title: RKO_shZNF280C_H3K27me3


title: RKO_shZNF280C_H3K4me1

status: Public on May 19 2022

type: SRA

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

country: China

institute: Shenzhen University

library_source: genomic

data_processing:
Raw reads were aligned to hg19 using bwa. The sam files were converted to bam with samtools.
MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage from Deeptools.

molecule: genomic DNA

organism: Homo sapiens

source_name: RKO colon cancer cells

growth_protocol: RKO cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 107 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 5-10 μg primary antibodies or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.
ChIP’s DNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. Fragments were amplified by PCR and PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit.

treatment_protocol: RKO colon cancer cells stably expressing a ZNF280C-targeting shRNA controlled by a tetracycline-inducible promoter were treated with or without 1 ug/ml doxycycline for 72 hours, and the cells were harvested for analysis as described below.

tag: cell type

value: RKO colon cancer cells

tag: shRNA

tag: antibody


title: RKO_shZNF280C_H3K27ac


title: RKO_shZNF280C-DOX_H3K4me3

tag: agent

value: doxycycline


title: RKO_shZNF280C-DOX_Rad21


title: Wild Type, E2, GRHL2, Rep 2 [WT_EG-2]

city: Madison

first: Elaine

last: Alarid

state: WI

address: 1111 Highland Avenue

department: McArdle Laboratory for Cancer Research, Department of Oncology and Carbone Comprehensive Cancer Center

country: USA

institute: University of Wisconsin - Madison

data_processing:
Quality control assessment of fastq files was performed using FASTQC. Adaptor trimming to remove Illumina adaptors was performed using Cutadapt through Trim Galore.
Reads were aligned to the hg38 genome with Bowtie2 using --local, and peaks were called with MACS2 using an FDR of 0.01 using the narrowPeak setting.
Bigwig files were generated using Deeptools bamCoverage.
Assembly: hg38
Supplementary files format and content: *.bed files are peaks called for each replicate
Supplementary files format and content: *bw files are for visualizing data for individual replicates in a genome browser

growth_protocol: MCF7 wild type and S118A knock-in cells were maintained in 10% CO2 at 37ᵒC with high-glucose (4.5 g/L) Dulbecco’s modified Eagles Medium (DMEM; Thermo Fisher, #11965092) supplemented with 10% HyClone fetal bovine serum (FBS; Cytiva, #SH30910.03), 100U/mL penicillin 100ug/mL streptomycin (1% Pen/Strep; Gibco, #15140-122), and 1mM sodium pyruvate (Gibco, #11360-070).

extract_protocol:
Cells were fixed for 10 minutes with 1.5% formaldehyde and quenched with 0.125M glycine. Nuclei were extracted from cell pellets and sonicated to shear DNA. DNA was immunoprecipitated using an anitbody against GRHL2 (Millipore Sigma, #HPA004820). DNA was purified after reverse-crosslinking using the Qiagen PCR purification kit (Qiagen, #28104).
Libraries were constructed using the NEBNext Ultra II DNA Library Prep kit (#E7103) and NEBNext Multiplex Oligos for Illumina (#E6440) according to vendor instructions. Samples were sequenced by paired-end 150bp sequencing on an Illumina NovaSeq 6000 by the Next Generation Sequencing department at the UW-Madison Biotechnology Center.

treatment_protocol: Cells were plated at a density of six million cells per 10cm plate with two plates per condition and were stripped of estrogens by culturing them for three days in phenol-red free DMEM supplemented with 10% charcoal stripped FBS (ssDMEM; Cytiva, #SH30910.03, stripped in-house), 100U/mL penicillin 100ug/mL streptomycin, 2mM L-glutamine (Thermo Fisher, #25030-081), and 1mM sodium pyruvate. Cells were treated with vehicle (0.1% EtOH) or 10nM 17β-estradiol (E2; Millipore Sigma #E2257) for 30 minutes.

tag: cell line

value: breast

tag: treatment

tag: chip antibody

tag: time

value: 30 min


title: RKO_shZNF280C-DOX_H3K27me3


title: Wild Type, E2, GRHL2, Rep 1 [WT_EG-1]


title: liver, Ctrl2

city: Nanjing

first: Zhenzhen

last: Sun

address: Guangzhou Road#72

institute: Children’s Hospital of Nanjing Medical University

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: txt file includes TPM, FPKM, Readcount values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Liver tissues were harvested and rapidly frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the instruction manual.
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 100 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).

tag: tissue

value: liver

value: Ten days after tamoxifen injection

tag: genotype

value: WT


title: RKO_shZNF280C-DOX_H3K4me1


title: RKO_shZNF280C-DOX_CTCF

value: CTCF


title: Wild-type-3

description: Expression_transgenic_matrix-FKPM_combined.txt

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on BGISEQ-500 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from MGISEQ-2000 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to generate the bam file of each sample from fastq with following parameters: -3 5 --local -x hg19 -U SE_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to identify the differentially expressed genes between groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each sample.

source_name: Wild-type mouse

extract_protocol:
Total RNA was extracted from  cells using Trizol reagent from Thermofisher according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: RKO colon cancer cells stably expressing a ZNF280C-targeting shRNA controlled by a tetracycline-inducible promoter were treated with or without 1 ug/ml doxycycline for 72 hours, and the cells were harvested for analysis as described below. For transgenic mice experiments, Zfp280c knock-out or wild-type C57BL/6J mice were sacrificed at 12 weeks of age and colon tissues were havested for transriptomic analysis as described below.

value: Wild-type


title: liver, Ctrl1


title: RKO_shZNF280C-DOX_input_rep1


title: RKO_shZNF280C-DOX_H3K27ac


title: RKO_shZNF280C_CTCF


title: RKO_shZNF280C_input_rep1


title: RKO_shZNF280C-DOX_input_rep2


title: Wild-type-2


title: S118A mut 2, Veh, GRHL2, Rep 1 [s118a-2_VG-1]

value: Veh


title: S118A mut 2, Veh, GRHL2, Rep 2 [s118a-2_VG-2]


title: S118A mut 2, E2, GRHL2, Rep 3 [s118a-2_EG-3]


title: ChIP_Input_CAKI-1_shKdm5b

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: Direct sequencing following sonication of x-linked chromatin

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

growth_protocol: NCI60 cancer cells were cultured in RPMI 1640 / 5% FBS media containing glutamine and pen/strep at 37oC with 5% CO2. Cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: cancer cell

tag: knockdown


title: RKO_shZNF280C_input_rep2


title: liver, Ctrl3


title: Wild-type-1


title: ChIP_Input_OVCAR-3_shKdm5b


title: S118A mut 2, E2, GRHL2, Rep 2 [s118a-2_EG-2]


title: Zfp280c knock-out-2

source_name: Zfp280c knock-out mouse

value: Zfp280c knock-out


title: S118A mut 1, Veh, GRHL2, Rep 3 [s118a-1_VG-3]


title: Zfp280c knock-out-3


title: S118A mut 2, E2, GRHL2, Rep 1 [s118a-2_EG-1]


title: ChIP_Input_OVCAR-4_shKdm5b


title: ChIP_Input_UACC-257_shKdm5b


title: ChIP_Input_A498_shKdm5b


title: S118A mut 2, Veh, GRHL2, Rep 3 [s118a-2_VG-3]


title: ChIP_Input_SK-MEL-5_shKdm5b


title: ChIP_Input_SK-MEL-28_shKdm5b


title: ChIP_Input_LOX_IMVI_shKdm5b


title: ChIP_Input_IGROV1_shKdm5b


title: ChIP_Input_UACC-62_shKdm5b


title: ChIP_Input_MALME-3M_shKdm5b


title: JTL670(fem-3)_EtOH_D1_48h_R3

city: Valhalla

first: Jian

last: Li

state: NY

address: 15 Dana Road

institute: New York Medical College

description:
TableS2_DE genes caused by HSF-1 depletion in soma.xlsx
edgeR_normcounts_glp1&fem3.tsv

data_processing:
RNA-seq reads were mapped to Ensembl WBcel235 genome using RNA STAR (Dobin et al., 2013) with --alignIntronMax 120000 to set the intron size, and --outFilterMultimapNmax 200 to allow multi-mapped reads. All paired-end reads were trimmed to 50 bp to make downstream mapping and analyses consistent.
The mapped reads were then subject to FeatureCounts in Rsubread (Liao et al., 2019) for quantification with the setting -p -B -P -C -M -O --fraction –largestOverlap. The settings in STAR and FeatureCounts enabled proper quantification of those heat shock genes (e.g. hsp-70 and hsp-16s) that are duplicated in C. elegans genome.
Differential expression (DE) analyses were then done using edgeR (Robinson et al., 2010) with default settings except of using Likelyhood Ratio Test and filtering out those lowly expressed genes with CPM (counts per million) value less than 1 in more than 75% samples. For each time point, to control for effects by auxin and by insertion of AID:GFP to HSF-1, we pooled EtOH treated CA1199 and EtOH treated JTL621 with auxin treated CA1199 to calculate the expression levels in control condition, and then compare them to auxin treated JTL621. This analysis reports only DE genes caused by HSF-1 depletion (as HSF-1 depletion vs. control).
Assembly: WS235/ce11
Supplementary files format and content: norm counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: young adults

growth_protocol: The HSF-1 AID animals in the wild-type background (JTL611) and the corresponding control animals that only express TIR1 in the soma (CA1200) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates (~500 worms per plate) at 20 °C for 51 hr to develop into young adults. The HSF-1 AID models in the longlived glp-1(e2141) temperature-sensitive mutant background (JTL667) and the control fem-3(q20) background (JTL670) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates at 25°C for 48 hr to develop into Day1 adults.

extract_protocol:
RNA was extracted using 300 uL Trizol reagent. Worms were vortexed continuously for 20 minutes at 4°C and then went through one cycle of freeze-thaw to help release RNA. Following this, RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) as per manufacturer’s instructions using on column DNase I digestion to remove genomic DNA.
Total RNAs were polyA enriched, and directional RNA-seq libraries were prepared using NEBNext Ultra II RNA library prep Kit.

treatment_protocol: For each condition, ~120 worms were transferred to either auxin or ethanol (EtOH) plates by picking, and kept for indicated time.

