title: SC324 2019-106-CORE

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

description:
SC324
10X Genomics scATACv1

data_processing:
For scRNA, FASTQ generation, demultiplexing, barcode assignment, gene counting and antibody counting were performed using 10X Genomics' Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For scATAC, FASTQ generation, demultiplexing, barcode assignment, and peak calling were performed using 10X Genomics' Cell Ranger-ATAC software v1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Data were aggregated and analyzed using the R packages Seurat v 4.0 and Signac v 1.0.9004 as well as Loupe Browser 3.1.1 (10X  Genomics)
Assembly: GRCh38 and hg19
Supplementary files format and content: 10x Genomics output scRNA files: raw_feature_bc_matrix.h5
Supplementary files format and content: 10x Genomics output scATAC files: fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv, summary.csv, raw_peak_bc_matrix.h5, filtered_peak_bc_matrix.h5, filtered_tf_bc_matrix.h5, peaks.bed, peak_annotation.csv, posssorted_bam.bam.bai

source_name: Lung

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of Liberase DL/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  For some lungs, certain cell populations were partially depleted with Miltenyi magnetic bead separation.  For scATAC, cells were lysed according to 10X Genomics' Nuclei Isolation for Single Cell ATAC Sequencing.  Cells or nuclei were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed per the manufacturer’s instructions (Single Cell 5' v1, Single Cell 3' v3, scATACv1 protocols, 10x Genomics). In short, for the scRNA protocols, lung cells were added to the master mix and loaded into the chip; subsequently, gel beads and partitioning oil were added into the chip which was then loaded into the Chromium instrument, generating the gel bead-in-emulsion (GEM). Once emulsified, cells were lysed and poly-A RNA transcribed to cDNA, adding an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and 10x Barcode. Silane DynaBeads were then used to clean up the pooled and barcoded cDNA which was then amplified by PCR.  SPRIselect reagent was used to select the appropriately sized fragments for library construction. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during the library construction protocol.  For scATAC, nuclei were incubated for one hour with the transposase then loaded into the Chromium instrument with barcoding reagents, gel beads, and partitioning oil.  Once emulsified, the P5 sequence and 10X barcode were added during the PCR GEM generation and barcoding steps.  The resulting 10x barcoded single-stranded DNA was then cleaned up with Silane Dynabeads and size selected with SPRIselect reagent.  Finally, a P7 sequence and a sample index were added during library construction via PCR.
scRNA and scATAC

value: Lung

value: Male

tag: disease status

value: normal control

tag: patientcorecode


title: SC316 2019-098-CORE

status: Public on Sep 02 2022

type: SRA

country: USA

description:
SC316
10X Genomics scATACv1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: age

tag: Sex

value: Female


title: SC336 2019-118-LT

description:
SC336
10X Genomics scATACv1

value: SSc


title: pooled (20) whole embryos solvent control RepD

city: Sasaktoon

first: Susari

last: Malala Irugal Bandaralage

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

description:
ME8-WT7-SDP
ME8_transcript1.txt

library_source: transcriptomic

data_processing:
https://galaxy.ecotoxxplorer.ca/
Raw files were trimmed to a minimum phred score of 20 and a minimum sequence length of 35 bases per paired read using Trim Galore!
Trimmed fastq files were pseudoaligned to the reference fathead minnow transcriptome (NCBI Acc# GCA_016745375.1) using Kallisto quant
Only features with at least 20 counts per million in at least 5 samples were kept for differential expression analyses. Significance of differentially expressed genes were assessed using DESeq2 in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05
Assembly: Fathead minnow (Pimephales promelas) reference transcriptome NCBI Acc# GCA_016745375.1 from Martinson, J., Bencic, D.C., Toth, G.P., Kostich, M.S., Flick, R.W., See, M.J., Lattier, D., Biales, A.D., Huang, W., n.d. De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure. https://doi.org/10.1101/2021.02.24.432777
Supplementary files format and content: csv - differential expression results using DESeq2
Supplementary files format and content: tabular - raw counts of all samples

molecule: total RNA

organism: Pimephales promelas

source_name: whole embryo bodies

growth_protocol: Fathead minnow embryos (20 embryos per replicate) were maternally exposed to graded concentrations (measured concentrations: solvent control, 0.576, 1.77, 5.89 mg/kg ) of HBCD  and reared in glass petri dishes in clean water, maintained at (23 oC, 16:8 light:dark cycle)

extract_protocol:
Total RNA was extracted from pools of 20 larvae using QIAGEN RNeasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Embryos were exposed via maternal transfer and reared in cllean water for  7-days post-fertilization in a flow-through  system.

value: whole embryo bodies

value: 7-days post-fertilization

tag: treatment

value: ethanol (EtOH)

tag: treatment (measured concentration)

value: solvent control


title: B006_T1 H3K27ac ChIPseq

city: Singapore

first: Pierce

middle: Kah Hoe

last: Chow

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Center Singapore

data_processing:
The reads in ChIP-seq data were first trimmed of the adapter and index sequences using BBDuk from BBTools (Bushnell, 2014). Read alignment and index generation were done using Bowtie2 (Langmead & Salzberg, 2012) and Samtools (Li, et al., 2009). Duplicated reads and unmapped reads were removed using Sambamba (Tarasov, et al., 2015). DeepTools bamCoverage (Ramírez, et al., 2014) was used to generate bigwig files for visualization
Assembly: hg38
Supplementary files format and content: bigwig

source_name: tumour

extract_protocol:
50 mg of snap frozen liver tissue was excised and pulverized into fine powder in liquid nitrogen. The samples were washed twice in cold 1X PBS with protease inhibitor, cross-linked with formaldehyde (1%) for 10 min at room temperature, quenched with glycine (125mM) for 5 min, and rinsed twice with cold 1X PBS. Lysis was performed for 30 minutes in cold lysis buffer (50mM HEPES-KOH, pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X, 0.1% Sodium deoxycholate, 0.1% SDS, Takara 1X protease inhibitors) to release nuclei. Pellets were centrifugated at 2,500G for 10 min at 4ºC to collect the nuclei pellet. Nuclei was sonicated in nuclei lysis buffer (50mM HEPES-KOH, pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X, 0.1% Sodium deoxycholate, 1% SDS, Takara, 1x protease inhibitor) using the Bioruptor sonicator to obtain chromatin fragments between 200 to 500 bp. The fragmented chromatin was immunoprecipitated overnight with 5 µg of H3K27ac antibody (catalogue #: ab4729, Abcam) and 50 µl of protein G beads (Invitrogen). Elution of DNA was done in 200 µl of elution buffer (50mM Tris-HCI, pH7.5 and 10mM EDTA), followed by decrosslinking which was performed at 65ºC overnight.
Library preparation was performed using eluted ChIP DNA with NEB ultra II library preparation kit, according to manufacturer’s protocol. 10-12 PCR cycles were performed using indexed primers and libraries size between 300 to 500 bp were selected. The libraries were sequenced at Macrogen using 2 x 150 bp read lengths.

tag: disease state

value: HCC

tag: chip antibody

value: H3K27ac (catalogue #:ab4729, Abcam

value: tumour

tag: library


title: C002_T3 H3K27ac ChIPseq


title: pooled (20) whole embryos solvent control RepC

description:
ME8-WT7-SCP
ME8_transcript1.txt


title: pooled (20) whole embryos solvent control RepB

description:
ME8-WT7-SBP
ME8_transcript1.txt


title: SC314 2019-095-CORE

description:
SC314
10X Genomics scATACv1


title: Serbp1 1st

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
First, the raw reads containing more than 2 N bases were discarded
FASTX Toolkit (version 0.0.13) was used to trim the adaptors and low-quality bases from sequencing reads. Short reads less than 16 nt were also removed.
The R Bioconductor package edgeR (Robinson, McCarthy et al. 2010) was used to identify DEGs. The cutoff criteria for identifying DEGs were set as false discovery rate < 0.05 and fold change > 2 or < 0.5.
TopHat2 was used to align the clean reads to the GRCh38 genome (Kim, Pertea et al. 2013), allowing up to 4 mismatches. Uniquely mapped reads were used for gene read number counting and fragments per kilobase of transcript per million fragments mapped (FPKM) calculation (Trapnell, Williams et al. 2010).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cells

growth_protocol: The pIRES-hrGFP-1a vector was digested for 2~3 h at 37°C by XhoI (NEB) and EcoRI.  Then, the enzyme-digested vector was run on a 1.0% agarose gel and purified with a Qiagen column kit.

extract_protocol:
HeLa cells were ground into fine powder to extract RNA. Total RNA was extracted with TRIzol (Ambion). RNA was purified with two phenol-chloroform treatments, and then the DNA was digested with RQ1 DNase (Promega, Madison, WI, USA). SmartSpec Plus (Bio-Rad, USA) was used to redetermine the quality and quantity of purified RNA by measuring the absorbance at 260 nm/280 nm (A260/A280). The integrity of RNA was verified by 1.5% agarose gel electrophoresis.
One microgram of the total RNA from each sample was used for RNA-seq library preparation with the VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). The polyadenylated mRNAs were converted into double-stranded cDNA after purification and fragmentation. The DNAs were ligated to VAHTS RNA Adapters (Vazyme) after end repair and A tailing. Heat-labile UDG was used to digest the purified ligation products corresponding to 200-500 bp, after which the fragments were amplified and purified. Single-stranded cDNA was quantified, stored at -80°C and sequenced.  The libraries were prepared following the manufacturer’s instructions. The Illumina HiSeq X Ten system was used for 150 nt paired-end sequencing, and high-throughput sequencing was performed. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to the Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: Total RNA was isolated from HeLa cells with TRIzol.   The oligo dT primer was used to reverse transcribe purified RNA to cDNA.   PCR amplification was used to synthesize the insert fragment.   The digested vector and the PCR insert were placed into a PCR microtube for ligation with a ClonExpress® II One Step Cloning Kit (Vazyme).   Then, the plasmids were transformed into an Escherichia coli strain.   The cells were plated onto LB agar plates containing 1 µL/ml ampicillin and incubated overnight at 37°C.   Universal primers (complementary to the backbone vector) were used to screen the colonies by colony PCR (28 cycles).   Sanger sequencing was used to verify the insert sequence.   The primer pairs used for Hot Fusion were designed with CE Design V1.04.   Each of the primers contains a gene-specific sequence and a 17–30 bp sequence of the pIRES-hrGFP-1a vector.

