title: CRISPRi_screen_High_r2

data_processing:
Library strategy: CRISPR screen
Alignment and read counting was performed using MAGeCK (0.5.9.3) with options [count --norm-method control] for all samples together (Li et al. 2014, Li et al. 2015).
Statistical analysis was performed using MAGeCK (0.5.9.3) with options [mle --norm-method control --max-sgrnapergene-permutation 350] (Li et al. 2014, Li et al. 2015)
Genome_build: -
Supplementary_files_format_and_content: Char_candidate_RE.txt: Characterization of the candidatate regulatory elements including genomic location, origin, length and number of guides
Supplementary_files_format_and_content: Char_guides.txt: Characterization of the gRNA library including location, orientation and sequence
Supplementary_files_format_and_content: raw_counts.txt: Raw counts of the individual samples assessed using MAGeCK count
Supplementary_files_format_and_content: mageck_mle.txt: Statistical analysis of the REs calculated using MAGeCK mle (normalized using the NT controls)

extract_protocol:
The PrimeFlow RNA assay (Thermofisher) was used according to the manufacturer’s recommendations. Specifically, the assay was performed in conical 96-well plates for a total of 200 million cells per replicate with 5 million cells per well  using Xist specific probes, labelled with Alexa-Fluor647 (VB1-14258). 20 million cells were snap-frozen after the two fixation steps to be used as the Unsorted fraction.  Samples were resuspended in PrimeFlow™ RNA Storage Buffer before flow cytometry. Here, four different populations were sorted according to Xist expression. In more detail, a Xist-negative population was taken from the bottom-15% of Xist-expressing cells. Three Xist-positive populations were taken in 15%-intervals from the top Xist-expressing cells (0-15% = High, 15-30% = Medium, 30-45% = Low). Around 11-15 million cells were recovered per fraction. After sorting, the cell pellets were snap-frozen and stored at -80°C.  DNA from frozen cell pellets was isolated through phenol/chloroform extraction. Cell pellets were thawed and resuspended in 250 µl of lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2 M NaCl and 5 mM DTT (Roth) in TE Buffer) and incubated overnight at 65°C. The next day 200 µg of RNAse A (Thermo Fisher Scientific) were added and the samples were incubated at 37°C for 1 h. 100 µg of Proteinase K (Sigma) were subsequently added, followed by a 1 h incubation at 50°C. Phenol/chloroform/isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed for 1 min and subsequently centrifuged at 16,000 x g for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 h. DNA was pelleted by centrifugation for 16,000 x g for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50 µl water.
The genomically integrated sgRNA cassette was amplified in two successive PCR reactions as described previously with minor modifications (Shalem et al. 2014). In order to ensure proper library coverage (>300x), 14.5 µg of each sample were amplified using the ReadyMix Kapa polymerase (Roche) with a total of 20 cycles and an annealing temperature of 55°C. Between 0.1-2 µg genomic DNA was amplified per 50 µl PCR reaction. In particular, in samples stained with Flow-FISH the PCR was inhibited at higher DNA concentrations such that up to 145 PCR reactions had to be performed per sample. Successful amplification was verified on a 1% agarose gel and the reactions were pooled. The PCR product was isolated and concentrated using the Zymo DNA Clean and Concentrator Kit. A second nested PCR was performed to attach sequencing adaptors and sample barcodes using 2.5-50µl of the product from the first PCR as template, with a total of 11 cycles and an annealing temperature of 55°C. Resulting amplicons were loaded on a 1% agarose gel and purified using the Nucleospin Gel and PCR clean-up kit (Macherey-Nagel). Libraries were sequenced paired-end 75bp on the NextSeq 500 platform yielding approximately 4*105 fragments per sample.

value: High

value: CRISPRi-Screen


title: TQ8

status: Public on Mar 04 2021

type: SRA

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

library_source: transcriptomic

data_processing:
Removing adaptors and quality filtering
Alignment against D. rerio precursors
Quantification using featureCounts
Differential expression using DESeq2
Genome_build: MirBase 22
Supplementary_files_format_and_content: Plain text. Raw and Normalized Counts

molecule: total RNA

organism: Colossoma macropomum

source_name: Muscle

growth_protocol: Controlled water conditions. Photoperiod 12/12h. Food twice a day.

extract_protocol:
TRIZOL
Truseq-small-rna-sample-prep

treatment_protocol: No treatment.

tag: tissue

value: muscle

tag: development stage

value: Juvenile


title: A549_FOSL1_FLAG cells treated with DEX for 12h - input control - rep1

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

country: USA

institute: Duke University

description: ChIP-seq

library_source: genomic

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Single-end reads were mapped using Bowtie (v1.0.0 PMID: 19261174) against hg38 genome with flags -v 2 -X 2000 --best --strata -m 1.
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads 200bp and converting the read counts to RPKMs.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig signal in RPMs

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Harvested plates at timepoints (0, 1, 4, 8, 12)
ChIP-seq libraries were prepared using a Kapa Hyper Prep kit.

treatment_protocol: Treated with 100 uM Dexamethasone

tag: time point

tag: cell line

value: adenocarcinomic human alveolar basal epithelial


title: CRISPRi_screen_Medium_r2

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: TX1072 XX SP107 cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)) at a density of 3.13*10^4 cells/cm2.

treatment_protocol: The TX SP107 mESC line, carrying an ABA-inducible dCas9-KRAB system, were passaged for two passages in Serum+LIF-containing medium before a total of 6.000.000 cells were transduced with viral supernatant of the sgRNA library (MOI = 0.3). Puromycin selection (1 ng/µl, Sigma) was started two days after transduction and kept for the rest of the experiment. At the next passage, the cells were transferred into a LIF-medium supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon). After two more passages,d ifferentiation was induced for 2 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates.

tag: condition

value: Medium

tag: replicate

tag: strain background

value: CAST / C57BL/6

tag: assay

tag: cell type

value: Mouse embryonic stem cells


title: CRISPRi_screen_High_r1


title: TQ6


title: lung_hypoxia_rep1

type: RNA

city: Xi'an

first: Shujuan

last: Xing

state: Shaanxi

address: 18 Yudou Road, Yanta District,

country: China

institute: Xi’an International University

description: Gene expression after hypoxia in lung

hyb_protocol: 1μl of 25 × Fragmentation Buffer and 5μl 10 × Blocking Agent were added to 1μg labeled cRNA, which were well mixed and incubated at 60℃ for 30 min for cleavage，finally, the labeled cRNA was diluted by adding 25μl 2 × GE Hybridization buffer. 50μl of hybridization solution was distributed to the Arraystar Mouse LncRNA Microarray V3.0. The microarray was in-cubated in Agilent hybrid oven at 65°C for 17 hours.

scan_protocol: The Agilent DNA microarray scanner (part number g2505c) was used to scan the chip.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to collect the probe signal. Genespring GX v12.1 software package of Agilent Technologies was used for data processing and screening of differentially expressed LncRNAs and mRNAs.

label_protocol: Total RNA were extracted from lung of mice and mRNA was purified by removal of rRNA(mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then each sample was amplified with random primers (ArrayStar Flash RNA labeling Kit, ArrayStar), which was transcribed into fluorescent CRNAs along the whole length of the transcript without 3 'bias, and the labeled cRNAs were purified with RNEasy Mini Kit (Qiagen). The specific activity and concentration of the labeled cRNAs (pmol Cy3/μg cRNA) were determined by nanodrop 1000 ultra micro spectrophotometer.

extract_protocol: Total RNA was extracted from the frozen lung tissues using TRIzol (Invitrogen, life Technologies, USA) according to the manufacturer’s protocol. RNA quality was measured by NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. 3 mice in each group were used for total RNA extraction.

treatment_protocol: The lung tissue was frozen in liquid nitrogen

tag: strain

value: lung

tag: Sex

value: male


title: CRISPRi_screen_Medium_r1


title: lung_ hypoxia-normoxia _rep2

description: Gene expression after hypoxia-normoxia in lung


title: lung_hypoxia_rep3

description: Gene expression after hypoxia in lung


title: lung_ hypoxia-normoxia _rep3


title: lung_hypoxia_rep2

description: Gene expression after hypoxia in lung


title: lung_normoxia_rep3

description: Gene expression after normoxia in lung


title: lung_normoxia_rep2

description: Gene expression after normoxia in lung


title: A549_FOSL1_FLAG cells treated with DEX for 01h - input control - rep3

description: ChIP-seq


title: TQ1


title: TQ2


title: CRISPRi_screen_Low_r2

value: Low


title: CRISPRi_screen_Low_r1


title: A549_FOSL1_FLAG cells untreated - input control - rep3

description: ChIP-seq


title: lung_ hypoxia-normoxia _rep1


title: A549_FOSL1_FLAG cells treated with DEX for 01h - input control - rep2

description: ChIP-seq


title: CRISPRi_screen_Negative_r2

value: Negative


title: A549_FOSL1_FLAG cells treated with DEX for 01h - input control - rep1

description: ChIP-seq


title: CRISPRi_screen_Negative_r1


title: A549_FOSL1_FLAG cells untreated - input control - rep2

description: ChIP-seq


title: CRISPRi_screen_Unsorted_r2

value: Unsorted


title: TQ3


title: lung_normoxia_rep1

description: Gene expression after normoxia in lung


title: A549_FOSL1_FLAG cells untreated - input control - rep1

description: ChIP-seq


title: CRISPRi_screen_Unsorted_r1


title: WT_14: BPA+/+_Replicate3

city: Copenhagen

first: Daniela

last: De Zio

state: Non United States Or Canada

address: Strandboulevarden 49

department: Cell Stress and Survival

country: Denmark

institute: Danish Cancer Society

data_processing:
Quality control of the reads and base-calling with FastQC available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc (Genomix4life).
Removal of adapter and very short reads with cutadapt described in Martin et al., EMBnet, 2011 (Genomix4life).
Reads alignment to Mus Musculus (mm10) using STAR version 2.5.3a with standard parameters for paired-reads described in Dobin et al., Bioinformatics, 2013 (Genomix4life).
Transcriptome expression quantification with featureCount (Genomix4life)
Genome_build: The reference track was the assembly mm10 obtained from Ensembl using iGenomes available at https://support.illumina.com/sequencing/sequencing_software/igenome.html (Genomix4life).
Supplementary_files_format_and_content: Excel file including Raw Counts and annotations for each sample.

source_name: 4-OHT induced cutaneous melanoma

extract_protocol:
On dry ice, the top skin of the tumour piece was carefully removed from each sample. After that, the samples were processed according to manufacturer's instructions with the Rneasy Plus Mini Kit from Qiagen (Cat. Number: 74134)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were shaved and treated with 4-hydroxytamoxifen (4-OHT) at 3-weeks of age. Mice were sacrificed 40d after treatment and induced melanoma samples were snap frozen with liquid N2 and stored at -80°C.

