title: HOK-16B CBD rep3

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

description: the immortalized human oral keratinocyte HOK-21B cell line

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: human oral keratinocyte

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

tag: cell line

value: human oral keratinocyte

value: treated with CBD


title: HOK-16B CBD rep2

status: Public on Jul 01 2021

type: SRA

country: China

description: the immortalized human oral keratinocyte HOK-20B cell line

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: FUS-DDIT3_CTCF_2

city: Gothenburg

first: Ayman

last: Osman

address: Medicinaregatan 1F

department: Laboratory medicine

country: Sweden

institute: Gothenburg University

library_source: genomic

data_processing:
Fastq files were aligned to hg38 reference genome using BWA.
Mapped bam files were used for peak calling by MACS2. Minimum FDR (q-value) cutoff for peak detection was set to 0.01
To visualize the peaks, ChIP signals (bigwig) were generated by bamcompare tool from deepTools using signal extraction scaling (SES) method, and the background signal were subtracted from ChIP signal.
Differential binding analysis was performed using DiffBind R/Bioconductor package. Motifs analysis were performed using (findMotifsGenome.pl) program from HOMER. Search for known motifs followed by de novo motif discovery were performed.
The DDIT3 microarray expression data was combined with DDIT3 ChIP-seq data using binding and expression target analysis (BETA) software to examine the effect of DDIT3 on regulation of gene. BETA basic was used with the following parameters: --da 500 -d 150000 -c 0.5 -g hg19.
Genome_build: hg38
Supplementary_files_format_and_content: BED

molecule: genomic DNA

source_name: HT1080 cell line

growth_protocol: Human parental fibrosarcoma cell line HT1080 and transfected clones were cultured at 37oC and 5% CO2 in RPMI 1640 medium supplemented with 2 mM L-glutamine, 50 U/ml penicillin, 50 g/ml streptomycin and 8% FCS (all Invitrogen). G418 (200 g/ml, Invitrogen) was added to the transfected cell clones to ensure stable expression of EGFP constructs in the cell population.

extract_protocol:
For chromatin immunoprecipitation, we used the iDeal ChIP-seq kit for Transcription Factors (Diagenode, cat No: C01010170). For cross-linking proteins with DNA, formaldehyde (37%) was mixed with Fixation Buffer (Diagenode), to a final concentration of 11% and added to the cultured cells medium in a proportion of 1:10, and incubated with gentle shaking at room temperature for 15 minutes. The reaction was stopped by adding glycine (1:10) for 5 minutes with gentle shaking at room temperature. The cells were collected by scraping and lysed with lysis buffers from Diagenode. chromatin was sheared by sonication using Bioruptor Pico sonication device (Diagenode, Belgium) (7 cycles, 30 seconds ON, 30 seconds OFF).
Chip-seq grade antibodies (H3K27ac #C15410196, H3K27me3 #C15410195, CTCF #C15410210, Diagenode), (DDIT3 #2895, Cell Signaling Technology) mixed with magnetic beads (Diagenode) were added to 250 µl of sheared chromatin and incubated under constant rotation at 4 ⁰C overnight. A volume of 2.5 µl was treated in the same but without antibody and used as input. The beads were washed with washing buffers from (Diagenode) and elution buffer was added and samples were incubated overnight at 65 ⁰C. for DNA purification  IPure beads v2 (Diagenode) were used. The beads were washed with washing buffers from (Diagenode), then resuspended with buffer C (Diagenode) and kept for further analysis.
Library preparation was performed by (Diagenode, Belgium). ChIP’d DNA was quantified using QuBit HS ds DNA kit. Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified (double-size selected) using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).
Libraries were pooled and sequenced with Illumina technology with single-end reads of 50bp length. Sequencing was performed by (Diagenode, Belgium).

value: fibrosarcoma cell line

tag: oncogene transfection

tag: antibody

value: CTCF


title: E12_G4_TNT_rep3

city: Boston

first: William

middle: T

last: Pu

state: MA

address: 300 Longwood Ave

country: USA

institute: Children's Hospital Boston

description: GATA4 bioChIP-seq

data_processing:
GATA4 bioChIP-seq:  Bowtie v1.1.1, m=1
GATA4 bioChIP-seq:  MACS2 v2.2.4, p 1e-5
GATA4 bioChIP-seq:  bamCoverage 3.3.1 --normalizeUsing RPKM --binSize 10 --smoothLength 20 -e 150
Genome_build: GATA4 bioChIP-seq:  mm10
Supplementary_files_format_and_content: GATA4 bioChIP-seq:  bigWig files represent reads per 1000 bp per 1 M reads.
Supplementary_files_format_and_content: GATA4 bioChIP-seq:  peak text files
ATAC-seq:  Bowtie v.2.2.9 (alignment)
ATAC-seq:  MACS2 v2.2.4 (peak-calling)
ATAC-seq:  bamCoverage 3.3.1 --normalizeUsing RPKM --binSize 10 --smoothLength 20 (create signal file)
Genome_build: ATAC-seq:  mm10
Supplementary_files_format_and_content: ATAC-seq:  bigWig files represent reads per 1000 bp per 1 M reads.
Supplementary_files_format_and_content: ATAC-seq:  peak text files
EC RNA-seq:  Star v2.7.3a (alignment)
EC RNA-seq:  featureCounts v1.6.3 -T 4 -s 1 (read counting)
Genome_build: EC RNA-seq: mm10
Supplementary_files_format_and_content: EC RNA-seq:  read counts per gene

organism: Mus musculus

source_name: E12.5 ventricular apex

extract_protocol:
GATA4 bioChIP-seq:  For each bioChIP-seq of GATA4, 15-20 E12.5 heart ventricles were harvested and crosslinked in 1% formaldehyde in PBS for 10 minutes at room temperature. Chromatin was fragmented using a microtip sonicator (Qsonica, S-3000) at 65% amplitude for 8 minutes. GATAfb and bound chromatin was pulled down by incubation with streptavidin beads (ThermoFisher Scientific, Cat#11206D)
GATA4 bioChIP-seq:   Libraries were constructed using the KAPA HyperPrep ChIP-seq library preparation kit (Roche, cat# 07962347001). Sequencing (75 nt single end) was performed on an Illumina NextSeq 500.
EC ATAC-seq:  For ATAC-seq of Tie2-Cre cell lineages, E12.5 Rosa26fsTrap;Tie2Cre mouse heart ventricles were dissected in ice cold PBS and dissociated to single cells with Neonatal Cardiomyocyte Isolation kit (Cellutron, cat#nc-6031). 40K GFP+ cells were sorted (BD FACSMelody) for each ATAC-seq library sample. For ATAC-seq of Cdh5(Pac)-CreERT2 labeled, Gata4 mutant and control cell lineages, 1mg tamoxifen dissolved in sunflower seed oil was administered to pregnant mice by gavage to induce the activity of Cre at E9.5. E12.5 heart ventricles were dissected in ice cold PBS and dissociated to single cells with the Neonatal Cardiomyocyte Isolation kit (Miltenyi). 20K GFP+ cells were sorted (BD FACSMelody) for each ATAC-seq library sample.
EC ATAC-seq:  The optimized-ATACSeq (omni-ATACSeq) libraries were generated from purified cells using the author’s recommended lysis steps and transposition protocol
EC ATAC-seq:  optimized-ATACSeq (omni-ATACSeq)
EC RNA-seq:  E12.5 Rosa26fsTrap;Tie2Cre mouse heart ventricles were dissected in ice cold PBS and dissociated to single cells with Neonatal Cardiomyocyte Isolation kit (Cellutron, cat#nc-6031). 60K GFP+ cells were sorted (BD FACSMelody) for each RNA sample.
EC RNA-seq:  RNA was prepared with RNeasy Micro Kit (Qiagen, Cat#74004). The polyadenylated RNA was purified by binding to oligo (dT) magnetic beads (ThermoFisher Scientific, 61005).
EC RNA-seq:  RNA-seq libraries were prepared with ScriptSeq v2 kit (Illumina, SSV 21106) according to the manufacturer’s instructions.

tag: age

tag: tissue

value: E12.5 ventricular apex

tag: lineage selectivity

value: Tnnt2-Cre activated biotinylation


title: CA1199_EtOH_2h_NHS_R1

city: Valhalla

first: Jian

last: Li

state: NY

address: 15 Dana Road

institute: New York Medical College

description:
Li_RNA_017
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.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.
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.
Genome_build: WS235/ce11

molecule: polyA RNA

organism: Caenorhabditis elegans

growth_protocol: The HSF-1 AID animals (JTL611 and JTL621) and the corresponding control animals that only express TIR1 (CA1200 and CA1199) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates (~500 worms per plate) for 51 hr to develop into young 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: Worms were transferred to either auxin or ethanol (EtOH) plates, and kept for 2 hours. Following this, worms were either directly collected or subjected to heat shock performed in a water bath pre-heated to 34°C. For heat shock, NGM plates were wrapped with parafilm and submerged for 30 min.

value: young adults

tag: tissue of tir1

value: germline

tag: strain

value: EtOH;NHS


title: Developing mouse embryo sections B09G01_S213

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

tag: genotype

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: CA1199_EtOH_2h_HS_R1

description:
Li_RNA_021
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: EtOH;HS


title: CA1200_EtOH_2h_NHS_R1

description:
Li_RNA_001
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv

value: soma


title: E12_G4_TNT_rep2

description: GATA4 bioChIP-seq


title: CA1199_Auxin_2h_NHS_R1

description:
Li_RNA_018
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: Auxin;NHS


title: Developing mouse embryo sections B08G06_S116


title: HOK-16B NC rep3

description: the immortalized human oral keratinocyte HOK-18B cell line

value: treated with vehicle excipient


title: HOK-16B CBD rep1

description: the immortalized human oral keratinocyte HOK-19B cell line


title: Developing mouse embryo sections B09G05_S21


title: Developing mouse embryo sections B08G05_S20


title: HOK-16B NC rep2

description: the immortalized human oral keratinocyte HOK-17B cell line


title: soma-HSF1_depletion-HS-PolII_ChIP_replicate1

description:
soma-depl-HS-Pol_combined_treat_pileup.bdg
Sample 20

data_processing:
Sequencing reads were mapped to a non-repeat-masked version of the C. elegans WS235 genome using bowtie2 (Langmead and Salzberg, 2012) with the command bowtie2 --no-unal --very-sensitive –dovetail. Mapped reads in coordinated pairs, and with fragment size no bigger than 600bp were kept for downstream analyses. Duplicate reads were filtered for each replicate using MACS2 (Zhang et al., 2008) command macs2 filterdup -g ce --keep-dup auto.
HSF-1 peaks were called for each ChIP replicate of the control (no HSF-1 depletion) paired with the corresponding input sample using the command macs2 callpeak -g ce -f BEDPE --call-summits -q 1e-6. Common HSF-1 peaks in the biological duplicates were kept for subsequent analyses.
Filtered reads from biological replicates were combined to generate the bedgragh files using the command macs2 pileup -B. Given average fragment size of ChIP DNA is almost identical in all conditions for either HSF-1 or Pol II, pair-end reads were shifted half of the fragment length toward the center to generate the bedgraph files.
To determine the genomic regions with significant HSF-1 occupancy change by HSF-1 depletion, the bedgraph files in the control condition (EtOH) and the depleted condition (auxin) were compared using the command macs2 bdgdiff -l 180 -C 10.
To visualize and compare the ChIP-seq data in genome browser views, the bedgraph files were normalized to reads per million using MACS2 callpeak -B –SPMR.
Genome_build: WS235
Supplementary_files_format_and_content: The bedgraph files were generated with MACS2 for combined reads from two replicates and shown as reads per million (RPM).