value: SERBP1 overexpression in HeLa  cell


title: C002_T2 H3K27ac ChIPseq


title: SC294 2019-049-LT

description:
SC294
10X Genomics scATACv1


title: pooled (20) whole embryos solvent control RepA

description:
ME8-WT7_SAP
ME8_transcript1.txt


title: C002_N H3K27ac ChIPseq

source_name: adjacent normal

value: adjacent normal


title: BMDM co-cultured 4T1 ADAM17 knock-out 2.8, repeat 3

city: Copenhagen

first: Marie

last: Kveiborg

state: non-US Resident

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
The data processing was perfomed according to standart BGI procdures: Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower  than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to  get the clean reads. Then we map those clean reads onto reference genome, followed  with novel gene prediction, SNP & INDEL calling and gene splicing detection. Finally,  we identify DEGs (differentially expressed genes) between samples and do clustering  analysis and functional annotations.
Gene Expression Analysis
We mapped clean reads to reference using Bowtie2\[9\], and then calculate gene
expression level with RSEM \[10\]. RSEM is a software package for estimating gene and
isoform expression levels from RNA-Seq data. Then, we calculate pearson correlation
between all samples using cor, perform hierarchical clustering between all samples
using hclust, perform PCA analysis with all samples using princomp, and draw the
diagrams with ggplot2 with fuctions of R.
Software information:
Bowtie2 :
Version: v2.2.5
Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --nomixed
--no-discordant -p 1 -k 200
Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml
RSEM :
Version: v1.2.12
Parameters: default
Website: http://deweylab.biostat.wisc.edu/ RSEM
DEG Detection
We detect DEGs with DEseq2 PossionDis as requested.DEseq2 is based on the
negative binomial distribution, performed as described at Michael I, et al.\[15\] PossionDis
is based on the poisson distribution, performed as described at Audic S, et al.\[16\]
Software information:
DEseq2:
Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05
PossionDis:
Parameters: Fold Change >= 2.00 and FDR <= 0.001
Assembly: mm10
Supplementary files format and content: Excel file including geneID, length, gene expression group wt, gene expression group ADAM17 knock-out, log2 change, adjusted p-value, direction of change, p-value, GO-term

organism: Mus musculus

source_name: Bone marrow derived macrophages

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), including DNase digestion. 200 ng of total RNA was used for the construction of sequencing libraries.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached  magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent  cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using  reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA  Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and  subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle  (ssDNA circle), which gave the final library.

tag: strain

value: Balb/c

tag: cell type

value: Bone marrow derived macrophages

value: Co-cultured with 4T1 ADAM17 knock-out


title: SC335 2019-118-LT

description:
SC335
10X Genomics 5PrimeV1

library_source: transcriptomic single cell

molecule: polyA RNA

value: Lung


title: SC256 2018-119-CORE

description:
SC256
10X Genomics scATACv1

value: Male


title: Ctrl 2nd

value: SERBP1 (control plasmid)


title: SC334 2019-114-CORE

description:
SC334
10X Genomics 5PrimeV1

value: normal control


title: HEP319_T3 H3K27ac ChIPseq


title: BMDM co-cultured 4T1 ADAM17 knock-out 2.8, repeat 2


title: SC333 2019-113-CORE

description:
SC333
10X Genomics 5PrimeV1


title: HEP319_T2 H3K27ac ChIPseq


title: BMDM co-cultured 4T1 wt, repeat 2

value: Co-cultured with 4T1 wt


title: HEP319_T1 H3K27ac ChIPseq


title: BMDM co-cultured 4T1 ADAM17 knock-out 2.8, repeat 1


title: primary human keratinocytes, CaCl2, D7, rep3

type: RNA

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to8x60K Human lncRNA Expression Microarray (Arraystar v4.01) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary human keratinocytes 1.8 mM CaCl2 D7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: We isolated primary human keratinocytes from fresh postoperative skin samples of children as described previously by Hildebrand et al. Primary human keratinocytes were cultured in EpiLife Medium (catalog No. MEPI500CA, GIBCO) supplemented with Human Keratinocyte Growth Supplement (catalog No. S0015, GIBCO). Keratinocytes were maintained in a humidified incubator at 37°C in the presence of 5% CO2. All keratinocytes have been passaged for fewer than 6 passages.

extract_protocol: RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of libraries.

treatment_protocol: Primary human keratinocytes were treated with 1.8 mM CaCl2

value: primary human keratinocytes

tag: time


title: primary human keratinocytes, CaCl2, D7, rep2


title: primary human keratinocytes, CaCl2, D7, rep1


title: primary human keratinocytes, CaCl2, D3, rep3

source_name: primary human keratinocytes 1.8 mM CaCl2 D3


title: primary human keratinocytes, CaCl2, D3, rep1


title: SC323 2019-106-CORE

description:
SC323
10X Genomics 5PrimeV1


title: primary human keratinocytes, CaCl2, D3, rep2


title: SC315 2019-098-CORE

description:
SC315
10X Genomics 5PrimeV1

value: Female


title: C57BL/6J, PPARαKO, Liver, GenX, Biol rep 4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: Processed data matrix column name: PFASdil87

data_processing:
All the generated raw sequencing reads were filtered, by removing reads with adaptors, reads with more than 3% of unknown bases, and low quality reads (score < 20). The SOAPnuke software developed by BGI was used for this, with parameters "-n 0.03 -l 20 -q 0.4 -A 0.28".
The tool Salmon (version 1.5.1) was used to map the cleaned reads to the GRCm39 mouse genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release M27). Salmon parameters used: -i ./salmon_index_M27 --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100 --threads 20
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport (version 1.22.0), to estimate gene level counts.
Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Before statistical analyses, nonspecific filtering of the count table was performed to increase detection power using the function filterByExpr implemented in the package edgeR (version3.36.0) with default settings. In essence, filtering was done based on the requirement that a gene should have an expression level greater than 10 counts per million reads (cpm) mapped, for at least 4 libraries across all 32 samples. Differences in library size were adjusted by the trimmed mean of M-values (TMM) normalization method, implemented in edgeR. Counts were transformed to log2(cpm) values and associated precision weights, and entered into the limma analysis pipeline (function voom).
Assembly: GRCm39
Supplementary files format and content: tab delimited txt file (TxImport.GeneLevel.counts.GEO.txt; matrix table with raw gene level counts for every gene (= unfiltered dataset) and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates) )
Supplementary files format and content: R-object (txi.counts.annotated.GEO.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (txi.lengthScaledTPM.annotated.GEO.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

source_name: Liver

growth_protocol: Male and female wildtype and PPARα−/− (PparαKO) mice that had been backcrossed on a pure C57BL/6J background for more than 10 generations were acquired from Jackson Laboratories (no. 000664 and 008154, respectively). The mice were further bred at the animal facility of Wageningen University under specific pathogen free conditions to generate the number of mice necessary for the experiments.

extract_protocol:
Total RNA from liver was obtained by homogenization using TRIzol reagent, followed by isolation and purification by Rneasy mini kit (Qiagen) according to manufacturer's instructions. RNA concentration was measured with a Nanodrop 1000 spectrometer and RNA integrity was determined using an Agilent 2100 Bioanalyzer with RNA 6000 microchips (Agilent Technologies).
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 100bp runs. At BGI, genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen, USA). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: At 9-11 weeks of age, male C57Bl/6J wildtype and PPARα−/− (PparαKO) mice received either regular drinking water, or drinking water containing 0.05 or 0.3 mg/kg bw/day PFOA, or 0.3 mg/kg bw/day GenX next to being fed a high-fat diet (45% kcal fat). After 20 weeks of exposure, mice were euthanized. To do this, mice were first anesthetized with isoflurane followed by blood collection via orbital puncture. Lean and fat mass were subsequently measured using EchoMRI 100V (EchoMedical Systems, Houston, TX, USA). Immediately thereafter, the mice were euthanized by cervical dislocation and tissues were collected. Liver tissue for RNA seq was snap frozen in liquid nitrogen and subsequently stored in -80.

value: Liver

tag: genotype

value: Ppar{alpha} KO

value: GenX 0.3 mg/kg bw/day

tag: diet

value: High fat diet (45% kcal fat)

value: 20 weeks


title: BMDM co-cultured 4T1 wt, repeat 1


title: HEP276_T3 H3K27ac ChIPseq

value: HCC

value: H3K27ac (catalogue #:ab4729, Abcam

value: tumour


title: HEP276_N H3K27ac ChIPseq

value: adjacent normal


title: HEP194_T2 H3K27ac ChIPseq


title: SC313 2019-095-CORE

description:
SC313
10X Genomics 5PrimeV1


title: SC293 2019-049-LT

description:
SC293
10X Genomics 3PrimeV3

value: SSc


title: HEP194_T3 H3K27ac ChIPseq


title: SC286 2019-039-LT

description:
SC286
10X Genomics 3PrimeV3

value: Lung


title: C57BL/6J, PPARαKO, Liver, GenX, Biol rep 3

description: Processed data matrix column name: PFASdil72

value: Male


title: C57BL/6J, PPARαKO, Liver, GenX, Biol rep 2

description: Processed data matrix column name: PFASdil57


title: primary human keratinocytes, CaCl2, D1, rep3

source_name: primary human keratinocytes 1.8 mM CaCl2 D1


title: primary human keratinocytes, CaCl2, D1, rep1


title: HEP194_T1 H3K27ac ChIPseq


title: primary human keratinocytes, CaCl2, D1, rep2


title: C57BL/6J, PPARαKO, Liver, GenX, Biol rep 1

description: Processed data matrix column name: PFASdil1


title: primary human keratinocytes, control, D0, rep3

source_name: primary human keratinocytes 1.8 mM CaCl2 D0

value: control


title: primary human keratinocytes, control, D0, rep2


title: primary human keratinocytes, control, D0, rep1


title: SC281 2019-027-LT

description:
SC281
10X Genomics 3PrimeV3


title: C57BL/6J, PPARαKO, Liver, PFOA0.3, Biol rep 4

description: Processed data matrix column name: PFASdil96

value: PFOA 0.3 mg/kg bw/day


title: B008_T5 H3K27ac ChIPseq


title: SC277 2019-022-CORE

description:
SC277
10X Genomics 3PrimeV3

value: normal control


title: Group 4_HH6_GFPneg_ATAC_1

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

description: 10869_10099_100378_HGHMCBGXB_A_HH6_AP2aE_ATAC_GFPneg_1_TCCTCTAC

data_processing:
Demultiplexing, bcl2fastq
Trimming, Group #1 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0, Groups #2-4 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0
Group #1 Alignment 'hisat2  --phred33 --rna-strandness RF --dta --no-unal' , Group #2 -4 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000'
Groups #2-4 Marking Duplicates, Picard MarkDuplicates
Filtering, samtools view, sort, index
Peak calling, MACS2 Group #2 callpeak -f BAMPE -g 2913022398  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73, Group #3, callpeak -f BAMPE -g 2913022398 -q 0.05 --call-summits Group #4, callpeak -f BAMPE -g 1218492533  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73
RNA-Seq Quantification Group #1 featureCounts -t exon -s 2 -g gene_id
Assembly: Group #1,2,3 UCSC hg38 Group #4 ENSEMBL galGal6
Supplementary files format and content: .narrowPeak, MACS2 peaks
Supplementary files format and content: .txt, FeatureCounts quantification file
Supplementary files format and content: .bam, alignment files

organism: Gallus gallus

source_name: Chicken HH6 GFPneg sorted ATAC 1

extract_protocol:
Groups #1-3 H1 cells were transfected with virus expressing either GFP or TFAP2A. After one week, transfected cells were isolated via FACS and then processed for various sequencing libraries. Group #4 Chicken embryos were electroporated with a TFAP2AE1-GFP reporter and subjected to FACS sorting. 10,000 GFP negative cells were collected and spun down before ATAC-Seq library construction
Group #1  30k sorted cells were used per sample. RNA was extracted using RNA-Aqueous Micro kit, normalized, and used for NEB Next Ultra II Directional RNA-Sequencing Kit, Group #2 30k sorted cells were used per sample. The OMNI-ATAC protocol was used for ATAC-Seq library prep, Group #3 CUT&RUN libraries with samples of 300k cells each were input normalized and contructed as in Rothstein & Simoes-Costa, Genome Research 2020, Group #4 10k sorted cells were used per sample. The OMNI-ATAC protocol was used for ATAC-Seq library prep.
Group #1 RNA-Seq, Group #2 ATAC-Seq, Group #3 CUT&RUN, Group #4 ATAC-Seq