value: cutaneous melanoma

value: Female

tag: genotype

value: Tyr::CreERT2/+; BrafV600E/+; Pten-/-; Ambra1+/+


title: A549_cJun_FLAG cells treated with DEX for 12h - input control - rep2

description: ChIP-seq


title: A549_cJun_FLAG cells treated with DEX for 12h - input control - rep1

description: ChIP-seq


title: WT_13: BPA+/+_Replicate2

value: Male


title: WT_12: BPA+/+_Replicate1


title: A549_cJun_FLAG cells treated with DEX for 08h - input control - rep2

description: ChIP-seq


title: A549_cJun_FLAG cells treated with DEX for 08h - input control - rep1

description: ChIP-seq


title: KO_11: BPA-/-_Replicate3

value: Tyr::CreERT2/+; BrafV600E/+; Pten-/-; Ambra1-/-


title: A549_cJun_FLAG cells treated with DEX for 04h - input control - rep3

description: ChIP-seq


title: KO_10: BPA-/-_Replicate2


title: A549_cJun_FLAG cells treated with DEX for 04h - input control - rep2

description: ChIP-seq


title: KO_9: BPA-/-_Replicate1


title: A549_cJun_FLAG cells treated with DEX for 04h - input control - rep1

description: ChIP-seq


title: A549_cJun_FLAG cells treated with DEX for 01h - input control - rep3

description: ChIP-seq


title: 10x Genomics sample 2 cell ranger counts

city: Nanjing

first: Yetao

last: Wang

state: Jiangsu

address: No. 12, Jiangwangmiao street,  Xuanwu District

department: Central Laboratory

institute: Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Sample 65 in sample_metadata.xlsx file
mRNA

data_processing:
For bulk RNA-Seq: The pooled reads were separated by CEL-Seq2 barcodes and mapped to the hg19 genome using Tophat (Kim et al., 2013) (version 2.0.14, default parameters). ESAT (Derr et al., 2016) was used to quantify aligned reads using a transcript annotation file containing all RefSeq genes filtered to select only ‘NM’ transcripts and extending the transcripts up to 1,000 bases past the end of the annotated 3’ end (-wExt 1000, -task score3p), multi-mapped reads (-multimap ignore) were discarded. DEBrowser was used to analyze the most varied genes, DESeq2 was used to perform differential expression analysis (Love et al., 2014). Data was transformed using rlog within DEseq2 and prcomp was used to calculate the PCs for principal component analysis (PCA).
For ATAC-Seq: Paired-end reads were filtered with trimmomatic (version 0.32), aligned with Bowtie2 (version 2.2.3) to a reference genome hg19. The duplicates were removed using Picard’s MarkDuplicates (version 0.32). To be able to accurately call the peaks, each aligned read was first trimmed to the 9-bases at the 5’ end, the region where the Tn5 transposase cuts the DNA. To smooth the peaks, the start site of the trimmed reads were extended up and down stream for 10 bases. Peaks were called 82% P3 + 18% supplement 1using these adjusted aligned reads with MACS2 (Zhang et al., 2008). The adjusted aligned reads were converted to tdf files using IGVTools (IGVtools count –w5) (version 2.3.31)(Robinson et al., 2011) for visualization. For motif analysis, motifs enriched in accessible regions within the enhancers and promoters of NK subsets or ILCs were found by findMotifsGenome from the HOMER2 package. The de-novo motifs found were matched against the HOCOMOCCO11 motif database (using the -mcheck option).
For single cell RNA-Seq: The Cell Ranger software package (10X Genomics) was used to perform sample demultiplexing, barcode processing, and single cell 3' gene counting. Default settings were used. The ﬁltered gene matrices generated by Cell Ranger were used as input into the open-source R package Seurat 3.0 (http://satijalab.org/seurat/) (Satija et al., 2015). FindNeighbors and FindClusters (using the default resolution of 0.6) were then run on the PCA reduction. FindMarkers was used to identify differentially expressed genes among clusters. Pseudotime analysis was done using monocle (version 2)(Qiu et al., 2017b). Cluster information (for color coding the cells for display) was imported from the Seurat analysis. The raw count data from the Seurat object was read into monocle and the standard workflow was followed: estimateSizeFactors, estimateDispersions, and detectGenes(min_expr=1) were called. Then the dispersion table was calculated and then subsetted to generate ordering genes with mean_expression >= 0.1 and dispersion_empirical >= dispersion_fit. The data was reduced to two dimensions and the cells were ordered (using the orderCells function). plot_cell_trajectory was used to create pseudotime trajectories and plot_genes_in_pseudotime (with its default settings, which rescales expression to relative values) used to show individual gene expression as a function of pseudotime.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: alldetected_*.xlsx files include reads for all detected genes.
Supplementary_files_format_and_content: *.tdf files for ATAC-Seq visualization.
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files for 10X Genomics samples.
Supplementary_files_format_and_content: bulk_RNA-Seq_primers_and_ATAC_Seq.xlsx: Each specific sample was assigned a unique barcode. The final library was amplified using uniform primers. This Excel file shows the unique barcode for each sample so that a specific sample can be extracted from the raw data files.
Supplementary_files_format_and_content: sample_metadata.xlsx: Excel file includes the metadata for individual samples.

source_name: human PBMCs

extract_protocol:
CEL-Seq2 method was used for constructing bulk RNA-Seq library (Genome Biol. 17, 77 (2016)).
ATAC-Seq protocol was based on Curr. Protoc. Mol. Biol. 109, 21.29.1–21.29.9 (2015).
Single cell RNA seq protocol was based on Single Cell 3’ Reagent Kits v2 (10x Genomics, 120234).

value: human peripheral blood

tag: hiv-1 positivity

value: HIV-1 negative


title: A549_cJun_FLAG cells treated with DEX for 01h - input control - rep2

description: ChIP-seq


title: donor2 ILCs ATAC-Seq

description: Sample 64 in sample_metadata.xlsx file

value: ILCs

tag: donor


title: A549_cJun_FLAG cells treated with DEX for 01h - input control - rep1

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: Incomplete intestinal metaplasia_donor 19

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: sample type


title: Incomplete intestinal metaplasia_donor 12


title: Incomplete intestinal metaplasia_donor 13


title: Incomplete intestinal metaplasia_donor 2


title: Incomplete intestinal metaplasia_donor 11


title: donor2 CD56negNK cells ATAC-Seq

description: Sample 63 in sample_metadata.xlsx file

value: CD56negNK cells


title: Incomplete intestinal metaplasia_donor 14


title: donor2 CD56dimNK cells ATAC-Seq

description: Sample 62 in sample_metadata.xlsx file

value: CD56dimNK cells


title: Incomplete intestinal metaplasia_donor 17


title: Complete intestinal metaplasia_donor 9

source_name: Intestinal metaplasia_complete subtype

value: Intestinal metaplasia_complete subtype


title: A549_cJun_FLAG cells untreated - input control - rep3

description: ChIP-seq


title: donor2 CD56hiNK cells ATAC-Seq

description: Sample 61 in sample_metadata.xlsx file

value: CD56hiNK cells


title: Incomplete intestinal metaplasia_donor 8


title: Incomplete intestinal metaplasia_donor 10


title: Incomplete intestinal metaplasia_donor 16


title: Complete intestinal metaplasia_donor 10


title: Incomplete intestinal metaplasia_donor 18


title: A549_cJun_FLAG cells untreated - input control - rep2

description: ChIP-seq


title: Incomplete intestinal metaplasia_donor 3


title: Complete intestinal metaplasia_donor 5


title: donor1 ILCs ATAC-Seq

description: Sample 60 in sample_metadata.xlsx file


title: Complete intestinal metaplasia_donor 4


title: Incomplete intestinal metaplasia_donor 5


title: Complete intestinal metaplasia_donor 8


title: Incomplete intestinal metaplasia_donor 1


title: Incomplete intestinal metaplasia_donor 4


title: Complete intestinal metaplasia_donor 11


title: A549_cJun_FLAG cells untreated - input control - rep1

description: ChIP-seq


title: Incomplete intestinal metaplasia_donor 6


title: donor1 CD56negNK cells ATAC-Seq

description: Sample 59 in sample_metadata.xlsx file


title: Incomplete intestinal metaplasia_donor 7


title: Complete intestinal metaplasia_donor 12


title: A549_JUND_FLAG cells treated with DEX for 12h - rep3

description: ChIP-seq


title: Incomplete intestinal metaplasia_donor 9


title: donor1 CD56dimNK cells ATAC-Seq

description: Sample 58 in sample_metadata.xlsx file


title: A549_JUND_FLAG cells treated with DEX for 12h - rep1

description: ChIP-seq


title: Complete intestinal metaplasia_donor 7


title: donor1 CD56hiNK cells ATAC-Seq

description: Sample 57 in sample_metadata.xlsx file


title: donors 1-6, CD56negNK cells sorted from PBMC culture

description:
Samples 51-56 in sample_metadata.xlsx file
mRNA
alldetected_different culture condition.xlsx

value: mixed sample (non-demultiplexed)


title: A549_JUND_FLAG cells treated with DEX for 08h - rep2

description: ChIP-seq


title: donors 1-6, CD56dimNK cells sorted from PBMC/CD4-PBMC/CD4-PBMC+IL-2 culture

description:
Samples 36-50 in sample_metadata.xlsx file
mRNA
alldetected_different culture condition.xlsx


title: A549_JUND_FLAG cells treated with DEX for 08h - rep1

description: ChIP-seq


title: A549_JUND_FLAG cells treated with DEX for 08h - rep3

description: ChIP-seq


title: Complete intestinal metaplasia_donor 6


title: donors 2-4, CD56hiNK/CD56dimNK/CD56negNK cells stimulated

description:
Samples 27-35 in sample_metadata.xlsx file
mRNA
alldetected_NK_stim_vs_no_stim.xlsx


title: A549_JUND_FLAG cells treated with DEX for 04h - rep1

description: ChIP-seq


title: donors 1-4, CD56hiNK/CD56dimNK/CD56negNK/ILC cells

description:
Samples 11-26 in sample_metadata.xlsx file
mRNA
alldetected_NK_vs_ILCs.xlsx


title: A549_JUND_FLAG cells treated with DEX for 01h - rep3

description: ChIP-seq


title: donors 1-5, Lin-CD45+CD56-CD127-/Lin-CD45+CD56-CD127+ cells

description:
Samples 1-10 in sample_metadata.xlsx file
mRNA
alldetected_CD127plus_vs_CD127minus.xlsx


title: Multifocal chronic atrohic gastritis_donor 12

source_name: Multifocal chronic atrohic gastritis

value: Multifocal chronic atrohic gastritis


title: H69M_K27Me3

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Aligned to hg19 with Bowtie2 with a setting of -k 1 and defalut parameters. Duplicates were marked by samtools (0.1.19).
Peaks were called using MACS1.4.2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: BED files with peaks

source_name: H69M cell line

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde for 10 min, washed in 5 mg/ml bovine serum albumin (BSA) before re-suspended in lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, 1× protease inhibitor cocktail) and sonicated with the Covaris M220 sonicator to obtain chromatin fragment lengths of 100-to-1,000 bp. Fragmented chromatin was diluted in IP buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and incubated with Protein G magnetic beads (Dynabeads, Thermo Fisher Scientific, Waltham, MA) pre-incubated with anti-H3K27Ac (ab4729, Abcam, Cambridge, UK) or anti-H3K27me3 (clone C36B1, Cell Signaling Technologies, Danvers, MA) antibodies. Immunoprecipitates were washed six times with wash buffer (50 mM HEPES pH 7.6, 0.5 M LiCl, 1 mM EDTA, 0.7% Na deoxycholate, 1% IGEPAL CA-630) and twice with TE buffer. Immunoprecipitated (or no IP input) DNA was treated with RNase A and Proteinase K on the beads, and recovered in 1% SDS and 0.1 M NaHCO3.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit (Cat# E7645, New England Biolabs, Ipswich, MA). Sequencing was performed on NextSeq500 (Illumina, San Diego, CA) for 38 nucleotides each from paired ends according to the manufacturer’s instructions.