source_name: HSF-1 depletion from the soma, 34C (HS)

growth_protocol: Age synchronization was achieved by treatment of alkaline hypochlorite solution and eggs were hatched in M9. L1 larvae were transferred to 10 cm NGM plates seeded with OP50 and grown at 20°C to young adult stage.

extract_protocol:
Animals were collected from NGM plates, washed with M9 and crosslinked with 2% formaldehyde in PBS at room temperature for 15 min. Crosslinking was quenched by incubation with 0.1M Tris (pH 7.5) for 5 min. Worms were then washed three times in M9 and once in cold FA buffer (50 mM HEPES/KOH pH7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxyholate, 150 mM NaCl with Roche Complete protease inhibitors). Worms were then resuspend in 600 ul of FA buffer and lysed by douncing in a Kontes 2 ml glass dounce, and sonicated in Bioruptor to yield 200 bp–600 bp size DNA fragments. Immunoprecipitation (IP) was set up using 0.5 ug of chromatin, and either 5 ul of anti-full length GFP antibody (Clontech, living colors), or 3 ug of anti-RNA Pol II antibody (8WG16, BioLegend) in FA buffer (1 ml total volume), and incubated at 4 ºC overnight on a rotating wheel. The next day, 30 ul of protein-G Dynabeads were added to each IP.
ChIP-seq libraries were prepared using Accel-NGS 2S kit as per manufacturer’s instructions.

treatment_protocol: Worms were transferred to either auxin (HSF-1 depletion) or ethanol (control) plates, and kept for 2 hours. Following this, worms were either directly collected or subjected to heat shock performed in a water bath pre-heated to 34°C. For heat shock, NGM plates were wrapped with parafilm and submerged for 30 min.

value: heat-shock

tag: chip antibody

value: Pol II


title: E12_G4_T2_rep3

description: GATA4 bioChIP-seq

value: Tie2-Cre activated biotinylation


title: soma-HSF1_depletion-HS-PolII_ChIP_replicate2

description:
soma-depl-HS-Pol_combined_treat_pileup.bdg
Sample 36


title: Developing mouse embryo sections B08G01_S212


title: E12_G4_T2_rep2

description: GATA4 bioChIP-seq


title: E12_G4_TNT_rep1

description: GATA4 bioChIP-seq


title: soma-HSF1_depletion-NHS-PolII_ChIP_replicate2

description:
soma-depl-NHS-Pol_combined_treat_pileup.bdg
Sample 35

source_name: HSF-1 depletion from the soma, 20C (NHS)

value: non-heat-shock


title: HOK-16B NC rep1

description: the immortalized human oral keratinocyte HOK-16B cell line

value: human oral keratinocyte


title: soma-HSF1_depletion-NHS-PolII_ChIP_replicate1

description:
soma-depl-NHS-Pol_combined_treat_pileup.bdg
Sample 19


title: Developing mouse embryo sections B07G06_S115


title: SAS_RT+HT_Rep3

city: Dresden

first: Oleg

middle: I

last: Chen

address: Handelallee 26

country: Germany

institute: OncoRay

data_processing:
The sequencing libraries were loaded on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions.
Image analysis and base calling were conducted by the NovaSeq Control Software.
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq
Differential gene expression was analyzed using the DESeq2 normalization analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: head-and-neck cancer cell line

growth_protocol: SAS and FaDu cells were seeded in 200 µl of regular DMEM per well in 96-well plates coated with 1.5% agarose (Sigma-Aldrich, Germany) for spheroid formation. All experiments were performed after 4 days of incubation, when spheroids of both cell lines reached a mean diameter ~ 400 µm.

extract_protocol:
Total cellular RNA was isolated from SAS and FaDu spheroids using the RNeasy Mini kit (QIAGEN, Germany) according to the manufacturer's protocol. RNA sequencing library preparations used the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA).
RNA-Seq libraries were prepared and sequenced by GENEWIZ (Leipzig, Germany) using the Illumina NovaSeq™ 6000 System.

treatment_protocol: FaDu and SAS spheroids treated with clinically relevant HT dose of 42.5°C for 60 minutes alone or in combination of single dose irradiation of 7 and 10 Gy for FaDu and SAS, respectively. All samples were collected 0.5 h after apropriate treatments.

value: SAS

tag: cell model

value: spheroids

value: Radiotherapy and Hyperthermia


title: E12_G4_T2_rep1

description: GATA4 bioChIP-seq

value: E12.5 ventricular apex


title: germline-HSF1_depletion-HS-PolII_ChIP_replicate2

description:
germline-depl-HS-Pol_combined_treat_pileup.bdg
Sample 40

source_name: HSF-1 depletion from the germline, 34C (HS)

value: young adults

value: germline


title: Developing mouse embryo sections B07G02_S307

value: E14 Mouse Embryo


title: SAS_RT+HT_Rep2


title: germline-HSF1_depletion-HS-PolII_ChIP_replicate1

description:
germline-depl-HS-Pol_combined_treat_pileup.bdg
Sample 24


title: Developing mouse embryo sections B07G01_S211

value: Sagigital section


title: cells_measurement_rep: 3T3-GN_H3K27ac_2

data_processing:
Bowtie2 v2.3.5.1
bamCoverage v3.3.1 --normalizeUsing RPKM --bl $mm10blacklist --binSize 10 --smoothLength 20 -e 150
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, normalized using RPKM

growth_protocol: Transduced cells were cultured in high glucose DMEM with 10% FBS with puromycin (2 μg/mL) and hygromycin (200 µg/mL) for three weeks. After three weeks of selection, cells were maintained in 0.5 μg/mL puromycin and 50 µg/mL hygromycin.

extract_protocol:
For ChIP-seq, the nuclei were sonicated in Sonication Buffer (20 mM Tris Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% NP40, 0.1% SDS, 1× PIC) using a Q800R3 Sonicator (Qsonica) with 65% amplitude for 40 minutes. Sheared DNA was incubated with 10 µg primary antibody (anti-HA, Cat#3724; anti-Flag, Cat#F1804; anti-H3K27ac, Cat#ab4729) at 4 °C overnight and then incubated with BSA-blocked Dynabeads Protein G for one hour.
KAPA HyperPrep ChIP-seq library preparation kits (Roche, cat# 07962347001) were used for library construction.

treatment_protocol: For ChIP-seq, 2x10^7 cells expressing HA-GATA4, Flag-NKX2-5, and Flag-ETS1 were cross-linked with 1% formaldehyde for 10 min at room temperature.

value: fibroblast

tag: chromatin feature

value: H3K27ac antibody


title: germline-HSF1_depletion-NHS-PolII_ChIP_replicate1

description:
germline-depl-NHS-Pol_combined_treat_pileup.bdg
Sample 23

source_name: HSF-1 depletion from the germline, 20C (NHS)


title: germline-control-HS-PolII_ChIP_replicate2

description:
germline-ctrl-HS-Pol_combined_treat_pileup.bdg
Sample 38

source_name: control, 34C (HS)


title: Developing mouse embryo sections B08G02_S308


title: SAS_RT+HT_Rep1


title: cells_measurement_rep: 3T3-GN_H3K27ac_3


title: germline-HSF1_depletion-NHS-PolII_ChIP_replicate2

description:
germline-depl-NHS-Pol_combined_treat_pileup.bdg
Sample 39


title: SAS_RT_Rep2

value: Radiotherapy


title: Developing mouse embryo sections B06G06_S114

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: soma-control-HS-PolII_ChIP_replicate1

description:
soma-ctrl-HS-Pol_combined_treat_pileup.bdg
Sample 18

value: soma


title: cells_measurement_rep: 3T3-GN_H3K27ac_1


title: cells_measurement_rep: 3T3-GE_H3K27ac_1


title: SAS_RT_Rep3


title: Developing mouse embryo sections B06G05_S18


title: cells_measurement_rep: 3T3-GE_H3K27ac_3


title: Developing mouse embryo sections B06G01_S210


title: SAS_HT_Rep3

value: Hyperthermia


title: Developing mouse embryo sections B06G02_S306


title: Developing mouse embryo sections B07G05_S19


title: cells_measurement_rep: 3T3-GE_H3K27ac_2


title: cells_measurement_rep: 3T3-G_H3K27ac_3


title: Developing mouse embryo sections B05G05_S17


title: germline-control-HS-PolII_ChIP_replicate1

description:
germline-ctrl-HS-Pol_combined_treat_pileup.bdg
Sample 22

value: heat-shock

value: Pol II


title: Developing mouse embryo sections B05G06_S113


title: SAS_RT_Rep1


title: SAS_HT_Rep1


title: SAS_HT_Rep2


title: cells_measurement_rep: 3T3-G_H3K27ac_2


title: Developing mouse embryo sections B05G02_S305


title: soma-control-HS-PolII_ChIP_replicate2

description:
soma-ctrl-HS-Pol_combined_treat_pileup.bdg
Sample 34


title: germline-control-NHS-PolII_ChIP_replicate2

description:
germline-ctrl-NHS-Pol_combined_treat_pileup.bdg
Sample 37

source_name: control, 20C (NHS)