tag: tissue/cell type

value: chicken embryos

value: TFAP2AE1-GFP Negative

tag: group


title: HH9NF_Sox2

data_processing:
Library strategy: CUT&RUN
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0
Alignment, bowtie2, Group #1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --x ~/genome/bowtie2-hg38/hg38 -I 10 -X 1000  Group #2 --x ~/genome/bowtie2-GRCg6a/GRCg6a
Marking Duplicates, Picard MarkDuplicates
Filtering, samtools view, sort, index
Peak calling, MACS2 Group#1 callpeak -f BAMPE -g 2913022398  -q 0.05 --call-summits, Group #2 -g 1218492533
Genome_build: Group #1, UCSC hg38
Genome_build: Group #2, ENSEMBL galGal6 (GRCg6a)
Supplementary_files_format_and_content: .narrowPeak, MACS2 peaks
Supplementary_files_format_and_content: .bed, peak file
Supplementary_files_format_and_content: .bam, alignment files

source_name: HH9 Neural Fold Dissection

extract_protocol:
Group #1 - Cultures were dissociated using Accutase and counted to normalize cell input. Group #2, cranial neural fold dissections in HH9 stage chicken embryos.
Libraries were cell input normalized and contructed as in Rothstein & Simoes-Costa, Genome Research 2020

tag: condition

value: No treatment

value: HH9 Neural Fold Dissection

tag: antibody

value: Sox2, R&D Systems (AF 2018) 1:50


title: C57BL/6J, PPARαKO, Liver, PFOA0.3, Biol rep 3

description: Processed data matrix column name: PFASdil95

tag: tissue

value: Liver

value: Ppar{alpha} KO

value: High fat diet (45% kcal fat)


title: C57BL/6J, PPARαKO, Liver, PFOA0.3, Biol rep 2

description: Processed data matrix column name: PFASdil80

value: 20 weeks


title: HH9NF_H3K27Ac_3


title: RCAS_YAP1-MAML2 rep3

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: RCAS_YAP1-MAML2 rep3

data_processing:
Sequencing was performed using an Illumina NovaSeq 6000 employing a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg38 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw values for each Sample.

source_name: tissue

growth_protocol: 30.000 HEK293 cells were seeded per well in 48 well plates and grown in DMEM (11995-073), 10% FBS, 1% PenStrep

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an S1 flow cell.

treatment_protocol: 16 hours after seeding cells were transfected with 300ng of plasmid DNA. 48 hours post-transfection, RNA was isolated (Qiagen Rneasy Mini Kit)

tag: transfected


title: RCAS_YAP1-MAML2 rep1

description: RCAS_YAP1-MAML2 rep1


title: B008_T2 H3K27ac ChIPseq

value: HCC

value: H3K27ac (catalogue #:ab4729, Abcam

value: tumour


title: HH9NF_Oct4_RD


title: ATAC_Oct4-Sox2-OE_2

data_processing:
Demultiplexing, bcl2fastq
Trimming, CutAdapt v2.10, -a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25 -j 0
Alignment, bowtie2, (Groups #1,#2 bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --threads 16 -x ~/genome/bowtie2-GRCg6a/GRCg6a -X 2000), (Group #3,  -x~/genome/hg38/hg38_bt2/GRCh38)
Mark Duplicates, picard MarkDuplicates
Filter Duplicates, samtools v1.9, samtools view -@ 16 -F 1804 -f 2
Call peaks, MACS2, (Groups #1,#2 macs2 callpeak -t "$FILE"  -n "$FILE" -f BAMPE -g 1218492533 -q 0.05 --call-summits  --nomodel --shift 37 --ext 73 -B --SPMR)(Group #3 -g 2913022398)
Combine datasets/R analysis, DiffBind
Genome_build: for Gallus gallus, ENSEMBL galGal6 (GRCg6a)
Genome_build: for Homo sapiens, UCSC hg38
narrowPeak, peak file from MACS2
.RDS, R data file, specifically the S3 Object of class DBA from DiffBind. Contains peak by sample count matrix.
.txt, tab-delim text file, peak by sample matrix for each experiment.

extract_protocol:
Group #1 - Cranial dissection and dissociation using Accumax, Group #2 - Half-head cranial dissection and dissociation using Accumax, Group #3 - culture dissociation using Accutase and counting to normalize cell input.
Cells were processed using the OMNI-ATAC-Seq protocol. Frozen cells were quickly thawed at 37℃ and ATAC-RSB buffer was added to a total volume of 1.5mL. Samples were centrifuged at 500rcf for 5 minutes at 4℃ and the supernatant was removed. Next, cells were resuspended in 100µl of ATAC-RSB-LYSIS and kept on ice for 3-5 minutes, depending on input cell type. To stop lysis, 1mL of ATAC-RSB-WASH was added to each sample and they were again centrifuged for 5 minutes at 500rcf. The supernatant was removed, and cells were resuspended in 50µl of OMNI-ATAC Mix (~100nM concentration of Illumina TDE1 enzyme). Cells were then tagmented on a mixing (500rpm) thermoblock at 37℃ for one hour. Tagmented DNA was recovered using a Qiagen MinElute Kit (#28204), with 21µl of elution buffer warmed to 55℃. Library amplification PCR was performed with the NEBNext Ultra II Q5 2X Master Mix (NEB #M0544S) using Nextera primers for 13-15 cycles.

treatment_protocol: 37C ex-ovo incubation, bilaterial electroporation of a control (TFAP2AE1-GFP, empty PCI-H2B-RFP) or overexpression (TFAP2AE1-GFP, PCI-OCT4-SOX2-H2B-RFP) vector, Cranial dissections, dissociation using Accumax, FACS sorting for GFP+/RFP+ neural crest cells, frozen in CryoStor media (Stem Cell Technologies #CS10), processed using OMNI-ATAC-Seq protocol

value: Cranial Dissection

value: OCT4-SOX2 Overexpression Cranial Dissection (GFP+/RFP+ cells)


title: B008_T1 H3K27ac ChIPseq


title: HEP264_N H3K27ac ChIPseq

value: adjacent normal


title: HEP264_T H3K27ac ChIPseq


title: RCAS_S94A-YAP1-MAML2 rep3

description: RCAS_S94A-YAP1-MAML2 rep3


title: RCAS_YAP1-MAML2 rep2

description: RCAS_YAP1-MAML2 rep2


title: C57BL/6J, PPARαKO, Liver, PFOA0.3, Biol rep 1

description: Processed data matrix column name: PFASdil16

tag: Sex

value: Male

value: PFOA 0.3 mg/kg bw/day


title: C57BL/6J, PPARαKO, Liver, PFOA0.05, Biol rep 4

description: Processed data matrix column name: PFASdil91

tag: treatment

value: PFOA 0.05 mg/kg bw/day


title: C57BL/6J, PPARαKO, Liver, PFOA0.05, Biol rep 3

description: Processed data matrix column name: PFASdil90


title: Group 4_HH6_GFPneg_ATAC_2

description: 10869_10099_100378_HGHMCBGXB_A_HH6_AP2aE_ATAC_GFPneg_2_CTAGTACG

source_name: Chicken HH6 GFPneg sorted ATAC 2

value: chicken embryos

value: TFAP2AE1-GFP Negative


title: C001_T3 H3K27ac ChIPseq


title: SC284 2019-029-LT

description:
SC284
10X Genomics 3PrimeV3

value: Lung

tag: age

tag: disease status

value: SSc

tag: patientcorecode


title: ATAC_Oct4-Sox2-OE_1

source_name: OCT4-SOX2 Overexpression Cranial Dissection


title: RCAS_S94A-YAP1-MAML2 rep2

description: RCAS_S94A-YAP1-MAML2 rep2


title: C001_N H3K27ac ChIPseq

tag: disease state

tag: chip antibody

tag: library


title: C57BL/6J, PPARαKO, Liver, PFOA0.05, Biol rep 2

description: Processed data matrix column name: PFASdil61

value: Liver

tag: strain

tag: time


title: RCAS_S94A-YAP1-MAML2 rep1

description: RCAS_S94A-YAP1-MAML2 rep1

tag: cell type


title: ATAC_Oct4-Sox2-Control_2

source_name: Control Cranial Dissection

value: Control Cranial Dissection (GFP+/RFP+ cells)


title: C57BL/6J, PPARαKO, Liver, PFOA0.05, Biol rep 1

description: Processed data matrix column name: PFASdil40

tag: genotype

value: Ppar{alpha} KO

tag: diet

value: High fat diet (45% kcal fat)


title: B003_T2 H3K27ac ChIPseq

value: HCC


title: ATAC_Oct4-Sox2-Control_1

tag: condition

tag: group


title: 11419_10946_112321_HVKM5BGXC_ATCACGAC_HH8_2

source_name: TFAP2AE1 GFP+ Sorted

treatment_protocol: 37C ex-ovo incubation, whole-embryo electroporation of ptk-TFAP2AE1-GFP, Cranial dissections, dissociation using Accumax, FACS sorting for GFP+ neural crest cells, frozen in CryoStor media (Stem Cell Technologies #CS10), processed using OMNI-ATAC-Seq protocol

value: NC

value: TFAP2AE1 GFP+ Sorted


title: C57BL/6J, PPARαKO, Liver, Control, Biol rep 4

description: Processed data matrix column name: PFASdil86

tag: tissue

value: Control

value: 20 weeks


title: B003_T1 H3K27ac ChIPseq

value: H3K27ac (catalogue #:ab4729, Abcam

value: tumour


title: 11306_10331_109900_HG3JFBGXC_TGGGTT_HH8_1


title: HEP325_T H3K27ac ChIPseq


title: RCAS_wtYAP1 rep1

description: RCAS_wtYAP1 rep1

tag: transfected

value: WT yap1


title: C57BL/6J, PPARαKO, Liver, Control, Biol rep 3

description: Processed data matrix column name: PFASdil84

tag: Sex

value: Male


title: 11419_10946_112321_HVKM5BGXC_TCCTCTAC_HH6_2


title: RCAS_GFP rep2

description: RCAS_GFP rep2

value: GFP


title: C57BL/6J, PPARαKO, Liver, Control, Biol rep 2

description: Processed data matrix column name: PFASdil63

tag: treatment


title: 11382_10331_111584_HT5YVBGXC_GAGGGG_HH6_1


title: HEP299_N H3K27ac ChIPseq

value: adjacent normal


title: HEP174_N H3K27ac ChIPseq


title: C57BL/6J, PPARαKO, Liver, Control, Biol rep 1

description: Processed data matrix column name: PFASdil4


title: 11419_10946_112321_HVKM5BGXC_ACCCAGCA_HH18_2


title: RCAS_GFP rep1

description: RCAS_GFP rep1


title: HEP098_T H3K27ac ChIPseq


title: C57BL/6J, WT, Liver, GenX, Biol rep 4

description: Processed data matrix column name: PFASdil93

value: Wildtype

value: GenX 0.3 mg/kg bw/day


title: C57BL/6J, WT, Liver, GenX, Biol rep 3

description: Processed data matrix column name: PFASdil24

value: Liver


title: 11382_10331_111585_HT5YVBGXC_AGGTTG_HH18_1


title: HEP098_N H3K27ac ChIPseq


title: C57BL/6J, WT, Liver, GenX, Biol rep 2

description: Processed data matrix column name: PFASdil9


title: 11419_10946_112321_HVKM5BGXC_ACAAACGG_HH16_2


title: RCAS_wtYAP1 rep3

description: RCAS_wtYAP1 rep3


title: 55B WES

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Library strategy: WES
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Sample de-multiplexing is performed using Illumina's CASAVA 1.8.2 software suite.
Sequencing reads were aligned to human genome build 38 (GRCh38/hg38) using the BWA-MEM  and then marks PCR duplicates using picard’s MarkDuplicates command.   Variants were called
The GATK 3.4 software was to call variants following the GATK Best Practices workflow.
Variants were annotated with ANNOVAR.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file with annotated variants