treatment_protocol: H69M cells were derived from H69 cells as in Canadas et al. 2014 (PMID 24284055).

value: Small cell lung cancer

tag: chip antibody

value: H3K27Me3 (Cell Signaling Technologies, clone C36B1)


title: Complete intestinal metaplasia_donor 2


title: A549_JUND_FLAG cells treated with DEX for 01h - rep1

description: ChIP-seq


title: Multifocal chronic atrohic gastritis_donor 13


title: A549_JUND_FLAG cells treated with DEX for 01h - rep2

description: ChIP-seq


title: H69M_K27Ac

value: H3K27Ac (Abcam, clone ab4729)


title: Complete intestinal metaplasia_donor 3


title: A549_JUND_FLAG cells untreated - rep3

description: ChIP-seq

source_name: A549_JUND_FLAG cells untreated - rep3


title: Multifocal chronic atrohic gastritis_donor 11


title: Complete intestinal metaplasia_donor 1


title: A549_JUND_FLAG cells untreated - rep2

description: ChIP-seq

source_name: A549_JUND_FLAG cells untreated - rep2


title: H69_K27Me3

source_name: NCI_H69 cell line


title: Multifocal chronic atrohic gastritis_donor 10


title: H69_K27Ac


title: A549_JUND_FLAG cells untreated - rep1

description: ChIP-seq

source_name: A549_JUND_FLAG cells untreated - rep1


title: Multifocal chronic atrohic gastritis_donor 7


title: A549_JunB_FLAG cells treated with DEX for 12h - rep3

description: ChIP-seq


title: Multifocal chronic atrohic gastritis_donor 1


title: H69M_input

value: Input


title: Multifocal chronic atrohic gastritis_donor 8


title: Multifocal chronic atrohic gastritis_donor 5


title: H69_input


title: Multifocal chronic atrohic gastritis_donor 6


title: Non-atrophic gastritis_donor 4

source_name: non atrophic gastritis

value: non atrophic gastritis


title: Multifocal chronic atrohic gastritis_donor 2


title: Non-atrophic gastritis_donor 7


title: Multifocal chronic atrohic gastritis_donor 3


title: Multifocal chronic atrohic gastritis_donor 4


title: Non-atrophic gastritis_donor 9


title: Non-atrophic gastritis_donor 5


title: Non-atrophic gastritis_donor 8


title: BCO6-Scaffolds

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

data_processing:
Paired-end reads were aligned to human genome (hg38) using STAR  (2.7.6a) with the default settings.
Subsampling was applied to have different samples with comparable reads using SAMtools(1.7).
The number of mapped fragments was quantified at gene level using featurecount (2.0.1) with the following parameters, -p -g gene_name, based on Gencode annotation (v30).
The R package DESeq2 (1.26.0 on R 3.6.1) was used for differential gene expression analysis and for generating PCA and heatmap plots. Vst normalized counts were generated using vst function from DESeq2, and transformed to Z-scores.
Pheatmap package was used to generate heatmap plots using either vst normalized counts or Z-scores as input.
R package fgsea (1.12.0) was used for GSEA analysis
Genome_build: hg38
Supplementary_files_format_and_content: Raw_gene_counts_matrix2.txt

source_name: human cholangiocyte organoids seeded on human ductal scaffolds

growth_protocol: Huch et al. Cell 2015 and Soroka et al. Hepatology 2018. For the cells cultured in 2D system, BCOs were seeded on fully empty human EHBD scaffolds.

extract_protocol:
Total RNA was collected after removal of the culture medium by adding 700µl of QIAzol lysis reagent (Qiagen) to a 24 well containing organoids (two 25µL BME/matrigel domes). RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer’s protocol16 and the concentration was measured using a NANOdrop 2000 (ThermoFisher)
500 ng of total RNA was used for library construction using KAPA RNA Hyper + RiboErase HMR kit (Roche 08098140702)

treatment_protocol: No treatment applied

value: ERCP organoids cultured on human ductal scaffolds


title: A549_JunB_FLAG cells treated with DEX for 12h - rep2

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 08h - rep3

description: ChIP-seq


title: Non-atrophic gastritis_donor 2


title: Normal mucosa_donor 9

source_name: Normal gastric mucosa

value: Normal gastric mucosa


title: Multifocal chronic atrohic gastritis_donor 9


title: Normal mucosa_donor 8


title: Non-atrophic gastritis_donor 6


title: BCO7-Scaffolds


title: Non-atrophic gastritis_donor 10


title: BCO5-Scaffolds


title: BCO5-3D

source_name: human cholangiocyte organoids

value: human cholangiocyte organoids generated from ERCP


title: Non-atrophic gastritis_donor 3


title: A549_JunB_FLAG cells treated with DEX for 08h - rep2

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 08h - rep1

description: ChIP-seq


title: Non-atrophic gastritis_donor 1


title: BCO6-3D


title: Normal mucosa_donor 5


title: A549_JunB_FLAG cells treated with DEX for 04h - rep3

description: ChIP-seq


title: Normal mucosa_donor 4


title: Normal mucosa_donor 7


title: Normal mucosa_donor 6


title: Normal mucosa_donor 10


title: A549_JunB_FLAG cells treated with DEX for 04h - rep2

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 12h - rep1

description: ChIP-seq


title: BCO7-3D


title: A549_JunB_FLAG cells treated with DEX for 04h - rep1

description: ChIP-seq


title: A549_JunB_FLAG cells treated with DEX for 01h - rep3

description: ChIP-seq


title: Normal mucosa_donor 3


title: A549_JunB_FLAG cells treated with DEX for 01h - rep2

description: ChIP-seq


title: NS12 NICD3 day 7

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Homo sapiens genome reference (GRCh38/hg38) using the TopHat component of Tuxedo Suite software, then cuffquant and cuffdiff were used for gene-level read counting and differentially expression analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text file includes locus, REFSEQ isoform id, Gene name and raw read counts for each transcript, in each sample

source_name: primary human bronchial epithelial cells (HBECs)

growth_protocol: Primary human bronchial epithelial cells (HBECs) from nonsmokers cultured on air-liquid interface (ALI) for up to 7 days. Briefly, 1 x 105 cells in 100 µl of BronchiaLifeTM epithelial airway medium (BLEAM) (Cat# LL-0023, Lifeline® Cell Technology, Oceanside, CA, USA) were seeded in the apical chamber of a 0.4 µm pore-sized Transwell® insert (Cat# 3470, Corning®, Corning, NY, USA) pre-coated with human type IV collagen (Cat# C7521, Sigma Aldrich, St. Louis, MO, USA) with 1 ml of BLEAM in the basolateral chamber (ALI day -2). The following day, fresh BLEAM media was replaced in the apical and basolateral chambers (100 µl and 1 ml, respectively). Following two days of submerged culture, media from the apical chamber was removed to expose the cells to air (ALI day 0), and 1 ml of HBTEC ALI differentiation medium (Cat# LM-0050, Lifeline® Cell Technology) supplemented with Penicillin (100 I.U./ml) - Streptomycin (100 µg/ml) was added to the basolateral chamber. The media was replaced every other day and the cells allowed to differentiate for up to 7 days.

extract_protocol:
Total RNA was extracted via direct lysis of cells in the ALI well using the PureLinkTM RNA mini kit (Cat# 12183018A, Thermo Scientific, Waltham, MA, USA) and included DNase treatment (Cat# 12185-010, Thermo Scientific) on the column to remove contaminating genomic DNA. RNA concentrations were measured with a NanoPhotometer® N60 (Implen, Westlake Village, CA, USA)
RNA-sequencing was performed on a NextSeq 500 Flowcell, High SR75 (Illumina, San Diego, CA, USA) following library preparation using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). The library preparation and sequencing were performed by the Clinical Genomics Core at the Oklahoma Medical Research Foundation

treatment_protocol: HBECs were infected with either Lenti-Control or Lenti-NICD3 at a multiplicity of infection of 50 (5 x 106 viral genomes/1 x 105 cells) at the time of seeding the cells on ALI to ensure that >90% of cells were infected (GFP+) with each virus. To aid virus infection, the BLEAM media was supplemented with 2 μg/ml of polybrene (catalog number TR-1003-G, Sigma Aldrich). The next day, fresh media was added to the wells and the standard ALI protocol was continued until the day of harvest.

tag: patient

value: nonsmoker donor 6

tag: treatment

value: day 7

value: HBEC (Primary human bronchial epithelial cells )