value: non-heat-shock


title: SAS_Control_Rep3

value: Control


title: SAS_Control_Rep2

value: SAS


title: germline-control-NHS-PolII_ChIP_replicate1

description:
germline-ctrl-NHS-Pol_combined_treat_pileup.bdg
Sample 21


title: cells_measurement_rep: 3T3-Ctrl_H3K27ac_3

value: control


title: SAS_Control_Rep1

value: spheroids


title: soma-control-NHS-PolII_ChIP_replicate2

description:
soma-ctrl-NHS-Pol_combined_treat_pileup.bdg
Sample 33


title: soma-control-NHS-PolII_ChIP_replicate1

description:
soma-ctrl-NHS-Pol_combined_treat_pileup.bdg
Sample 17


title: FaDu_RT+HT_Rep3

value: FaDu

value: Radiotherapy and Hyperthermia


title: Developing mouse embryo sections B04G05_S16


title: Developing mouse embryo sections B05G01_S209


title: Developing mouse embryo sections B04G01_S208


title: FaDu_HT_Rep3


title: Developing mouse embryo sections B04G02_S304


title: FaDu_RT+HT_Rep2


title: FaDu_RT+HT_Rep1


title: cells_measurement_rep: 3T3-GN_NKX2-5_3

value: FLAG antibody


title: soma-HSF1_depletion-NHS-input

description:
HSF-1_ChIP_peaks.xlsx
Sample 3

value: young adults


title: cells_measurement_rep: 3T3-GN_NKX2-5_2


title: FaDu_HT_Rep2


title: cells_measurement_rep: 3T3-Ctrl_H3K27ac_2


title: cells_measurement_rep: 3T3-GN_NKX2-5_1


title: Developing mouse embryo sections B03G05_S15

value: E14 Mouse Embryo

value: Sagigital section


title: soma-HSF1_depletion-HS-input

description:
HSF-1_ChIP_peaks.xlsx
Sample 4


title: germline-HSF1_depletion-HS-input

description:
HSF-1_ChIP_peaks.xlsx
Sample 8

value: germline


title: Developing mouse embryo sections B03G06_S111


title: cells_measurement_rep: 3T3-G_H3K27ac_1

value: fibroblast

value: H3K27ac antibody


title: Developing mouse embryo sections B04G06_S112


title: cells_measurement_rep: 3T3-GN_GATA4_3

value: HA antibody


title: Developing mouse embryo sections B03G02_S303


title: cells_measurement_rep: 3T3-Ctrl_H3K27ac_1


title: FaDu_RT_Rep3

value: Radiotherapy


title: Developing mouse embryo sections B02G06_S110


title: germline-control-NHS-input

description:
HSF-1_ChIP_peaks.xlsx
common-NHS-HSF1-peaksummits(EtOH).bed
Sample 5


title: soma-control-HS-input

description:
HSF-1_ChIP_peaks.xlsx
common-HS-HSF1-peaksummits(EtOH).bed
Sample 2

value: heat-shock

value: soma


title: germline-HSF1_depletion-NHS-input

description:
HSF-1_ChIP_peaks.xlsx
Sample 7

value: non-heat-shock


title: Developing mouse embryo sections B03G01_S207


title: FaDu_HT_Rep1

value: Hyperthermia


title: FaDu_RT_Rep2


title: germline-control-HS-input

description:
HSF-1_ChIP_peaks.xlsx
common-HS-HSF1-peaksummits(EtOH).bed
Sample 6


title: soma-control-NHS-input

description:
HSF-1_ChIP_peaks.xlsx
common-NHS-HSF1-peaksummits(EtOH).bed
Sample 1


title: soma-HSF1_depletion-HS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
soma-depl-HS-HSF1_combined_treat_pileup.bdg
Sample 28

value: GFP


title: cells_measurement_rep: 3T3-GE_ETS1_2


title: cells_measurement_rep: 3T3-GN_GATA4_2


title: cells_measurement_rep: 3T3-GN_GATA4_1


title: Developing mouse embryo sections B02G01_S206


title: Developing mouse embryo sections B02G02_S302


title: cells_measurement_rep: 3T3-GE_ETS1_3


title: soma-HSF1_depletion-HS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
soma-depl-HS-HSF1_combined_treat_pileup.bdg
Sample 12


title: Developing mouse embryo sections B02G05_S14


title: Developing mouse embryo sections B01G02_S301


title: Developing mouse embryo sections B01G05_S13


title: FaDu_Control_Rep3

value: spheroids

value: Control


title: germline-HSF1_depletion-HS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
germline-depl-HS-HSF1_combined_treat_pileup.bdg
Sample 32


title: cells_measurement_rep: 3T3-GE_GATA4_1


title: 1995_2

city: Wenzhou

first: Yangyang

last: Pan

address: 183 guangchang Road, Lucheng District

department: Pediatric Dentistry,

institute: Wenzhou Medical University

data_processing:
Base-calling, and quality value calculations were performed using the Illumina GA Pipeline (version 1.6)
High quality reads in each sample were mapped to the reference genome of Streptococcus mutans UA159. Analysis tool: Bowtie2 Version 2.3.5
Gene and isoform abundances of paired-end RNA-Seq data were quantified using RSEM Version 1.3.1
Edger software Version 3.24.3 was used to compare the  differentially expressed genes between the two groups
Genome_build: Streptococcus mutans UA159 chromosome
Supplementary_files_format_and_content: Table with gene counts and TPM for every gene and every sample

organism: Streptococcus mutans

source_name: cells

growth_protocol: All cells were incubated in BHI broth under anaerobic conditions (90% N2, 5%H2, 5% CO2) at 37°C

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.0, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, ≥100ng/μl, ≥2μg) was used to construct sequencing library
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 2μg of total RNA. Shortly, ribosomal RNA (rRNA) depletion instead of poly(A) purification is performed by Ribo-Zero Magnetic kit (epicenter) and then all mRNAs were broken into short (200nt) fragments by adding fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). When the second strand cDNA was synthesized, dUTP was incorporated in place of dTTP. Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. The second strand cDNA with dUTP was recognized and degraded by UNG enzyme. Libraries were size selected for cDNA target fragments of 200bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq×TEN (2 × 150bp read length).The processing of original images to sequences, base-calling, and quality value calculations were performed using the Illumina GA Pipeline (version 1.6), in which 150bp paired-end reads were obtained. A Perl program was written to select clean reads by removing low-quality sequences, reads with more than 5% of N bases (unknown bases) and reads containing adaptor sequences

treatment_protocol: All cells were grown to mid-log phase

value: SMU_1995c deletion mutant

tag: backgound strain


title: 1995_3


title: Developing mouse embryo sections B01G01_S205


title: FaDu_Control_Rep2

value: FaDu


title: cells_measurement_rep: 3T3-GE_ETS1_1

value: FLAG antibody


title: cells_measurement_rep: 3T3-N_NKX2-5_2


title: cells_measurement_rep: 3T3-GE_GATA4_3


title: FaDu_RT_Rep1


title: Developing mouse embryo sections B01G06_S109

value: E14 Mouse Embryo


title: Developing mouse embryo sections A12G05_S12

value: Sagigital section


title: cells_measurement_rep: 3T3-E_ETS1_3

source_name: ΝΙΗ3Τ3-ΕΤS1


title: soma-HSF1_depletion-NHS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
soma-depl-NHS-HSF1_combined_treat_pileup.bdg
Sample 11

value: young adults


title: FaDu_Control_Rep1


title: soma-HSF1_depletion-NHS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
soma-depl-NHS-HSF1_combined_treat_pileup.bdg
Sample 27


title: cells_measurement_rep: 3T3-GE_GATA4_2

value: fibroblast


title: Chimeric_High_inflorescence_1cm_RNA-seq

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

data_processing:
For Bisulfite-Seq data, the adaptor sequences and low-quality reads were trimmed using trim_galore(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The clean data were mapped against genome using bismark(v0.19.0). CGmaptools(v0.1.1) was used to calculate the methylation level of the 2-kb sequences upstream and downstream of all genes and transposable elements (http://rice.plantbiology.msu.edu/). A personal Python script was  used to visualize the methylation level.
For RNA-seq data, the adaptor sequences and low-quality reads were trimmed using trim_galore(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).The clean reads were mapped against replaced genome using Tophat2 (v2.1.1)[5] with default parameters. Cufflinks (v2.0.0) was used to quantify the relative expression of the genes and calculate any differentially expressed genes (Fold change ≥ 1, adjusted p-value<0.01). To visualize the RNA-seq expression level, bedtools was used to calculate the coverage and normalize the data per million mapped reads. A Python script was used to visualize the data.
For smallRNA-seq data, The adaptor sequences and low-quality RNA-seq reads were trimmed using trim_galore, and reads shorter than 18 nt or longer than 30 nt were discarded. MicroRNA (http://www.mirbase.org/ftp.shtml), transfer RNA (http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), ribosomal RNA (Rice Genome Annotation MSU7.0), small nucleolar RNA, and small nuclear RNA  (https://www.arb-silva.de/no_cache/download/archive/release_132/Exports/) sequences were also removed. The remaining clean reads were aligned to the  replaced MSU7.0 rice genome using Bowtie (v 1.1.1), allowing 2 mismatches and requiring mapping to a unique site. The siRNA enrichment was calculated in 10-kb windows with normalized reads, and only windows with at least three reads were further analysed. To visualize the level of siRNA expression, bedtools was used to calculate the coverage and normalize the data per million mapping reads. A  Python script was used to visualize the data.
Genome_build: About 7-kb sequence containing LOC_Os01g41370 was amplified from ZH11 and sequenced. This sequence was used to replace the LOC_Os01g41370 sequence in the MSU7.0 rice genome assembly, which was identified using BLASTn. The replaced MSU7.0 rice genome was used in our analysis.

organism: Oryza sativa Japonica Group

source_name: Chimeric High inflorescence 1cm

growth_protocol: The Epi-lf mutant was identified in a screen of an anther-cultured population of Japonica rice (Oryza sativa ssp. japonica; variety ZhongHua11; ZH11) in 2005. The mutant phenotype of Epi-lf was stably inherited over more than 20 generations. The mutant and WT rice plants were planted in paddy fields under natural conditions or in glasshouses with a day temperature of 30°C and a night temperature of 24°C.