source_name: Human derived cell line

growth_protocol: Cells were grown in monolayer in RPMI + 10% FBS + Penicillin-streptomycin and amphotericin at 37ºC, 5% CO2 for 3 days

extract_protocol:
Genomic DNA was extracted using QiaAmp DNA Mini Kit
1 µg of genomic DNA was sheared to a mean fragment length of about 140 base pairs using focused acoustic energy (Covaris E210). Exome sequencing was performed by exome capture using the IDT xGen capture probe panel with an additional "spike-in" of ~2,500 regions, totaling ~620 kb, of RefGene coding regions that were not included or were poorlycovered by the IDT panel. Captured fragments were sequenced using 101 base pair paired-end sequencing reads in an Illumina NovaSeq 6000 with a S4 flowcell according to Illumina protocols.

tag: setting

value: growiing in mouse brain

value: osimertimib

tag: treatment time

value: at resistance


title: RCAS_wtYAP1 rep2

description: RCAS_wtYAP1 rep2


title: 11306_10331_109903_HG3JFBGXC_CCACTC_HH16_1


title: HEP325_N H3K27ac ChIPseq

value: HCC


title: B014_T H3K27ac ChIPseq

source_name: tumour


title: B014_N H3K27ac ChIPseq


title: RCAS_GFP rep3A

description: RCAS_GFP rep3


title: C57BL/6J, WT, Liver, GenX, Biol rep 1

description: Processed data matrix column name: PFASdil7

value: High fat diet (45% kcal fat)


title: 54A WES


title: C57BL/6J, WT, Liver, PFOA0.3, Biol rep 4

description: Processed data matrix column name: PFASdil70

value: PFOA 0.3 mg/kg bw/day


title: 11419_10946_112321_HVKM5BGXC_GAAACCCA_HH14_2

value: NC

value: TFAP2AE1 GFP+ Sorted


title: 54B WES


title: B012_T H3K27ac ChIPseq

value: H3K27ac (catalogue #:ab4729, Abcam


title: 11306_10331_109902_HG3JFBGXC_TTGACC_HH14_1


title: C57BL/6J, WT, Liver, PFOA0.3, Biol rep 3

description: Processed data matrix column name: PFASdil39

value: 20 weeks


title: B012_N H3K27ac ChIPseq


title: Rv2D WES

value: growing in culture

value: vehicle

value: 24 hours


title: C57BL/6J, WT, Liver, PFOA0.3, Biol rep 2

description: Processed data matrix column name: PFASdil38

value: Male


title: Cv2D WES


title: 11419_10946_112321_HVKM5BGXC_CACCACAC_HH12_2


title: 11419_10946_112321_HVKM5BGXC_CAGATCCA_HH12_1


title: ATAC_DN67_MED12_stim

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

data_processing:
reads were trimmed with fastp
reads were aligned to hg38 with hisat2
reads were deduplicated using picard
peaks were called using macs2
normalized bigwig files were generated using Rtracklayer
Genome_build: hg38
Supplementary_files_format_and_content: bigwig genome wide signal track

source_name: primary T cells

extract_protocol:
ATACseq: Approximately 100k CAR-T cells were used from each sample. Nuclei were isolated with ATAC-LB (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) . ChIP: CAR-T cells (3 x 106) were double crosslinked by 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30 minutes followed by 10 minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level – 10, Duty Cycle – 5, PIP – 140, Cycles/Burst – 200, Time – 4 minutes). Sheared chromatin was immunoprecipitated overnight.
ATACseq libraries were prepared with Nextera DNA Library Preparation Kit (Illumina). ChIPseq libraries were prepared with Ovation Ultralow Library System V2 (Tecan).

treatment_protocol: cells were stimulated with anti-idiotye antibody for 3 hours

value: stimulated


title: C57BL/6J, WT, Liver, PFOA0.3, Biol rep 1

description: Processed data matrix column name: PFASdil10

value: Wildtype


title: B011_T H3K27ac ChIPseq

value: tumour


title: B011_N H3K27ac ChIPseq

source_name: adjacent normal

value: adjacent normal


title: 55A WES

value: growiing in mouse brain

value: osimertimib


title: HEP549_T H3K27ac ChIPseq

value: HCC


title: C57BL/6J, WT, Liver, PFOA0.05, Biol rep 4

description: Processed data matrix column name: PFASdil74

value: Liver

value: PFOA 0.05 mg/kg bw/day

value: High fat diet (45% kcal fat)


title: 11306_10331_109901_HG3JFBGXC_TGGTCA_HH10_1

value: NC

value: TFAP2AE1 GFP+ Sorted


title: C57BL/6J, WT, Liver, PFOA0.05, Biol rep 3

description: Processed data matrix column name: PFASdil45

value: 20 weeks


title: 11419_10946_112321_HVKM5BGXC_ACAGTGGT_HH10_2


title: HEP549_N H3K27ac ChIPseq

value: H3K27ac (catalogue #:ab4729, Abcam


title: C57BL/6J, WT, Liver, PFOA0.05, Biol rep 2

description: Processed data matrix column name: PFASdil34


title: C57BL/6J, WT, Liver, PFOA0.05, Biol rep 1

description: Processed data matrix column name: PFASdil13


title: HEP532_N H3K27ac ChIPseq


title: HEP532_T H3K27ac ChIPseq


title: 12_neg_ASH_GAGTGG

description: 9846_10946_79261_HGM37BGX7_12_neg_ASH_GAGTGG_R1

data_processing:
Demultiplexing, bcl2fastq
Trimming, CutAdapt v2.10, -j 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=25
Alignment, Hisat2 v2.1.0, -p 16 --phred33 --rna-strandness R --dta --no-unal -x ~/genome/HiSat2_ENSEMBL_galGal6/ENSEMBL_galGal6
Sort and Index, samtools v1.9, samtools sort samtools index
Quantification, featureCounts v1.6.2, ./BAM/*.BAM -T 16 -t exon -s 2 -g gene_id -a ~/genome/Gallus_gallus.GRCg6a.99.gtf -o ./counts/featureCounts.txt
Genome_build: Ensembl galGal6 (GRCg6a)
Supplementary_files_format_and_content: featureCounts.txt, (Tab delim) all samples gene-level quantification
featureCountsFiltered.txt, (Tab delim) Filtered samples gene-level quantification, also better formated for easy understanding

source_name: GFP- Embryonic Head Sorted

growth_protocol: 37C ex-ovo incubation

extract_protocol:
Cranial portions of chicken heads were dissected and dissociated using Accumax. For each sample, around 20 heads were pooled for FACS sorting. GFP+ neural crest and GFP- embryonic head cells were captured by directly sorting into RNA Aqueous micro kit.
Stranded RNA-Seq was performed with NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB #E7765) according to manufactuors' instructions.

treatment_protocol: whole-embryo electroporation of ptk-TFAP2AE1-GFP.

tag: hh stage (time)

value: Whole Embryo (WE)

value: GFP- Embryonic Head Sorted


title: 14_neg_ASH_ATTCCT

description: 9846_10946_79263_HGM37BGX7_14_neg_ASH_ATTCCT_R1


title: C57BL/6J, WT, Liver, Control, Biol rep 4

description: Processed data matrix column name: PFASdil56

value: Male

value: Control


title: ATAC_DN59_AAVS1_stim

value: stimulated


title: ATAC_DN59_MED12_stim


title: 14_pos_ASH_ACTGAT

description: 9846_10946_79262_HGM37BGX7_14_pos_ASH_ACTGAT_R1

value: Neural Crest (NC)


title: HEP229_N H3K27ac ChIPseq

tag: disease state

value: adjacent normal


title: C57BL/6J, WT, Liver, Control, Biol rep 3

description: Processed data matrix column name: PFASdil50

value: Wildtype


title: HEP193_N H3K27ac ChIPseq

tag: chip antibody


title: ATAC_DN67_MED12_unstim

value: unstimulated


title: C57BL/6J, WT, Liver, Control, Biol rep 2

description: Processed data matrix column name: PFASdil31


title: ATAC_DN63_AAVS1_stim


title: HEP262_T H3K27ac ChIPseq

value: HCC

value: tumour

tag: library


title: 10_pos_ASH_GTGGCC

description: 9846_10946_79258_HGM37BGX7_10_pos_ASH_GTGGCC_R1


title: ATAC_DN67_AAVS1_stim


title: ATAC_DN63_MED12_stim


title: C57BL/6J, WT, Liver, Control, Biol rep 1

description: Processed data matrix column name: PFASdil17

value: Liver

tag: strain


title: ATAC_DN63_AAVS1_unstim


title: Cartilage,  Ossification, 85 day 3

city: BeiJing

first: lei

last: xiang

address: No. 31, Xinjiekou east street, Xicheng district

institute: Jishuitan Hospital

data_processing:
The constructed library was used Qubit®2.0 Fluorometer to detect the concentration and Agilent2100 to detect the size.
The qualified library is sequenced by Illumina Novaseq 6000.
The original data are preprocessed to remove the joint sequence and low-quality reads. The data preprocessing software was used Seqtk.
Normalize the Fragments (trimmed mean of M values), and then calculate the FPKM value of each gene.
The preprocessed sequence was analyzed by genomic mapping using HISAT2 software.
Assembly: NCBI Sus_scrofa.Sscrofa10

organism: Sus scrofa domesticus

source_name: Cartilage

extract_protocol:
The sample was extracted RNA by the RNA extraction Kit(RNeasy Mini Kit ,Cat#74106, Qiagen)
Magnetic beads were used to remove rRNA. Next, the RNA removed from rRNA was subjected to fragmentation, double-stranded cDNA synthesis, degradation of the second strand, end repair, addition of A to the 3 'end, junction and amplification experiments.