tag: tissue of tir1

value: soma

tag: strain

value: Auxin

tag: time point


title: JTL670(fem-3)_Auxin_D1_24h_R3

value: EtOH


title: ChIP_Input_K-562_shKdm5b


title: JTL670(fem-3)_Auxin_D1_48h_R3


title: ChIP_Input_CCRF-CEM_shKdm5b

source_name: CCRF-CEM

value: CCRF-CEM


title: S118A mut 1, Veh, GRHL2, Rep 1 [s118a-1_VG-1]


title: S118A mut 1, Veh, GRHL2, Rep 2 [s118a-1_VG-2]


title: ChIP_Input_HL-60_shKdm5b


title: S118A mut 1, E2, GRHL2, Rep 3 [s118a-1_EG-3]


title: ChIP_Input_NCI-H522_shKdm5b


title: S118A mut 1, E2, GRHL2, Rep 2 [s118a-1_EG-2]


title: Zfp280c knock-out-1


title: JTL670(fem-3)_EtOH_D1_24h_R3


title: ChIP_Input_NCI-H322M_shKdm5b


title: JTL670(fem-3)_Auxin_D1_8h_R3


title: ChIP_Input_NCI-H226_shKdm5b


title: ChIP_Input_HOP-92_shKdm5b


title: ChIP_Input_NCI-H23_shKdm5b


title: ChIP_Input_U251_shKdm5b


title: Input, WT Vehicle [Input]

description: Input

value: Input


title: ChIP_Input_EKVX_shKdm5b

source_name: EKVX

value: EKVX


title: JTL670(fem-3)_EtOH_D1_8h_R3


title: S118A mut 1, E2, GRHL2, Rep 1 [s118a-1_EG-1]


title: ChIP_Input_T-47D_shKdm5b


title: siGRHL2, Veh, GRHL2, Rep 3 [GV-G3]

data_processing:
library strategy: CUT&RUN
Quality control assessment of fastq files was performed using FASTQC. Adaptor trimming to remove Illumina adaptors was performed using Cutadapt through Trim Galore.
Reads were aligned to the hg38 genome using Bowtie2 using the --very-sensitive-local and --dovetail flags. Aligned fragments were filtered for a maximum fragment length of 120bp using alignmentSieve from Deeptools.
Bam files from replicates were merged using Samtools merge. Peaks were called with MACS2 using IgG as a control and an FDR cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: *bed files are from peaks called on bam files that were the result of merging all replicate bams for a given condition together
Supplementary files format and content: *bw files were created from bam files that were result of merging all replicate bams for a given condition together and can be used for visualization on a genome browser

growth_protocol: MCF7 cells were maintained in 10% CO2 at 37ᵒC with high-glucose (4.5 g/L) Dulbecco’s modified Eagles Medium (DMEM; Thermo Fisher, #11965092) supplemented with 10% HyClone fetal bovine serum (FBS; Cytiva, #SH30910.03), 100U/mL penicillin 100ug/mL streptomycin (1% Pen/Strep; Gibco, #15140-122), and 1mM sodium pyruvate (Gibco, #11360-070).

extract_protocol:
Following treatment, samples were processed for CUT&RUN using the CUTANA ChIC/CUT&RUN Kit (Epicypher, #14-1048; protocol from user manual version 2.0).
Library prep was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7103) and NEBNext Multiplex Oligos for Illumina (NEB, #E6440), with changes made to the protocol to improve the capture of smaller TF fragments: the inactivation temperature after end-repair was changed to 50°C for 1 hour, the bead size-selection ratio in the adaptor cleanup step was increased to 1.75x, and the bead size-selection ratio in the PCR cleanup step was increased to 1.2x. Samples were sequenced by paired-end 150bp sequencing on an Illumina NovaSeq 6000 by the Next Generation Sequencing department at the UW-Madison Biotechnology Center.

treatment_protocol: MCF7 cells were cultured in 10cm plates in for one day. On day two, cells were seeded at a density of 350,000 cell/well in 6 well plates in Pen/Strep free media and reverse transfected with 62.5pmol of either All Stars Negative control siRNA (siCtrl; Qiagen, #1027280) or siGRHL2 (Santa Cruz Biotechnology, #sc-77606) using 7µg of Lipofectamine 2000 (Thermo Fisher Scientific, #11668019). After 24 hours, the media was changed to the appropriate media containing Pen/Strep. The following day, cells were removed from the plates using brief trypsinization and assessed for viability using trypan blue (Gibco, #15250-061). 0.5 million viable cells were aliquoted into 1.5mL Eppendorf tubes and treated with E2 or vehicle for 30min while rotating at 37ᵒC.

value: GRHL2 (Millipore Sigma, #HPA004820)


title: siGRHL2, Veh, Santa Cruz pS118-ER, Rep 2 [GV-SC2]

value: breast

value: pS118-ER (Santa Cruz, #sc-12915)


title: ChIP_Input_MCF7_shKdm5b


title: siGRHL2, Veh, Santa Cruz pS118-ER, Rep 1 [GV-SC1]

value: 30 min


title: ChIP_Input_CAKI-1_shLuc_ctrl

value: shLuc


title: siGRHL2, Veh, GRHL2, Rep 2 [GV-G2]


title: JTL667(glp-1)_Auxin_D1_24h_R3


title: JTL667(glp-1)_EtOH_D1_48h_R3


title: siGRHL2, Veh, GRHL2, Rep 1 [GV-G1]


title: ChIP_Input_OVCAR-3_shLuc_ctrl


title: JTL667(glp-1)_Auxin_D1_8h_R3


title: ChIP_Input_OVCAR-4_shLuc_ctrl


title: ChIP_Input_SNB-75_shKdm5b


title: ChIP_Input_IGROV1_shLuc_ctrl


title: JTL667(glp-1)_Auxin_D1_48h_R3


title: ChIP_Input_SF-539_shKdm5b


title: ChIP_Input_UACC-62_shLuc_ctrl


title: siGRHL2, Veh, ER, Rep 3 [GV-ER3]

value: ER (Epicypher #13-2012)


title: JTL667(glp-1)_EtOH_D1_8h_R3


title: JTL670(fem-3)_Auxin_D1_48h_R2


title: ChIP_Input_A498_shLuc_ctrl


title: ChIP_Input_BT-549_shKdm5b


title: ChIP_Input_UACC-257_shLuc_ctrl


title: JTL667(glp-1)_EtOH_D1_24h_R3


title: siGRHL2, E2, Santa Cruz pS118-ER, Rep 2 [GE-SC2]


title: ChIP_Input_SK-MEL-28_shLuc_ctrl


title: siGRHL2, E2, Santa Cruz pS118-ER, Rep 1 [GE-SC1]


title: ChIP_Input_SK-MEL-5_shLuc_ctrl


title: JTL670(fem-3)_EtOH_D1_48h_R2


title: ChIP_Input_HL-60_shLuc_ctrl


title: ChIP_Input_CCRF-CEM_shLuc_ctrl


title: ChIP_Input_NCI-H522_shLuc_ctrl


title: ChIP_Input_MALME-3M_shLuc_ctrl


title: ChIP_Input_K-562_shLuc_ctrl


title: JTL670(fem-3)_EtOH_D1_24h_R2


title: ChIP_Input_NCI-H322M_shLuc_ctrl


title: siGRHL2, Veh, ER, Rep 1 [GV-ER1]


title: ChIP_Input_LOX_IMVI_shLuc_ctrl


title: siGRHL2, E2, GRHL2, Rep 2 [GE-G2]


title: siGRHL2, Veh, ER, Rep 2 [GV-ER2]


title: siGRHL2, E2, GRHL2, Rep 1 [GE-G1]


title: JTL670(fem-3)_Auxin_D1_8h_R2


title: ChIP_Input_EKVX_shLuc_ctrl


title: ChIP_Input_NCI-H23_shLuc_ctrl


title: JTL670(fem-3)_EtOH_D1_8h_R2


title: ChIP_Input_HOP-92_shLuc_ctrl


title: JTL667(glp-1)_EtOH_D1_48h_R2


title: siGRHL2, E2, ER, Rep 3 [GE-ER3]


title: ChIP_Input_U251_shLuc_ctrl


title: ChIP_Input_NCI-H226_shLuc_ctrl


title: JTL667(glp-1)_Auxin_D1_24h_R2


title: JTL670(fem-3)_Auxin_D1_24h_R2


title: ChIP_Input_SNB-75_shLuc_ctrl


title: ChIP_Input_SF-539_shLuc_ctrl


title: siGRHL2, E2, ER, Rep 2 [GE-ER2]


title: ChIP_Input_MCF7_shLuc_ctrl


title: ChIP_Input_T-47D_shLuc_ctrl


title: siGRHL2, E2, ER, Rep 1 [GE-ER1]


title: ChIP_Input_BT-549_shLuc_ctrl


title: siGRHL2, E2, GRHL2, Rep 3 [GE-G3]


title: JTL667(glp-1)_EtOH_D1_24h_R2


title: siCtrl, E2, Santa Cruz pS118-ER, Rep 2 [CV-SC2]


title: JTL667(glp-1)_Auxin_D1_8h_R2


title: H3K4me3_CAKI-1_shKdm5b_rep1

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: JTL667(glp-1)_EtOH_D1_8h_R2


title: H3K4me3_CAKI-1_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_A498_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_A498_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL670(fem-3)_Auxin_D1_48h_R1


title: siCtrl, E2, Santa Cruz pS118-ER, Rep 1 [CV-SC1]


title: H3K4me3_OVCAR-4_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_OVCAR-3_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: JTL670(fem-3)_EtOH_D1_48h_R1


title: H3K4me3_OVCAR-3_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL670(fem-3)_Auxin_D1_24h_R1


title: JTL670(fem-3)_EtOH_D1_24h_R1


title: siCtrl, Veh, IgG, Rep 1 [CV-IgG1]

value: IgG (Epicypher, #13-0042)


title: H3K4me3_UACC-62_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_IGROV1_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_IGROV1_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: JTL670(fem-3)_Auxin_D1_8h_R1


title: siCtrl, Veh, H3K4me3, Rep 3 [CV-H3]

value: Veh


title: siCtrl, Veh, H3K4me3, Rep 2 [CV-H2]


title: H3K4me3_UACC-257_shKdm5b_rep2

description: Chromatin IP against H3K4me3

value: cancer cell


title: H3K4me3_UACC-257_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: siCtrl, Veh, H3K4me3, Rep 1 [CV-H1]


title: JTL670(fem-3)_EtOH_D1_8h_R1


title: H3K4me3_SK-MEL-5_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_SK-MEL-5_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: siCtrl, Veh, IgG, Rep 3 [CV-IgG3]


title: siCtrl, Veh, GRHL2, Rep 3 [CV-G3]


title: H3K4me3_OVCAR-4_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL667(glp-1)_Auxin_D1_48h_R1


title: H3K4me3_MALME-3M_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: siCtrl, Veh, IgG, Rep 2 [CV-IgG2]


title: H3K4me3_SK-MEL-28_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: JTL667(glp-1)_EtOH_D1_48h_R1


title: H3K4me3_SK-MEL-28_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: siCtrl, Veh, GRHL2, Rep 2 [CV-G2]


title: H3K4me3_MALME-3M_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_UACC-62_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_LOX_IMVI_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL667(glp-1)_Auxin_D1_24h_R1


title: H3K4me3_K-562_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_K-562_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_LOX_IMVI_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: JTL667(glp-1)_EtOH_D1_24h_R1


title: JTL667(glp-1)_Auxin_D1_8h_R1


title: H3K4me3_HL-60_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL667(glp-1)_EtOH_D1_8h_R1


title: siCtrl, Veh, ER, Rep 2 [CV-ER2]


title: H3K4me3_CCRF-CEM_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_CCRF-CEM_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: siCtrl, Veh, ER, Rep 1 [CV-ER1]


title: JTL611 Auxin NHS 24 h_R3

description:
TableS2_DE genes caused by HSF-1 depletion in soma.xlsx
edgeR_normcounts_24h_CA1200&JTL611.tsv


title: JTL611 EtOH NHS 24h_R3


title: H3K4me3_NCI-H522_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: siCtrl, E2, Santa Cruz pS118-ER, Rep 1 [CE-SC1]


title: H3K4me3_NCI-H322M_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_NCI-H322M_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: siCtrl, E2, Santa Cruz pS118-ER, Rep 2 [CE-SC2]