extract_protocol:
Total RNA was extracted from different tissues using TRIzol reagent (Thermo Fisher Scientific). The first-strand cDNA was synthesized using 1 μg RNA and ReverTra Ace qPCR RT Master Mix with gDNA Remover (Toyobo), according to the manufacturer’s instructions, using 29 PCR cycles to amplify the LF transcripts and 23 PCR cycles for Actin1. The RT-PCR analysis was repeated three times with similar results. Genomic DNA was isolated from the flag leaves of WT and tillers with different phenotypes of Epi-lf using the CTAB method. Briefly, 1 μg of genomic DNA was treated with sodium bisulphite using the Qiagen EpiTect Bisulfite kit, according to the manufacturer’s instructions. The treated DNA was dissolved in 15 mL distilled water, and 3 μL of this solution was used as the template in a 50-μL PCR (94°C for 4 min; followed by 40 cycles of 94°C for 30 s , 55°C for 30 s and 60°C for 30 s; with a final 60°C for 10 min).The PCR products were purified and cloned into pEASY-T5-Blunt Zero Cloning Kit vectors.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: variety

value: Inflorescence

tag: developmental stage


title: UA159_3

value: wild type


title: soma-control-HS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
common-HS-HSF1-peaksummits(EtOH).bed
soma-ctrl-HS-HSF1_combined_treat_pileup.bdg
Sample 26


title: germline-control-HS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
common-HS-HSF1-peaksummits(EtOH).bed
germline-ctrl-HS-HSF1_combined_treat_pileup.bdg
Sample 14

value: germline


title: cells_measurement_rep: 3T3-N_NKX2-5_3

tag: cell line

tag: cell type


title: germline-HSF1_depletion-NHS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
germline-depl-NHS-HSF1_combined_treat_pileup.bdg
Sample 15

tag: treatment


title: Developing mouse embryo sections A11G06_S107

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: germline-HSF1_depletion-HS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
germline-depl-HS-HSF1_combined_treat_pileup.bdg
Sample 16

value: heat-shock


title: soma-control-HS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
common-HS-HSF1-peaksummits(EtOH).bed
soma-ctrl-HS-HSF1_combined_treat_pileup.bdg
Sample 10

value: soma


title: 1995_1


title: germline-HSF1_depletion-NHS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
germline-depl-NHS-HSF1_combined_treat_pileup.bdg
Sample 31

value: non-heat-shock


title: Chimeric_semi-High_inflorescence_1cm_RNA-seq

source_name: Chimeric semi-High inflorescence 1cm

value: Oryza sativa ssp. japonica; variety ZhongHua11


title: Developing mouse embryo sections A12G06_S108


title: Developing mouse embryo sections A12G01_S204


title: Chimeric_Dwarf_inflorescence_1cm_RNA-seq

source_name: Chimeric Dwarf inflorescence 1cm


title: cells_measurement_rep: 3T3-N_NKX2-5_1


title: Developing mouse embryo sections A11G02_S299


title: germline-control-NHS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
common-NHS-HSF1-peaksummits(EtOH).bed
germline-ctrl-NHS-HSF1_combined_treat_pileup.bdg
Sample 29

value: GFP


title: cells_measurement_rep: 3T3-E_ETS1_1


title: Developing mouse embryo sections A12G02_S300


title: UA159_1


title: Developing mouse embryo sections A11G05_S11


title: UA159_2


title: germline-control-HS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
common-HS-HSF1-peaksummits(EtOH).bed
germline-ctrl-HS-HSF1_combined_treat_pileup.bdg
Sample 30


title: cells_measurement_rep: 3T3-E_ETS1_2


title: WT_inflorescence_1cm_RNA-seq

source_name: WT inflorescence 1cm


title: Chimeric_semi-High_inflorescence_5cm_RNA-seq 2

source_name: Chimeric semi-High inflorescence 5cm


title: Developing mouse embryo sections A11G01_S203


title: cells_measurement_rep: 3T3-G_GATA4_1

value: HA antibody


title: soma-control-NHS-HSF1_ChIP_replicate2

description:
HSF-1_ChIP_peaks.xlsx
common-NHS-HSF1-peaksummits(EtOH).bed
soma-ctrl-NHS-HSF1_combined_treat_pileup.bdg
Sample 25


title: cells_measurement_rep: 3T3-G_GATA4_3


title: cells_measurement_rep: 3T3-GN_ATAC_2

data_processing:
Bowtie2 v2.2.9
removeChrom.py to remove ChrM
picardtools MarkDuplicates
bamCoverage v3.3.1 --normalizeUsing RPKM --bl $mm10blacklist --binSize 10 --smoothLength 20
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, normalized using RPKM

extract_protocol:
Purified nuclei for transposase treatment.
Libraries were constructed with Optimized ATAC-Seq (OmniATAC-seq) protocol.

treatment_protocol: Harvest cells with cell lifters, 50K cells were used for each replicate.

value: ATAC

tag: reagent


title: Developing mouse embryo sections A10G05_S10


title: cells_measurement_rep: 3T3-G_GATA4_2


title: Developing mouse embryo sections A10G06_S106


title: cells_measurement_rep: 3T3-GN_ATAC_3


title: Chimeric_semi-High_inflorescence_5cm_RNA-seq 1


title: Developing mouse embryo sections A10G02_S298


title: Chimeric_Dwarf_inflorescence_5cm_RNA-seq

source_name: Chimeric Dwarf inflorescence 5cm


title: EM donor3 aCD3/28+L2

city: NYC

first: Adam

last: Mor

department: Medicine

institute: CUIMC

description: Norm_Count_all_genes_all_ samples.xlsx

data_processing:
Expression count (STAR) analysis performed using BasePair software
Differential expression (DESeq2, compare 2 groups) performed using BasePair software. In each cell subset (naïve, CM ,EM) - each treatment (aCD3/28, aCD3/28+PDL1, aCD3/28+PDL2) was compared to the unstimulated condition
Genome_build: hg19
Supplementary_files_format_and_content: Normalized counts of all genes in all samples

source_name: Primary human EM CD4+ T cells

growth_protocol: Mononuclear cells were isolated from whole blood of healthy donors by Lymphoprep density gradient (Stemcell). CD4 Naive, CM and EM T cell subsets were isolated by the appropriate microbeads kits (Miltenyi), following the manufacturer’s protocols. Isolated cells were allowed to rest in RPMI 1640 media (supplemented with 10% heat inactivated fetal bovine serum, 1% penicillin - streptomycin, 1X non-essential amino acids, and 1mM sodium pyruvate) for 24 hours.

extract_protocol:
Total RNA was isolated from the stimulated cells using RNeasy Mini Prep (Qiagen)
Illumina low input RNA

treatment_protocol: Rested cells were resuspended at 1E6 cells/mL of the above media containing 1 µg/mL anti-CD28 (CD28.2, Biolegend) and plated on 48 well plates pre-coated with either 5 µg/mL anti-CD3 and 5 µg/mL Isotype control antibody, 5 µg/mL anti-CD3 and 5 µg/mL PD-L1, or 5 µg/mL anti-CD3 and 5 µg/mL PD-L2 for 18 hours at 0.5 mL media per well.

value: Primary human EM CD4+ T cells

value: anti-CD3, anti-CD28, PD-L2

tag: donor #


title: soma-control-NHS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
common-NHS-HSF1-peaksummits(EtOH).bed
soma-ctrl-NHS-HSF1_combined_treat_pileup.bdg
Sample 9

tag: age


title: cells_measurement_rep: 3T3-GN_ATAC_1


title: Chimeric_High_inflorescence_5cm_RNA-seq

source_name: Chimeric High inflorescence 5cm

tag: tissue


title: WT_inflorescence_5cm_RNA-seq

source_name: WT inflorescence 5cm


title: Developing mouse embryo sections A10G01_S202

source_name: E14 saggital sections 8-10um thick


title: cells_measurement_rep: 3T3-GE_ATAC_3


title: germline-control-NHS-HSF1_ChIP_replicate1

description:
HSF-1_ChIP_peaks.xlsx
common-NHS-HSF1-peaksummits(EtOH).bed
germline-ctrl-NHS-HSF1_combined_treat_pileup.bdg
Sample 13

tag: tissue of tir1


title: Chimeric_semi-High_inflorescence_2cm_RNA-seq 2

source_name: Chimeric semi-High inflorescence 2cm


title: cells_measurement_rep: 3T3-GE_ATAC_2


title: EM donor3 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx

value: anti-CD3, anti-CD28, PD-L1


title: Developing mouse embryo sections A09G05_S9

value: E14 Mouse Embryo


title: CM donor3 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx

source_name: Primary human CM CD4+ T cells

value: Primary human CM CD4+ T cells


title: EM donor3 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx

value: unstimulated


title: Developing mouse embryo sections A09G06_S105

value: Sagigital section


title: Developing mouse embryo sections A09G02_S297


title: cells_measurement_rep: 3T3-N_ATAC_3

value: fibroblast


title: Chimeric_High_inflorescence_2cm_RNA-seq

source_name: Chimeric High inflorescence 2cm

value: Inflorescence


title: cells_measurement_rep: 3T3-GE_ATAC_1


title: Developing mouse embryo sections A08G06_S104


title: Developing mouse embryo sections A09G01_S201


title: cells_measurement_rep: 3T3-N_ATAC_1


title: cells_measurement_rep: 3T3-N_ATAC_2


title: WT_inflorescence_2cm_RNA-seq

source_name: WT inflorescence 2cm


title: CM donor3 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx


title: Chimeric_Dwarf_inflorescence_2cm_RNA-seq

source_name: Chimeric Dwarf inflorescence 2cm


title: CM donor3 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx


title: Developing mouse embryo sections A08G05_S8


title: cells_measurement_rep: 3T3-E_ATAC_3


title: cells_measurement_rep: 3T3-E_ATAC_2


title: EM donor3 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx

value: anti-CD3, anti-CD28


title: Developing mouse embryo sections A08G02_S296


title: Naive donor3 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx

source_name: Primary human Naive CD4+ T cells

value: Primary human Naive CD4+ T cells


title: Developing mouse embryo sections A08G01_S200


title: cells_measurement_rep: 3T3-G_ATAC_3


title: CM donor3 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx


title: LF_5Aza_treat_RNA-seq

source_name: Epi-lf 5Aza treat

value: leaf

value: 10 days


title: Developing mouse embryo sections A07G06_S103


title: cells_measurement_rep: 3T3-E_ATAC_1


title: LF_nontreat_RNA-seq

source_name: Epi-lf nontreat


title: Naive donor3 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx


title: WT_nontreat_RNA-seq

source_name: WT nontreat


title: Naive donor3 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx


title: cells_measurement_rep: 3T3-G_ATAC_1


title: EM donor2 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx


title: cells_measurement_rep: 3T3-ctrl_ATAC_3

value: control


title: Developing mouse embryo sections A07G01_S199


title: cells_measurement_rep: 3T3-G_ATAC_2


title: Chimeric_semi-High_inflorescence_2cm_RNA-seq 1


title: LF_embryo_RNA-seq

source_name: Epi-lf embryo

value: embryo


title: EM donor2 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx


title: LF_endosperm_RNA-seq

source_name: Epi-lf endosperm

value: endosperm


title: Naive donor3 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx


title: Developing mouse embryo sections A07G02_S295


title: Developing mouse embryo sections A07G05_S7


title: WT_embryo_RNA-seq

source_name: WT embryo


title: WT_endosperm_RNA-seq

source_name: WT endosperm


title: LF_dwarf_RNA-seq

source_name: Epi-lf dwarf leaf

value: 50 days


title: EM donor2 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx

source_name: Primary human EM CD4+ T cells

value: Primary human EM CD4+ T cells


title: Developing mouse embryo sections A06G02_S294


title: WT_5Aza_treat_RNA-seq

source_name: WT 5Aza treat


title: CM donor2 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx

value: anti-CD3, anti-CD28, PD-L2


title: Nef_plate_3_scRNA-seq

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals, library 3

data_processing:
Alignment of the Celseq2 reads was performed using the mapandgo. Following merging of the reads generated in multiple lanes and removal of the reads that lack Celseq2 barcodes, the data was trimmed using Trimgalore (version 0.4.3107) that employs cutadapt108 to remove the Illumina library adapters and fastQC109 reads with low quality base-calls at the end of the reads.
Alignment of the reads to the mm10 reference genome was done STAR (version 2.5.3a110), and single-cell libraries were de-multiplexed using the barcoded present in preloaded primer sequences.
Following UMI correction, reads were adjusted for the possibility of false assignment of reads from different mRNAs as duplicates due to the low chance of having the same UMI on different mRNA molecules. This was the final count file used for the analysis.
bc_celseq2.tsv contains barcode information used to assign reads to each cell (well)
Genome_build: mm10
Supplementary_files_format_and_content: *.tsv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. The first column lists the official gene symbol followed by the functional annotation of hte gene and the chromosome name, separated by a double underscore.