treatment_protocol: Cut up the tissue pieces on the ice, put the tissue  into a mortar, add an appropriate amount of liquid nitrogen, grind quickly, and then add liquid nitrogen after the liquid nitrogen is reduced, grind it repeatedly for 3 times. The ground tissue fluid was used for the extraction of RNA

value: Cartilage

value: Primary cell

tag: source

value: Chondrocytes and osteocytes

value: Osteogenesis of cartilage


title: ATAC_DN63_MED12_unstim


title: 16_1_neg_ASH_CCGTCC

description: 9846_10946_79257_HGM37BGX7_16_1_neg_ASH_CCGTCC_R1

tag: cell type


title: B020_N H3K27ac ChIPseq

value: H3K27ac (catalogue #:ab4729, Abcam


title: 12_pos_ASH_CGTACG

description: 9846_10946_79260_HGM37BGX7_12_pos_ASH_CGTACG_R1

value: TFAP2AE1 GFP+ Sorted


title: ATAC_DN59_MED12_unstim

tag: genotype


title: Cartilage,  Ossification, 85 day 2


title: 16_1_pos_ASH_ATGTCA

description: 9846_10946_79256_HGM37BGX7_16_1_pos_ASH_ATGTCA_R1


title: Cartilage,  Ossification, 85 day 1


title: B018_N H3K27ac ChIPseq


title: B020_T H3K27ac ChIPseq


title: 10_neg_ASH_GTTTCG

description: 9846_10946_79259_HGM37BGX7_10_neg_ASH_GTTTCG_R1

value: Whole Embryo (WE)

value: GFP- Embryonic Head Sorted


title: Cartilage,  Ossification, 45 day 2


title: ATAC_DN59_AAVS1_unstim


title: 16_1_2_neg_ASH_AGTTCC

description: 9846_10946_79255_HGM37BGX7_16_1_2_neg_ASH_AGTTCC_R1


title: Cartilage,  Ossification, 45 day 3


title: 16_1_2_pos_ASH_AGTCAA

description: 9846_10946_79254_HGM37BGX7_16_1_2_pos_ASH_AGTCAA_R1


title: H3K27Ac_DN67_MED12_stim

value: H3K27ac (Abcam - ab4729)


title: B017_T H3K27ac ChIPseq


title: B017_N H3K27ac ChIPseq


title: H3K27Ac_DN63_MED12_stim

value: stimulated


title: Cartilage,  Ossification, 45 day 1


title: 10_neg_lib_GCCAAT

description: 9846_10946_79253_HGM37BGX7_10_neg_lib_GCCAAT_R1


title: ATAC_DN67_AAVS1_unstim


title: H3K27Ac_DN67_AAVS1_stim


title: B016_T H3K27ac ChIPseq


title: 10_pos_lib_TTAGGC

description: 9846_10946_79252_HGM37BGX7_10_pos_lib_TTAGGC_R1

value: Neural Crest (NC)


title: B016_N H3K27ac ChIPseq

value: adjacent normal


title: HEP262_N H3K27ac ChIPseq


title: H3K27Ac_DN63_AAVS1_stim


title: 8_pos_lib_CGATGT

description: 9846_10946_79250_HGM37BGX7_8_pos_lib_CGATGT_R1


title: jy111_biol rep4

city: San Diego

first: Spencer

middle: S

last: Gang

address: Bonner Hall #4205, 7835 Trade St. Suite 100

department: Division of Biological Sciences

institute: University of California, San Diego

description: pals-25(jy111) L4 44h

data_processing:
Reads were aligned to C. elegans genome WS235 using Rsubreads in R studio
Reads were counted using Featurecounts in Rstudio
Transcript abundance was quantified with limma-voom in Galaxy
Assembly: WormBase Release WS235
Supplementary files format and content: txt files of CPM for each sample for all genes. Limma-voom performed exculding undetected and lowly expressed genes (CPM of less than 0.5)

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Synchronized L1 worms for wild-type, pals-22(jy3), pals-22(jy3) pals-25(jy9), and pals-25(jy111) worm strains were prepared by bleaching gravid adults to isolate embyros in M9 buffer that hatched into starved L1s. L1s were grown for 44 hours, or 48 hours for pals-22(jy3), to the L4 life stage.

extract_protocol:
Tri reagent (Molecular Research Center) and BCP reagent followed by isopropanol and ethanol washes. Total RNA resuspended in nuclease-free watar and further purified using Rneasy Mini kit (Qiagen). Final RNA reuspended in nuclease-free water. RNA quality assessed with a TapeStation system (Agilent) prior to library preparation.
Library constructed by the University of California, San Diego Institute for Genomic Medicine following Illumina Stranded mRNA Prep standard protocols

treatment_protocol: Nematode Growth Media agar plates supplemented with E. coli OP50-1 at 20°C

value: Whole animal

tag: cell line


title: jy111_biol rep3

description: pals-25(jy111) L4 44h


title: H3K27Ac_DN59_MED12_stim


title: jy111_biol rep2

description: pals-25(jy111) L4 44h


title: H3K27Ac_DN59_AAVS1_stim


title: 6_pos_lib_ATCACG

description: 9846_10946_79248_HGM37BGX7_6_pos_lib_ATCACG_R1

tag: condition


title: HEP200_T8 H3K27ac ChIPseq


title: jy111_biol rep1

description: pals-25(jy111) L4 44h


title: HEP200_T7 H3K27ac ChIPseq


title: jy3jy9_biol rep4

description: pals-22(jy3) pals-25(jy9) L4 44h

value: pals-22(jy3) pals-25(jy9)


title: H3K27Ac_DN67_AAVS1_unstim

value: unstimulated


title: HH12_mGFP_1_GTGAAA

description: 9279_5515_70280_HTNMMBGX3-HJNG2BGX5_MR15R-HH12-mGFP-1_GTGAAA_R1

tag: group


title: HH10_mGFP_2_GTAGAG

description: 9279_5515_70281_HTTM3BGX5-HJNG2BGX5_MR14R-HH10-mGFP-2_GTAGAG_R1


title: jy3jy9_biol rep3

description: pals-22(jy3) pals-25(jy9) L4 44h

tag: tissue


title: 8_neg_lib_ACAGTG

description: 9846_10946_79251_HGM37BGX7_8_neg_lib_ACAGTG_R1


title: H3K27Ac_DN63_MED12_unstim


title: jy3jy9_biol rep2

description: pals-22(jy3) pals-25(jy9) L4 44h


title: H3K27Ac_DN63_AAVS1_unstim


title: HH16_pGFP_2_CAACTA

description: 9279_5515_70279_HHTM3BGX5-HJNG2BGX5_MR20R-HH16-pGFP-2_CAACTA_R1


title: HEP152_T10 H3K27ac ChIPseq

value: HCC

value: tumour


title: HH16_mGFP_2_CATGGC

description: 9236_5515_69217_HHTM3BGX5_MR24-HH16-mGFP-2_CATGGC_R1


title: H3K27Ac_DN59_MED12_unstim


title: 01567_N H3K27ac ChIPseq


title: jy3jy9_biol rep1

description: pals-22(jy3) pals-25(jy9) L4 44h


title: HeLa, High+OVA

city: Daejeon

first: Hyun

middle: Ahm

last: Sohn

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

data_processing:
base calling was conducted through an integrated primary analysis software called RTA (Real Time  Analysis).
The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq
Adapters are trimmed away with Trim Galore 0.6.4 (>Q30)
Reads are mapped with paired end mapping of STAR 2.7.3a
Mapped reads are quantified and normalized with cufflinks 2.2.1
Assembly: GRCh38
Supplementary files format and content: Excel file includes CPM values for each Sample

source_name: HeLa cell line

growth_protocol: Each cell line were routinely grown in DMEM  supplemented with 10% fetal bovine serum and 100 U/ml penicillin. Cell lines were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
HeLa cells were washed with PBS, and RNA was harvested using  RNA Prep Kit (Qiagen) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For  knockdown of NDRG3 and control,  siRNA(50nM) were treated in HeLa cell line.

value: HeLa

value: Cervical cancer cells

value: OVA

tag: cell confluency

value: High density


title: HeLa, High+siPTRK 2

value: PTPRK knockdown


title: jy3_biol rep4

description: pals-22(jy3) L4 48h


title: HH14_pGFP_3_ATGAGC

description: 9236_5515_69214_HHTM3BGX5_MR18-HH14-pGFP-3_ATGAGC_R1

value: TFAP2AE1 GFP+ Sorted


title: 6_neg_lib_TGACCA

description: 9846_10946_79249_HGM37BGX7_6_neg_lib_TGACCA_R1

value: Whole Embryo (WE)


title: jy3_biol rep2

description: pals-22(jy3) L4 48h


title: HeLa, High+siPTRK 1


title: H3K27Ac_DN67_MED12_unstim


title: RNApol _DN67_AAVS1_stim

value: RNAPIIpS2 Abcam - ab5095


title: HeLa, High+siCtrl

value: siCtrl


title: HH8_mGFP_3_AGTTCC

description: 9236_5515_69211_HHTM3BGX5_MR12-HH8-mGFP-3_AGTTCC_R1

value: GFP- Embryonic Head Sorted


title: HH12_mGFP_2_GTGGCC

description: 9236_5515_69213_HHTM3BGX5_MR16-HH12-mGFP-2_GTGGCC_R1


title: HH6_mGFP_3_CTTGTA

description: 9236_5515_69210_HHTM3BGX5_MR10-HH6-mGFP-3_CTTGTA_R1


title: HEP152_T7 H3K27ac ChIPseq

value: H3K27ac (catalogue #:ab4729, Abcam


title: RNApol _DN67_MED12_stim

value: stimulated


title: RNApol _DN63_AAVS1_stim


title: N2_biol rep4

description: wild-type L4 44h

value: Whole animal

value: WT


title: MCL Patient 4

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

description: single cell poly-A RNA

data_processing:
Base-calling, alignment, filtering, and generation of normalized abundance measurements was performed using cellranger v3.1.0 with standard parameters.
Genome_build: Hg38
Supplementary_files_format_and_content: Processed data files are in either tab separated value or matrix market format.  All processed files are gzipped.

source_name: PBMCs, CD19 depleted, methanol-fixed

growth_protocol: PBMC were collected from MCL patients by density gradient centrifugation and CD19+ B cells were depleted.

extract_protocol:
CD19-depleted PBMC were fixed in methanol and stored at -80C prior to further processing.  Cells were then rehydrated and washed according to the published 10X genomics protocol.
Single cells were captured, barcoded cDNA was amplified and libraries were constructed using the 10X Single Cell 3' v3 kit according to the manufacturer's instructions.

treatment_protocol: No treatments were administered.

value: CD19-depleted PBMC

value: MCL

tag: age at diagnosis

tag: Sex

value: male

tag: collection date

tag: Stage

value: IV


title: MCL Patient 3

description: single cell poly-A RNA


title: RNApol _DN63_MED12_stim

tag: treatment


title: jy3_biol rep1

description: pals-22(jy3) L4 48h


title: HH14_mGFP_3_CACGAT

description: 9236_5515_69216_HHTM3BGX5_MR22-HH14-mGFP-3_CACGAT_R1

tag: hh stage (time)


title: H3K27Ac_DN59_AAVS1_unstim

value: unstimulated

tag: chip antibody

value: H3K27ac (Abcam - ab4729)


title: HH12_pGFP_2_GATCAG

description: 9236_5515_69209_HHTM3BGX5_MR8-HH12-pGFP-2_GATCAG_R1

value: Neural Crest (NC)


title: RNApol _DN59_MED12_stim


title: MCL Patient 2

description: single cell poly-A RNA

tag: disease state


title: N2_biol rep3

description: wild-type L4 44h


title: jy3_biol rep3

description: pals-22(jy3) L4 48h


title: N2_biol rep2

description: wild-type L4 44h


title: HH8_pGFP_3_TGACCA

description: 9236_5515_69207_HHTM3BGX5_MR4-HH8-pGFP-3_TGACCA_R1


title: HH10_pGFP_3_GCCAAT

description: 9236_5515_69208_HHTM3BGX5_MR6-HH10-pGFP-3_GCCAAT_R1


title: RNApol _DN59_AAVS1_stim


title: R2 scRNA-seq

data_processing:
The data from sequencer was processed using bcl2fastq progam provided by the vendor (10X genomics).  This program demultiplexes the data.
The resulting output was procssed using cellranger program provided by the vendor (10X genomics).  This program aligns, the reads, and uses the barcode information to generate diigital gene expression matrix data.
The data was filtered, normalized (SCTransform), and clustered in Seurat (version 3) within R.
After principal component analysis, first 30 principal components were used for clustering.  The data was further visualized using Seurat 3 and R.
Genome_build: hg38
Supplementary_files_format_and_content: Average gene expression excel for average gene expression per cluster.