title: NS12 NICD3 day 3

value: day 3


title: NS12 NICD3 day 0

value: day 0


title: Normal mucosa_donor 2


title: NS12 NICD3 day 5

value: day 5


title: A549_JunB_FLAG cells treated with DEX for 01h - rep1

description: ChIP-seq

tag: tissue

value: adenocarcinomic human alveolar basal epithelial


title: NS12 GFP day 7

value: Lenti-Control

tag: time point


title: A549_JunB_FLAG cells untreated - rep3

description: ChIP-seq

source_name: A549_JunB_FLAG cells untreated - rep3

tag: cell line


title: NS12 GFP day 5


title: Normal mucosa_donor 1


title: A549_JunB_FLAG cells untreated - rep2

description: ChIP-seq

source_name: A549_JunB_FLAG cells untreated - rep2


title: NS12 GFP day 3


title: A549_JunB_FLAG cells untreated - rep1

description: ChIP-seq

source_name: A549_JunB_FLAG cells untreated - rep1


title: Intestinal_adyacent_normal tissue_donor 21

source_name: Normal paired_adyacent  to tumor

value: Normal paired_adyacent  to tumor


title: Intestinal_adyacent_normal tissue_donor 24


title: NS12 GFP day 0


title: Intestinal_adyacent_normal tissue_donor 20


title: A549_FOSL2_FLAG cells treated with DEX for 12h - rep3

description: ChIP-seq


title: Intestinal_adyacent_normal tissue_donor 17


title: Intestinal_adyacent_normal tissue_donor 19


title: NS11 NICD3 day 7

value: nonsmoker donor 5


title: A549_FOSL2_FLAG cells treated with DEX for 12h - rep2

description: ChIP-seq


title: Intestinal_adyacent_normal tissue_donor 18


title: Intestinal_adyacent_normal tissue_donor 23


title: NS11 NICD3 day 5


title: Intestinal_adyacent_normal tissue_donor 16


title: A549_FOSL2_FLAG cells treated with DEX for 12h - rep1

description: ChIP-seq


title: Intestinal_adyacent_normal tissue_donor 22


title: Intestinal_adyacent_normal tissue_donor 12


title: NS11 NICD3 day 3


title: Diffuse_adyacent_normal tissue_donor10


title: Intestinal_adyacent_normal tissue_donor 15


title: A549_FOSL2_FLAG cells treated with DEX for 08h - rep3

description: ChIP-seq


title: NS11 NICD3 day 0


title: Diffuse_adyacent_normal tissue_donor5


title: Intestinal_adyacent_normal tissue_donor 14


title: Diffuse_adyacent_normal tissue_donor11


title: Diffuse_adyacent_normal tissue_donor7


title: A549_FOSL2_FLAG cells treated with DEX for 08h - rep2

description: ChIP-seq


title: NS11 GFP day 7


title: Diffuse_adyacent_normal tissue_donor3


title: Diffuse_adyacent_normal tissue_donor4


title: Intestinal_adyacent_normal tissue_donor 13


title: NS11 GFP day 5


title: A549_FOSL2_FLAG cells treated with DEX for 04h - rep3

description: ChIP-seq


title: Diffuse_adyacent_normal tissue_donor1


title: NS11 GFP day 3


title: A549_FOSL2_FLAG cells treated with DEX for 04h - rep2

description: ChIP-seq


title: NS11 GFP day 0


title: A549_FOSL2_FLAG cells treated with DEX for 04h - rep1

description: ChIP-seq


title: Diffuse_adyacent_normal tissue_donor8


title: Intestinal_cancer tissue_donor 24

source_name: Tumor biopsy intestinal subtype

value: Tumor biopsy intestinal subtype


title: A549_FOSL2_FLAG cells treated with DEX for 08h - rep1

description: ChIP-seq


title: Diffuse_adyacent_normal tissue_donor2


title: Diffuse_adyacent_normal tissue_donor9


title: Intestinal_cancer tissue_donor 21


title: Diffuse_adyacent_normal tissue_donor6


title: A549_FOSL2_FLAG cells treated with DEX for 01h - rep3

description: ChIP-seq


title: NS10 NICD3 day 7

value: nonsmoker donor 4


title: NS10 NICD3 day 5


title: A549_FOSL2_FLAG cells treated with DEX for 01h - rep2

description: ChIP-seq


title: Intestinal_cancer tissue_donor 16


title: ORF5-PK15 2

city: Seoul

first: Chang-Yong

last: Choi

address: 145, Anam-ro, Seongbuk-gu

department: Department of Biotechnology

country: South Korea

institute: Korea University

description: viral protein expression

data_processing:
Tophat v2.0.13 incorporates the Bowtie v2.2.3 algorithm to perform the alignment
Tophat initially removes a portion of the reads based on the quality information accompanying each read before it maps reads to the reference genome
Transcript assembly and abundance estimation using Cufflinks v2.2.1
The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) from Cufflinks
Genes with one more than zeroed FPKM values in the samples were excluded. To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes
Genome_build: GCF_000003025.5
Supplementary_files_format_and_content: Excel spreadsheet format which includes contents; 1) Gene_symbol, 2) NCBI Protein accession ID, 3) Product, 4) Fold change, 5) Volume, 6) GOmap stat, 7) GOmap genes, 8) KEGG stat, 9) KEGG genes

organism: Sus scrofa

source_name: PK15 cell line

extract_protocol:
Total RNA was isolated from PK15 cells using TRIzol reagent according to the manufacturer's instructions.
In order to construct cDNA libraries with the TruSeq mRNA LT library kit (Illumina, USA), 1 g of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100 nt paired-end sequencing by Illumina HiSeq4000 (Illumina)

value: kidney

value: epithelial cell

tag: transfection

value: PCV2ORF5/pLNCX2 (ORF5-PK15)


title: ORF5-PK15 3

description: viral protein expression


title: NS10 NICD3 day 0


title: ORF5-PK15 1

description: viral protein expression


title: Intestinal_cancer tissue_donor 23


title: A549_FOSL2_FLAG cells treated with DEX for 01h - rep1

description: ChIP-seq


title: Intestinal_cancer tissue_donor 17


title: A549_FOSL2_FLAG cells untreated - rep3

description: ChIP-seq

source_name: A549_FOSL2_FLAG cells untreated - rep3


title: Ovary-Control-6 (C6)

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, the clean reads were mapped onto the reference mouse genome mm10 using the bowtie2 (version 2.1.0)
The mapped tags were then aligned against miRBase (version 22.1), and read counts were calculated through customized script.
Reads per million mapped reads (RPM) were calculated.
The target genes of DEmiRs were predicted through miRTarbase database
Genome_build: mm10
Supplementary_files_format_and_content: Xlsx file includes matrix table with raw miRNA reads count and RPM values for every miRNA and every sample

source_name: ovary

extract_protocol:
Total RNA was extracted from ovarian tissue samples by using TRIzol reagents (Invitrogen, Waltham, Massachusetts, USA) as recommended by the manufacturer. The total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running 1.5% agarose gel electrophoresis and staining with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
One microgram of total RNA was used to construct the small RNA-seq libraries by TruSeq® Small RNA Library Prep Kit (NEB, San Diego, California, USA) following the manufacturer’s protocol. The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

value: ovary

value: ICR

value: No treatment

tag: age

value: 8 weeks


title: Intestinal_cancer tissue_donor 20


title: Intestinal_cancer tissue_donor 12


title: Intestinal_cancer tissue_donor 19


title: Intestinal_cancer tissue_donor 15


title: Mock-PK15 3

value: pLNCX2 (Mock-PK15)


title: NS10 GFP day 7

value: day 7

value: HBEC (Primary human bronchial epithelial cells )


title: Intestinal_cancer tissue_donor 13


title: Ovary-Control-3 (C3)


title: NS10 GFP day 5

value: day 5


title: Intestinal_cancer tissue_donor 18


title: A549_FOSL2_FLAG cells untreated - rep1

description: ChIP-seq

source_name: A549_FOSL2_FLAG cells untreated - rep1

value: adenocarcinomic human alveolar basal epithelial


title: Mock-PK15 2


title: Diffuse_cancer tissue_donor11

source_name: Tumor biopsy diffuse subtype

value: Tumor biopsy diffuse subtype


title: Ovary-Control-2 (C2)


title: Mock-PK15 1


title: A549_FOSL2_FLAG cells untreated - rep2

description: ChIP-seq

source_name: A549_FOSL2_FLAG cells untreated - rep2


title: NS10 NICD3 day 3

value: day 3


title: NS10 GFP day 3

value: Lenti-Control


title: Ovary-PCOS-4 (P4)

value: Offspring born in DHT exposure during pregnancy


title: Ovary-PCOS-3 (P3)


title: A549_FOSL1_FLAG cells treated with DEX for 12h - rep2

description: ChIP-seq


title: NS10 GFP day 0

value: nonsmoker donor 4

value: day 0


title: NS9 NICD3 day 7

value: nonsmoker donor 3


title: Diffuse_cancer tissue_donor2


title: Intestinal_cancer tissue_donor 22

value: Tumor biopsy intestinal subtype


title: Diffuse_cancer tissue_donor5


title: Diffuse_cancer tissue_donor10


title: Ovary-PCOS-2 (P2)

value: ovary


title: NS9 NICD3 day 5


title: A549_FOSL1_FLAG cells treated with DEX for 12h - rep1

description: ChIP-seq


title: Diffuse_cancer tissue_donor6


title: Endothelial 2H11 cells treated with BMP4 and Palovarotene_rep1

city: Houston

first: GUOYU

last: YU

state: TX

address: 1515 Holcombe Blvd, Houston,

department: Translational Molecular Pathology

institute: MD Anderson Cancer Center

data_processing:
Sequence quality was examined using the FastQC.
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to reference genome using Hisat2 software.
The aligned reads were assembled to transcripts by StringTie and FPKMs were computed.
The differentially expression of the genes and transcripts were analyzed using Ballgown R package.
rMATS was used to analzye alternative splicing events.
Genome_build: GENCODE mouse GRCm38
Supplementary_files_format_and_content: Gene/transcript expression levels in FPKM

molecule: polyA RNA

source_name: axillary lymph node/vascular epithelium

extract_protocol: Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT)  magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina HiSeq 4000 system.

treatment_protocol: Strave 2H11 cells and use BMP4 or BMP4 plus Palovarotene treat cells for 48 hours

value: axillary lymph node/vascular epithelium

value: BMP4 and Palovarotene treated for 48 hours


title: Diffuse_cancer tissue_donor4


title: A549_FOSL1_FLAG cells treated with DEX for 08h - rep3

description: ChIP-seq


title: Diffuse_cancer tissue_donor7


title: Ovary-PCOS-1 (P1)

value: ICR

value: 8 weeks


title: NS9 NICD3 day 3


title: Endothelial 2H11 cells treated with BMP4_rep3

value: BMP4 treated for 48 hours


title: MO 5: NSD3 Morpholino Replicate 5

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
Reads were trimmed with Trimmomatic (version 0.32) and mapped to the Gallus_gallus GRCg6a genome (Ensembl) using STAR (version 2.5.3a).
Gene abundance estimates were determined with Ensembl version 100 annotations for Galgal6 using Rsubread (version 1.28.1).
Differential gene expression was determined with DESeq2 ( version 1.28.1)
Genome_build: GRCg6a
Supplementary_files_format_and_content: xlsx: lists of differentially expressed genes and FPKM values; bigWig: genome wide transcript coverage data.

organism: Gallus gallus

source_name: cranial neural folds

growth_protocol: Fertilized eggs were obtained from Sunnyside Eggs (Beaver Dam, WI) and Hoover’s Hatchery (Rudd, IA). Eggs were incubated in humidified incubators (G.Q.F. Manufacturing, Savannah, GA) at 39°C until the desired developmental stage.

extract_protocol:
Cranial neural fold explants were placed in Ringer’s saline on ice for a maximum of 1 hour. Neural fold explants were homogenized in TRIzol Reagent (ThermoFisher Scientific, Waltham, MA) and stored at -80°C until bilateral cranial neural folds from 60 embryos of each condition were collected. These homogenized samples were then pooled in groups of 12, creating five biological replicates for each condition. Total RNA was isolated by TRIzol extraction, then cleaned by following the RNA Cleanup protocol with RNeasy spin columns (QIAGEN, Velencia, CA).
Poly(A)+ RNA was selected from total RNA using the Illumina TruSeq stranded mRNA kit (San Diego, CA).

treatment_protocol: Hamburger and Hamilton (HH) stage 4 to 5 embryos were bilaterally electroporated with 0.5 mM mmMO or NSD3 MO and 300 ng/µL pCS2+myc (Turner and Weintraub, 1994) carrier DNA.

value: 0.5mM NSD3 MO

tag: developmental stage

value: 5-7 somite chick embryos

tag: number of animals

value: Pool of 12 embryos


title: Diffuse_cancer tissue_donor9

value: Tumor biopsy diffuse subtype


title: NS9 GFP day 7

value: day 7

tag: cell type

value: HBEC (Primary human bronchial epithelial cells )


title: NS9 NICD3 day 0


title: Diffuse_cancer tissue_donor3


title: MO 4: NSD3 Morpholino Replicate 4


title: Diffuse_cancer tissue_donor1


title: Intestinal_cancer tissue_donor 14


title: NS9 GFP day 5

value: Lenti-Control

value: day 5


title: Endothelial 2H11 cells treated with BMP4_rep2

tag: strain


title: A549_FOSL1_FLAG cells treated with DEX for 04h - rep3

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: A549_FOSL1_FLAG cells treated with DEX for 04h - rep2

description: ChIP-seq


title: Endothelial 2H11 cells treated with BMP4_rep1


title: Diffuse_cancer tissue_donor8


title: A549_FOSL1_FLAG cells treated with DEX for 01h - rep3

description: ChIP-seq


title: NS9 GFP day 3

value: nonsmoker donor 3

value: day 3


title: MO 1: NSD3 Morpholino Replicate 1


title: A549_FOSL1_FLAG cells treated with DEX for 04h - rep1

description: ChIP-seq


title: RNA_TX1072_XO_d4_r1

data_processing:
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BAM files were split according to the strand of the reads using a custom shell script
BigWig tracks were created using deepTools (2.0) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] for TT-seq and [bamCoverage -bs 10 --normalizeUsing CPM -ignore chrX chrY] for RNA-seq (Ramírez et al. 2016). They were then visualized using the UCSC Genome Browser (Kent et al. 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks

source_name: Mouse embryonic stem cells

growth_protocol: TX1072 XXΔXic and TX1072 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon).