extract_protocol:
RNA was extracted by 2x heat lysis (65C) in 384 well, which were immediately used for downstream single cell RNA sequencing reactions (Celseq2)
Single-cell RNA sequencing was performed with Cel-seq2 at the Single Cell Discoveries (Utrecht, NL), as described by Hashimshony et al., 2016 and Muraro et al., 201625,106. Plates contained preloaded barcoded poly-T primers that specifically amplify the mRNA and introduce a 6bp unique molecular identifier (UMI), an 8bp cell barcode and a T7 RNA polymerase binding site. In addition, plates were pre-loaded with ERCC spike-ins that allowed quality control of reactions in individual wells. Cells were lysed by heating at 65C for 5 min followed by rapid chilling on ice for 2 min (twice). mRNA was reversed transcribed using Superscript II (ThermoFisher Scientific) and converted into second stranded DNA by DNA polymerase I (ThermoFisher Scientific). Material from each plate was then pooled, cleaned up using Ampure beads (Beckman Coulter, #A63881) and amplified by in vitro transcription overnight using the MEGAscript T7 transcription kit (ThermoFisher Scientific, # AMB1334). Following a second round of clean up, amplified RNA was measured using the Agilent RNA 6000 pico chips (Agilent # 5067-1513), reverse-transcribed using random hexamer primers that introduce Truseq Small RNA kit RP1 primer binding sites (Illumina) and finally converted into DNA libraries using custom rpi primers (RNA PCR Primer Index) adapted from the Truseq Small RNA kit (Illumina)106. Following two rounds of Ampure bead clean up and quality control using the Agilent High Sensitivity DNA Kit (5067-4626), libraries were sent for sequencing at the Utrecht Sequencing Facility (USEQ, Life Sciences faculty, Utrecht University) for paired end sequencing (26bp for read 1 and 50bp for read 2) by Nextseq500. 5 plates were combined for a full sequencing run, which yielded ~300M assigned to the libraries.

treatment_protocol: For fasting, animals were food restructed for 24h

tag: strain

tag: condition

value: fed

value: Lepr+ cells from the hypothalamus


title: cells_measurement_rep: 3T3-ctrl_ATAC_2

tag: genotype

value: ATAC


title: Nef_plate_2_scRNA-seq

description: Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals, library 2


title: CM donor2 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx

value: Primary human CM CD4+ T cells

value: unstimulated


title: Nef_plate_5_scRNA-seq

description: Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals following 24 of fasting, library 4

value: fasted


title: Developing mouse embryo sections A06G05_S6

source_name: E14 saggital sections 8-10um thick

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: LF_Normal_rep2_RNA-seq

source_name: Epi-lf noraml leaf


title: Naive donor2 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx

value: Primary human Naive CD4+ T cells


title: Developing mouse embryo sections A05G05_S5


title: LF_CHD1_rep2_RNA-seq

source_name: Epi-lf CHD1 leaf

value: leaf


title: Developing mouse embryo sections A05G06_S101


title: Nef_plate_1_scRNA-seq

description: Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals, library 1


title: cells_measurement_rep: 3T3-ctrl_ATAC_1

value: fibroblast


title: EM donor2 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx


title: Developing mouse embryo sections A06G01_S198


title: LF_CHD1_rep1_RNA-seq


title: Developing mouse embryo sections A05G02_S293


title: Developing mouse embryo sections A06G06_S102


title: LF_Normal_rep1_RNA-seq


title: WT_endosperm_BS-seq


title: Naive donor2 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx

value: anti-CD3, anti-CD28


title: CM donor2 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx

source_name: Primary human CM CD4+ T cells

value: anti-CD3, anti-CD28, PD-L1


title: Developing mouse embryo sections A04G06_S100


title: Naive donor2 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx


title: LF_endosperm_BS-seq

value: endosperm


title: Developing mouse embryo sections A05G01_S197


title: Naive donor2 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx


title: SPOCmut#H1(iXist-ChrX)_3hDox_H2AK119ub1

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Mapping: Raw fastq read pairs were mapped to the “N-masked” mm10 genome by bowtie2 (v2.2.6) using parameters “--very-sensitive --no-discordant --no-mixed -X 2000”
Filtering: Alignment files were  filtered to remove unmapped read pairs and PCR duplicates (picard-tools MarkDuplicates)
bedGraph generation: Alignments files were processed into bedGraph format by genomeCoverageBed (BEDtools) and normalised to the total library size of the sample.
BigWig generation: BigWig files were generated from normalized bedGraph files using bedGraphToBigWig (kentutils) with default parameters.
250kb windows: The custom script ExtractInfoFrombedGraph_AtBed.py (https://github.com/guifengwei) was used on normalized bedGraph files to extract values of H2AK119ub1 enrichment for 250 kb windows spanning whole X chromosome or the 103.5Mb region of ChrX1 proximal to Xist that can be allelically-assigned. Line graphs displayed in report were generated in R by subtraction of Uninduced from Induced (Dox-NoDox) samples of these 250kb windows for each clone/replicate.
Genome_build: mm10
Supplementary_files_format_and_content: text (tables of enrichment for 250KB windows); bigwig

source_name: mESC_iXist-ChrX_female (XX)

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating.

extract_protocol:
Native ChIP-seq using buffers supplemented with 10 mM of the deubiquitinase inhibitor N-ethylmaleimide (Sigma, E3876-5G) throughout. Briefly, 50 million ES cells (or for 24h data sets, 40 million mES cells with 10 million Drosophila SG4 cells as spike-in) were lysed in RSB (10 mM Tris pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) for 5 min on ice with gentle inversion. Nuclei were resuspended in 1 ml of RSB + 0.25 M sucrose + 3 mM CaCl2, treated with 200 U of MNase (Fermentas) for 5 min at 37 °C, quenched with 4 µl of 1 M EDTA, then centrifuged at 5000 r.p.m. for 5 min. The supernatant was transferred to a fresh tube as fraction S1. The chromatin pellet was incubated for 1 h in 300 µl of nucleosome release buffer (10 mM Tris pH 7.5, 10 mM NaCl, 0.2 mM EDTA), carefully passed five times through a 27G needle and then centrifuged at 5000 r.p.m. for 5 min. The supernatant from this S2 fraction was combined with S1 as soluble chromatin extract. For each ChIP reaction, 100 µl of chromatin was diluted in Native ChIP incubation buffer (10 mM Tris pH 7.5, 70 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton) to 1 ml and incubated with 4ul H2AK119ub1 Ab (Cell Signalling Technology, #8240) overnight at 4 °C. Samples were incubated for 1 h with 40 µl protein A agarose beads pre-blocked in Native ChIP incubation buffer with 1 mg/ml BSA and 1 mg/ml yeast tRNA, then washed for a total of four times in Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton) and once in TE. The DNA was eluted with 1% SDS and 100 mM NaHCO3, and was purified using the ChIP DNA Clean and Concentrator kit (Zymo Research).
Libraries were prepared from 50ng ChIP DNA using NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1μg/mL) to the culture medium for 3h or 24h.

value: 129S x Cast

value: mESC

tag: Sex

value: female

tag: genotype/variation

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain

tag: chip antibody

value: anti-H2AK119ub1 (CST #8240S, rabbit mAb D27C4)


title: EM donor1 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx

value: Primary human EM CD4+ T cells

value: anti-CD3, anti-CD28, PD-L2


title: SpenKO#C4(iXist-ChrX)_3hDox_H2AK119ub1

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); deletion of Spen RRM domain (full KO)


title: Developing mouse embryo sections A04G02_S292


title: EM donor1 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx


title: LF_CHD2_rep1_BS-seq

tag: variety

value: 50 days


title: Developing mouse embryo sections A04G01_S196

value: E14 Mouse Embryo


title: SPOCmut#C11(iXist-ChrX)_0hDox_H2AK119ub1


title: SPOCmut#C11(iXist-ChrX)_3hDox_H2AK119ub1


title: SPOCmut#H1(iXist-ChrX)_0hDox_H2AK119ub1


title: WT_embryo_BS-seq

value: embryo

tag: developmental stage


title: LF_CHD1_rep1_BS-seq


title: EM donor1 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx


title: Developing mouse embryo sections A03G05_S3

value: Sagigital section


title: LF_embryo_BS-seq


title: LF_Normal_rep1_BS-seq

source_name: Epi-lf normal leaf

value: leaf


title: Developing mouse embryo sections A04G05_S4


title: WT_rep1_BS-seq

source_name: WT leaf


title: Developing mouse embryo sections A03G06_S99


title: EM donor1 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx

value: unstimulated


title: CM donor1 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx

value: Primary human CM CD4+ T cells

value: anti-CD3, anti-CD28


title: Developing mouse embryo sections A03G02_S291


title: SpenKO#C3(iXist-ChrX)_3hDox_H2AK119ub1

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); deletion of Spen RRM domain (spurious truncated product)


title: CM donor1 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx


title: WT(iXist-ChrX)_0hDox_H2AK119ub1

value: 129S x Cast

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)


title: LF_Medium_BS-seq

source_name: Epi-lf medium leaf


title: WT(iXist-ChrX)_3hDox_H2AK119ub1

value: mESC

value: female


title: Developing mouse embryo sections A02G05_S2


title: CM donor1 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx


title: Developing mouse embryo sections A03G01_S195


title: Developing mouse embryo sections A02G02_S290


title: Naive donor1 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx

source_name: Primary human Naive CD4+ T cells

value: Primary human Naive CD4+ T cells

value: anti-CD3, anti-CD28, PD-L1


title: Developing mouse embryo sections A02G06_S98


title: CM donor1 aCD3/28+L1

description: Norm_Count_all_genes_all_ samples.xlsx


title: SPOCmut#E7(iXist-ChrX)_Dox_24h_input

description: Input gDNA, includes reads from Drosophila genome for spike-in calibration.