title: H3K4me3_NCI-H23_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: CA1200 Auxin NHS 24h_R3

description:
TableS1_DE genes caused by auxin.xlsx
edgeR_normcounts_24h_CA1200&JTL611.tsv


title: H3K4me3_NCI-H522_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: siCtrl, Veh, ER, Rep 3 [CV-ER3]


title: siCtrl, E2, GRHL2, Rep 3 [CE-G3]


title: siCtrl, Veh, GRHL2, Rep 1 [CV-G1]


title: CA1200 EtOH NHS 24 h_R3


title: H3K4me3_NCI-H226_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_HL-60_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: siCtrl, E2, GRHL2, Rep 2 [CE-G2]


title: H3K4me3_NCI-H226_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL611 Auxin NHS 8h_R3

description:
TableS2_DE genes caused by HSF-1 depletion in soma.xlsx
edgeR_normcounts_8hr_CA1200&JTL611.tsv


title: H3K4me3_HOP-92_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_HOP-92_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: siCtrl, E2, GRHL2, Rep 1 [CE-G1]


title: JTL611 EtOH NHS 8h_R3


title: H3K4me3_EKVX_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: siCtrl, E2, ER, Rep 3 [CE-ER3]


title: siCtrl, E2, ER, Rep 2 [CE-ER2]


title: H3K4me3_U251_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_EKVX_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_NCI-H23_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: CA1200 EtOH NHS 8h_R3

description:
TableS1_DE genes caused by auxin.xlsx
edgeR_normcounts_8hr_CA1200&JTL611.tsv


title: H3K4me3_U251_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: H3K4me3_SNB-75_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL611 Auxin NHS 24 h_R2


title: H3K4me3_SF-539_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: JTL611 EtOH NHS 24h_R2


title: UCLA1, D4 PGCLC aggregate cells

city: Los Angeles

first: Tsotne

last: Chitiashvili

state: CA

address: 615 Charles E Young Dr S

institute: University of California - Los Angeles

data_processing:
scRNA-seq reads were aligned to human hg38 genome assembly using 10X Genomics Cell ranger v3.4. Expression matrixes generated by Cell Ranger were imported to Scanpy or Seurat for downstream analysis. All gene that were expressed in less than 5 cells were discarded and cells with less than 250 detected genes were filtered out. Data was scaled by detected number of UMIs and mitochondrial gene percentage. Cells were clustered by Louvain algorithm and UMAP package was used to visualize cells in 2D plot.
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Differentiated cells

extract_protocol: scRNA-seq libraries were generated immediately after tissue dissociation using 10X Genomics Chromium instrument and Chromium single cell 3’ reagent kit V3. Each individual run was designed to target 10000 cells per library. Libraries were generated according to manufacturer’s instructions and library fragment size distribution was determined by BioAnalyzer instrument. Afterwards libraries were pulled together and sequenced on Illumina Novaseq 6000 platform, at average depth of 200-300 million reads per sample.

treatment_protocol: Fetal tissues were processed 24-48 hours after the termination. Upon arrival, tissues were gently washed with PBS and placed in dissociation buffer. Dissociation buffer consisted of Collagenase IV 10mg/ml (Life Technologies #17104-019), Dispase II 250 ug/ml (Life Technologies #17105041), DNAseI 1:1000 (Sigma 4716728001), 10% FBS (Life technologies 10099141) diluted in PBS. Tissues were dissociated for 15 minutes at 370C. After every 5 minutes tissues were pipetted against the bottom of Eppendorf tube. Cells were centrifuged for 5 minutes at 500g and resuspended in PBS+0.04% BSA. Cells were strained through 40mincron strainer. Afterwards cells were stained with FGFR3 antibody and DAPI. Sorted for DAPI negative FGFR3 positive cells. Sorted cells from week 8 and week 13 ovaries were mixed at 1:3 ratio accordingly and cell concentration was adjusted to 800-1200 cells per microliter and immediately used for scRNA-seq.

tag: age

value: Day 4

value: PGCLC aggregate cells

tag: cell source

value: differentiated from UCLA1 human embryonic stem cells


title: CA1200 Auxin NHS 24h_R2

value: soma

value: Auxin


title: H3K4me3_T-47D_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_SF-539_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: siCtrl, E2, ER, Rep 1 [CE-ER1]


title: H3K4me3_T-47D_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: RE_CAKI-1_shLuc_ctrl

description: RNA-Seq

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The rpkm.txt measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

growth_protocol: Cancer cells were cultured in RPMI 1640 / 5% FBS media containing glutamine and pen/strep at 37oC with 5% CO2. Cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
RNA was harvest using RNeasy Qiagen kits.
Library preparation was performed using a New England Biolabs NEBNext Ultra II RNA Library Prep Kit for Illumina.


title: H3K4me3_MCF7_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: CA1200 EtOH NHS 24 h_R2

value: EtOH


title: FGFR3 sorted ovarian cells

source_name: Prenatal Gonads

value: Week 8 and Week 13

value: prenatal ovaries

value: FGFR3 sorted ovarian cells


title: H3K4me3_BT-549_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_BT-549_shKdm5b_rep1

description: Chromatin IP against H3K4me3


title: RE_CAKI-1_shKdm5b

description: RNA-Seq


title: H3K4me3_MCF7_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: JTL611 Auxin NHS 8h_R2


title: RE_A498_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_CAKI-1_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: RE_A498_shKdm5b

description: RNA-Seq


title: H3K4me3_CAKI-1_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: JTL611 EtOH NHS 8h_R2


title: H3K4me3_A498_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_SNB-75_shKdm5b_rep2

description: Chromatin IP against H3K4me3


title: CA1200 Auxin NHS 8h_R2


title: H3K4me3_A498_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: OV_OVCAR-4_shLuc_ctrl

description: RNA-Seq


title: CA1200 EtOH NHS 8h_R2


title: H3K4me3_OVCAR-4_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_OVCAR-4_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: JTL611 EtOH NHS 24h_R1


title: OV_OVCAR-3_shKdm5b

description: RNA-Seq


title: H3K4me3_OVCAR-3_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: JTL611 Auxin NHS 24 h_R1


title: H3K4me3_OVCAR-3_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: NCI/ADR-RES


title: OV_IGROV1_shLuc_ctrl

description: RNA-Seq


title: OV_OVCAR-3_shLuc_ctrl

description: RNA-Seq


title: CA1200 Auxin NHS 24h_R1


title: CA1200 EtOH NHS 24 h_R1


title: H3K4me3_IGROV1_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Probiotic curative treatment (biol rep 3)

city: Tours

first: Cyril

last: Poupet

address: 31 avenue Monge

department: Faculty of pharmacy

country: France

institute: University of Tours

data_processing:
The quality scores across all bases of all reads and the N (non-attributed bases) content across all bases were determined for each condition with the FastQC software from the Babraham Institute.
The research of contaminants is carried out using FastQ Screen.
The reads were aligned on reference genome using Bowtie2 software (C. elegans (WBcel235, UCSC)). Reads which did not aligned on C. elegans genome were excluded from further analysis.
Retained reads were counted using featureCounts software (version 1.6.4) and analysis of differential expression was achieved by the package DESeq2. Gene expression changes with adjusted p-value of less than 0.05 were declared differentially expressed and considered for further analysis.
Assembly: C. elegans WBcel235 (UCSC)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: whole organism

growth_protocol: Wild-type worms were synchronized using the bleach / NaOH methods. L1 larvae were allowed to grow on E. coli OP50 lawn for 48 hours at 20°C (until they reached L4 / young adult stage)

extract_protocol:
Cell walls were disrupted using glass beads and a Precellys device. Total RNA was extracted using the TRIzol reagent and chloroform method. Any DNA present in the samples was removed using the DNase treatment and removal kit.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Preparation Kit following manufacturer's protocols.

treatment_protocol: Worms were put in presence of E. coli OP50, L. rhamnosus Lcr35 or C. albicans only during 4 hours. For the preventive treatment, worms were firstly fed on E. coli OP50 or Lcr35 for 4 hours then infected with C. albicans for 2 hours. For the curative treatment, worms were firstly infected with C. albicans for 2 hours then fed on E. coli OP50 or Lcr35 for 4 hours.

value: whole organism

value: C. elegans + C. albicans ATCC 10231 (2h) then L. rhamnosus Lcr35 (4h)


title: Curative treatment control condition (biol rep 4)

value: C. elegans + C. albicans ATCC 10231 (2h) then E. coli OP50 (4h)


title: H3K4me3_IGROV1_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)

value: shLuc


title: Probiotic curative treatment (biol rep 2)


title: Probiotic curative treatment (biol rep 1)


title: Curative treatment control condition (biol rep 3)


title: OV_IGROV1_shKdm5b

description: RNA-Seq


title: Curative treatment control condition (biol rep 1)


title: JTL611 EtOH NHS 8h_R1


title: JTL611 Auxin NHS 8h_R1


title: ME_UACC-62_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_UACC-62_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Probiotic preventive treatment (biol rep 4)

value: C. elegans + L. rhamnosus Lcr35 (4h) then C. albicans ATCC 10231 (2h)


title: OV_OVCAR-4_shKdm5b

description: RNA-Seq

value: cancer cell


title: ME_UACC-62_shKdm5b

description: RNA-Seq


title: H3K4me3_UACC-62_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: Probiotic preventive treatment (biol rep 3)


title: ME_UACC-257_shLuc_ctrl

description: RNA-Seq


title: Curative treatment control condition (biol rep 2)


title: H3K4me3_UACC-257_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: CA1200 EtOH NHS 8h_R1


title: ME_UACC-257_shKdm5b

description: RNA-Seq


title: H3K4me3_UACC-257_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: Probiotic preventive treatment (biol rep 2)


title: Probiotic preventive treatment (biol rep 1)


title: ME_SK-MEL-5_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_SK-MEL-5_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Preventive treatment control condition (biol rep 4)

value: C. elegans + E. coli OP50 (4h) then C. albicans ATCC 10231 (2h)


title: Preventive treatment control condition (biol rep 2)


title: Preventive treatment control condition (biol rep 3)


title: ME_SK-MEL-28_shLuc_ctrl

description: RNA-Seq


title: ME_SK-MEL-28_shKdm5b

description: RNA-Seq


title: ME_SK-MEL-5_shKdm5b

description: RNA-Seq


title: dCas9::VP64 replicate 3

city: Berlin

first: Michael

last: Ristow

state: CH

address: Charitéplatz 1

department: Inst. Exp. Endocrinology

country: Germany

institute: Charite Berlin

description:
dCas9::VP64
Library: Illumina Truseq Nano

data_processing:
data analysis framework used: SUSHI
quality controlled reads aligned to reference genome Ensembl WBcel235 using the STAR aligner
expression counts were computed using featureCounts in the 458 Bioconductor package Subread
differential expression analysis was performed using edgeR
NA
Assembly: Ensembl WBcel235 (GCF_000002985.6)
Supplementary files format and content: One Excel table (.xlsx),containing FPKMs, normalized counts and additional information for all samples

source_name: Whole nematodes

growth_protocol: Adult nematodes (wild-type N2 or dCas9::VP64) were allowed to lay eggs for four to nine hours and the resulting eggs incubated for 64 h at 20 °C on NGM agar plates inoculated with E. coli OP50 bacteria to obtain a synchronized population of young adult nematodes. The resulting synchronized populations were incubated for an additional 48 h at 20 °C with continuous supply of HT115 scrambled bacteria as a food source.

