours. FBS was removed once cell-cell junctions reappeared at approximately 1-1.5 weeks. RPEs were cultured on scaffolds for 8 weeks and collected for processing. RPE differentiation studies were performed in triplicate from three separate cell stocks and with cells simultaneously plated onto laminin-coated chamber slides, Transwell™ only, electrospun soy scaffolds or PCL scaffolds seated and affixed to a Transwell™.

value: iPSC derived retinal pigment epithelium (RPE)

value: Soy


title: Time restricted feeding 19:00 Participant: 1

description:
Sample ID: RF029.R.T13
RESTRICT.txt
TRF T13 Participant: 1


title: Unrestricted feeding 23:00 Participant: 1

description:
Sample ID: RF029.U.T17
RESTRICT.txt
URF T17 Participant: 1


title: RPE_Soy.2


title: HCC1428-LTED-66_SAR439859 (30nM)

description:
novel selective estrogen degrader
HCC1428-LTED-66_CTCGAACA


title: RPE_Soy.1


title: Time restricted feeding 07:00 Participant: 1

description:
Sample ID: RF029.R.T1
RESTRICT.txt
TRF T1  Participant: 1


title: RPE_PCL.3

source_name: Homo sapiens iPSC derived RPE differentiated on PCL

value: PCL


title: RPE_PCL.1


title: RPE_PCL.2


title: RNA_P0_PSG_Dnmt3l_KO2

city: Vancouver

first: Kenjiro

last: Shirane

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

description:
RNA_P0_PSG_Dnmt3l_KO_2
strand-specific RNAseq

data_processing:
ChIP-seq: Reads were aligned to the mouse genome (mm10) using bwa (Li and Durbin 2009). PCR duplicates were removed by Picard-tools (http://broadinstitute.github.io/picard) and remaining reads with low mapping quality (MAPQ < 5) were excluded by Samtools (http://www.htslib.org/). Smoothed bigWig files were generated by deeptools (Ramírez et al., 2014) with BINSIZE=100 and SMOOTHLENGTH=1000 options.
WGBS: Reads with adaptor sequences at the 5’-end or low-quality bases at the 3’-end were trimmed by Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and the remaining reads were then aligned to the mouse genome (mm10) using Bismark (Krueger and Andrews 2011) with bowtie2 and pbat options (Langmead and Salzberg 2012). Reads that were not aligned with paired-end mode were then separately mapped to mm10 using single-end mode. bismark_methylation_extractor was used for extracting methylated and unmethylated counts of each CpG.
RNA-seq: Reads were aligned to the mouse genome (mm10) and transcripts using STAR (Dobin et al., 2013) with --sjdbGTFfile and --twopassMode Basic options.
Aligned reads were converted to bigWig format using bedtools (Quinlan et al., 2010) and bedGraphToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: p0 prospermatogonia

extract_protocol:
Testes were isolated and incubated at 37℃ for 5-8 minutes in 0.25% trypsin/0.5 mM EDTA/DNaseⅠ/PBS with serial pipetting to obtain single cell suspensions. After quenching the reaction with fetal bovine serum (FBS), cells were washed once with FACS buffer (2% FBS/1 mM EDTA/PBS), stained with Propidium Iodide (PI) and passed through a 35 μm cell strainer (Falcon). FACS was carried out on a BD Influx. Following removal of doublet/triplet cells, OCT3/4-EGFP+ (PI-) cells were sorted.
Total RNA extracted was from 2~3 K cells by using RNeasy micro kit (Qiagen) with on-column DNaseⅠ treatment. rRNA was depleted by NEBNext rRNA Depletion Kit (NEB) and cDNA was synthesized by NEBNext RNA First Strand Synthesis Module (NEB) and double-stranded using NEBNext UltraII Directional RNA Second Strand Synthesis Module (NEB). Following purification of double-stranded DNA by AMPure XP beads, library was constructed as described previously with modifications (Brind'Amour et al., 2015). Briefly, end repair and A-tailing were performed using NEBNext UltraII End Repair/dA-Tailing Module (NEB) and ligation was carried out using NEBNext Ultra II Ligation Module (NEB) with an in-house adaptor which is compatible with Illumina sequencers. After purification of adaptor-ligated products by AMPure XP beads, libraries were amplified with unique indexing primers for 12-14 cycles. Following purification of the amplified libraries by AMPure XP beads, libraries were pooled, run on 2% E-Gel EX Gel (ThermoFisher Scientific) and the fragments from 200-600 bp was excised and purified by Zymoclean Gel DNA Recovery Kit (Zymo Research).