extract_protocol:
The lysates were pre-cleared by centrifugation and per 10.000.000 cells supplemented with 2.4ng equimolar mix of in vitro transcribed S4U-labelled and unlabeled ERCC spike-ins, as described by Schwalb et al., 2016. Total RNA was extracted from Trizol with chloroform. In short, 200ul chloroform was mixed per ml lysate and phase separated by centrifugation in phase-lock tubes. RNA was precipitated from the aqueous phase with Isopropanol supplemented with 0.1 mM DTT and centrifugation for 10 minutes at 16.000x g and 4°C. The RNA pellet was washed once with 75% Ethanol and resuspended in Nuclease free water. Residual genomic DNA was removed in solution with DNaseI (Qiagen) following the manufacturer’s guidelines. The total RNA was purified for a second round with the Direct-zol RNA Miniprep Plus kit (Zymo Research) by following the manufacturer’s guidelines but in addition including 100 mM DTT in all wash buffers to prevent oxidation of S4U-labeled RNA. For each TT-seq reaction 300ug of purified RNA was divided over 2 Covaris MicroTubes and fragmented on the Covaris S2 platform for 10 s, 1% duty cycle, intensity 2, 1 cycle, 200 cycles/burst. Each corresponding sample was pooled and 3ug taken aside for quality control (BioAnalzyer fragment size check and spike-in qRT-PCR) and for NGS as input total RNA.  The remaining S4U-treated RNA (~260ul) was biotinylated by adding to 400 ul Biotin-HPDP (0.5ug/ul in DMSO)  100 ul 10x Biotinylation buffer and incubated for 1.5 hours on a thermoblock at 37°C with 750 rpm agitation. To clean up any unreacted Biotin-HPDP, the biotinylated RNA was extracted with phenol:chloroform (PCI) 5:1, pH 4.5) (Ambion). For this an equal volume of PCI was mixed with the biotinylated RNA and phase separated by centrifuging in phase-lock tubes at 12,000x g for 5 min. The aqueous phase was collected, mixed with an equal volume of Isoproponol and 1:10 volume of 5 M NaCl, and centrifuged at 16,000x g for 15 min 4°C to precipitate the biotinylated RNA. The RNA pellet was washed twice with 500ul 75% ethanol and dissolved in 50ul RNase-free water. Nascent biotinylated RNAs were enriched with MACS streptavidin μBeads.
Nascent RNA samples were subjected to strand-specific RNA-seq library preparation with the KAPA RNA HyperPrep kit with RiboErase (Illumina, #KR1351), which included 1st and 2nd strand synthesis and ribosomal RNA depletion, by following the manufacturers guidelines. The libraries were subjected to Illumina NGS PE75 (for TX1072 XXΔXic) on the HiSeq 4000 platform or PE100 (for TX1072 XO) on the NovaSeq 500 platform with approximately 100 million fragments per sample.

treatment_protocol: Differentiation was induced for 0, 2 or 4 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates. Cells were metabolically labeled with culture medium containing 750 μM 4-Thiouridine (S4U) (Sigma Aldrich) for 5 minutes at 37 °C and 5% CO2.

value: TX1072 XO

tag: condition

value: Day 4

tag: replicate

tag: strain background

value: CAST / C57BL/6

tag: assay

value: RNA-seq

value: Mouse embryonic stem cells


title: MO 2: NSD3 Morpholino Replicate 2


title: mmMO 4: Control Morpholino Replicate 4

value: 0.5mM mmMO


title: A549_FOSL1_FLAG cells treated with DEX for 01h - rep1

description: ChIP-seq


title: RNA_TX1072_XO_d0_r2

value: Day 0


title: RNA_TX1072_XO_d4_r2


title: mmMO 3: Control Morpholino Replicate 3

value: 5-7 somite chick embryos


title: NS9 GFP day 0

value: day 0


title: A549_FOSL1_FLAG cells treated with DEX for 01h - rep2

description: ChIP-seq


title: mmMO 5: Control Morpholino Replicate 5

value: Pool of 12 embryos


title: MO 3: NSD3 Morpholino Replicate 3

value: 0.5mM NSD3 MO


title: RNA_TX1072_XO_d0_r1


title: A549_FOSL1_FLAG cells untreated - rep2

description: ChIP-seq

source_name: A549_FOSL1_FLAG cells untreated - rep2


title: RNA_TX1072_XO_d2_r2

value: Day 2


title: NS8 NICD3 day 0

value: nonsmoker donor 2

value: HBEC (Primary human bronchial epithelial cells )


title: NS8 NICD3 day 7

value: day 7


title: TT_TX1072_XO_d4_r2

data_processing:
Library strategy: TT-seq
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BAM files were split according to the strand of the reads using a custom shell script
BigWig tracks were created using deepTools (2.0) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] for TT-seq and [bamCoverage -bs 10 --normalizeUsing CPM -ignore chrX chrY] for RNA-seq (Ramírez et al. 2016). They were then visualized using the UCSC Genome Browser (Kent et al. 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks

value: TT-seq


title: RNA_TX1072_XO_d2_r1


title: NS8 NICD3 day 5

value: day 5


title: NS8 NICD3 day 3

value: day 3


title: A549_cJun_FLAG cells treated with DEX for 12h - rep1

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: NS8 GFP day 5

value: Lenti-Control


title: TT_TX1072_XO_d2_r1

value: TX1072 XO

value: CAST / C57BL/6


title: mmMO 1: Control Morpholino Replicate 1

value: 0.5mM mmMO


title: A549_cJun_FLAG cells treated with DEX for 12h - rep2

description: ChIP-seq


title: A549_FOSL1_FLAG cells untreated - rep3

description: ChIP-seq

source_name: A549_FOSL1_FLAG cells untreated - rep3


title: TT_TX1072_XO_d4_r1

value: Day 4

value: Mouse embryonic stem cells


title: TT_TX1072_XO_d2_r2


title: TT_TX1072_XO_d0_r2

value: Day 0


title: A549_FOSL1_FLAG cells untreated - rep1

description: ChIP-seq

source_name: A549_FOSL1_FLAG cells untreated - rep1


title: A549_cJun_FLAG cells treated with DEX for 08h - rep1

description: ChIP-seq


title: NS8 GFP day 0

source_name: primary human bronchial epithelial cells (HBECs)

value: day 0


title: A549_cJun_FLAG cells treated with DEX for 08h - rep2

description: ChIP-seq


title: NS8 GFP day 7


title: Control E1 F3 generation

city: Liege

first: David

last: Lopez Rodriguez

state: Liege

address: Avenue de l'Hopital 11

department: GIGA-Neuroscience

country: Belgium

institute: University of Liege

data_processing:
Intial basecalling using Illumina RTA 1.18.64
Barcode and adapter sequence was removed using Trimmomatic v0.33 ILLUMINACLIP  TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:10:34 HEADCROP:13
Alignment using Tophat2 v2.1 to rat rn6
Splice junction mapping using Tophat2 v. 2.1
Mapping to Ensembl build 83 using Bioconductor Rsubread package using default parameters except countMultiMappingReads = TRUE, AllowMultiOverlaps = TRUE
Genome_build: rat rn6, Ensembl build 83 annotation

organism: Rattus norvegicus

source_name: 21-day old female rat ancestrally exposed (F3 generation) to an EDC mixture through the maternal lineage

extract_protocol:
MBH-PoA tissue was removed, flash frozen on dry ice and mRNA was prepared for RNA sequencing before sending it to the OSU Center for genome Research and Biocomputing for library preparation and sequencing using a HiSeq 2500 instrument.  Four samples per lane were sequenced with a target density of 300 million reads per lane using a single-read 100 cycle protocol.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exposure to an EDC mixture via the maternal lineage thorugh food from 2 weeks before gestion until the end of lactation

value: 21 day-old

value: Wistar rat

value: EDC mixture

value: Hypothalamus (MBH-PoA)

tag: generation

tag: gender

value: female


title: Control E3 F3 generation


title: Control E2 F3 generation


title: Control C4 F3 generation

source_name: 21-day old female rat ancestrally exposed (F3 generation) to vehicle through the maternal lineage

value: Control (Vehicle)


title: mmMO 2: Control Morpholino Replicate 2

value: 5-7 somite chick embryos

value: Pool of 12 embryos


title: A549_cJun_FLAG cells treated with DEX for 04h - rep3

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: NS6 NICD3 day 5

tag: patient

value: nonsmoker donor 1

value: day 5

value: HBEC (Primary human bronchial epithelial cells )


title: cHiC_TX1072_XO_d2_r2

data_processing:
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.4). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’.
Mapping, filtering and deduplication of the short reads were performed with the HiCUP pipeline (0.7.04) with options [no size selection, Nofill: 1, Format: Sanger] (Wingett et al., 2015). The pipeline employed bowtie2 (2.3.5.1) (Langmead and Salzberg 2012)
Juicer tools (1.19.02) was used to generate binned contact maps from valid and unique read pairs with MAPQ ≥ 30 (Durand et al. 2016) and to normalize contact maps by Knight and Ruiz (KR) matrix balancing (Knight and Ruiz 2013).
For the generation of contact maps, only reads pairs mapping to the genomic region (chrX:103,190,001-103,950,000) were considered. Afterwards KR-normalized maps were exported at 10-kb bin size.
Genome_build: mm10
Supplementary_files_format_and_content: hic: KR-normalized, 10kb-binned contact maps from valid and unique read pairs (MAPQ >= 30) of the individual replicates

extract_protocol:
Cells were were disassociated with 0.1% (w/v) accutase for 7 min at 37 °C. Cells were counted and 2 * 10^6 cells were transferred in a 50-ml falcon tube through a 40-μm cell strainer and complemented with 10% FBS/PBS. 37% formaldehyde (Sigma-Aldrich) was added to a final concentration of 2% cells fixed for 10 min at room temperature. Crosslinking was quenched by adding glycine (final concentration; 125 mM). Fixed cells were washed twice with cold PBS and lysed using fresh lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA with protease inhibitor) to isolate nuclei. After 10-min incubation in ice, cell lysis was assessed microscopically. Nuclei were centrifuged for 5 min at 480g, washed once with PBS and snap frozen in liquid N2.
3C libraries were prepared from fixed nuclei as described previously (Despang et al 2019). In summary, nuclei pellets were thawed on ice and subjected to DpnII digestion, ligation and decrosslinking. Re-ligated products were sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 2 cycles of 60 s each, set mode: frequency sweeping, temperature: 4–7 °C). Adapters were then added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect library and indexed for sequencing (100 bp, paired end) following manufacturer’s instructions. The custom-designed SureSelect library was described to capture informative GATC fragments within chrX:102238718-105214261 (mm10) using GOPHER, as described previously (Hansen et al. 2019).