extract_protocol:
For C. elegans total RNA isolation, nematodes collected from synchronized plates were washed three times with ice-cold S-Buffer and flash-frozen in liquid nitrogen. Afterwards, 500 µl ice-cold TRI Reagent (Molecular Research Center, #TR118) was added to the ground pellet. RNA was extracted based on the phenol-chloroform extraction method. Concentration of the resulting RNA was measured with an LVis plate on a CLARIOstar microplate reader (BMG LABTECH) and stored at -80 °C until further use.
Illumina Truseq Nano

treatment_protocol: All nematodes were fed HT115 scrambled bacteria starting from the first day of adulthood

value: Whole nematodes

value: HT115 scrambled


title: Wild-type N2 replicate 3

description:
Wild-type N2 (Bristol)
Library: Illumina Truseq Nano

value: Wild-type N2 (Bristol)


title: H3K4me3_SK-MEL-28_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: LOX IMVI


title: dCas9::VP64 replicate 2


title: CA1200 Auxin NHS 8h_R1

value: soma

value: Auxin


title: dCas9::VP64 replicate 1


title: Preventive treatment control condition (biol rep 1)


title: H3K4me3_MALME-3M_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3

value: SR


title: ME_MALME-3M_shLuc_ctrl

description: RNA-Seq


title: Wild-type N2 replicate 1


title: Pathogen control condition (biol rep 3)

value: C. elegans + C. albicans ATCC10231 (4h)


title: replicate 2, scRNAseq

city: Bar Harbor

first: Gregory

middle: W.

last: Carter

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description: 10x Genomics v3 3' Gene Expression

data_processing:
FASTQ files for all samples were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v1.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For all single cell samples,  R1 contains a 98bp biological read. For all samples, R2 contains a 14bp cell barcode and R3 contains 10bp UMI barcode.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format. Rows correspond to genes in the order provided in genes.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

source_name: RPE cells

extract_protocol:
Mice at P36 were sacrificed by asphyxiation with carbon dioxide and cervical dislocation. Eyes were enucleated and placed immediately in a dish of 1x phosphate-buffered saline (PBS) on wet ice. Eyes were punctured below the limbus with a 20 g needle, gripped at the cornea with straight forceps, and cut circumferentially below the limbus with angled Vannas microdissection scissors. After removing the cornea, iris, and lens, and trimming the optic nerve flush with the sclera, the retina was immediately peeled from the posterior eyecup. The peeled eyecup was then placed in 1.0 ml prewarmed 0.5% trypsin-EDTA (Thermofisher, 15400-054) and incubated for 30 min at 37 ˚C under an atmosphere containing 5% CO2. Following incubation, the interior of the eyecup was grasped at the optic nerve with forceps and the entire eyecup was drawn out of the solution and resubmerged repeatedly to release RPE sheets. When no additional sheets were released, the remaining tissue containing the choroid and sclera was discarded. The solutions containing RPE sheets from both eyes were pooled with 8.0 ml of ice-cold collection buffer in a gentleMACS C tube (Miltenyi Biotec, Bergisch Gladbach, North Rhine-Westphalia, Germany) and disrupted using protocol C of a gentleMACS Dissociator (Miltenyi Biotec). Samples were centrifuged at 300g for 10 min at 4 ˚C and resuspended by triturating the pellet in 250 µl DMEM (Thermo Fisher Scientific, 11054-020) containing 2% fetal bovine serum, 2 mM EDTA. Calcium-AM (0.63 µl) was added from a 40 µM working stock and samples were incubated for 15 min. Cells negative for DAPI and positive for calcein-AM staining were sorted into DMEM contain 20% fetal bovine serum, 1x N1 medium supplement (Sigma N6530-5BL), 1x MEM non-essential amino acids (Thermo Fisher Scientific, 11140050), 2 mM GlutaMAX-I (Thermo Fisher Scientific, A128601), 0.25 mg/ml taurine (Millipore Sigma T0625), 20 ng/ml hydrocortisone (Millipore Sigma, H0396), and 13 ng/ml triiodothyronine (Millipore Sigma, T5516) using a 100 µm nozzle on a FACSAria II cell sorter (BD Biosciences, San Jose, CA, USA). Collected samples were centrifuged at 300g for 10 min at 4 ˚C and resuspended in 0.04% bovine serum albumin.
A volume of the suspension containing 8,000–12,000 cells was loaded in a single channel of a Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA, USA) and barcoded cDNA libraries were prepared using a Chromium Single Cell 3’ Chip Kit v2 (10x Genomics) according to the manufacturer’s protocol. Amplified cDNA from each channel was used to construct a sequencing library (Illumina, San Diego, CA, USA). cDNA and libraries were checked for quality on a 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and quantified by KAPA qPCR. Sequencing was performed on an NextSeq500 System (Illumina, San Diego, CA, USA) using 150-cycle sequencing to an average depth of 50,000 reads per cell.

value: RPE cells

tag: Sex

value: male

value: 4-5 weeks old


title: H3K4me3_MALME-3M_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

tag: cell type


title: Wild-type N2 replicate 2


title: ME_MALME-3M_shKdm5b

description: RNA-Seq


title: H3K4me3_SK-MEL-5_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: ME_LOX_IMVI_shKdm5b

description: RNA-Seq


title: ME_LOX_IMVI_shLuc_ctrl

description: RNA-Seq


title: replicate 1, scRNAseq

description: 10x Genomics v3 3' Gene Expression


title: Pathogen control condition (biol rep 1)

value: whole organism


title: Pathogen control condition (biol rep 2)


title: H3K4me3_SK-MEL-28_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: H3K4me3_LOX_IMVI_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: shLuc


title: H3K4me3_LOX_IMVI_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Probiotic control condition (biol rep 3)

value: C. elegans + L. rhamnosus Lcr35 (4h)


title: LE_K-562_shLuc_ctrl

description: RNA-Seq

value: cancer cell


title: H3K4me3_K-562_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Probiotic control condition (biol rep 2)


title: LE_K-562_shKdm5b

description: RNA-Seq


title: H3K4me3_K-562_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: CCRF-CEM


title: Probiotic control condition (biol rep 1)


title: LE_HL-60_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_HL-60_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Colon, SZN1326p_48hr, replicate 1, scRNA-seq

city: South San Francisco

first: Russell

last: Fletcher

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina read data was processed (demultiplexing, barcoded processing, gene counting and aggregation) using the 10x Genomics Cellranger (version 3.0.2) pipeline on the mm10-3.0.0 version of the mouse transcriptome.
Assembly: mm10
log2 normalized counts matrix as tab delimited text file
batch, experimental condition, cell type data in tab delimited text file

source_name: transverse colon

growth_protocol: Mice were obtained from Jackson Laboratories (Bar Harbor, ME, USA). All animal experimentation was in accordance with the ‘‘Guide for the Care and Use of Laboratory Animals’’ prepared by the National Academy of Sciences. Protocols for animal experimentation were approved by the Surrozen Institutional Animal Care and Use Committee. 7-week-old C57Bl/6J female mice were acclimatized 4-5 per cage a minimum of two days prior to the experiment. Mice were kept 12/12-hour light/dark cycle in a 30% to 70% humidity environment and room temperature ranging from 20°C to 26°C.

extract_protocol:
Transverse colon was isolated from each animal and feces were removed. After a brief wash in cold PBS, the colon was cut longitudinally, and the tissue was cut into 3-4 mm length fragments. Tissue fragments were incubated in pre-warmed (37 °C) PBS with 5 mM EDTA in a shaker at 37 °C at 150 rpm for 15 minutes. After 15 minutes, the tubes containing the samples were vigorously shaken for 10 seconds to release more epithelial cells. The epithelial cells floating in suspension were removed to a new tube and centrifuged at 200 rcf for two minutes. The residual tissue containing the remaining epithelia and stroma/lamina propria was then incubated in 8-12.5 mL of lamina propria dissociation buffer (AdvDMEM/F12 with 10 mM HEPES, 0.2 % FBS, DNAse1 (80 U/mL), Liberase TM (0.2 mg/mL), and 1 % antibiotic/antimycotic) at 37 °C for 30 minutes with horizontal shaking at 150 rpm. After pelleting, the epithelial cells were resuspended in 1 mL of TrypLE with DNase1, incubated at 37 °C for five minutes, and then triturated with a P1000 pipette for 30 seconds. After trituration, 10 mL of PBS plus 50 U/mL DNAse1 were added to the epithelial cells, and they were centrifuged at 500 rcf, 4 °C, and the supernatant was removed. Epithelial cells were then washed one time in FACS buffer (HBSS, 2% FBS, 10 mM HEPES, 1 mM sodium pyruvate, and 1% Pen-strep or antibiotic/antimycotic solution) before another round of centrifugation and final resuspension in 0.5 mL of FACS buffer. Following 30 minutes of dissociation in LP dissociation buffer, the remaining tissue fragments and suspension were centrifuged at 500 rcf for five minutes. Supernatant was removed down to 1 mL, and the sample was triturated with a P1000 until the solution was homogeneous and all tissue fragments had dissociated. After trituration, the sample was centrifuged at 500 rcf for 5 minutes at 4 °C and washed in FACS buffer prior to resuspension in 1 mL of FACS buffer in preparation for FACS. All cells were passed through a 40-micron filter prior to FACS. DAPI was used to assess viability, and only DAPI-negative cells were collected. Cells were collected from the epithelial fraction and then from the epithelial/lamina propria fraction and combined (1:5 ratio) and counted on a hemocytometer prior to cell capture.
Standard 10x Genomics Chromium 3’ v3 scRNA-seq reagents (PN1000075) were used. Approximately 4000-4500 cells were loaded per channel. Cells from one animal replicate were captured per channel. Standard 10x Genomics Chromium 3’ v3 scRNA-seq RT, cDNA amplification, and sequencing library preparation protocols were followed. Multiplexed sequencing libraries were sequenced on Illumina Nova Seq 6000 S1 lanes, averaging about 50,000 reads per cell.

treatment_protocol: For the acute DSS model, mice were treated with 4% DSS in their drinking water throughout the duration of the experiment. DSS-treated animals were dosed with 10 mg/kg SZN-1326-p or an anti-GFP antibody on day 4 of the DSS treatment. On day 5 and 6, we collected cells from two uninjured mice and from three replicates each for anti-GFP and SZN-1326-p-treated DSS animals. Each animal was considered a replicate.

value: transverse colon

value: colon cells


title: Colon, SZN1326p_48hr, replicate 2, scRNA-seq

description: 10x Genomics


title: Negative control condition (biol rep 2)

value: C. elegans + E. coli OP50 (4h)


title: Colon, anti-GFP_48hr, replicate 3, scRNA-seq

description: 10x Genomics


title: Negative control condition (biol rep 1)


title: H3K4me3_HL-60_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: Colon, anti-GFP_48hr, replicate 2, scRNA-seq

description: 10x Genomics


title: H3K4me3_CCRF-CEM_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: LE_CCRF-CEM_shLuc_ctrl

description: RNA-Seq


title: Colon, SZN1326p_48hr, replicate 3, scRNA-seq

description: 10x Genomics


title: shRNA CDAN1 (codanin-1) rep2

city: New Haven

first: Gary

last: Kupfer

address: 333 Cedar St

institute: Yale

data_processing:
The reads from the sequencer were trimmed for quality and aligned with the hg19 reference genome using TopHat2.
The aligned reads were processed with hg19 reference anotation from UCSC with cuffdiff to generate the expression abundance estimates and differential gene expression information.
The cuffdiff outputs were processed with cummeRbund in R to generate visualizations of the data.
Genome_build: hg19 UCSC
Supplementary_files_format_and_content: FPKM table with FPKM values for each of the samples.