tag: strain background

tag: developmental stage

value: postnatal day 0

tag: genotype/variation

value: Dnmt3l KO


title: RPE_Transwell.3

source_name: Homo sapiens iPSC derived RPE differentiated on Transwell

value: Transwell


title: HCC1428-LTED-60_Fulvestrant (30nM)

description:
Standard of care, selective estrogen degrader
HCC1428-LTED-60_CAAGAAGC

tag: cell line


title: RNA_P0_PSG_Dnmt3l_Control1

description:
RNA_P0_PSG_Dnmt3l_HET_1
strand-specific RNAseq

value: Dnmt3l HET


title: RNA_P0_PSG_Nsd1_KO2

description:
RNA_P0_PSG_Nsd1_KO_2
strand-specific RNAseq

value: Nsd1 KO


title: RNA_P0_PSG_Dnmt3l_KO1

description:
RNA_P0_PSG_Dnmt3l_KO_1
strand-specific RNAseq


title: RPE_Transwell.2


title: RPE_Transwell.1


title: RNA_P0_PSG_Dnmt3l_Control2

description:
RNA_P0_PSG_Dnmt3l_HET_2
strand-specific RNAseq


title: RPE_Chamber.2

source_name: Homo sapiens iPSC derived RPE differentiated on laminin-coated chamber slide

value: laminin-coated chamber slide


title: RPE_Chamber.3


title: RNA_P0_PSG_Nsd1_KO1

description:
RNA_P0_PSG_Nsd1_KO_1
strand-specific RNAseq


title: RNA_P0_PSG_Nsd1_Control1

description:
RNA_P0_PSG_Nsd1_HET_1
strand-specific RNAseq

value: Nsd1 HET


title: RPE_Chamber.1


title: RNA_P0_PSG_Nsd1_Control2

description:
RNA_P0_PSG_Nsd1_HET_2
strand-specific RNAseq


title: RNA_E16.5_PSG_Dnmt3l_KO2

description:
RNA_E16.5_PSG_Dnmt3l_KO_2
strand-specific RNAseq

source_name: e16.5 prospermatogonia

value: embryonic day 16.5


title: RNA_E16.5_PSG_Dnmt3l_KO1

description:
RNA_E16.5_PSG_Dnmt3l_KO_1
strand-specific RNAseq


title: Treg_aCD3-TNFR2_Donor3

city: Leiden

first: Mark

last: Mensink

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

description: Sample 18: 5076_24_64_sort_38_tTreg_aCD3-TNFR2_ATTCCTT

data_processing:
The 65 bp single end reads were mapped to the human reference genome (hg38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: peripheral blood

growth_protocol: Naïve Tconv and Treg cells were sorted from human buffy coats from male healthy donors (Sanquin) by flow cytometry. Human sorted Tconv and Treg cells were plated in 96-well round bottom plates (Greiner; 1x10^4 cells per well) and cultured in IMDM (Gibco, Life Technologies), supplemented with 8% FCS (Sigma), penicillin/streptomycin (Roche) and 300 IU/mL IL-2 (DuPont Medical) (T cell medium) at 37 °C/5% CO2. Activating mAbs to CD3 (clone CLB-T3/4.E, Sanquin, 0.1 µg/ml) and CD28 (clone CLB-CD28/1, Sanquin, 0.2 µg/ml,) were used for T cell expansion. From day 7 to 14, T cells (5x10^5 cells/mL) were plated in 24-well plates (Greiner). After 1 or 2 weeks of culture, Tconv and Treg cells (1 x 10^6 cells/mL) were cultured in 6-well plates (Corning) for 4 days in fresh T cell medium supplemented with 300 IU/mL IL-2, but without anti-CD3/CD28 mAbs. Dead cells were removed by Ficoll density gradient centrifugation prior to restimulation experiments.

extract_protocol:
Restimulated T cells were washed in cold PBS and resuspended in RLT buffer (Qiagen). Total RNA isolation was performed according to manufacturer’s protocol using the RNeasy MinElute Cleanup Kit (Qiagen) including an on-column DNAse digestion (Qiagen). Quality and quantity of the total RNA were assessed on a 2100 Bioanalyzer using a Nano chip (Agilent).
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0. Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Following the expansion protocol, 1x10^5 T cells were treated with anti-CD3, anti-CD3/CD28 or anti-CD3/TNFR2 (clone MR2-1, Hycult Biotech) agonistic mAbs for 24 hours, in the presence of IL-2, and were subsequently harvested for whole transcriptome analysis.