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain


title: SpenKO#C3(iXist-ChrX)_0hDox_H2AK119ub1

value: anti-H2AK119ub1 (CST #8240S, rabbit mAb D27C4)


title: SPOCmut#H1(iXist-ChrX)_Dox_24h_input


title: Developing mouse embryo sections A02G01_S194


title: genomic DNA from primary tumor sample 10 [PT.10]

type: genomic

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC arrays using standard Illumina protocol

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

data_processing:
Beta values were obtained using GenomeStudio (Illumina). Beta values were normalized using BMIQ. Multimapping CpGs, CpGs close to SNPs, meQTLs, CpGs with Detection P-values > 0.05 in any sample, CpGs with standard deviation < 0.05 and CpGs outside promoter region (TSS1500, TSS200, 5’UTR), were filtered.
matrix processed value definition: BMIQ normalized and filtered Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: primary tumor sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from frozen tissue using the AllPrep DNA/RNA/Protein method (Qiagen, Hilden, Germany), according to standard instructions.

tag: disease stage

value: Untreated

tag: epithelial fraction

tag: ar gene amplification

value: No


title: genomic DNA from primary tumor sample 12 [PT.12]


title: Naive donor1 unstimulated

description: Norm_Count_all_genes_all_ samples.xlsx

tag: cell type

tag: treatment


title: genomic DNA from primary tumor sample 8 [PT.8]


title: Naive donor1 aCD3/28+L2

description: Norm_Count_all_genes_all_ samples.xlsx

value: anti-CD3, anti-CD28, PD-L2

tag: donor #


title: SPOCmut#H1(iXist-ChrX)_NoDox_0h_input


title: SpenKO#C4(iXist-ChrX)_0hDox_H2AK119ub1

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); deletion of Spen RRM domain (full KO)


title: Developing mouse embryo sections A01G06_S97

tag: tissue

value: E14 Mouse Embryo

value: Sagigital section


title: genomic DNA from primary tumor sample 11 [PT.11]


title: genomic DNA from primary tumor sample 6 [PT.6]


title: genomic DNA from primary tumor sample 7 [PT.7]


title: Naive donor1 aCD3/28

description: Norm_Count_all_genes_all_ samples.xlsx


title: genomic DNA from primary tumor sample 9 [PT.9]


title: Developing mouse embryo sections A01G01_S193


title: SpenKO#D4(iXist-ChrX)_NoDox_0h_input


title: TEADi_A

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

description: ad_TEADi (Treatment)

data_processing:
Reads were trimmed using Trimmomatic 0.36 for adapters and low-quality bases
alignment to the human reference genome, hg19, was performed using STAR 2.5.1.
Gene counts were calculated using Quantify to annotation model with Ensembl Transcripts release 75 (Partek E/M, PartekFlow 8.0.19.0819)
Counts were filtered to exclude genes with maximum <=5.0 counts with Partek Flow 8.0.19.0819
Counts were added +1 and gene expression was normalized to TMM using PartekFlow 8.0.19.0819
TMM values were used for differential analysis to identify genes that are differentially expressed using the GSA function in PartekFlow 8.0.19.0819 with q value calculation, by comparing the TEADi expressing cells vs GFP expressing cells.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include TMM values and GSA analysis for all samples

source_name: SCC9 cells

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2, in DMEM/F12 Media with 10% FBS and 400 ng/ml hydrocortisone

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq mRNA Prep Kit RS-122-2101

treatment_protocol: Cells were transduced one day after plating with a multiplicity of infection (MOI) of 25 with adeno-GFP (control) or adeno-TEADi

tag: cell line

value: TEAD inhibitor protein (TEADi)


title: TEADi_B

description: ad_TEADi (Treatment)


title: genomic DNA from primary tumor sample 4 [PT.4]


title: Developing mouse embryo sections A01G05_S1


title: SPOCmut#E7(iXist-ChrX)_NoDox_0h_input

tag: strain


title: genomic DNA from primary tumor sample 5 [PT.5]


title: genomic DNA from primary tumor sample 3 [PT.3]


title: TEADi_C

description: ad_TEADi (Treatment)


title: WT(iXist-ChrX)_Dox_24h_input_Rep2


title: GFP_C

description: ad_GFP (control)

value: control GFP


title: SpenKO#C3(iXist-ChrX)_NoDox_0h_input

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); deletion of Spen RRM domain (spurious truncated product)


title: Developing mouse embryo sections A01G02_S289


title: OSC - Nxf2-KD - LamDam_rep2

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

data_processing:
Library strategy: DamID-seq
Hi-C: HiCExplorer v3.3 software (Ramirez et al., 2018) was used for the calculation of HiC matrix, and GENOVA v1.0 was used for visualizing the results. Two replicates were performed per knockdown, and hicCorrelate was used to calculate correlation between replicate samples. Due to the high correlation between replicates, samples were combined by using hicSumMatrices for the further analysis. Bins of too low or high coverage were removed and the HiC matrix was iteratively corrected by ICE using hicCorrectMatrix. HiC matrix was further normalized between different knockdown samples using hicNormalize. TADs were defined using hicFindTADs function and matrixes were converted into ginteractions file using hicConvertFormat.
DamID-seq: Adapters were removed using cutadapt, and reads shorter than 50nt after adapter removal was discarded. damidseq_pipeline (Marshall and Brand, 2015) was used to map the reads to Drosophila melanogaster (dm3) genome, followed by normalization and background reduction. We used q-value cutoff 0 (to include multi-mapped reads), and fragment size of 300. Due to the high correlation of replicate samples, two replicate reads were merged for the further analysis. After mapping of DamID-seq reads to the genome, log2 ratio of LamDam/Dam was calculated and bedgraph file was generated using damidseq_pipeline.
ChIP-seq: For ChIP-seq analysis, adapters were removed from the reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 2.2.9 (Langmead and Salzberg, 2012) with the default parameters. MACS 1.4.2 (Zhang et al., 2008) was used for peak calling and generation of wig files.
Genome_build: dm3
Supplementary_files_format_and_content: Hi-C: ginteractions file (tsv format) generated using HiCExplorer v3.3 (Ramirez et al., 2018)
Supplementary_files_format_and_content: DamID-seq: bedgraph file generated using damidseq_pipeline v1.4.5 (Marshall and Brand, 2015)
Supplementary_files_format_and_content: ChIP-seq: wig file generated using MACS v1.4.2 (Zhang, 2008)

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells

growth_protocol: Ovarian somatic cells (OSCs) was established in the previous studies (Niki et al., 2006; Saito et al., 2009). OSCs were cultured in Shield and Sang M3 Insect Medium (Caisson Laboratories) supplemented with 10% fly extract, 10% fetal bovine serum, 0.6 mg/ml glutathione, and 10 μg/ml insulin.

extract_protocol:
Hi-C: Hi-C using OSCs were performed as described previously (Ulianov et al., 2016) with some minor modifications. OSCs were fixed with 1% formaldehyde for 10min, and stored at -80 degrees before usage. 5 x 10^5 cells were lysed and chromatin digested using 30G needle. Chromatin digestion was performed using HindIII restriction enzyme. Ends were filled with biotin-14-dCTP followed by blunt-end ligation. Proteins were reverse crosslinked form the cells, and DNA purification was performed. Biotin was removed from un-ligated ends and DNA was sonicated using covaris S220 (covaris). Sonicated DNA was used for biotin pull down by streptavidin conjugated to Dynabeads Streptavidin C1 beads (Invitrogen). Pulled-down DNA was used as the template to construct DNA library.
DamID-seq: Dam-ID-seq was performed as described previously (Pickersgill et al., 2006) with some modifications to analyze methylated sequences using deep-sequencing rather than microarray. DamID vectors were transfected into OSCs using Nucleofector, one day before cell harvest. pNDamMyc plasmid (van Steensel and Henikoff, 2000) was a kind gift from Dr. Bas van Steensel. Lamin was cloned into pNDamMyc vector as described previously (Pickersgill et al., 2006). Genome DNA precipitation, DpnI digestion, adapter ligation, DpnII digestion, PCR, and PCR cleanup was performed as described within “Van Steensel Lab version 28/08/2006” protocol. Obtained DNA was used as the template to prepare deep sequencing library.
ChIP-seq: ChIP was performed as described previously (Iwasaki et al., 2016). Briefly, OSCs (3×107) were fixed, lysed, and their nuclei were isolated using truChIP Chromatin Shearing Kits (Covaris), in accordance with the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), and then diluted with ChIP buffer. DNA–protein complexes were incubated with antibody on Dynabeads-Protein G for 4 h, at 4 degrees. Beads were washed with ChIP buffer, high-salt lysis buffer, and wash buffer followed by TE. After reversing cross-linking for 12–16 h at 65 degrees, samples were treated with RNase for 30 min at 37 degrees and Proteinase K for 60 min at 55 degrees. DNA was then recovered.
DNA library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), in accordance with the manufacturer’s instructions.

treatment_protocol: For the transfection of siRNAs into OSCs, 200 pmol siRNA duplex was nucleofected into 3.0 × 10^6 cells using the Cell Line 96-well Nucleofector Kit SF (Lonza) and program DG150 of the 96-well Shuttle Device (Lonza). The siRNAs were transfected twice for 4-day KD, and once for 2-day KD. Co-transfection of siRNA and plasmid DNA was performed using the Cell Line Nucleofector Kit V (Lonza) and program T-029 of the Nucleofector II Device (Lonza).

value: Ovarian Somatic Cells


title: GFP_B

description: ad_GFP (control)


title: WT(iXist-ChrX)_NoDox_0h_input_Rep2

value: 129S x Cast

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)


title: SpenKO#C3(iXist-ChrX)_Dox_24h_input

value: mESC

value: female


title: OSC - Nxf2-KD - LamDam_rep1


title: hESC_prime_brg-2

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description:
Primed hESCs shBRG1#2
TCCCAGC-11

data_processing:
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs

source_name: Embryonic stem cells

growth_protocol: Conventional (primed) human ESCs were maintained on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers and passaged using Collagenase (1 mg/mL) or manual methods. Primed human ESCs were cultured in human ESC medium (hESM) [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (Gibco HI FBS, 10082-147), 5% KnockOut Serum Replacement (Invitrogen), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Naive human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium [DMEM (Invitrogen) supplemented with 10% FBS (Gibco HI FBS, 10082-147), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza) and 0.1 mM β-mercaptoethanol (Sigma)]. For conversion of pre-existing primed human ESC lines, we seeded 2 x 105 trypsinized single cells on a MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (Stemgent, 10 μM). 2 days later medium was switched to 5i/L/A or 4i/L/A (no IM12)-containing naive human ESC medium. Following an initial wave of cell death, naive colonies appeared within 10 days and were expanded polyclonally using Accutase (Gibco) on a MEF feeder layer. Naive human pluripotent cells were derived and maintained in serum-free N2B27-based media supplemented with inhibitors and cytokines. 500 mL of medium was generated by including: 240 mL DMEM/F12 (Invitrogen; 11320), 240 mL Neurobasal (Invitrogen; 21103), 5 mL N2 supplement (Invitrogen; 17502048), 10 mL B27 supplement (Invitrogen; 17504044), 10 μg recombinant human LIF (made in-house), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Lonza), 50 µg/ml BSA (Gibco Fraction V, 15260), and the following small molecules and cytokines: PD0325901 (Stemgent, 1 μM), IM-12 (Enzo, 1 μM or 0 µM), SB590885 (R&D systems, 0.5 μM), WH4-023 (A Chemtek or Selleckchem, 1 μM), Y-27632 (Stemgent, 10 μM) and Activin A (Peprotech, 10 ng/mL). All naïve hESC experiments were conducted in 5% O2, 5% CO2.