treatment_protocol: Differentiation was induced for 0 or 2days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates.

value: TX1072 XO

value: Day 2

value: CAST / C57BL/6

value: Capture Hi-C


title: Control E4 F3 generation

tag: treatment


title: A549_FOSL1_FLAG cells treated with DEX for 12h - rep3

description: ChIP-seq

tag: tissue


title: Endothelial 2H11 cells treated with BMP4 and Palovarotene_rep3

value: axillary lymph node/vascular epithelium

value: BMP4 and Palovarotene treated for 48 hours


title: Control C3 F3 generation

value: 21 day-old

value: Wistar rat


title: NS8 GFP day 3

value: nonsmoker donor 2

value: Lenti-Control

tag: time point

value: day 3


title: NS6 NICD3 day 3


title: cHiC_TX1072_XO_d2_r1

tag: cell line

value: Mouse embryonic stem cells


title: A549_cJun_FLAG cells treated with DEX for 04h - rep1

description: ChIP-seq


title: NS6 NICD3 day 7

value: day 7


title: Control C2 F3 generation

value: Control (Vehicle)

value: Hypothalamus (MBH-PoA)

value: female


title: NS6 NICD3 day 0

value: nonsmoker donor 1

value: day 0

value: HBEC (Primary human bronchial epithelial cells )


title: cHiC_TX1072_XXdXic_d2_r2

value: TX1072 XXdXic

value: Day 2

value: CAST / C57BL/6


title: A549_cJun_FLAG cells treated with DEX for 01h - rep3

description: ChIP-seq

value: adenocarcinomic human alveolar basal epithelial


title: cHiC_TX1072_XO_d0_r1

value: TX1072 XO

value: Day 0

value: Capture Hi-C


title: Control C1 F3 generation

value: 21 day-old

value: Wistar rat


title: NS6 GFP day 7

value: Lenti-Control


title: A549_cJun_FLAG cells treated with DEX for 01h - rep2

description: ChIP-seq


title: Control E4 F1 generation

source_name: 21-day old female rat in utero exposed (F1 generation) to an EDC mixture through the maternal lineage

value: EDC mixture


title: NS6 GFP day 5

value: day 5


title: cHiC_TX1072_XXdXic_d2_r1

value: Mouse embryonic stem cells


title: A549_cJun_FLAG cells treated with DEX for 04h - rep2

description: ChIP-seq


title: NS6 GFP day 3

value: day 3


title: cHiC_TX1072_XXdXic_d0_r2


title: Control E3 F1 generation

value: Hypothalamus (MBH-PoA)

value: female


title: NS6 GFP day 0

value: nonsmoker donor 1

value: day 0

value: HBEC (Primary human bronchial epithelial cells )


title: A549_cJun_FLAG cells treated with DEX for 01h - rep1

description: ChIP-seq


title: Control E2 F1 generation


title: cHiC_TX1072_XXdXic_d0_r1

value: TX1072 XXdXic

value: CAST / C57BL/6


title: A549_cJun_FLAG cells untreated - rep2

description: ChIP-seq

source_name: A549_cJun_FLAG cells untreated - rep2

value: adenocarcinomic human alveolar basal epithelial


title: Endothelial 2H11 cells treated with BMP4 and Palovarotene_rep2

value: axillary lymph node/vascular epithelium

value: BMP4 and Palovarotene treated for 48 hours


title: ea_RH_4_D

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_RH_4_v3_filtered_feature_bc_matrix.h5

data_processing:
Instrument Models: Illumina HighSeq4000 and NOVASEQ6000
Pipeline version: bcl2fastq 2.20.0.422
Sequencing kits: HiSeq 3000/4000 PE and S2
Sequencing software: HCS HD 3.4.0.38 and HCS 1.6.0
Basecall softwares: RTA 2.7.7 and RTA v3.4.4
BaseQual encoding Phred+33
Read alignment and transcript quantification were conducted using cellRanger v3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: filtered and unfiltered counts files and metadata
Supplementary_files_format_and_content: cell metadata table
Supplementary_files_format_and_content: Seurat object

source_name: brain tumor xenograft

growth_protocol: C57BL/6J wild-type (wt) mice were purchased from Charles River. Mice were bred according to local regulatory authorities (breeding approval reference Z124I02). All mice were 7-10 weeks of age at use. Mice were kept under specific pathogen-free conditions at the animal facility of the DKFZ Heidelberg.

extract_protocol:
Tumors were dissociated after d7 (early) and d28 (late) and FACS purified based on CD45-expression using anti-CD45.2 (clone 30-F11, BioLegend, San Diego, USA)
10x libraries were prepared from FACS-purified CD45+ cells in a single run.
10x Single Cell 3' v2 Kit

treatment_protocol: 1 x 10E4 GL261 tumor cells were diluted in 2 µl sterile PBS (Sigma-Aldrich) and stereotactically implanted into the right hemisphere of 7-10 weeks old female C57BL/6J mice (coordinates: 2 mm right lateral of the bregma and 1 mm anterior to the coronal suture with an injection depth of 3mm below the dural surface) using a 10µl Hamilton micro-syringe driven by a fine step stereotactic device (Stoelting).

value: early timepoint

tag: genotype

value: GL261 episomally overexpressing R132H-mutated IDH1 xenograft

value: FACS-sorted CD45+ cells


title: Control E1 F1 generation

tag: age

value: 21 day-old

value: Wistar rat

value: EDC mixture


title: A549_cJun_FLAG cells untreated - rep1

description: ChIP-seq

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Single-end reads were mapped using Bowtie (v1.0.0 PMID: 19261174) against hg38 genome with flags -v 2 -X 2000 --best --strata -m 1.
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads 200bp and converting the read counts to RPKMs.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig signal in RPMs

source_name: A549_cJun_FLAG cells untreated - rep1


title: Control C4 F1 generation

source_name: 21-day old female rat in utero exposed (F1 generation) to vehicle through the maternal lineage

value: Control (Vehicle)


title: A549_cJun_FLAG cells untreated - rep3

description: ChIP-seq

source_name: A549_cJun_FLAG cells untreated - rep3


title: ea_RH_4_C


title: TAPR1 KO (B37c24) day 21

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

department: Department of Medicine

country: Canada

institute: University of Montreal

description:
TAPR1_KO_sgRNA_read_counts.txt
sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed.
Supplementary_files_format_and_content: sgRNA read counts per sample as a tab-delimited text file

source_name: Nalm-6 pre-B lymphoid cell line

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Genomic DNA was extracted and purified using the Gentra Cell Puregene kit (QIAGEN, cat. # 158388).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: NALM-6 cells (wild-type or TAPR1 KO) were transduced with the TKOv3 library for 2 days followed by selection with puromycin for 4 days 48h post-transduction. Cells were propagated for another 21 days with addition of fresh media at each cell passage.

tag: sample type

value: pooled sgRNA library

tag: genotype/variation

value: TAPR1 KO


title: TAPR1 KO (B38c13) day 21


title: Wild-type replicate B, day 21

value: wild type


title: ea_RH_4_B

tag: cell type


title: TT_TX1072_XO_d0_r1

value: TX1072 XO

value: Day 0

value: TT-seq

value: Mouse embryonic stem cells


title: Wild-type replicate A, day 21


title: Control C3 F1 generation

tag: strain

value: Hypothalamus (MBH-PoA)

value: female


title: ea_RH_4_A


title: Control C2 F1 generation


title: M4319-Sal-abs-5

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description:
raw_counts.csv
normalized_counts.csv

data_processing:
Reads were trimmed to remove adapter sequence and low-quality base calls using Trimmomatic v0.38
Reads were aligned to the rat genome rn06 using HISAT2 v2.1.0
Aligned reads were mapped to known transcripts from Ensembl genes version 94 using GenomicAlignments v1.16.0
Differentially epxressed genes were identified using DESeq2 v1.20.0 with a Benjamini-Hochberg estimated false discovery rate of 0.1 used as a threshold for statistical significance.
Sample F4329-Sal-3 failed to cluster with other samples and was omitted from further processing.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Counts per gene per sample in CSV format.

source_name: Left ventricular tissue

growth_protocol: Male and female Sprague Dawley rats (Charles River Laboratories, strain code 001) were pair housed in standard cages with free access to food and water and were maintained on a 12 hour / 12 hour light / dark schedule (lights on at 07:00).

extract_protocol:
Hearts were either isolated on day 11 (24 hours after the last saline /methamphetamine injection) or isolated 30 days after the last saline / methamphetamine injection to investigate the effects of a 30 day period of abstinence on myocardial gene expression. Total RNA was isolated using Trizol (Thermo Fisher, Waltham, MA) according to the manufacturer’s instructions.
RNA libraries were prepared from each heart using the Truseq RNA mRNA library prep kit from Illumina (San Diego, CA).  RNA sequencing (2 x 50 paired end reads; 20 million reads / sample) was performed on an Illumina HiSeq1500 sequencer.

treatment_protocol: Adult male and female rats (8 weeks of age) received daily (10:00) subcutaneous injections with methamphetamine (5 mg/ kg/day) or saline for 10 consecutive days.

tag: Sex

value: M

value: Saline

tag: abstinence

value: Yes


title: M4318-Sal-abs-4

description:
raw_counts.csv
normalized_counts.csv


title: M4320-Sal-abs-6

description:
raw_counts.csv
normalized_counts.csv


title: ea_RH_3_D

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_RH_3_v3_filtered_feature_bc_matrix.h5

value: early timepoint

value: GL261 episomally overexpressing R132H-mutated IDH1 xenograft

value: FACS-sorted CD45+ cells


title: Control C1 F1 generation

value: 21 day-old

value: Wistar rat


title: M4317-Sal-abs-3

description:
raw_counts.csv
normalized_counts.csv


title: TAPR1 targeting sgRNA knockout clone 6

data_processing:
Reads were aligned using Bowtie2.2.5, with default parameters, to all RefSeq transcripts (as at April, 2018). Alignments with fewer than 2 inserted or deleted bases and a maximum edit distance of 5 (i.e. the sum of inserted, deleted, or mismatched bases) were counted to generate read counts per transcript, and reads mapping to transcripts produced from the same gene locus were summed together to generate read counts per gene.
Read counts from different sequencing lanes for the same sample were summed.
The tabulated read counts per gene in cells of a given knockout line (e.g. TERT-disrupted or TAPR1-disrupted) were analyzed for differential expression relative to non-targetting controls using the DESeq2 pipeline with the SARtools package on R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read counts per gene

extract_protocol:
RNA from 1 million clonal NALM-6 cells of the indicated genotypes was extracted using the QIAGEN Mini Rneasy kit according to the manufacturer's protocol. RNA purity was assessed using a nanodrop spectrophotometer (260/280 nm) and RNA was quantified by QuBit (ABI). RNA quality was assessed with a Bioanalyzer RNA 6000 Nano assay on a 2100 Bioanalyzer (Agilent Technologies).
One microgram of total RNA was used for library preparation, which was carried out using the KAPA mRNAseq Hyperprep kit (KAPA, #KK8581). Libraries were quantified using QuBit and Bioanalyzer instruments, and diluted to 10 nM before normalization by qPCR using the KAPA library quantification kit (KAPA, #KK4973). Libraries were then pooled to equimolar concentration.