source_name: peripheral blood

growth_protocol: Mobilized adult peripheral blood CD34+ cells were cultured in a 4-phase culture system (expansion and erythroid differentiation I, II, and III) over 21 days at 37°C in 5% CO2. Experiments were performed using cells from different donors.

extract_protocol:
Total RNA was isolated on day 12 of the erythroid culture using with TRIzol (Invitrogen) or the RNeasy kit (QIAGEN). DNA contamination was removed with DNase I treatment (Roche). RNA concentration and purity (A260/A280 above 1.8) were assessed using a Nanodrop ND-8000 spectrophotometer (NanoDrop Technologies).
RNA libraries were prepared for sequencing using the high-throughput Illumina platform at the Yale Center for Genome Analysis.

treatment_protocol: Knockdown of codanin-1 was achieved by viral transduction with pLKO.1-puro-CMV-TagRFP shRNA lentiviral vector targeting 2 different regions of CDAN1 (shRNA CDAN1) or non-targeting (shRNA Control) as a control. Cells were expanded for 24 hours and then mixed with viral supernatant and 4 μg/ml polybrene (Sigma-Aldrich) and spun at 1,800 rpm for 90 minutes at 37°C. After 72 hours, TagRFP+ cells were sorted by FACS and returned to culture.

value: hematopoietic stem cells

tag: day of erythroid induction (21 days in total)

tag: genotype/variation

value: CDAN1 (codanin-1) knockdown


title: Colon, anti-GFP_48hr, replicate 1, scRNA-seq

description: 10x Genomics


title: Colon, Uninjured_48hr, replicate 2, scRNAseq

description: 10x Genomics


title: H3K4me3_CCRF-CEM_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: shRNA CDAN1 (codanin-1) rep1


title: H3K4me3_NCI-H522_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Colon, Uninjured_48hr, replicate 1, scRNAseq

description: 10x Genomics


title: LC_NCI-H522_shLuc_ctrl

description: RNA-Seq


title: LE_CCRF-CEM_shKdm5b

description: RNA-Seq


title: shRNA Control

value: control


title: LC_NCI-H522_shKdm5b

description: RNA-Seq


title: H3K4me3_NCI-H522_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: Colon, SZN1326p_24hr, replicate 3, scRNA-seq

description: 10x Genomics


title: LC_NCI-H322M_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_NCI-H322M_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: LE_HL-60_shKdm5b

description: RNA-Seq


title: Colon, SZN1326p_24hr, replicate 2, scRNA-seq

description: 10x Genomics


title: Colon, SZN1326p_24hr, replicate 1, scRNA-seq

description: 10x Genomics


title: LC_NCI-H322M_shKdm5b

description: RNA-Seq


title: GATA1 ChIP-Seq

data_processing:
The reads were trimmed for length and quality using custom scripts.
bwa mem was used to align the trimmed reads to the hg19 (UCSC reference) version of the reference genome.
The MACS2 algorithm was used on the aligned files to generate peaks.
For both GATA, and GK1 the same IgG was used as control.
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak file generated by MACS2

growth_protocol: K562 cells were cultured in RPMI1640, 10% FBS, and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
30 million K562 cells per sample were cross-linked for 10 minutes at room temperature with 1% formaldehyde. Nuclei were isolated and sonicated in lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) on a Diagenode Standard Bioruptor for 18 cycles at 20 seconds each with 60 seconds rest between cycles. Sonicated lysates were then immunoprecipitated by overnight incubation at 4°C with Dynabeads magnetic protein G beads (Thermofisher) bound with antibody against protein of choice.
ChIP samples were converted into libraries by the Yale Center for Genome Analysis facility using the Illumina ChIP sequencing library preparation kit and sequenced using the high-throughput Illumina platform.

value: erythroleukemia cells

value: GATA1 (N6, sc-265X, Santa Cruz)


title: IgG ChIP-Seq

value: IgG (sc-2027, Santa Cruz)


title: H3K4me3_NCI-H23_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: LC_NCI-H23_shKdm5b

description: RNA-Seq


title: RA d4 lateg1 EsrrbPlus7

city: jerusalem

first: Muhammad

last: Awawdy

address: The Hebrew University, The Edmond J. Safra Campus - Givat Ram

country: Israel

institute: Hebrew university of jerusalem

data_processing:
Illumina output was analyzed using an in-house Perl script that produced a reads matrix that was aligned using RSEM with Bowtie. The resulting matrix was analyzed in R
For bulk data analysis the transcript per million (TPM) values were used to compare between libraries
scRNA-seq data was analyzed using the Seurat v2.4 pipeline
cells with more than 10,000 unique molecular identifiers were retained for further analysis. A global-scaling normalization was performed on the filtered dataset using “LogNormalize” with a scale factor of 10,000. Identification of highly variable genes was performed with the following parameters: x.low.cutoff = 0.2, x.high.cutoff = 5, y.cutoff = 0.5, and y.high.cutoff = 10. Cell-to-cell variation in gene expression driven by batch, cell alignment rate, and the number of detected molecules were regressed out and a linear transformation was applied. A principal component analysis was performed on the scaled data with 12 principal components. Clustering was done with resolution of 0.6, and tSNE or UMAP was using for visualization.
CHIP-seq Sequencing data were aligned using Bismark and Bowtie (https://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf) using paired-ended approach. TDF genomic browser files were produced using IGV count. We applied HOMER to find peaks using ChIP-seq criteria and used BEDTools to intersect bins with genomic intervals such as promoters, genes, and predicted enhancers.
Genome_build: mm9, GRC38

source_name: R1 mESC cell line

growth_protocol: ESCs were seeded on 0.1% gelatin-coated plates (Sigma-Aldrich, G1393) and grown in ES medium (Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5671), 10% fetal bovine serum (FBS, Biological Industries, 04-007-1A), 1 mM sodium pyruvate (Biological Industries, 03-042-1B), 0.1 mM nonessential amino acids (Biological Industries, 01-340-1B), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, M3148), 1000 U/ml LIF (Mercury, ESG1107)). The cells were maintained at an incubator at 37 °C with 5% CO2 humidified air. For pluripotent conditions, 3 µM CHIR99021 (PeproTech, SM-2520691-B) and 0.2 µM PD0325901 (PeproTech, SM-3911091-B) were added to the ES medium.

extract_protocol:
mRNA extraction was performed using Invitrogen Dynabeads mRNA DIRECT Purification Kit (61011) according to the protocol included with the kit.
The library for differential gene expression analysis was prepared using 100-1000 ng of mRNA. First, RNA was fragmented using an RNA fragmentation kit (Ambion, AM8740) following the manufacturer’s protocols. Fragmented RNA was purified with 1.4x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 10 μl TE buffer (10 mM Tris–HCl, pH 8.0, 0.1 mM EDTA). The resulting fragmented RNA was reverse transcribed using an oligo dT primer: First, 10 μl of RNA were mixed with 2 μl of 50 μM oligo dT primer (Bio-Rad, 1725038) and 1 μl of 25 mM dNTP mix (NEB, N0447S), and samples were incubated for 3 minutes at 65 °C and transferred to ice. The following components were added to the reaction, for a total volume of 20 μl: 4 μl of 5x First-Strand SuperScript III buffer (Invitrogen, 18080044), 2 μl of 0.1 M DTT (Invitrogen, 18080044), 1 μl murine RNase inhibitor (NEB, M0314L), and 1 μl of 200 U/μL SuperScript III RT enzyme (Invitrogen, 18080044). The reaction product (in the form of a cDNA:RNA hybrid) was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 16 μl TE buffer as described above. For second-strand synthesis, 16 μl of the digestion reaction product were combined with 2 μl second-strand synthesis (SSS) buffer and 1 μl of SSS enzyme mix of mRNA Second Strand Synthesis Module kit (NEBNext, E6111S) and incubated at 16 °C for 2.5 hours, followed by 20 minutes at 65 °C. The resulting product was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted with 20.4 μl TE buffer. cDNA edges were repaired using End-It DNA End-Repair Kit (Danyel Biotech, ER81050) by combining the 20.4 μl sample with 3 μl 10X End-repair Buffer, 3 μl 2.5 mM dNTPs, 3 μl 10 mM ATP, and 0.6 μl END-IT enzyme mix at room temperature for 45 minutes, followed by purification with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and elution with 32 μl TE buffer. Klenow-mediated addition of an adenine to the 3’ end of the DNA fragments was performed using the Klenow fragment (3'→5' exo-) kit (NEB, M0212L) by combining the 32 μl sample with 5 μl 10X Klenow Buffer NEB 2, 10 μl 1 mM dATP, and 0.6 μl 5 U/μl Klenow (3’-5’ exo-) at 37 °C for 30 minutes, followed by purification with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and elution with 8 μl TE buffer. Illumina library adaptors were added to the resulting cDNA fragment using DNA ligase (NEB, M2200S) by incubation with 5 μl 2x Ligase Buffer, 0.5 μl adapter Oligo mix (1:10 in H2O), and 0.5 μl 1 U/ml DNA Ligase at room temperature for 15 minutes. The ligated product was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 11.5 μl TE buffer. The resulting libraries were PCR amplified using standard PE1/PE2 full-length primer mix containing Illumina library indices for multiplexing (sequences are given in Supplementary Table X). Each PCR reaction contained 11.5 μl post-RT cDNA library, 12.5 μl 2x KAPA HiFi HotStart PCR mix (Zotal, KK-KK2601), and 1 μl of 25 μM 2p Fixed (+barcode) and 2p Fixed primer mix (Supplementary Table 3). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 32 μl TE buffer. A 15-μl aliquot of each resulting library was run in a 2% agarose gel, and size selection for the desired 200-800 bp DNA library fragments was performed using PureLink DNA gel extraction kit (Invitrogen, K210012). Library quality was confirmed by Agilent 2200 TapeStation Nucleic Acids System.  The in vitro transcription sequencing (IVT) library was prepared using 75-100 ng of mRNA, extracted as described above. First-strand synthesis was performed using SuperScript III Reverse Transcriptase (Invitrogen, 18080044) and the T7RTPolyT primer (Supplementary Table X) at 50 °C for 2 hours followed by 15 minutes at 70 °C and 1 minute at 4 °C. To remove unused primers and primer dimers, the reaction product was combined with 20 μl digestion mix containing 5 μl ExoI (NEB, M0293S), 5 μl HinFI (NEB, R0155S), 5 μl ExoI buffer (NEB, B0293S), 5 μl CutSmart buffer (NEB, B7204S), and 30 μl nuclease-free water and incubated for 1 hour at 37 °C and 10 minutes at 80 °C. The reaction product (in the form of a cDNA:RNA hybrid) was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 13.5 μl TE buffer. For second-strand synthesis, the 13.5 μl digestion reaction product was combined with 1.5 μl SSS buffer and 1 μl of SSS enzyme mix from the mRNA Second Strand Synthesis Module kit (NEBNext, E6111S) and incubated at 16 °C for 2.5 hours, followed by 20 minutes at 65 °C. For linear amplification by in vitro transcription, 16 μl of SSS reaction products were combined with 24 μl HiScribe T7 High Yield RNA Synthesis Kit (NEB, E2040S) reagent mix containing 4 μl T7 Buffer, 4 μl ATP, 4 μl CTP, 4 μl GTP, 4 μl UTP, and 4 μl T7 enzyme mix. The reaction was incubated at 37 °C for 13 hours, and the resulting RNA was purified with 1.3x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted with 20 μl TE buffer. Aliquots of 9 μl of each sample were frozen for backup at -80 °C, 2 μl of each sample was directly analyzed, and the remaining 9 μl were used in subsequent library preparation steps. RNA was fragmented using the RNA fragmentation kit (Ambion, AM8740) by combining 9 μl sample with 1 μl of RNA fragmentation reagent and incubating at 70 °C for 2 minutes. After transfer to ice, 40 μl fragmentation stop mix containing 5 μl fragmentation stop solution and 35 μl TE buffer was added. Fragmented RNA was purified with 1.4x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 10 μl TE buffer. The resulting amplified and fragmented RNA was reverse transcribed using a random hexamer primer (IDT) as follows: First, 10 μl of RNA were mixed with 2 μl of 100 μM PvG748-SBS12-RT random hexamer primer (Supplementary Table X) and 1 μl of 10 mM dNTP mix (NEB, N0447S), incubated for 3 minutes at 65 °C and transferred to ice. The following components were then added to the reaction for a total volume of 20 μl: 4 μl of 5x First-Strand SuperScript III buffer (Invitrogen, 18080044), 1 μl 0.1 M DTT (Invitrogen, 18080044), 1 μl murine RNase inhibitor (NEB, M0314L), and 1 μl of 200 U/µL SuperScript III RT enzyme (Invitrogen, 18080044). Following reverse transcription, the reaction volume was raised to 50 μl by adding 30 μl nuclease-free water, and the resulting cDNA was purified with 1.2x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 11.5 μl TE buffer. Library amplification was performed using 12.5 µl 2x KAPA HiFi HotStart ReadyMix PCR kit (Zotal, KK-KK2601) and 1 μl of 25 μM 2p fixed primers (Supplementary Table X). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 30 μl nuclease-free water. Aliquots of 15 μl of each library were run in 2% agarose gels, and size selection for the desired 200-600 bp DNA library fragments was performed using PureLink DNA gel extraction kit (Invitrogen, K210012). Library quality was confirmed using the Agilent 2200 TapeStation Nucleic Acids System (Agilent).  For scRNA-seq, encapsulation of cells with Reverse Transcription mix (IGEPAL CA-630- Sigma-Aldrich I8896-50ML , SuperScript III Reverse Transcriptase Invitrogen 18080044, Deoxynucleotide (dNTP) Solution Set Ornat N0446S, D,L-DITHIOTHREITOL Bio-Lab 000448235200, TRIS-HCL  1 M STOCK SOLUTIONS  PH 7.5  B 1L Sigma-Aldrich T2319-1L, RNase Inhibitor, Murine NEB M0314L) and gels with unique molecular identifiers was performed using the FLUIGENT Smart Microfluidics Pump Syste