extract_protocol:
Nano-sized droplets containing a single cell with the bar-coded gel bead were generated using the Chromium controller (10x Genomics)
10x Genomics (Single Cell 3′ Library Kit V3)


title: HeLa, Low

value: HeLa

value: Cervical cancer cells

value: no treatment

value: Low density


title: RNApol _DN67_MED12_unstim

value: RNAPIIpS2 Abcam - ab5095


title: MCL Patient 1

description: single cell poly-A RNA


title: HH6_pGFP_3_CGATGT

description: 9236_5515_69206_HHTM3BGX5_MR2-HH6-pGFP-3_CGATGT_R1

value: TFAP2AE1 GFP+ Sorted


title: BM4 scRNA-seq


title: RNApol _DN59_MED12_unstim


title: Supralumbar_Uninjured_biol_rep2

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

description: 10X Genomics

data_processing:
Illumina NovaSeq 6000 used for base-calling
CellRanger pipeline (10X Genomics) used for base-cell demultiplexing, alignment, read filtering, and UMI counting.
Low quality cells removed based on total UMI count
Software: CellRanger (7.0.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Mice were anesthetized with isoflurane and promptly decapitated. The brain and brainstem were dissected out and placed in ice-cold slushy artificial cerebrospinal fluid (Hearing et al., 2013) for one minute. Brains were then sectioned in the sagittal plane at 500-micron intervals using Adult Mouse Brain Slicer Matrix on ice (Zivic Instruments BSMAS005-2). A total of nine sections were created from each animal including a midline section and four sections moving lateral into each hemisphere. Neurons retrogradely labelled from lumbar spinal cord were then micro dissected using a stereomicroscope and fluorescence adapter (NIGHTSEA SFA-GR).  The three sections from the left hemisphere and one midline section were dissected and flash frozen in a 1.5mL Eppendorf DNA LoBind Microcentrifuge tube. The three sections from the right hemisphere were then collected and flash frozen with identical conditions, as mentioned above. Samples were then stored at -80 °C until FACS sorting. To prepare cell nuclei on the day of library preparation frozen tissue was promptly transferred from -80 °C storage to a chilled 2mL dounce with chilled Nuclei EZ Lysis Buffer (Sigma-Aldrich N 3408). Sample was dounced 25 times with pestle A and 20 times with pestle B. The dounced sample was then transferred to a chilled 15mL conical tube and an additional 2mL of Nuclei EZ Lysis Buffer was added and gently mixed by inversion. The sample incubated on ice for 5 minutes and then was centrifuged at 500G at 4 °C. The supernatant was removed, and the pellet was resuspended in 4mL of Nuclei EZ Lysis Buffer. The sample again was incubated on ice and centrifuged at 500G at 4 °C for 5 minutes. Following the centrifugation, the supernatant was removed, and the pellet resuspended in 500uL of Nuclei Suspension Buffer (2% BSA, 40U/uL RNase Inhibitor (Invitrogen Ref. AM2684), 1X PBS). The resuspended solution was then filtered through a 20um filter and moved directly to the FACS machine. The collection tube for the sorted nuclei was coated with 5% BSA and contained the 10X Genomics master mix. We initially gate out debris using side scatter area (SSC-A) vs forward scatter area (FSC-A) and forward scatter width (FSC-W) vs forward scatter area (FSC-A). To eliminate doublets, the nuclei that pass through the gates above were then gated by side scatter width (SSC-W) vs side scatter height (SSC-H). Nuclei that passed through all the above gates were then filtered by level of fluorescence so that only the brightest were collected. With the above parameters, the FACS machine was set to collect 5,000 nuclei in five to seven minutes.
Sample libraries were prepared according to Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-1000269), according to the manufacture protocol (10X Genomics, CG000204 Rev D).

tag: strain

value: Brain

tag: preparation

value: cell nuclei


title: unsorted total pituitary cells from R26-LSL-eYFP

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

address: 101 Nicolls Road

institute: Stony Brook University

description: We also prepared single-cell RNA libraries from 2 male R26-Eyfp control mice (1 from each corresponding litter of the Cre-positive samples), which were dispersed but did not undergo FACS, as a second pool in order for our analyses to include all pituitary cell-types.

data_processing:
Samples were demultiplexed with Cellranger Single Cell Software Suite 3.1.0
Binary sequence alignment maps were converted into the loom format using velocyto.py (La Manno et al. 2018), which were then analyzed in R using the ‘Seurat’ 3.1.2 package (Butler et al. 2018; Stuart et al. 2019).
Core Seurat functions were used to read in loom files, integrate samples, generate uniform manifold approximation and projection (UMAP) plots, calculate clusters, perform differential gene expression analyses, and generate plots of expression data.
Assembly: fastq files aligned to a modified University of California Santa Cruz mm10 (GRCm38) reference genome containing amended annotation for the Prop1 3’ untranslated region (Cheung et al. 2018b) and the Eyfp sequence (https://www.ncbi.nlm.nih.gov/nuccore/LC171744.1, positions 2933-3640).
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)
Supplementary files format and content: loom format matrix created by velocyto.py

source_name: pituitary

extract_protocol:
Pituitary tissue was dissected and dispersed using an enzymatic mix of collagenase, trypsin, and DNaseI for 4 hrs (cells sorted for Tshb-Cre sample), and dispersed cells prepared for scRNAseq library preparation. Dispersed cells were resuspended in HBSS/0.4%BSA.
Single-cell RNA libraries were prepared by the University of Michigan’s Advanced Genomics Core under a standardized pipeline on the 10x Genomics Chromium platform and controller, following manufacturer’s instructions for Single Cell 3’ v3 reagents, and sequenced on the NovaSeq6000 platform with an S4 chip.  From our previous description in Cheung et al., 2018 Endocrinology: Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting post-GEM reverse transcription product was cleaned up using DynaBeads MyOne silane beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA) cleaned and quantified, and then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by KAPA quantitative PCR for Illumina adapters (Roche, Pleasanton, CA) and size was determined by Agilent TapeStation D1000 tapes. Read 1 primer sequences were added to the molecules during GEM incubation. P5, P7, and sample index and read 2 primer sequences were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. Libraries were generated with unique sample indices for each sample.

value: pituitary

tag: sample type

value: 2 male

tag: cell type

value: total pituitary cells

tag: age


title: PC9 scRNA-seq

tag: cell line


title: RNApol _DN63_MED12_unstim

tag: genotype


title: HH14_mGFP_2_CACCGG

description: 9235_5515_69200_HTNMMBGX3_MR21-HH14-mGFP-2_CACCGG_R1

tag: condition

value: Whole Embryo (WE)

tag: group

value: GFP- Embryonic Head Sorted


title: Supralumbar_Uninjured_biol_rep3

description: 10X Genomics

tag: tissue


title: HH14_pGFP_2_GAGTGG

description: 9235_5515_69198_HTNMMBGX3_MR17-HH14-pGFP-2_GAGTGG_R1


title: Supralumbar_Uninjured_biol_rep1

description: 10X Genomics


title: HH16_pGFP_1_ATTCCT

description: 9235_5515_69199_HTNMMBGX3_MR19-HH16-pGFP-1_ATTCCT_R1


title: RNApol _DN63_AAVS1_unstim


title: mouse NLS-2SA-YAP1 rep3

description: mouse NLS-2SA-YAP1 rep3

data_processing:
Sequencing was performed using an Illumina NovaSeq 6000 employing a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC mm10 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw values for each Sample.

growth_protocol: DF1 cells were grown in DMEM (11995-073), 10% FBS, 1% PenStrep and transfected with RCAS-YAP1-MAML2-v2 or RCAS-NLS-2SA-YAP1. 1-2 weeks post-transfection, transfected DF1 cells were injected into the subarachnoid space of p0-p3 Nestin/tv-a Cdkn2a null mice. Mice were observed for signs of tumor growth and euthanized at appropriate times. Tumors were flash frozen in liquid nitrogen, ground up using a motor and pestor (on dry ice) and RNA was extracted using the Qiagen RNAeasy Mini kit

treatment_protocol: untreated

tag: tumor

tag: source region

value: extra cranial


title: SaOS-2 CRISPR-UHRF1 [ATAC-seq]

city: Irvine

first: Claudia

middle: A

last: Benavente

state: CA

address: 839 Medical Sciences Ct, Sprague Hall 108

institute: University of California, Irvine

data_processing:
Reads were trimmed by Illumina adapters and base quality scores >20 and mapped to the hg19 genome with Bowtie2 (--dovetail -X 2000).
Duplicated reads were removed. Blacklist regions on the genome were excluded.
Peaks were called using MACS2 (-p 0.0001 -g mm -f BAMPE --nomodel --nolambd).
BigWig files were created using bedGraphToBigWig.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: bigWig files

source_name: osteosarcoma cell line

growth_protocol: 143B were cultured in MEM (Gibco), with 10% BCS, penicillin/streptomycin, and 0.015mg/ml BrdU. SJSA-1 were cultured in RPMI (Gibco), with 10% BCS and penicillin/streptomycin. SaOS-2 were cultured in McCoy’s 5A (Gibco), with 10% BCS and penicillin/streptomycin.

extract_protocol:
Approximately 50,000 cells were harvested for ATAC-seq for each replicate.
ATAC-seq was performed as previously described (Buenrostro et al. 2015, Nature 523:486-490).

treatment_protocol: Cells were transduced with lentivirus: CRISPR-VO= lentiCRISPRv2 (Addgene) or CRISPR-UHRF1= plentiCRISPRv2 with UHRF gRNA (gRNA sequence: TCAATGAGTACGTCGATGCT; GenScript). Followed by puromycin selection.

value: Osteosarcoma cell line

tag: experimental condition

value: UHRF1 KO


title: RNApol _DN59_AAVS1_unstim

tag: treatment

value: unstimulated


title: YFP FAC-sorted cells from Tshb-Cre; R26-LSL-eYFP

description: We dissected pituitary glands from 3 male and 1 female Tshb-Cre; R26-Eyfp mouse (2 males from one litter and one male and one female from a second litter) and dispersed cells for FACS using EYFP fluorescence in one pool.