treatment_protocol: Gene disruptions in NALM-6 cells were carried out using CRISPR-Cas9 editing using sgRNAs as described in this study. Clonal isolates of AAVS1 non-tarteting controls (NT), TERT-disrupted (TERT KO) or TAPR1-disrupted cells (TAPR1 KO) were isolated by single cell sorting. Indel efficiency and clonal genotyping was performed on genomic DNA using target locus PCR amplification and sanger sequencing.

value: TAPR1 targeting sgRNA knockout


title: TAPR1 targeting sgRNA knockout clone 5


title: HEK293_Amoto_rep3

city: Los Angeles

first: Minjie

last: Zhang

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

description: crosslinked total RNA

data_processing:
Sequencing data were preprocessed to remove adapters form the 5'end and 3’end using Trimmomatic software; PCR duplicates are removed using splitFastqLibrary (in the icSHAPE pipeline)
Reads were mapped to hg38 or mm10 genome using STAR program.
The primary mapping alignments were filtered to remove low-confidence segments, rearranged and classified into six different types using gaptypes.py (https://github.com/zhipenglu/CRSSANT).
Filtering alignments were assembled to DGs and NGs using the crssant.py script (https://github.com/zhipenglu/CRSSANT).
Bedtools v2.25.0 was used to annotate gapped and chimeric alignments.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: bam files contain grouped snRNA structures and interactions; BEDPE file contains disjoint RNA structures and interaction.

source_name: HEK293T cells

growth_protocol: HEK293T and HeLa cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) + 10% fetal bovine serum (FBS, Gibco) + Pen/Strep antibiotic, in 37°C incubator with 5% CO2.

extract_protocol:
TNA method was used to extract crosslinked RNA.
Library was prepared using optimized PARIS protocol (Lu. et al. Cell, 2016).

treatment_protocol: 0.5 mg/ml AMT or Amotosalen in vivo crosslinking; mRNAs were enriched using Poly(A)Purist™ MAG Kit (Invitrogen); EVD68 viral RNA is enriched using seven antisense oligos.

value: HEK293T cells

value: embryonic kidney cells

tag: passages


title: HEK293_Amoto_rep4

description: crosslinked total RNA


title: ea_RH_3_C


title: ea_RH_3_B


title: HEK293_Amoto_rep2

description: crosslinked total RNA


title: M4315-Sal-abs-1

description:
raw_counts.csv
normalized_counts.csv


title: TAPR1 targeting sgRNA knockout clone 3


title: TAPR1 targeting sgRNA knockout clone 2


title: ea_RH_3_A


title: ea_RH_2_D

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_RH_2_v3_filtered_feature_bc_matrix.h5


title: TAPR1 targeting sgRNA knockout clone 4


title: M3999-Sal-6

description:
raw_counts.csv
normalized_counts.csv

value: No


title: HEK293_Amoto_rep1

description: crosslinked total RNA


title: M3998-Sal-5

description:
raw_counts.csv
normalized_counts.csv


title: HEK293_AMT_rep4

description: crosslinked total RNA


title: TAPR1 targeting sgRNA knockout clone 1


title: TERT targeting sgRNA knockout clone 3

value: TERT targeting sgRNA knockout


title: HEK293_AMT_rep3

description: crosslinked total RNA


title: ea_RH_2_C


title: M3997-Sal-4

description:
raw_counts.csv
normalized_counts.csv


title: HEK293_AMT_rep2

description: crosslinked total RNA


title: ea_RH_2_B


title: M3993-Sal-2

description:
raw_counts.csv
normalized_counts.csv


title: TERT targeting sgRNA knockout clone 2


title: M3994-Sal-3

description:
raw_counts.csv
normalized_counts.csv


title: HEK293_AMT_rep1

description: crosslinked total RNA


title: M4316-Sal-abs-2

description:
raw_counts.csv
normalized_counts.csv


title: ea_RH_1_D

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_RH_1_v3_filtered_feature_bc_matrix.h5


title: TERT targeting sgRNA knockout clone 1


title: AAVS1 non-targeting sgRNA knockout clone 3

value: AAVS1 non-targeting sgRNA knockout


title: YAP-TFE3 shZZZ3 rep2

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads from the SW872 line was aligned against the ensembl reference ‘hg38’
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample ...

source_name: SW872 liposarcoma cells ATCC

growth_protocol: SW872 cells stably expressing TAZ-CAMTA1 or YAP-TFE3 with stable knockdown of YEATS2 or ZZZ3

extract_protocol:
Total RNA was isolated using the PureLink™ RNA mini kit (Invitrogen-ThermoFisher Scientific).  On-column DNase (Invitrogen) treatment was performed according to manufacturer’s instructions
Illumina TruSeq stranded mRNA sample preparation kit

tag: transduction

value: YAP-TFE3 shZZZ3


title: ea_RH_1_C


title: M3992-Sal-1

description:
raw_counts.csv
normalized_counts.csv


title: AAVS1 non-targeting sgRNA knockout clone 2


title: YAP-TFE3 shZZZ3 rep1


title: ea_RH_1_B


title: M4314-Meth-abs-6

description:
raw_counts.csv
normalized_counts.csv

value: Methamphetamine


title: A549_FOSL1_FLAG cells treated with DEX for 08h - rep1

city: Durham

first: Charles

last: Gersbach

address: 101 science drive rm 2323

institute: Duke University

description: ChIP-seq

extract_protocol:
Harvested plates at timepoints (0, 1, 4, 8, 12)
ChIP-seq libraries were prepared using a Kapa Hyper Prep kit.

treatment_protocol: Treated with 100 uM Dexamethasone

value: adenocarcinomic human alveolar basal epithelial


title: M4313-Meth-abs-5

description:
raw_counts.csv
normalized_counts.csv

value: M


title: YAP-TFE3 shYEATS2 rep2

value: YAP-TFE3 shYEATS2


title: AAVS1 non-targeting sgRNA knockout clone 1


title: ea_RH_1_A


title: M4312-Meth-abs-4

description:
raw_counts.csv
normalized_counts.csv

value: Yes


title: YAP-TFE3 shYEATS2 rep1


title: 42A_BIBR1532_20_uM_d20

description: sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed.
Read counts from all control samples were summed.
Genome_build: For Nalm-6 screens: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core RefSeq gene-targeting sgRNA set of of the library.
Supplementary_files_format_and_content: Tab-separated sgRNA read counts per sample

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 7 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks and compounds were added (20 µM BIBR1532 or DMSO 0.1% v/v) and propagated for 20 days. Fresh media and compound was added at each cell passage. Untreated controls (replicates A, B) were also propagated for 15 or 22 days respectively.

value: pooled sgRNA library

value: Treated with 20 uM BIBR1532 20 days


title: ea_RH_2_A

value: early timepoint

value: GL261 episomally overexpressing R132H-mutated IDH1 xenograft

value: FACS-sorted CD45+ cells


title: M4311-Meth-abs-3

description:
raw_counts.csv
normalized_counts.csv


title: YAP-TFE3 shNon-targeting rep2

value: YAP-TFE3 shNon-targeting


title: M4310-Meth-abs-2

description:
raw_counts.csv
normalized_counts.csv


title: 7_days_DOX_and_22_days_post_DOX_A

description: sgRNAs PCR-amplified from genomic DNA

value: No treatment control 22 days A


title: M4309-Meth-abs-1

description:
raw_counts.csv
normalized_counts.csv


title: 7_days_DOX_and_22_days_post_DOX_B

description: sgRNAs PCR-amplified from genomic DNA

value: No treatment control 22 days B


title: ea_WT_4_B

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_WT_4_v3_filtered_feature_bc_matrix.h5

value: GL261 episomally overexpressing wildtype IDH1 xenograft


title: TAZ-CAMTA1 shZZZ3 rep2

value: TAZ-CAMTA1 shZZZ3


title: 7_days_DOX_and_15_days_post_DOX_B

description: sgRNAs PCR-amplified from genomic DNA

value: No treatment control 15 days B


title: ea_WT_4_C


title: ea_WT_4_A


title: TAZ-CAMTA1 shZZZ3 rep1


title: M4338-Meth-6

description:
raw_counts.csv
normalized_counts.csv

value: No


title: 7_days_DOX_and_15_days_post_DOX_A

description: sgRNAs PCR-amplified from genomic DNA

value: No treatment control 15 days A


title: ea_WT_3_D

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_WT_3_v3_filtered_feature_bc_matrix.h5


title: DMSO_control_0_1percent_d20

description: sgRNAs PCR-amplified from genomic DNA

value: 0.1% v/v DMSO control 20 days


title: TAZ-CAMTA1 shYEATS2 rep2

value: TAZ-CAMTA1 shYEATS2


title: M4337-Meth-5

description:
raw_counts.csv
normalized_counts.csv

value: M

value: Methamphetamine


title: TAZ-CAMTA1 shYEATS2 rep1


title: M4336-Meth-4

description:
raw_counts.csv
normalized_counts.csv


title: YAP-TFE3 shNon-targeting rep1


title: ea_WT_3_B


title: M4335-Meth-3

description:
raw_counts.csv
normalized_counts.csv


title: at-leaf-HiC-replicate2_col_wt_x_col_wt

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Arabidopsis thaliana F1-leaf of Columbia-0
Total DNA
processed data file: Leaf_R1_R2_100000_iced.matrix
processed data file: Leaf_R1_R2_200000_iced.matrix

data_processing:
Raw mHi-C data were mapped to the Col-0 reference genome of Arabidopsis (TAIR10) with a two-step approach incorporated in the Hic-Pro software (version 2.9.0) (Servant et al. 2015). First, reads were mapped to the reference genome using the bowtie2 end-to-end algorithm followed by a second mapping of the 5′ fraction of the unmapped reads containing the ligation site. Uniquely mapping reads from both mapping steps were retained in a single alignment file. Multiple hits, singletons and read pairs that did not map close to a restriction site or within the expected fragment size were discarded. Subsequently, uninformative read pairs, including invalid ligation products and PCR artifacts, were removed. The remaining valid read pairs involving two different restriction fragments were used to generate contact maps with 100 kb and 200 kb genomic bin sizes. The raw contact matrices were normalised to minimise biases due to GC content, mappability and effective fragment length with a sparse-based implementation of the iterative correction method embedded in HiC-Pro (Imakaev et al. 2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_iced.matrix: Normalized contact maps for two resolutions (100kb and 200kb) for merged replicates of both conditions. Columns: bin_i / bin_j / counts_ij

organism: Arabidopsis thaliana

source_name: AT F1-leaf

growth_protocol: All seeds were surface sterilized (70%, 30% ethanol 10min), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
To examine the tissue-specific spatial organization of chromatin, we adopted the previously published genome-wide high-resolution in situ Hi-C method  (Flyamer et al. 2017). The major step involved in the preparation of mHi-C library is HCHO-crosslinking, permeabilization followed by restriction enzyme digestion proximity-dependent ligation events between cross-linked restriction-digested chromatin fragments.
Sequencing libraries were constructed using Ovation Rapid DR Multiplex System 1-8 (NuGEN) with 300-800 bp size selection according to the manufacturer’s instructions.
Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.