treatment_protocol: RA (Sigma-Aldrich, R2625) dissolved in dimethyl sulfoxide (ENCO, 0219605580) at 1 μM in LIF-free media with 10% FBS, on 0.1% gelatin-coated plates.

value: R1 mESC cell line

tag: developmental stage

value: Embrionic stem cells in early differentiation

tag: state

value: RA differentiation

tag: differentiated days


title: LC_NCI-H23_shLuc_ctrl

description: RNA-Seq

tag: cell line


title: Colon, anti-GFP_24hr, replicate 2, scRNA-seq

description: 10x Genomics

tag: treatment


title: Colon, anti-GFP_24hr, replicate 3, scRNA-seq

description: 10x Genomics

tag: tissue


title: H3K4me3_NCI-H23_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

tag: chip antibody

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: RA d4 lateg1 EsrrbPlus5


title: LC_NCI-H226_shKdm5b

description: RNA-Seq

tag: knockdown


title: Colon, anti-GFP_24hr, replicate 1, scRNA-seq

description: 10x Genomics

tag: genotype


title: H3K4me3_NCI-H226_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3

value: shLuc


title: LC_NCI-H226_shLuc_ctrl

description: RNA-Seq


title: RA d4 lateg1 esrrbminus3


title: RA d4 lateg1 esrrbminus2


title: Colon, Uninjured_24hr, replicate 2, scRNAseq

description: 10x Genomics


title: H3K4me3_HOP-92_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_NCI-H322M_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: EKVX


title: H3K4me3_NCI-H226_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: cancer cell


title: LC_HOP-92_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_HOP-92_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: RA d4 lateg1 esrrbminus1


title: LC_EKVX_shLuc_ctrl

description: RNA-Seq


title: Day7 2E’/PTX  siPD-L1 4

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC v.0.11.3 was used to observe read quality
Fastp was used to remove adapter sequences
STAR was used to map reads to the genome of mus_musculus
FeatureCounts on stranded mode was used to count reads mapping to genes
edgeR was used to identify differentially expressed genes
biomaRt was used to annotate genes using Ensembl annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel File containing count matrix for mouse genes

source_name: C57BL/6 mice

growth_protocol: Tumor growth was monitored by measuring the size

extract_protocol:
RNA isolated using Rnasy Qiagen kit
Tru-Seq stranded Illumina protocol, per manufacturer instructions

treatment_protocol: B16F10 tumor cells (1 × 106) were subcutaneously inoculated in the upper flank of the right hind limb of C57BL/6 mice. When tumor size reached ~150 mm3, the mice were treated with an intratumoral injection of D5W, 2E’, 2E’/PTX, 2E’/PTX/siNeg or 2E’/PTX/siPD-L1.

value: CT26 tumor cells

value: 2E'/PTX and siPD-L1

tag: time

value: day 7


title: Day7 2E’/PTX  siPD-L1 3


title: LF-4

city: Beijing

first: Zhixiu

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
Fastp (0.18.0)  was used to control and filter the raw read data. Clean reads were obtained after removing reads containing adapters, reads with an N ratio exceeding 10%, reads with all A bases, and low-quality reads. The reads were filtered further to obtain high-quality clean reads.
Bowtie 2 (2.2.8) was used to align the high-quality clean reads against species-specific ribosomal sequences and sequences that aligned to ribosomal RNA were removed.
The reads that were filtered out of ribosomal RNA were aligned to the duck reference genome (CAU-Wild 1.0) using the alignment software Tophat2 (2.1.1).
Cufflink (2.1.1) software was used to assemble transcripts based on the Tophat2 alignment results.
Multiple sequence assemblies were merged using cuffmerge and filtered to generate unique annotation files for transcripts that may have been artificially introduced with assembly errors for subsequent differential analysis.
Assembly: Anas platyrhynchos (mallard) CAU__Wild1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each sample ...

organism: Anas platyrhynchos

source_name: F2 duck population

growth_protocol: All ducks were farmed under the same breeding conditions. Food and water were provided ad libitum.

extract_protocol:
Abdominal fat were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The PrimeScript RT reagent Kit with gDNA Eraser was used to reverse transcribe the RNA to generate cDNA following the manufacturer’s instructions. A cDNA library was then constructed and sequenced on the Illumina HiSeqTM 4000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 42 day after birth

tag: duck  type

value: duck with the low abdominal fat ratios (LF)

value: abdominal fat


title: LC_HOP-92_shKdm5b

description: RNA-Seq


title: H3K4me3_EKVX_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: Colon, Uninjured_24hr, replicate 1, scRNAseq

description: 10x Genomics

value: transverse colon

value: colon cells


title: Cod1 ChIP-Seq

value: erythroleukemia cells

value: Codanin-1 (homemade antibody raised against N-terminal fragment of codanin-1, amino acids 123-142, ProteinTech)


title: LF-3

tag: age


title: H3K4me3_U251_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_EKVX_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3

value: COLO 205


title: LF-2


title: LC_EKVX_shKdm5b

description: RNA-Seq


title: CNS_U251_shLuc_ctrl

description: RNA-Seq


title: Day7 2E’/PTX  siPD-L1 1


title: LF-1


title: Day7 2E’/PTX  siNeg 3

value: 2E'/PTX and siNeg


title: CNS_U251_shKdm5b

description: RNA-Seq


title: CNS_SNB-75_shLuc_ctrl

description: RNA-Seq


title: HF-3

value: duck with the high abdominal fat ratios (HF)


title: CNS_SNB-75_shKdm5b

description: RNA-Seq


title: HF-2


title: Day7 2E’/PTX  siNeg 2


title: CNS_SF-539_shLuc_ctrl

description: RNA-Seq


title: Day7 2E’/PTX  siPD-L1 2


title: H3K4me3_SF-539_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: CNS_SF-539_shKdm5b

description: RNA-Seq


title: Day7 2E’/PTX  siNeg 1


title: Day7 D5W 3

value: dextrose 5% in water


title: RKO_shZNF280C_H3K27me3-rep2

data_processing:
Raw reads were aligned to hg19 using bwa. The sam files were converted to bam with samtools.
MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage from Deeptools.

source_name: RKO colon cancer cells

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 10^7 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 5-10 μg primary antibodies or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.
ChIP’s DNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. Fragments were amplified by PCR and PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit.

tag: cell line background

value: RKO

value: stably expressing a ZNF280C-targeting shRNA controlled by a tetracycline-inducible promoter


title: HF-1


title: HF-4


title: H3K4me3_T-47D_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3

value: cancer cell

value: shLuc


title: Day7 D5W 2

value: CT26 tumor cells

value: day 7


title: Day7 2E’/PTX  siNeg 4


title: H3K4me3_SF-539_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: BR_T-47D_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_T-47D_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: BR_T-47D_shKdm5b

description: RNA-Seq


title: H3K4me3_U251_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: RKO_shZNF280C_H3K27ac-rep2


title: H3K4me3_SNB-75_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: H3K4me3_SNB-75_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: RKO_shZNF280C_SMCHD1


title: Day7 D5W 1


title: BR_MCF7_shKdm5b

description: RNA-Seq


title: RKO_shZNF280C-DOX-SMCHD1

value: 1 ug/ml doxycycline for 72 h


title: Day 0 control 2

value: untreated

value: day 0


title: H3K4me3_MCF7_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: RKO_shZNF280C-DOX_H3K27me3-rep2


title: BR_BT-549_shLuc_ctrl

description: RNA-Seq


title: H3K4me3_BT-549_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3

value: HS 578T


title: RKO_shZNF280C-DOX_H3K27ac-rep2


title: Day 0 control 1


title: H3K4me3_BT-549_shLuc_ctrl_rep1

description: Chromatin IP against H3K4me3


title: BR_MCF7_shLuc_ctrl

description: RNA-Seq


title: S6Skin

status: Public on May 18 2022

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression

organism: Sciurus carolinensis

source_name: Skin

growth_protocol: Wild caught

extract_protocol:
Tissues were extracted from recently (<12hr) deceased or euthanized animals and flash frozen in liquid nitrogen. Animals not euthanized in lab were kept at 4°C and processed within 12hr of death. Frozen tissues were pulverized using a Cell Crusher piston chilled with liquid nitrogen to produce uniform powdered tissue. Approximately 30mg of frozen tissue powder was used for Trizol RNA extraction. Contaminating DNA was removed from RNA samples using Purelink DNase kit along with Purelink RNA columns. Purified RNA quality was checked using agarose gel examination for rRNA integrity and Qubit analysis
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
Ribo-depletion for RNAseq