value: 3 male + 1 female pituitary mixed

value: pituitary YFP+ cells

value: Tshb-Cre; R26-LSL-eYFP


title: HH10_mGFP_1_ATGTCA

description: 9235_5515_69196_HTNMMBGX3_MR13R-HH10-mGFP-1_ATGTCA_R1

tag: hh stage (time)


title: SaOS-2 CRISPR-VO [ATAC-seq]

value: Non-targeting CRISPR


title: MED12_DN67_AAVS1_stim

value: stimulated

tag: chip antibody

value: MED12 Bethyl laboratories - A300-774A


title: mouse NLS-2SA-YAP1 rep2

description: mouse NLS-2SA-YAP1 rep2

source_name: tissue


title: SJSA-1 CRISPR-UHRF1 #10 [ATAC-seq]


title: RNApol _DN67_AAVS1_unstim

value: RNAPIIpS2 Abcam - ab5095


title: N2_biol rep1

description: wild-type L4 44h

value: Whole animal

value: WT


title: HH8_mGFP_1_AGTCAA

description: 9235_5515_69195_HTNMMBGX3_MR11-HH8-mGFP-1_AGTCAA_R1


title: C2 scRNA-seq


title: mouse NLS-2SA-YAP1 rep1

description: mouse NLS-2SA-YAP1 rep1

value: extra axial


title: MED12_DN63_AAVS1_stim


title: MED12_DN59_AAVS1_stim


title: HH16_mGFP_1_CAGGCG

description: 9235_5515_69201_HTNMMBGX3_MR23-HH16-mGFP-1_CAGGCG_R1


title: SJSA-1 CRISPR-VO [ATAC-seq]


title: mouse YAP1-MAML2-v2 rep7

description: mouse YAP1-MAML2-v2 rep7

value: intra ventricular


title: 143B CRISPR-UHRF1 #7 [ATAC-seq]


title: MED12_DN67_AAVS1_unstim


title: HH12_pGFP_1_ACTTGA

description: 9235_5515_69193_HTNMMBGX3_MR7-HH12-pGFP-1_ACTTGA_R1

value: Neural Crest (NC)

value: TFAP2AE1 GFP+ Sorted


title: MED12_DN63_AAVS1_unstim


title: HH10_pGFP_2_ACAGTG

description: 9235_5515_69192_HTNMMBGX3_MR5-HH10-pGFP-2_ACAGTG_R1


title: mouse YAP1-MAML2-v2 rep5

description: mouse YAP1-MAML2-v2 rep5

value: extra cranial


title: MED12_DN59_AAVS1_unstim


title: HH8_pGFP_1_TTAGGC

description: 9235_5515_69191_HTNMMBGX3_MR3-HH8-pGFP-1_TTAGGC_R1


title: SaOS-2 CRISPR-UHRF1 [RNA-seq]

description: processed data file: merged_fpkm.tsv

data_processing:
Reads were trimmed by base quality scores >20 and mapped to the hg19 genome with HiSat2.
Counts per gene were calculated by counting reads mapping to constitutive exons using featureCount.
FPKM were calculated using Cufflinks.
Counts for each gene were then analyzed with the R package DESeq2 to identify differentially expressed genes. A 5% false discovery rate cutoff was used for significance.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: merged_fpkm.tsv: Tab-separated text file includes FPKM values.

extract_protocol:
Total RNA was isolated using the RNA Micro Kit (Qiagen).
500 ng of total RNA was used to create the RNA-seq library following the manufacturer’s protocol from purification, mRNA fragmentation through the adenylation of end-repaired cDNA fragments and cleanup (TruSeq Stranded mRNA, Illumina). The collected sample was cleaned with AMPure XP beads (Beckman Coulter) and eluted in 20 μl of 10 mM Tris buffer, pH 8, 0.1% Tween 20. 500 ng of total RNA was used to create the RNA-seq library following the manufacturer’s protocol from purification, mRNA.

value: Osteosarcoma cell line


title: 143B CRISPR-VO [ATAC-seq]


title: mouse YAP1-MAML2-v2 rep6

description: mouse YAP1-MAML2-v2 rep6


title: HH6_pGFP_2_ATCACG

description: 9235_5515_69190_HTNMMBGX3_MR1-HH6-pGFP-2_ATCACG_R1


title: SJSA-1 CRISPR-UHRF1 #5 [ATAC-seq]

value: UHRF1 KO


title: mouse YAP1-MAML2-v2 rep4

description: mouse YAP1-MAML2-v2 rep4


title: HH6_mGFP_2_GGCTAC

description: 9235_5515_69194_HTNMMBGX3_MR9-HH6-mGFP-2_GGCTAC_R1

value: Whole Embryo (WE)

value: GFP- Embryonic Head Sorted


title: MED1_DN67_MED12_stim

value: MED1 Bethyl laboratories - A300-793A


title: mouse YAP1-MAML2-v2 rep3

description: mouse YAP1-MAML2-v2 rep3


title: HH12_mGFP_V4_2_TAATCG

description: 10406_10331_89151_HLYH2BGX9_HH12_mGFP_V4-2_TAATCG_R1


title: SaOS-2 CRISPR-VO [RNA-seq]

description: processed data file: merged_fpkm.tsv


title: HH12_pGFP_V4_2_CCAACA

description: 10406_10331_89150_HLYH2BGX9_HH12_pGFP_V4-2_CCAACA_R1


title: MED1_DN63_MED12_stim


title: SJSA-1 CRISPR-UHRF1 #10 [RNA-seq]

description: processed data file: merged_fpkm.tsv


title: SJSA-1 CRISPR-UHRF1 #5 [RNA-seq]

description: processed data file: merged_fpkm.tsv


title: MED1_DN67_AAVS1_stim


title: mouse YAP1-MAML2-v2 rep1

description: mouse YAP1-MAML2-v2 rep1


title: mouse YAP1-MAML2-v2 rep2

description: mouse YAP1-MAML2-v2 rep2


title: MED1_DN63_AAVS1_stim


title: HH12_mGFP_V4_1_CATTTT

description: 10406_10331_89149_HLYH2BGX9_HH12_mGFP_V4-1_CATTTT_R1


title: SJSA-1 CRISPR-VO [RNA-seq]

description: processed data file: merged_fpkm.tsv


title: HH12_pGFP_V4_1_CATGGC

description: 10406_10331_89148_HLYH2BGX9_HH12_pGFP_V4-1_CATGGC_R1


title: MED1_DN59_MED12_stim


title: HH16calz_neg_CTTGTA

description: 10262_10946_86634_HFK7NBGX9_HH16calz_neg_CTTGTA_R1


title: MED1_DN59_AAVS1_stim


title: 143B CRISPR-VO [RNA-seq]

description: processed data file: merged_fpkm.tsv


title: KO

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
More than two billion scRNA-seq reads were processed and analyzed with the default parameters of CellRanger single-cell software suite (v3.1.0). Base calling files (BCLs) generated by Illumina sequencer were demultiplexed according to the sample index.
Sequences were then aligned to the mm10 reference for whole transcriptome analysis.
Loupe browser and Seurat (v4.0.0) were used to perform visualization, quality control, normalization, scaling, PCA dimension reduction, clustering, and differential expression analysis
Cells with UMI count of greater than 30,000, fewer than 500 or greater than 6,000 genes, and >10% of total expression from mitochondrial genes were excluded
The remaining 11,651 cells were unsupervised clustered after aligning the top 12 dimensions and setting resolution to 0.5. The identity for each cluster was assigned according to marker genes for known non-parenchymal cell types in the mouse  liver
Genome_build: mm10
Supplementary_files_format_and_content: .rds files contain Seurat objects with the count matrix as an RNA assay, and identified cell clusters in the @meta.data field.

source_name: liver non-parenchymal cells

extract_protocol:
8 hours after LPS treatment, mice were sacrificed and largest liver lobe of n=3 mice from same group were pooled together and grinded with gentleMACS™ Dissociators. Mouse hepatic parenchymal cells were digested and non-parenchymal cells were isolated by Mouse Liver Dissociation Kit (Miltenyi Biotec). Isolated cells passed through 40-um cell strainer were treated with Red Blood Cell Lysis Solution (Miltenyi Biotec) to lyse blood cells. To acquire cells with >90% viability, dead cells were removed with Dead Cell Removal Kit (Miltenyi Biotec). Briefly, cells were pelleted by centrifugation at 300g for 5 minutes and resuspended in buffer containing dead cell removal microbeads and incubated at room temperature for 15 minutes. Cell suspension was applied to the MS columns (MACS Cat# 130-042-201) and effluent containing live cells was collected. Live cells were then centrifuged at 300g for 5 minutes, resuspended in cold 0.04% BSA/PBS and counted with Bio-Rad’s TC20TM automated cell counter. Live cells were prepared for scRNA-seq with the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics) according to the user guide. Briefly, ~4800 cells were wrapped into each gel-beads in emulsion (GEMs, 10X Genomics) at a concentration of 500-1000 cells/uL on Single Cell 3’ Chips v3 (10x Genomics) by using 10X Chromium controller.
For reverse transcription incubation, GEMs were transferred to Bio-Rad C1000 Touch™ Thermal Cycler, followed by post GEMs–RT Cleanup, cDNA Amplification according to the manufacturer’s instructions. Qubit™ dsDNA HS Assay Kit (Invitrogen) was used to quantified cDNA concentration and single cell transcriptome libraries were constructed using the 10x Chromium Single Cell 3’ Library (10x Genomics, v3 barcoding chemistry). Quality control was performed with Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies). Libraries were then purified, pooled and analyzed on Illumina NovaSeq 6000 S2 Sequencing System with 150-bp paired-end reads.

treatment_protocol: 6–8-week-old mice are intraperitoneally injected with 20 mg/kg LPS from E. coli O111:B4 or PBS.

value: liver non-parenchymal cells

value: i.p. injected with PBS for 8 hours


title: MED1_DN67_MED12_unstim

value: unstimulated


title: WT_LPS

value: i.p. injected with LPS for 8 hours

value: wild type


title: HH16calz_pos_CAGATC

description: 10262_10946_86633_HFK7NBGX9_HH16calz_pos_CAGATC_R1


title: WT


title: HH8v3_neg_GCCAAT

description: 10262_10946_86632_HFK7NBGX9_HH8v3_neg_GCCAAT_R1


title: MED1_DN67_AAVS1_unstim


title: HH8v3_pos_ACAGTG

description: 10262_10946_86631_HFK7NBGX9_HH8v3_pos_ACAGTG_R1


title: ZT 18 IgA+ PC replicate 5

city: Manchester

first: Matthew

last: Hepworth

address: AV Hill Building

country: United Kingdom

institute: University of Manchester

data_processing:
FPKM values were generated
Heatmap outputs were generated in GraphPad Prism
Supplementary_files_format_and_content: Matrix table with raw gene counts or FPKM normalised values for every gene and every sample

source_name: IgA+ Plasma Cells (small intestinal)

extract_protocol:
Collagenase D and Dnase I isolation of single cell small intestinal lamina propria cells (see methods of above manuscript)
Sort-purfication of CD138+ IgA+ Plasma Cells via fluorscence activated cell sorting (FACS)
Samples lysed in Qiagen RLT buffer and processed as per manufacturer's instructions (RNA mini kit)
Normalised RNA was used to generate libraries using NEB Next Ultra RNA library Prep Kit (Illumina). Indices were included to multiplex samples and mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesised using random hexamer primers followed by second strand cDNA synthesis. Following end repair, A-tailing, adaptor ligation and size section libraries were further amplified and purified and insert size validated on an Agilent 2100, and quantified using quantitative PCR (qPCR). Libraries were then sequenced on an Illumina NovaSeq 6000 S4 flowcell with PE150 according to results from library quality control and expected data volume.