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the SMARTer Directional cDNA Library Construction Kit (Clontech, 634933). Libraries were sequenced on an Illumina HiSeq3000 1 × 50 platform.

treatment_protocol: Human ESCs were infected with the lentivirus in the presence of 6 ug/ml polybrene (Millipore). Infected cells were plated on mitomycin C inactivated DR4 feeder cells and selected with 1 ug/ml of puromycin for 5 days since 48 h after transduction.

value: Embryonic stem cells

tag: culture condition

value: Primed

value: BRG knockdown


title: OSC - Nxf2-KD - Dam_rep1


title: SpenKO#D4(iXist-ChrX)_Dox_24h_input


title: genomic DNA from primary tumor sample 1 [PT.1]

value: Untreated


title: WT(iXist-ChrX)_NoDox_0h_input_Rep1


title: OSC - Nxf2-KD - Dam_rep2


title: WT(iXist-ChrX)_Dox_24h_input_Rep1


title: SPOCmut#H1(iXist-ChrX)_Dox_24h_H2AK119ub1

description: Includes reads from Drosophila genome for spike-in calibration.

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain

value: anti-H2AK119ub1 (CST #8240S, rabbit mAb D27C4)


title: genomic DNA from non-malignant sample 12 [N.12]

source_name: non-malignant sample

value: No


title: genomic DNA from non-malignant sample 10 [N.10]


title: genomic DNA from non-malignant sample 9 [N.9]


title: hESC_prime_ntc

description:
Primed hESCs non-targeting control
GCAGGGG-9

tag: genotype

value: non-targeting control


title: hESC_prime_brg-1

description:
Primed hESCs shBRG1#1
AGATACT-10


title: OSC - Piwi-KD - LamDam_rep2

value: Piwi-KD


title: genomic DNA from primary tumor sample 2 [PT.2]


title: hESC_prime_untransfected

description:
Primed hESCs untransfected
TATCTTA-8

value: untransfected


title: genomic DNA from non-malignant sample 11 [N.11]


title: GFP_A

description: ad_GFP (control)

value: control GFP


title: SPOCmut#H1(iXist-ChrX)_NoDox_0h_H2AK119ub1


title: OSC - Piwi-KD - Dam_rep2


title: SPOCmut#E7(iXist-ChrX)_NoDox_0h_H2AK119ub1


title: SpenKO#D4(iXist-ChrX)_Dox_24h_H2AK119ub1

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); deletion of Spen RRM domain (spurious truncated product)


title: OSC - Piwi-KD - Dam_rep1

value: Ovarian Somatic Cells


title: genomic DNA from non-malignant sample 8 [N.8]


title: genomic DNA from non-malignant sample 7 [N.7]


title: hESC_naive_brg-1

description:
Naive hESCs shBRG1#1
TGGTCTC-6

value: Naive


title: OSC - Piwi-KD - LamDam_rep1


title: SPOCmut#E7(iXist-ChrX)_Dox_24h_H2AK119ub1

value: 129S x Cast


title: OSC - EGFP-KD - LamDam_rep2

value: EGFP-KD


title: OSC - EGFP-KD - Dam_rep2


title: genomic DNA from non-malignant sample 6 [N.6]


title: hESC_naive_brm-3

description:
Naive hESCs shBRM#3
AGCGCCG-5

value: BRM knockdown


title: SpenKO#C3(iXist-ChrX)_Dox_24h_H2AK119ub1

value: mESC

value: female


title: hESC_naive_brm-2

description:
Naive hESCs shBRM#2
CATCGCG-4

value: Embryonic stem cells


title: OSC - EGFP-KD - LamDam_rep1


title: hESC_naive_brm-1

description:
Naive hESCs shBRM#1
TACAGAC-3


title: hESC_naive_brg-2

description:
Naive hESCs shBRG1#2
TTCGCTG-7

value: BRG knockdown


title: genomic DNA from non-malignant sample 5 [N.5]

value: Untreated


title: OSC - EGFP-KD - Dam_rep1


title: genomic DNA from non-malignant sample 3 [N.3]


title: SpenKO#C3(iXist-ChrX)_NoDox_0h_H2AK119ub1

value: anti-H2AK119ub1 (CST #8240S, rabbit mAb D27C4)


title: hESC_naive_untransfected

description:
Naive hESCs untransfected
ACGTCTG-1


title: OSC - HP1-KD-2days - HiC_rep1

description: HP1merge_40kb.ICEcor.Norm.ginteractions.tsv

data_processing:
Hi-C: HiCExplorer v3.3 software (Ramirez et al., 2018) was used for the calculation of HiC matrix, and GENOVA v1.0 was used for visualizing the results. Two replicates were performed per knockdown, and hicCorrelate was used to calculate correlation between replicate samples. Due to the high correlation between replicates, samples were combined by using hicSumMatrices for the further analysis. Bins of too low or high coverage were removed and the HiC matrix was iteratively corrected by ICE using hicCorrectMatrix. HiC matrix was further normalized between different knockdown samples using hicNormalize. TADs were defined using hicFindTADs function and matrixes were converted into ginteractions file using hicConvertFormat.
DamID-seq: Adapters were removed using cutadapt, and reads shorter than 50nt after adapter removal was discarded. damidseq_pipeline (Marshall and Brand, 2015) was used to map the reads to Drosophila melanogaster (dm3) genome, followed by normalization and background reduction. We used q-value cutoff 0 (to include multi-mapped reads), and fragment size of 300. Due to the high correlation of replicate samples, two replicate reads were merged for the further analysis. After mapping of DamID-seq reads to the genome, log2 ratio of LamDam/Dam was calculated and bedgraph file was generated using damidseq_pipeline.
ChIP-seq: For ChIP-seq analysis, adapters were removed from the reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 2.2.9 (Langmead and Salzberg, 2012) with the default parameters. MACS 1.4.2 (Zhang et al., 2008) was used for peak calling and generation of wig files.
Genome_build: dm3
Supplementary_files_format_and_content: Hi-C: ginteractions file (tsv format) generated using HiCExplorer v3.3 (Ramirez et al., 2018)
Supplementary_files_format_and_content: DamID-seq: bedgraph file generated using damidseq_pipeline v1.4.5 (Marshall and Brand, 2015)
Supplementary_files_format_and_content: ChIP-seq: wig file generated using MACS v1.4.2 (Zhang, 2008)


title: WT(iXist-ChrX)_Dox_24h_H2AK119ub1_Rep3

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)


title: genomic DNA from non-malignant sample 4 [N.4]

value: No


title: WT(iXist-ChrX)_NoDox_0h_H2AK119ub1_Rep3


title: OSC - EGFP-KD-2days - HiC_rep2

description: EGFP_forHP1merge_40kb.ICEcor.Norm.ginteractions.tsv


title: genomic DNA from bone metastasis sample 70 [Met.70]

source_name: bone metastasis sample

value: Castration-resistant prostate cancer

tag: meta-c class

value: MetA

value: Yes

tag: ar activity score

tag: proliferation score

tag: mca class

value: Positive


title: SpenKO#D4(iXist-ChrX)_NoDox_0h_H2AK119ub1

tag: Sex

tag: genotype/variation

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); deletion of Spen RRM domain (spurious truncated product)

tag: chip antibody


title: OSC - EGFP-KD-2days - HiC_rep1

value: Ovarian Somatic Cells


title: Gefitinib 2

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

country: France

institute: Inserm

data_processing:
Trimming of first 15bp of each read to eliminate compositional bias
STAR alignment in 2 passes with default parameters against Ensembl human genome GRCh38
Read count extraction with HTSeq-count
Only "protein coding" genome features were kept for subsequent processing
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: notch-counts-all.txt
Supplementary_files_format_and_content: normalized-counts-coding.txt

source_name: NSCLC cell line

growth_protocol: Cells were cultured in RPMI1640 containing 10 % FCS  in an atmosphere of humidified 5% CO2 at 37°C and passed twice a week.

extract_protocol:
total RNA were extracted using the Rneasy kit from qiagen. RNA integrity was checked with the Agilent RNA 6000 nano kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 72 h with DBZ (250 nM) (or DMSO as vehicle), then serum-starved overnight and treated with 1µM gefitinib for the final 6h of incubation.

value: PC9ER cells (PMID:   29212784)

value: Gefitinib 1microM

value: NSCLC


title: WT(iXist-ChrX)_NoDox_0h_H2AK119ub1_Rep2

value: 129S x Cast

value: mESC


title: WT(iXist-ChrX)_Dox_24h_H2AK119ub1_Rep2

value: female


title: genomic DNA from non-malignant sample 1 [N.1]

tag: disease stage

tag: epithelial fraction


title: Gefitinib 1

tag: cell type


title: Gefitinib 3

tag: treatment


title: WT(iXist-ChrX)_Dox_24h_H2AK119ub1_Rep1


title: OSC - Egg-KD - HiC_rep2

description: EGGmerge_40kb.ICEcor.Norm.ginteractions.tsv

value: Egg-KD


title: OSC - HP1-KD-2days - HiC_rep2


title: WT(iXist-ChrX)_NoDox_0h_H2AK119ub1_Rep1


title: Control 3

value: DMSO


title: genomic DNA from non-malignant sample 2 [N.2]

value: Untreated

tag: ar gene amplification


title: genomic DNA from bone metastasis sample 68 [Met.68]

value: MetB

value: Negative


title: OSC - Egg-KD - HiC_rep1


title: hESC_naive_ntc

description:
Naive hESCs non-targeting control
GTCGATA-2

value: Embryonic stem cells

value: Naive

value: non-targeting control


title: genomic DNA from bone metastasis sample 67 [Met.67]

value: Castration-resistant prostate cancer

value: MetA

value: Yes


title: Control 2

value: PC9ER cells (PMID:   29212784)