treatment_protocol: No treatment

value: Skin


title: S6Lung

source_name: Lung

value: Lung


title: H3K4me3_MCF7_shLuc_ctrl_rep2

description: Chromatin IP against H3K4me3


title: S5Heart

source_name: Heart

value: Heart


title: S5Skin


title: S6Liver

source_name: Liver

value: Liver


title: S5Kidney

source_name: Kidney

value: Kidney


title: S6Kideny


title: Day 0 control 3


title: S5Liver


title: S5Lung


title: S6Heart


title: S4Kidney


title: S4Liver


title: S4Skin


title: S4Lung


title: S4Heart


title: S3Skin


title: S3Lung


title: S3Liver


title: BR_BT-549_shKdm5b

description: RNA-Seq


title: S1Kidney


title: S1Lung


title: S1Skin


title: S3Heart


title: S3Kidney


title: S1Heart


title: CA1200 Auxin NHS 8h_R3

source_name: young adults

tag: tissue of tir1

value: soma

tag: strain

tag: agent

value: Auxin

tag: time point


title: RS4Heart

organism: Tamiasciurus hudsonicus


title: RS4Brain

source_name: Brain

value: Brain


title: RS4Liver


title: RS2Liver


title: RS3Lung


title: RS3Liver


title: RS3Kidney


title: RS3Heart


title: RS2Lung


title: RS3Brain


title: S1Liver


title: RS1Lung


title: RS2Kidney


title: RS1Heart


title: R4Kidney

organism: Rattus rattus


title: R4Lung


title: RS2Heart


title: RS1Brain


title: RS1Liver


title: RS4Kidney


title: R4Heart


title: R4Liver


title: R3Liver


title: R3Lung


title: R4Skin


title: R3Heart


title: R3Kidney


title: RS1Kidney


title: R3Brain


title: R2Lung


title: R2Kidney


title: R1Kidney


title: R1Heart


title: R1Lung


title: P5Skin

organism: Cuniculus paca


title: R1Liver


title: P5Lung


title: P5Liver


title: P3Skin


title: P4Skin


title: P3Lung


title: R4Brain


title: P3Brain


title: P2Liver


title: P2Lung


title: P2Skin


title: P1Heart


title: P3Liver


title: P1Liver


title: P1Skin


title: B9Spleen_S6

organism: Castor canadensis

source_name: Spleen

value: Spleen


title: B9Skin_S31


title: P1Kidney


title: P2Brain


title: B9Lung_S16


title: R2Heart


title: B9Liver_S26


title: B9Heart_S11


title: B9Kidney_S21


title: B8Spleen_S5


title: R2Liver


title: P5Brain


title: P5Kidney


title: B8Skin_S30


title: B8Kidney_S20


title: B7Skin_S29


title: B8Liver_S25


title: B8Brain_S34


title: B7Kidney_S19


title: B7Spleen_S4


title: B7Liver_S24


title: B7Lung_S14


title: B5Spleen_S2


title: B7Brain_S33


title: B5Skin_S27


title: B6Skin_S28


title: B6Kidney_S18


title: B5Heart_S8


title: B5Lung_S13


title: B8Heart_S10


title: B3Lung_S12


title: B6Brain_S32


title: B9Brain_S35


title: B8Lung_S15


title: B3Heart_S7


title: B5Kidney_S17


title: ASM5Skin

organism: Acomys russatus


title: ASM5Lung


title: B6Spleen_S3


title: ASM5LiverR


title: B3Liver_S22


title: ASM5Heart


title: ASM5Brain


title: ASM4Skin


title: B6Heart_S9


title: ASM4Lung


title: ASM4LiverR


title: ASM4Kidney


title: ASM4Heart


title: ASM4Brain


title: ASM3SKin

source_name: SKin

value: SKin


title: ASM3Lung


title: ASM2Lung


title: ASM2Skin


title: ASM3Kidney


title: ASM2Brain


title: ASM2LiverR


title: ASM2Heart


title: ASM1Skin


title: ASM3LiverR


title: ASM1Brain


title: ASM3Brain


title: ASM1Kidney


title: ASM2Kidney


title: AMS1Lung


title: ASM1LiverR


title: ASM3Heart


title: Tumor_rep109

type: RNA

city: Créteil

first: Virginie

last: Firlej

address: Ur Trepca

institute: UPEC TrePca

hyb_protocol: Samples were hybridized with GeneChip Human Exon HTA2.0 Arrays (Affymetrix) and scanned at the IC Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data have been analyzed by Genosplice society as previously described

label: biotin

source_name: Tumor

label_protocol: All protocols were carried out according to Affymetrix instructions

growth_protocol: tissues were collected directly after prostatectomie by an anapathomopathologist and freeze at -80°C

extract_protocol: RNA was extracted from prostate tissues. with the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.   RNA was extracted from prostate tissues. with the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: tumor

tag: gleason

tag: Stage


title: Tumor_rep115


title: Tumor_rep110


title: Tumor_rep114


title: Tumor_rep113


title: Tumor_rep105


title: Tumor_rep104


title: Tumor_rep101


title: Tumor_rep106


title: Tumor_rep111


title: B6Liver_S23


title: Tumor_rep99


title: Tumor_rep108


title: Tumor_rep102


title: Tumor_rep112


title: Tumor_rep98


title: Tumor_rep103


title: Tumor_rep96


title: Tumor_rep93


title: Tumor_rep95


title: Tumor_rep94


title: Tumor_rep107


title: Tumor_rep97


title: ASM5Kidney


title: Tumor Hormono-resistant__rep13

source_name: Tumor Hormono-resistant


title: Tumor Hormono-resistant__rep11


title: Tumor_rep100


title: Tumor Hormono-resistant__rep10


title: Tumor Hormono-resistant__rep12


title: Tumor Hormono-resistant__rep9


title: Tumor Hormono-resistant__rep6


title: Tumor Hormono-resistant__rep7


title: Tumor_rep92


title: Tumor Hormono-resistant__rep8


title: Tumor_rep88


title: Tumor_rep90


title: Tumor_rep85


title: Normal_rep9

source_name: Normal

value: normal prostate


title: Tumor_rep83


title: Tumor_rep82


title: Tumor_rep87


title: Tumor_rep73


title: Tumor_rep75


title: Tumor_rep74


title: Tumor_rep81


title: Tumor_rep80


title: Tumor_rep72


title: Tumor_rep78


title: Tumor_rep79


title: Tumor_rep76


title: Tumor_rep69


title: Tumor_rep91


title: Tumor_rep89


title: Tumor_rep71


title: Tumor_rep86


title: Tumor_rep70


title: Tumor_rep64


title: Tumor_rep77


title: Tumor_rep56


title: Tumor_rep66


title: Tumor_rep62


title: Tumor_rep58


title: Tumor_rep67


title: Tumor_rep68


title: Tumor_rep54


title: Tumor_rep51


title: Tumor_rep55


title: Tumor_rep65


title: Tumor_rep63


title: Tumor_rep61


title: Tumor_rep48


title: Tumor_rep60


title: Tumor_rep59


title: Tumor_rep57


title: Tumor_rep45


title: Tumor_rep49


title: Tumor_rep46


title: Tumor_rep53


title: Tumor_rep50


title: Tumor_rep44


title: Tumor_rep47


title: ASM1Heart


title: Tumor_rep52


title: Tumor_rep43


title: Tumor_rep42


title: Tumor_rep33


title: Tumor_rep40


title: Tumor_rep35


title: Tumor_rep39


title: Tumor_rep41


title: Tumor_rep29


title: Tumor_rep37


title: Tumor_rep38


title: Tumor_rep32


title: Tumor_rep27


title: Tumor_rep25


title: Tumor_rep26


title: Tumor_rep36


title: Tumor_rep24


title: Tumor_rep34


title: Tumor_rep30


title: Tumor_rep31


title: Tumor_rep23


title: Tumor_rep22


title: Tumor_rep20


title: Tumor_rep28


title: Tumor_rep15


title: Tumor_rep21


title: Tumor Hormono-resistant__rep5


title: Tumor_rep18


title: Tumor_rep14


title: Tumor_rep19


title: Tumor Hormono-resistant__rep4


title: Tumor_rep13


title: Tumor_rep10


title: Tumor_rep9


title: Tumor_rep16


title: Tumor Hormono-resistant__rep1


title: Tumor_rep11


title: Tumor_rep12


title: Tumor Hormono-resistant__rep2


title: Tumor Hormono-resistant__rep3


title: Normal_rep6


title: Tumor_rep8


title: Tumor_rep84


title: Normal_rep7


title: Normal_rep5


title: Normal_rep8


title: Tumor_rep4


title: Tumor_rep6


title: Tumor_rep7


title: Normal_rep4


title: Normal_rep3


title: Tumor_rep5


title: Tumor_rep1


title: CHO 42.5°C_1h_C4

city: Szeged

first: Zsolt

last: Torok

address: Temesvari krt. 62.

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre

data_processing:
Base-calling software: DRAGON and bcl2fastq
Trimming: CLCBio GW, Trim Reads 2.2 (parameters: Quality trim = Yes, Quality limit = 0.01, Ambiguous trim = Yes, Ambiguous limit = 2, Trim adapter list = Illumina_TruSeq_LT_and_TruSeq_HT, Automatic read-through adapter trimming = Yes, Use colorspace = No, Remove 5' terminal nucleotides = Yes, Number of 5' terminal nucleotides = 15, Remove 3' terminal nucleotides = No, Discard short reads = Yes, Minimum number of nucleotides in reads = 50, Discard long reads = No, Save discarded sequences = No, Save broken pairs = No, Create report = Yes)
Read Mapping: CLCBio GW, RNA-Seq Analysis 2.17 (parameters: Reference type = Genome annotated with genes and transcripts, Reference sequence = CHOK1GS_HDv1_genome, Gene track = Cricetulus_griseus_chok1gshd.CHOK1GS_HDv1.99_Gene, mRNA track = Cricetulus_griseus_chok1gshd.CHOK1GS_HDv1.99_mRNA, Use spike-in controls = no, Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = No, Auto-detect paired distances = Yes, Strand specific = Both, Maximum number of hits for a read = 10, Count paired reads as two = No, Expression value = Total counts, Calculate expression for genes without transcripts = No, Create report = Yes, Create fusion gene table = No, Create list of unmapped reads = No)
Assembly: Cricetulus griseus, CHOK1GS_HDv1
Supplementary files format and content: Total counts of reads mapped on  Cricetulus griseus genes. (File format: CSV)
Supplementary files format and content: Raw counts

organism: Cricetulus griseus

source_name: CHO cells

growth_protocol: CHO (ATCC CCL-61, Manassas, VA) cells were cultured in Ham’s F-12K nutrient mix 10% supplemented with fetal bovine serum (Gibco) and 1% penicillin/ streptomycin (Sigma-Aldrich) and grown at 37 °C in a humidified 5% CO2 atmosphere. The cells were seeded at 250 cells/mm2, in tissue culture plates (VWR) 24 h prior to experiments to ensure logarithmic growth during treatments.