tag: ecotype

value: Col_wt x Col_wt

value: leaf

value: 4 weeks


title: at-leaf-HiC-replicate1_col_wt_x_col_wt


title: M4303-Meth-2

description:
raw_counts.csv
normalized_counts.csv


title: TAZ-CAMTA1 shNon-targeting rep2

value: TAZ-CAMTA1 shNon-targeting


title: ea_WT_3_A

value: early timepoint

value: FACS-sorted CD45+ cells


title: TAZ-CAMTA1 shNon-targeting rep1


title: ea_WT_2_D

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_WT_2_v3_filtered_feature_bc_matrix.h5


title: M4302-Meth-1

description:
raw_counts.csv
normalized_counts.csv


title: ea_WT_4_D


title: ea_WT_2_C


title: F4342-Sal-abs-6

description:
raw_counts.csv
normalized_counts.csv

value: F

value: Saline

value: Yes


title: at-endosperm-HiC-replicate1_col_wt_x_col_wt

description:
Arabidopsis thaliana F1-endosperm of Columbia-0
Total DNA
processed data file: Endo_R1_R2_100000_iced.matrix
processed data file: Endo_R1_R2_200000_iced.matrix

source_name: AT F1-Endosperm

value: Endosperm


title: ea_WT_3_C

value: GL261 episomally overexpressing wildtype IDH1 xenograft


title: F4341-Sal-abs-5

description:
raw_counts.csv
normalized_counts.csv


title: ea_WT_2_B


title: ibat_ctrl9

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

data_processing:
Sequencing software: HiSeq Control Software 2.2.58 Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64 fastq-file generation: CASAVA BCL2FASTQ Conversion Software 1.8.3
Sequenced reads with masked adaptor sequence were mapped to the murine genome, NCBI build 38, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM).
Genome_build: murine NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

source_name: primary adipocytes

extract_protocol:
Primary adipocytes were washed with ice-cold PBS, placed on ice and scraped into Trisure (Bioline). Total RNA was prepared from Trisure (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were constructed from total RNA (TruSeq RNA Sample Prep kit v2 (Illumina)).

tag: source organ

value: interscapular BAT

value: C57BL/6N UCP1 reporter


title: H3K27ac ChIP_Input_TFE3_Rep2

data_processing:
BCL basecalls were converted to FASTQ with Illumina 'bcl2fastq"
fastq data were processed using the 'bcbio-nextgen.py' pipeline in "chip-seq" mode.   Genome build was "GRCh37".
reads were trimmed with "atropos", aligned with 'bwa', and peaks called with 'macs2' running in "narrowPeak" mode.  Peaks with FDR p-value < 0.05 were accepted.

growth_protocol: SW872 cells were stably transduced and grown to 90% confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Cells were cross-linked and prepared using the SimpleChIP Enzymatic Chromatin IP KIt according to manufacturer's instructions. Flag tagged proteins were immunoprecipated with the anti-DYKDDDDK rabbit monoclonal antibody (Cell Signaling)
The SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina was used to prepare the DNA library according to manufacturer's instructions

tag: antibody


title: H3K27ac ChIP_TFE3_Rep2


title: ibat_ctrl15


title: ea_WT_2_A


title: H3K27ac ChIP_Input_TFE3_Rep1


title: H3K27ac ChIP_TFE3_Rep1


title: ea_WT_1_D

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
ea_WT_1_v3_filtered_feature_bc_matrix.h5


title: F4305-Sal-abs-4

description:
raw_counts.csv
normalized_counts.csv

tag: treatment


title: H3K27ac ChIP_Input_YAP_TFE3_Rep2


title: ea_WT_1_C


title: ibat_ctrl11


title: ibat_ctrl13


title: F4301-Sal-abs-2

description:
raw_counts.csv
normalized_counts.csv


title: ibat_fgf16


title: at-endosperm-HiC-replicate2_col_wt_x_col_wt

tag: tissue


title: F3995-Sal-abs-1

description:
raw_counts.csv
normalized_counts.csv


title: H3K27ac ChIP_Input_YAP_TFE3_Rep1


title: ibat_fgf14


title: ea_WT_1_A

tag: time point


title: H3K27ac ChIP_YAP_TFE3_Rep1

tag: cell line


title: ibat_fgf12


title: F4332-Sal-6

description:
raw_counts.csv
normalized_counts.csv

value: No


title: SC10

city: Creteil

first: Celine

last: Colnot

state: Val de Marne

address: 8 rue du Général Sarrail

department: INSERM U955, IMRB

country: France

institute: Univ Paris Est Créteil, INSERM

data_processing:
Fastq files were processed with the CellRanger pipeline with the default’s parameters
Reads were align against the mm10 reference genome
Filtered features barcodes matrices were used to perform data analysis
Data processing were performed using Seurat v3.1.2 with the following parameters: Cells expressing between 350 and 8000 genes and expressing less that 20% of mitochondrial gene were retained for analysis, genes expressed in less than 5 cells were not taken into account. 20 first principal component were used for the dimensional reduction.
Genome_build: mm10
Supplementary_files_format_and_content: filtered raw count, barcodes and features names

source_name: Skeletal muscle Prx1-derived cells GFP+ at d5 post-polytrauma

extract_protocol:
GFP+ FACS sorted cells from Prx1Cre;mTmG mice
Libraries were generated using Chromium Single Cell 3’Library & Gel Bead Kit v.2 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1000 cells/µL in PBS+0,04% FBS and 20 000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR.

treatment_protocol: no injury or after tibial fracture or after polytrauma

tag: strain background

tag: day post-injury

value: Skeletal muscle


title: H3K27ac ChIP_Input_YAP5SA_Rep2


title: ibat_fgf10


title: F4331-Sal-5

description:
raw_counts.csv
normalized_counts.csv


title: F4304-Sal-abs-3

description:
raw_counts.csv
normalized_counts.csv


title: F4330-Sal-4

description:
raw_counts.csv
normalized_counts.csv


title: SC_9

source_name: Skeletal muscle Prx1-derived cells GFP+ at d3 post-polytrauma


title: H3K27ac ChIP_YAP5SA_Rep2


title: SC5

source_name: Skeletal muscle Prx1-derived cells GFP+ at d5 post-fracture


title: F4329-Sal-3


title: F4328-Sal-2

description:
raw_counts.csv
normalized_counts.csv


title: iwat_ctrl5

value: inguinal WAT


title: iwat_ctrl3


title: SC4

source_name: Skeletal muscle Prx1-derived cells GFP+ at d3 post-fracture


title: H3K27ac ChIP_YAP5SA_Rep1


title: SC3

source_name: Skeletal muscle Prx1-derived cells GFP+ at d0 (uninjured)


title: H3K27ac ChIP_CAMTA1_Rep2


title: iwat_fgf8


title: iwat_ctrl1


title: H3K27ac ChIP_YAP_TFE3_Rep2


title: ea_WT_1_B

tag: genotype


title: F4308-Meth-abs-6

description:
raw_counts.csv
normalized_counts.csv

value: Methamphetamine


title: Breat Tumor Control 60 min

city: Irvine

first: Jered

last: Haun

address: Nat Sci II 3107

department: Biomedical Engineering

institute: University of California, Irvine

data_processing:
Alignmnet of libraries was completed using 10x Genomics Cell Ranger 3.1.0
Each library was aligned to an indexed mm10 reference genome
Libraires from each set were normalized with Cell Rnager Aggr, to normalize mean reads per cells across each libraries
Genome_build: mm10
Supplementary_files_format_and_content: mtx, features, barcodes

source_name: Breast tumor

extract_protocol:
Kidneys and mammary tumor were dissected, minced into ~ 1 mm3  pieces, and processed using either the microfluidic platform (15 and 60 min digestion device intervals, single pass through integrated dissociation/filter device) or control (60 min digest) using 0.25% type I collagenase. Recovered cells were centrifuged (400xg, 5 min), treated with 100 Units of DNase I for 5 min at 37°C, and washed by centrifugation into PBS+. Samples were then incubated with RBC lysis buffer for 5 min on ice, centrifuged, and resuspended in PBS+. Cells were stained with SytoxBlue (Life Technologies, Carlsbad, CA, USA) prior to FACS (FACSAria Fusion, BD Biosciences, Franklin Lakes, NJ) to remove dead cells and ambient RNA. Sorted live single cells (SytoxBlue-neg) were centrifuged and resuspended at a concentration of 1000 cells/µL in PBS with 0.04% BSA. The 10x Chromium system (10x Genomics, Pleasanton, CA) was then used for droplet-enabled scRNA-seq. Oil, cells, reagents, and beads were loaded onto an eight-channel microfluidic chip. Lanes were loaded with ~17,000 cells from each of the samples, determined using an automated cell counter (Countess II, Invitrogen, Carlsbad, CA).
Library generation for 10x Genomics Single Cell Expression v3 chemistry was performed according to manufacturer’s instructions.

value: MMTV-PyMT

value: Breast tumor

tag: age

value: 10 weeks

tag: protocol

value: Control

value: 60 min


title: F4327-Sal-1

description:
raw_counts.csv
normalized_counts.csv


title: H3K27ac ChIP_Input_CAMTA1_Rep2


title: F4306-Meth-abs-4

description:
raw_counts.csv
normalized_counts.csv


title: iwat_fgf4

tag: strain


title: Breast Tumor Platform 60 min

value: Platform


title: iwat_fgf6


title: iwat_ctrl7


title: F4307-Meth-abs-5

description:
raw_counts.csv
normalized_counts.csv

tag: Sex

value: F


title: H3K27ac ChIP_Input_CAMTA1_Rep1


title: Breast Tumor Platform 15 min

value: 15 min


title: Kidney Platform 15 min

source_name: Kidney

value: Kidney

value: 12 weeks


title: iwat_fgf2


title: H3K27ac ChIP_CAMTA1_Rep1


title: H3K27ac ChIP_Input_YAP5SA_Rep1


title: Kidney Platform 60 min


title: F3991-Meth-abs-1

description:
raw_counts.csv
normalized_counts.csv

tag: abstinence

value: Yes


title: H3K27ac ChIP_TAZ_CAMTA1_Rep2


title: F4000-Meth-abs-3

description:
raw_counts.csv
normalized_counts.csv


title: H3K27ac ChIP_Input_TAZ_CAMTA1_Rep1


title: ctrl2 BAT

source_name: immortalized preadipocytes

extract_protocol:
Preadipocytes were washed with ice-cold PBS, placed on ice and scraped into Trisure (Bioline). Total RNA was prepared from Trisure (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were constructed from total RNA (TruSeq RNA Sample Prep kit v2 (Illumina)).

value: interscapular BAT

tag: agent


title: Mouse_brain_snoRNA

description: crosslinked snoRNA

source_name: Mouse brain tissue

value: brain

tag: cell type

value: whole brain tissues

value: four weeks


title: ctrl3 BAT


title: H3K27ac ChIP_TAZ_CAMTA1_Rep1

tag: transduction


title: Mouse_brain_mRNA

description: crosslinked mRNA

source_name: whole brain tissue

value: whole brain tissue

value: 4 weeks


title: F4334-Meth-6

description:
raw_counts.csv
normalized_counts.csv

value: Methamphetamine

value: No