value: Regulatory CD4+ T cell

value: IL-2 and anti-CD3/TNFR2 agonistic mAbs

tag: individual


title: Treg_aCD3_Donor3

description: Sample 16: 5076_21_61_sort_38_tTreg_aCD3_CGTACGT

value: IL-2 and anti-CD3 agonistic mAb


title: Treg_aCD3-CD28_Donor3

description: Sample 17: 5076_22_62_sort_38_tTreg_aCD3-28_GAGTGGA

value: IL-2 and anti-CD3/CD28 agonistic mAbs


title: RNA_E16.5_PSG_Dnmt3l_Control2

description:
RNA_E16.5_PSG_Dnmt3l_HET_2
strand-specific RNAseq


title: RNA_E16.5_PSG_Dnmt3l_Control1

description:
RNA_E16.5_PSG_Dnmt3l_HET_1
strand-specific RNAseq


title: RNA_E16.5_PSG_Nsd1_KO2

description:
RNA_E16.5_PSG_Nsd1_KO_2
strand-specific RNAseq


title: RNA_E16.5_PSG_Nsd1_KO1

description:
RNA_E16.5_PSG_Nsd1_KO_1
strand-specific RNAseq


title: RNA_E16.5_PSG_Nsd1_Control2

description:
RNA_E16.5_PSG_Nsd1_HET_2
strand-specific RNAseq


title: Tconv_aCD3-CD28_Donor3

description: Sample 14: 5076_18_57_sort_38_Tconv_aCD3-28_GTGAAAC

value: Conventional CD4+ T cell


title: Tconv_aCD3-TNFR2_Donor3

description: Sample 15: 5076_20_59_sort_38_Tconv_aCD3-TNFR2_GTTTCGG


title: Tconv_aCD3_Donor3

description: Sample 13: 5076_17_56_sort_38_Tconv_aCD3_GTCCGCA


title: Treg_aCD3-TNFR2_Donor1

description: Sample 12: 5076_16_49_sort_29_tTreg_aCD3-TNFR2_CCGTCCC


title: RNA_E16.5_PSG_Nsd1_Control1

description:
RNA_E16.5_PSG_Nsd1_HET_1
strand-specific RNAseq


title: Treg_aCD3-CD28_Donor1

description: Sample 11: 5076_14_47_sort_29_tTreg_aCD3-28_AGTTCCG


title: Tconv_aCD3-TNFR2_Donor1

description: Sample 9: 5076_12_44_sort_29_Tconv_aCD3-TNFR2_CTTGTAA


title: H3K36me3_Setd2_KO_FGO

source_name: fully-grown oocyte

extract_protocol:
Ovaries were incubated in 2 mg/mL collagenaseA/0.2% trypsin/PBS at 37℃ for 10-20 minutes with serial pipetting and the same volume of M2 medium was added. Oocytes were then passed into 0.1% BSA/PBS and collected into drops of M2 medium. Oocytes with surrounding somatic cells were passed through several times into pulled glass capillaries to exclude somatic cells from oocytes and oocytes were collected in drops of M2 medium. Oocytes were then passed through 3-5 times into 0.1%BSA/PBS drops and collected.
ULI-N-ChIP-seq protocol (Brind'Amour et al., 2015) was used for generating ChIP-seq libraries with some modifications. Briefly, chromatin was fragmentated by MNase (NEB), diluted in native ChIP buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 150 mM NaCl; 0.1% Triton X-100) containing 1 mM PMSF and EDTA-free protease inhibitor cocktail (Roche) and sonicated 10 second sonication cycles for 3 times with low power (Bioruptor). Following pre-clearing of chromatin fragments with protein A and G beads (ThermoFisher Scientific) or Dynabeads M-280 Sheep anti-Mouse IgG beads (ThermoFisher Scientific), chromatin fragments were split and incubated with each of the histone methylation antibodies at 4 degree for overnight. Following purification of ChIPed DNA by AMPure XP beads, end repair and A-tailing were performed using NEBNext UltraII End Repair/dA-Tailing Module (NEB) and ligation was carried out using NEBNext Ultra II Ligation Module (NEB) with an in-house adaptor which is compatible with Illumina sequencers. After purification of adaptor-ligated products by AMPure XP beads, libraries were amplified with unique indexing primers for 12-14 cycles. Following purification of the amplified libraries by AMPure XP beads, libraries were pooled, run on 2% E-Gel EX Gel (ThermoFisher Scientific) and the fragments from 200-600 bp was excised and purified by Zymoclean Gel DNA Recovery Kit (Zymo Research).

value: 3-4-week old

value: Setd2 KO

tag: chip antibody

value: H3K36me3 (EpiCypher, SKU13-0031)


title: Input_Setd2_KO_FGO


title: Treg_aCD3_Donor1

description: Sample 10: 5076_13_46_sort_29_tTreg_aCD3_AGTCAAC

tag: cell type


title: Treg_aCD3-TNFR2_Donor2

description: Sample 6: 5076_8_34_sort_33B_tTreg_aCD3-TNFR2_ACTTGAA


title: Tconv_aCD3-CD28_Donor1

description: Sample 8: 5076_10_42_sort_29_Tconv_aCD3-28_TAGCTTA


title: Tconv_aCD3_Donor1

description: Sample 7: 5076_9_41_sort_29_Tconv_aCD3_GATCAGA


title: H3K36me3_WT_FGO

value: WT


title: H3K36me2_Setd2_KO_FGO

value: H3K36me2 (Cosmo Bio, MABI0332)


title: Input_WT_FGO


title: H3K36me2_WT_FGO


title: Treg_aCD3-CD28_Donor2

description: Sample 5: 5076_6_32_sort_33B_tTreg_aCD3-28_GCCAATA


title: H3K36me3_P12_GO

source_name: p12 growing oocyte

value: postnatal day 12


title: Tconv_aCD3-TNFR2_Donor2

description: Sample 3: 5076_4_29_sort_33B_Tconv_aCD3-TNFR2_TGACCAA


title: H3K36me2_P12_GO