extract_protocol:
For the analysis of heat induced transcriptome, cells were collected and prepared with NucleoSpin RNA isolation kit for total RNA (Macherey-Nagel). Isolation of RNA samples were performed according to the manufacturer’s instructions. Briefly, 10^6 cells were seeded on culture plates for 24h prior to heat treatments which included 4 bio-logical repeats of 4 sample groups (37 °C, 40 °C for 1 h, 6 h and 42.5 °C for 1 h). Then cells were collected per sample on an RNA binding column, which was followed by a DNase treatment to remove DNAs from samples. The quality and the quantity of the extracted RNAs were determined by NanoDrop 2000/2000c Spectrophotometer and Qubit Fluorometer (both from Thermo Fisher Scientific), and byTapeStation (Agilent).
Sequencing library preparation was performed using Tru Seq RNA Library Preparation Kit (Illumina), according to the manufacturer’s instructions and sequenced on Illumina NextSeq instrument using 2 x 150 bp paired end sequencing chemistry.

treatment_protocol: CHO cells were seeded on culture plates for 24h prior to heat treatments which included 4 bio-logical repeats of 4 sample groups (37 °C, 40 °C for 1 h, 6 h and 42.5 °C for 1 h)

value: CHO (ATCC CCL-61)

value: Heat shock:42.5degreeC


title: CHO 40°C_1h_B2

value: Heat shock:40degreeC


title: CHO 40°C_1h_C2


title: CHO 40°C_6h_A3


title: CHO 42.5°C_1h_B4


title: Tumor_rep3


title: CHO 40°C_6h_C3


title: CHO 40°C_1h_A2


title: CHO 42.5°C_1h_A4


title: CHO 40°C_6h_B3


title: Normal_rep1


title: Normal_rep2


title: 47SVEC

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

institute: Pacific Northwest National Laboratory

data_processing:
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the mouse genome using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Assembly: Genome Reference Consortium Mouse Build 39 (https://www.ncbi.nlm.nih.gov/genome/?term=txid10090)
Supplementary files format and content: .txt files represent number of raw read counts mapping to each gene

source_name: SVEC endothelial cells

growth_protocol: standard culture protocols

extract_protocol:
Full length cDNA was generated from single cell using SMART-Seq v4 Plus according to the manufacture protocol. The cDNA quality is determined by 5200 Agilent Fragment analyzer.
For RNA‐Seq, SMART-Seq v4 Plus(c at#R400753) was used to generate template library for sequencing on illumina NextSeq550 platform according to the manufacture protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2.5 kit 150 cycles (cat#20024907).

value: SVEC


title: CHO 42.5°C_1h_D4


title: 45SVEC


title: 46SVEC


title: 48SVEC


title: CHO Ctrl_D1


title: CHO Ctrl_A1


title: 43SVEC


title: 2_combination_products_replicate2

city: Bethesda

first: Anupama

last: Khare

state: MD

address: 37 Convent Drive

institute: National Cancer Institute

data_processing:
Reads were cut with Cutadapt. Sequence AGATCGGAAGAGC was removed.
Reads were trimmed with Trimmomatic for single end using leading (3), trailing (3), sliding window (4-15), and minimum length of 10.
Rockhopper was run to match reads to P. aeruginosa UCBPP-PA14 genome and compare expression levels.
Genome_build: RefSeq NC_008463.1
Supplementary_files_format_and_content: txt files were generated using Rockhopper
Supplementary_files_format_and_content: Raw Counts  Normalized Counts   RPKM Expression

organism: Pseudomonas aeruginosa PA14

source_name: bacterial cells

growth_protocol: P. aeruginosa was grown in a modified M63 medium shaking at 300 rpm at 37C to OD600 = 0.5 before treatment.

extract_protocol:
RNA Purification Plus Kit (Norgen)
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: 25% (v/v) of media, media with the indicated products, or S. aureus supernatant was added to the sample.

value: 120 min

value: 80 microM staphylopine, 1000 microM DTPA, 500 microM deferoxamine, 150 microM citrate, and 150 microM acetoin in media


title: Tumor_rep2


title: 2_combination_products_replicate1


title: 44SVEC


title: CHO 40°C_1h_D2


title: CHO Ctrl_B1


title: 41SVEC


title: 42SVEC


title: 2_acetoin_replicate1

value: 150 microM acetoin in media


title: 40SVEC


title: Tumor_rep17


title: 2_acetoin_replicate2


title: 39SVEC


title: 2_citrate_replicate1

value: 150 microM citrate in media


title: 2_citrate_replicate2


title: 38SVEC


title: CHO Ctrl_C1


title: 37SVEC


title: 2_staphylopine_replicate2

value: 80 microM staphylopine in media


title: 2_DTPA_deferoxamine_replicate1

value: 1000 microM DTPA and 500 microM deferoxamine in media


title: 35SVEC


title: 33SVEC


title: 36SVEC


title: 2_supernatant_replicate1

value: S. aureus supernatant


title: 34SVEC


title: 2_media_replicate2

value: media


title: 2_media_replicate1


title: 30SVEC


title: 31SVEC


title: 20_combination_products_replicate2


title: 29SVEC


title: 2_DTPA_deferoxamine_replicate2


title: 28SVEC


title: 20_acetoin_replicate2

value: 20 min


title: 20_acetoin_replicate1


title: 20_citrate_replicate2


title: 25SVEC


title: 26SVEC


title: 24SVEC


title: 23SVEC


title: 20_DTPA_deferoxamine_replicate1


title: 20_DTPA_deferoxamine_replicate2


title: 2_supernatant_replicate2


title: 21SVEC


title: 2_staphylopine_replicate1


title: 22SVEC


title: 20_staphylopine_replicate2


title: 20_supernatant_replicate2


title: 32SVEC


title: CHO 40°C_6h_D3


title: 20_staphylopine_replicate1


title: 19SVEC


title: 20_media_replicate2


title: 20_media_replicate1


title: 20_combination_products_replicate1


title: 17SVEC


title: 27SVEC


title: 16SVEC


title: 20_supernatant_replicate1


title: 20_citrate_replicate1


title: 18SVEC


title: Initial_replicate2

value: 0 min


title: Initial_replicate1


title: 15SVEC


title: 14SVEC


title: 13SVEC


title: 12SVEC


title: 11SVEC


title: 20SVEC


title: 10SVEC


title: Sample_229: genomic DNA from PDB case 229

type: genomic

city: Doha

first: Omar

middle: M E

last: Albagha

address: Qatar Foundation

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: Blood Sample

hyb_protocol: Bisulfite conversion was performed on 500µg of DNA. DNA methylation profiling was performed using the Illumina Infinium HumanMethylation 450K array (Illumina, USA) by following the manufacturerís protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The R package RnBeads version 1.10.8

label: Cy5 and Cy3

source_name: White blood cells_229

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using standard protocols.

tag: gender

value: Female

tag: sample type

value: Blood

tag: disease state

value: Paget’s disease of bone (PDB)

tag: cell type

value: White blood cells

tag: array


title: Sample_231: genomic DNA from PDB case 231

description: Blood Sample

source_name: White blood cells_231


title: 9SVEC

tag: cell line


title: Sample_230: genomic DNA from PDB case 230

description: Blood Sample

source_name: White blood cells_230


title: Sample_228: genomic DNA from PDB case 228

description: Blood Sample

source_name: White blood cells_228

value: Male


title: Sample_226: genomic DNA from PDB case 226

description: Blood Sample

source_name: White blood cells_226


title: 7SVEC


title: Sample_225: genomic DNA from PDB case 225

description: Blood Sample

source_name: White blood cells_225


title: Sample_223: genomic DNA from PDB case 223

description: Blood Sample

source_name: White blood cells_223


title: 5SVEC


title: Sample_224: genomic DNA from PDB case 224

description: Blood Sample

source_name: White blood cells_224


title: 6SVEC


title: 4SVEC


title: Sample_227: genomic DNA from PDB case 227

description: Blood Sample

source_name: White blood cells_227


title: Sample_220: genomic DNA from PDB case 220

description: Blood Sample

source_name: White blood cells_220


title: Sample_232: genomic DNA from PDB case 232

description: Blood Sample

source_name: White blood cells_232


title: 3SVEC


title: Sample_221: genomic DNA from PDB case 221

description: Blood Sample

source_name: White blood cells_221


title: Sample_219: genomic DNA from PDB case 219

description: Blood Sample

source_name: White blood cells_219


title: 8SVEC


title: 2SVEC


title: 1SVEC


title: Sample_217: genomic DNA from PDB case 217

description: Blood Sample

source_name: White blood cells_217

value: Date _5


title: Sample_222: genomic DNA from PDB case 222

description: Blood Sample

source_name: White blood cells_222


title: 48C10

source_name: C10 alveolar type II epithelial cells


title: Sample_218: genomic DNA from PDB case 218

description: Blood Sample

source_name: White blood cells_218


title: Sample_216: genomic DNA from PDB case 216

description: Blood Sample

source_name: White blood cells_216


title: 47C10


title: 46C10


title: 44C10


title: Sample_214: genomic DNA from PDB case 214

description: Blood Sample

source_name: White blood cells_214

value: Date _1


title: Sample_215: genomic DNA from PDB case 215

description: Blood Sample

source_name: White blood cells_215


title: Sample_212: genomic DNA from PDB case 212

description: Blood Sample

source_name: White blood cells_212


title: 45C10


title: Sample_213: genomic DNA from PDB case 213

description: Blood Sample

source_name: White blood cells_213


title: 41C10


title: Sample_211: genomic DNA from PDB case 211

description: Blood Sample

source_name: White blood cells_211


title: 42C10


title: 40C10


title: Sample_210: genomic DNA from PDB case 210

description: Blood Sample

source_name: White blood cells_210


title: 38C10


title: Sample_209: genomic DNA from PDB case 209

description: Blood Sample

source_name: White blood cells_209


title: 39C10


title: 37C10


title: 36C10


title: Sample_207: genomic DNA from PDB case 207

description: Blood Sample

source_name: White blood cells_207


title: Sample_205: genomic DNA from PDB case 205

description: Blood Sample

source_name: White blood cells_205


title: Sample_206: genomic DNA from PDB case 206

description: Blood Sample

source_name: White blood cells_206


title: 34C10


title: 33C10


title: 35C10


title: Sample_204: genomic DNA from PDB case 204

description: Blood Sample

source_name: White blood cells_204


title: 31C10


title: 32C10


title: Sample_201: genomic DNA from PDB case 201

description: Blood Sample

source_name: White blood cells_201


title: Sample_202: genomic DNA from PDB case 202

description: Blood Sample

source_name: White blood cells_202


title: 30C10


title: 43C10


title: Sample_208: genomic DNA from PDB case 208

description: Blood Sample

source_name: White blood cells_208


title: 29C10

source_name: C10 alveolar type II epithelial cells


title: Sample_200: genomic DNA from PDB case 200

description: Blood Sample

source_name: White blood cells_200


title: Sample_199: genomic DNA from PDB case 199

description: Blood Sample

source_name: White blood cells_199


title: Sample_197: genomic DNA from PDB case 197

description: Blood Sample

source_name: White blood cells_197

value: Date _3


title: 27C10


title: 24C10