title: OSC - H1-KD - HiC_rep2

description: H1merge_40kb.ICEcor.Norm.ginteractions.tsv

value: Ovarian Somatic Cells


title: genomic DNA from bone metastasis sample 66 [Met.66]

value: MetC


title: OSC - H1-KD - HiC_rep1


title: WT_2

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015)
Biological read: read1 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: WT normal colon

growth_protocol: in vivo mouse model

extract_protocol:
Mouse epithelial cell suspensions were obtained by standard dissociation (refer to manuscript). Viable cells were enriched with MACS. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

treatment_protocol: standard AOM/DSS regimen or injection with tamoxifen (refer to manuscript)

tag: tissue

value: WT normal colon


title: OSC - EGFP-KD - HiC_rep1 [forEGGH1]

description: EGFP_forEGGH1merge_40kb.ICEcor.Norm.ginteractions.tsv

tag: cell line

value: EGFP-KD


title: genomic DNA from bone metastasis sample 65 [Met.65]

value: No

value: Positive


title: OSC - EGFP-KD - HiC_rep2 [forEGGH1]


title: genomic DNA from bone metastasis sample 69 [Met.69]


title: Adj_normal_2

source_name: adj normal colon Lrig1;Apc

value: adj normal colon Lrig1;Apc


title: WT_1


title: genomic DNA from bone metastasis sample 64 [Met.64]


title: C. frutescens Fruit

city: New Delhi

first: Nirala

last: Ramchiary

address: lab-229, school of life sciences, JNU, New Delhi - 110067

department: School of life sciences

country: India

institute: Jawaharlal Nehru University

data_processing:
miRNA profiling
Supplementary_files_format_and_content: miRNAs and counts

organism: Capsicum frutescens

source_name: Fruit

growth_protocol: For small RNA, one genotype each from Bhut jolokia (C. chinense) and C. frutescens (Accesion 4) with contrasting fruit characters was selected. The seeds of Bhut jolokia and Acc. 4 were surface sterilized with 4% sodium hypochlorite, germinated in the petri-dish using moist germination paper and transfer to glass house in pots after one week and grown at 24-26°C with 16 hours light period until fruit setting and maturity. For fruit tissues, samples were collected at various fruit developmental stages such as 5 Day Post Anthesis (DPA), 10DPA, 20DPA, Breaker (30-45DPA), and Mature (45-60 DPA). All the fruit stages were pooled and considered as the fruit tissue sample. The fully expanded fresh leaf and flower buds of different size and age along with stem were collected from healthy matured glass house grown plants.

extract_protocol:
The RNA Extraction was carried out using Macherey-Nagel NucleoSpin RNA kit (MN, US). The total RNA were pooled from the three biological replicates from the individual tissue samples. Further, the quality, and the quantity of RNAs was estimated with Bioanalyzer (Agilent) plant Nano kit.
For small RNA library preparation, RNA samples with 260/280 ratio of 1.9–2.0 and RNA integrity number (RIN) of ≥ 8 were selected. The sRNA libraries were prepared by using TruSeq Small RNA sample preparation kit (Illumina, US). Each sRNA library was sequenced using Illumina Genome Analyser II at Genotypic Technologies Pvt. Ltd, Bangalore, India.

value: Fruit


title: C. frutescens Flower

source_name: Flower

value: Flower


title: genomic DNA from bone metastasis sample 63 [Met.63]

value: Negative


title: C. frutescens Stem

source_name: Stem

value: Stem


title: genomic DNA from bone metastasis sample 62 [Met.62]


title: Apc_tumor_1

source_name: tumor Lrig1;Apc

value: tumor Lrig1;Apc


title: AOM/DSS_3

source_name: AOM/DSS tumor

value: AOM/DSS tumor


title: OSC - Nxf2-KD - HiC_rep1

description: NXF2merge_40kb.ICEcor.Norm.ginteractions.tsv


title: C. frutescens Leaf

source_name: Leaf

value: Leaf


title: Control 1

value: DMSO

value: NSCLC


title: OSC - EGFP-KD - HiC_rep2 [forNXF2]

description: EGFP_forNXF2merge_40kb.ICEcor.Norm.ginteractions.tsv


title: Pooled sera_51132

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622685.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

organism: Streptococcus pyogenes

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: Pooled sera

tag: strain

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar

value: M1T1 clone


title: AOM/DSS_2


title: OSC - EGFP-KD - HiC_rep1 [forNXF2]

value: Ovarian Somatic Cells


title: genomic DNA from bone metastasis sample 61 [Met.61]

value: Castration-resistant prostate cancer

tag: meta-c class

value: MetA

value: Yes

tag: ar activity score

tag: proliferation score

tag: mca class


title: genomic DNA from bone metastasis sample 60 [Met.60]

tag: disease stage

tag: epithelial fraction

value: Positive


title: AOM/DSS_1


title: Pooled sera_51131


title: genomic DNA from bone metastasis sample 59 [Met.59]

tag: ar gene amplification


title: genomic DNA from bone metastasis sample 58 [Met.58]

value: MetC


title: RNA-seq of WT cells after 24 h growth in YEME liquid medium at 30C in the presence of congocidine 1µg/ml - replicate 3

city: Gif-sur-Yvette

first: Stéphanie

middle: Germaine

last: Bury-Moné

address: 1 Avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell

description: Library prepared with Total RNA Stranded (reversely stranded) kit => The R1 file corresponds to antisense orientation, and R2 to the sense orientation.

data_processing:
STAR software was used for mapping RNA-seq to the reference genome (genome-build-accession NCBI_Assembly: GCF_001267885.1) containing only one terminal inverted repeat (TIR), to avoid any biases associated to multiple mapping within the duplicated extremities of the genome (since the two TIR sequences are indiscernible).
FeatureCounts program was used to quantify reads in sense and antisense orientation generated from RNA-sequencing technology in terms of “Gene” feature according to S. ambofaciens ATCC 23877 most recent annotation (GCF_001267885.1_ASM126788v1_genomic.gff – released on the 06/15/2020).
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
mapping against Streptomyces ambofaciens chromosome (without considering the Terminal Inverted Repeats):  bowtie2 --very-sensitive local
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Binning at  10kb.
Genome_build: Streptomyces ambofaciens ATCC 23877
Supplementary_files_format_and_content: RNA-seq data in txt format. 791x791 normalized contact matrix in txt format for the 3C-seq data.

organism: Streptomyces ambofaciens ATCC 23877

source_name: WT cells

growth_protocol: Twenty million spores of S. ambofaciens ATCC 23877 were inoculated in 100 ml of media before growth at 30°C in a shaking agitator (220 rpm, INFORS HT multitron standard). Media composition: MP5 medium (7 g/l yeast extract, 20.9 g/l MOPS, 5 g/l NaCl, 1 g/l NaNO3, 36 ml/l glycerol – pH 7.5) , or YEME medium 10.3 % saccharose (3 g/l yeast extract, 5 g/l bactotryptone, 3 g/l malt extract, 10 g/l glucose, 103 g/l saccharose; pH 7.0-7.2)

extract_protocol:
Pellets were washed with 1 ml of DEPC water, centrifuged for 5 min at 16,000 g at 4°C, and homogenized with glass beads (≤ 106 µm; G4649, SIGMA) in 350 µl of lysis buffer (RNeasy Plus Mini Kit, QIAGEN) supplemented with 10 µl/ml β-mercaptoethanol. Samples were processed 3 times for 45 sec each in FastPrep-24TM 5G instrument (MP Biomedicals) at setting 6 with 1 min cooling between the stages. After centrifugation for 10 min at 16,000 g at 4°C, total RNAs were isolated from the supernatants using RNeasy Plus Mini Kit (QIAGEN) and gDNA Eliminator columns, following manufacturer’s recommendations. To remove genomic DNA, RNA samples were incubated from 30 min at 37°C with 20 U of RNase-free DNase I (Roche) in a final reaction volume of 30 µl. RNA were then cleaned up using the RNeasy Mini Kit (QIAGEN), following manufacturer’s recommendations. The absence of DNA in the preparations was checked by PCR on an aliquot. RNA samples were quantified using QubitTM RNA HS Assay kit (ThermoFischer Scientific), following manufacturer’s recommendations.  Total RNA quality was assessed on an Agilent Bioanalyzer 2100, using RNA 6000 pico kit (Agilent Technologies). 500 ng of total RNA were treated with DNAse (Baseline Zero DNAse, Epicentre) prior to ribosomal RNA depletion using the RiboZero bacteria magnetic Kit from Illumina according to the manufacturer recommendations. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion.
Libraries were pooled in equimolar proportions and sequenced (Paired-end 2x43 bp) on an Illumina NextSeq500 instrument, using a NextSeq 500 High Output 75 cycles kit. Demultiplexing has been done (bcl2fastq.gz2 V2.2.18.12) and adapters (adapter_3p_R1: AGATCGGAAGAGCACACGTCTGAACT; adapter_3p_R2: AGATCGGAAGAGCGTCGTGTAGGGA) were trimmed with Cutadapt1.15, only reads longer than 10 bp were kept.

treatment_protocol: 25 ml (for samples harvested after 24 h growth) or 10 ml of cultures (for other time points) were added to an equal volume of cold ethanol. Cells were then harvested through centrifugation for 15 min at 4,000 g at 4°C, and stored at -20°C.

tag: genotype

value: WT


title: Adj_normal_1

tag: tissue

value: adj normal colon Lrig1;Apc


title: TNFa 6 [BH181212-sample-7]

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

state: CA

address: 1450 Biggy Street

department: MMI

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v3.5.3) with default parameter settings
Gencode M20 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: TNFa_sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated ILC2s after 3 i.p. injections of 1µg rm-IL33 were stimulated with rm-IL-2 (10ng/mL) and rm-IL-7 (10ng/mL) at 37°C with rmTNFa (40ng/mL) or PBS control for 48 hours.

value: BALB/c

tag: age

value: 6 weeks

tag: treatment

value: TNFa

value: lung

tag: cell type

value: sorted ILC2s


title: Pooled sera_51133

tag: growth media

tag: strain

tag: growth time

tag: growth phase


title: TNFa 5 [BH181212-sample-6]


title: TNFa 4 [BH181212-sample-5]


title: RNA-seq of WT cells after 24 h growth in YEME liquid medium at 30C in the presence of congocidine 1µg/ml - replicate 1


title: PBS 3 [BH181212-sample-3]

source_name: PBS_sorted ILC2s

value: PBS


title: RNA-seq of WT cells after 24 h growth in YEME liquid medium at 30C in the presence of congocidine 1µg/ml - replicate 2


title: genomic DNA from bone metastasis sample 57 [Met.57]

value: No

value: Negative


title: genomic DNA from bone metastasis sample 56 [Met.56]


title: Pooled sera_51128

value: Pooled sera

value: 2 hrs exposure to sera

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar

value: M1T1 clone