value: Wild Type

tag: background strain

tag: zeitgeber time


title: Col-0, 3d control, rep3

city: Umea

first: Clement

last: Boussardon

address: Umeå Plant Science Centre Department of Plant Physiology Umeå University

department: Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

description: Novogene Technology Co., Ltd (HiSeq platforms, paired-end 150 bp sequencing strategy)

data_processing:
The quality of the raw sequence data was assessed using FastQC, v0.11.4. Residual ribosomal RNA (rRNA) contamination was assessed and filtered using SortMeRNA using the rRNA sequences provided with SortMeRNA.
Data were then filtered to remove adapters and trimmed for quality using Trimmomatic. After both filtering steps, FastQC was run again to ensure that no technical artefacts were introduced. Read counts were obtained using kallisto (v0.43.0) with the parameters quant -b 100 --pseudobam -t 1 --rf-stranded and using the TAIR10 cDNA sequences as a reference (retrieved from the TAIR resource).
The kallisto abundance values were imported into R using the Bioconductor58 (v3.3) tximport package. For the data quality assessment and visualization, the read counts were normalized using a variance stabilizing transformation as implemented in DESeq2.
Statistical analysis of gene and transcript differential expression (DE) between conditions was performed in R using the Bioconductor DESeq2 package (v1.14.1), with the following model: ~Line*Hours to account for both the genotype (WT or rpn12a-236) and harvesting time (d0, h6, d1, d3, d6).
FDR adjusted p-values were used to assess significance; a common threshold of 1% was used.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include z-score for each replicate/genotype/time point

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: WT and rpn12a-236 plants were grown under short-day photoperiod, and samples of leaf blades were collected at 8 am, for the 0 day, 1 day, 3 days, 6 days time points for IDL/light control treatments and at 2 pm, for the 6 hours time point for IDL/light control treatments.

extract_protocol:
For all conditions, three biological replicates were used, each of them being a pool of two leaves from independent plants. RNA was extracted from approximately 40 mg of frozen material using an EZNA plant RNA kit following provider recommendations (Omega Bio-tek, R6834-01).
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

value: Leaf

tag: ecotype

tag: time

value: 3 day

value: Wild type

value: Light control


title: Col-0, 6d control, rep2

value: 6 day


title: MED1_DN63_MED12_unstim


title: MED1_DN63_AAVS1_unstim


title: ZT 18 IgA+ PC replicate 4


title: Col-0, 6d control, rep1


title: Col-0, 6d control, rep3


title: HH6v3_neg_TGACCA

description: 10262_10946_86630_HFK7NBGX9_HH6v3_neg_TGACCA_R1

tag: cell type


title: ZT 18 IgA+ PC replicate 3


title: HH6v3_pos_CGATGT

description: 10262_10946_86629_HFK7NBGX9_HH6v3_pos_CGATGT_R1

source_name: TFAP2AE1 GFP+ Sorted

value: Neural Crest (NC)

value: TFAP2AE1 GFP+ Sorted


title: Col-0, 3d control, rep2


title: MED1_DN59_MED12_unstim


title: ZT 18 IgA+ PC replicate 2


title: KO_LPS

tag: strain


title: 143B CRISPR-UHRF1 #7 [RNA-seq]

description: processed data file: merged_fpkm.tsv

tag: cell line

value: Osteosarcoma cell line

value: UHRF1 KO


title: MED1_DN59_AAVS1_unstim

tag: genotype


title: Col-0, 3d control, rep1


title: CCD-18Co cells, TGF-beta, ZNF281 siRNA, biol rep 3

city: Roma

first: valerio

last: fulci

address: Vle regina Elena, 324

department: Dipartimento di Medicina Molecolare

country: Italy

institute: Università i Roma "La Sapienza"

data_processing:
TopHat2 alignment to hg38, gencode v31 GTF file. Other options:--library-type fr-firststrand
Htseq-count, command line options:  -f bam -s reverse -m intersection-strict --secondary-alignments=ignore –supplementary-alignments=ignore
Assembly: hg38, gencode v31
Supplementary files format and content: read counts at gene level, as assessed by htseq-count

growth_protocol: CCD18-Co cells were grown in MEM (S-51416C, Sigma) supplemented with 10% FBS, penicillin/streptomycin, 2mM L-glutamine, 1mM Sodium pyruvate

extract_protocol:
1x10^6 cells were lysed in 300ul of Trizol and RNA was purified using Direct-zol™ RNA MiniPrep Kit (Zymo Research), following manufacturer’s protocol.
TruSeq stranded total RNA with Ribo-Zero

treatment_protocol: At day 1, CCD18-Co cells were seeded to be 60%- 70% confluent at the day of transfection. At day 2, 10nM siRNA ZNF281 (Silencer™ pre-designed siRNA, Ambion) or Silencer™ Select Negative Control No. 1 siRNA (Ambion) were transfected using Lipofectamine RNAiMAX Reagent (Life Technologies), following manufacturer’s protocol. At day 3, the medium was replaced with low-serum starvation medium (MEM complemented with 0.5% FBS, penicillin/streptomycine, 2mM L-glutamine, 1mM Sodium pyruvate). At day 4, TGF-β1 (10,ng/mL) was added to low-serum starvation medium for 24h.

value: Colon fibroblast cell line

value: ZNF281 siRNA

value: TGF-beta


title: RNAseq_DN67_MED12_stim

data_processing:
Sequencing libraries were prepared by Novogene (Sacramento, CA) and 150 bp paired end sequencing at a depth of 3 x 10e7 reads per sample was obtained using the Illumina NovaSeq6000 platform
FASTQ files were generated by Novogene.
Transcripts were quantified with Salmon
DESeq2 was used to generate TPM (transcripts per million)
Genome_build: hg38
Supplementary_files_format_and_content: Data transcripts per million summarized to gene level. Each column in the table is a sample. Each row is a gene.

extract_protocol:
Total RNA was extracted from fresh cells using the Qiagen Rneasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stimulated


title: ZT 18 IgA+ PC replicate 1


title: Col-0, 1d control, rep3

value: 1 day


title: ZT 12 IgA+ PC replicate 5


title: CCD-18Co cells, ZNF281 siRNA, biol rep 3

value: control


title: CCD-18Co cells, TGF-beta, CTRL siRNA, biol rep 3

value: CTRL siRNA


title: Col-0, 1d control, rep2


title: ZT 12 IgA+ PC replicate 4

value: Wild Type


title: RNAseq_DN67_AAVS1_stim


title: Col-0, 1d control, rep1

value: Leaf


title: ZT 12 IgA+ PC replicate 3


title: RNAseq_DN63_MED12_stim


title: CCD-18Co cells, CTRL siRNA, biol rep 3


title: Col-0, 6h control, rep3

value: 6 hours


title: CCD-18Co cells, ZNF281 siRNA, biol rep 2


title: RNAseq_DN59_MED12_stim


title: CCD-18Co cells, TGF-beta, ZNF281 siRNA, biol rep 2


title: RNAseq_DN63_AAVS1_stim


title: ZT 12 IgA+ PC replicate 2


title: Col-0, 6h control, rep2

value: Wild type


title: ZT 12 IgA+ PC replicate 1


title: RNAseq_DN67_MED12_unstim

value: unstimulated


title: RNAseq_DN59_AAVS1_stim


title: CCD-18Co cells, CTRL siRNA, biol rep 2


title: Col-0, 6h control, rep1

value: Light control


title: CCD-18Co cells, TGF-beta, CTRL siRNA, biol rep 2


title: ZT 6 IgA+ PC replicate 5


title: Col-0, 6d IDL, rep3

value: 6 day

value: Individually darkened leaf


title: ZT 6 IgA+ PC replicate 4


title: CCD-18Co cells, TGF-beta, ZNF281 siRNA, biol rep 1


title: Col-0, 6d IDL, rep2


title: ZT 6 IgA+ PC replicate 3


title: RNAseq_DN63_MED12_unstim


title: Col-0, 6d IDL, rep1


title: ZT 6 IgA+ PC replicate 2


title: Col-0, 3d IDL, rep3

value: 3 day


title: CCD-18Co cells, CTRL siRNA, biol rep 1


title: RNAseq_DN59_MED12_unstim


title: CCD-18Co cells, TGF-beta, CTRL siRNA, biol rep 1


title: ZT 6 IgA+ PC replicate 1


title: Group 3_H1_hTFAP2A_Sox2_2

description: 12793_10099_147167_HGHM3BGXK_H1_hTFAP2A_Sox2_2_GTAGAGAT

data_processing:
library strategy: CUT&RUN
Demultiplexing, bcl2fastq
Trimming, Group #1 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0, Groups #2-4 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0
Group #1 Alignment 'hisat2  --phred33 --rna-strandness RF --dta --no-unal' , Group #2 -4 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000'
Groups #2-4 Marking Duplicates, Picard MarkDuplicates
Filtering, samtools view, sort, index
Peak calling, MACS2 Group #2 callpeak -f BAMPE -g 2913022398  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73, Group #3, callpeak -f BAMPE -g 2913022398 -q 0.05 --call-summits Group #4, callpeak -f BAMPE -g 1218492533  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73
RNA-Seq Quantification Group #1 featureCounts -t exon -s 2 -g gene_id
Assembly: Group #1,2,3 UCSC hg38 Group #4 ENSEMBL galGal6
Supplementary files format and content: .narrowPeak, MACS2 peaks
Supplementary files format and content: .txt, FeatureCounts quantification file
Supplementary files format and content: .bam, alignment files

source_name: Human H1 ESC TFAP2A Overexpressing 2

extract_protocol:
Groups #1-3 H1 cells were transfected with virus expressing either GFP or TFAP2A. After one week, transfected cells were isolated via FACS and then processed for various sequencing libraries. Group #4 Chicken embryos were electroporated with a TFAP2AE1-GFP reporter and subjected to FACS sorting. 10,000 GFP negative cells were collected and spun down before ATAC-Seq library construction
Group #1  30k sorted cells were used per sample. RNA was extracted using RNA-Aqueous Micro kit, normalized, and used for NEB Next Ultra II Directional RNA-Sequencing Kit, Group #2 30k sorted cells were used per sample. The OMNI-ATAC protocol was used for ATAC-Seq library prep, Group #3 CUT&RUN libraries with samples of 300k cells each were input normalized and contructed as in Rothstein & Simoes-Costa, Genome Research 2020, Group #4 10k sorted cells were used per sample. The OMNI-ATAC protocol was used for ATAC-Seq library prep.
Group #1 RNA-Seq, Group #2 ATAC-Seq, Group #3 CUT&RUN, Group #4 ATAC-Seq

tag: tissue/cell type

value: Human H1-derived cells

value: TFAP2A Overexpression

tag: antibody

value: Sox2, R&D Systems (AF 2018) 1:50


title: RNAseq_DN63_AAVS1_unstim


title: Col-0, 3d IDL, rep1

tag: tissue


title: Col-0, 3d IDL, rep2


title: RNAseq_DN59_AAVS1_unstim


title: ZT 0 IgA+ PC replicate 4


title: ZT 0 IgA+ PC replicate 3


title: ZT 0 IgA+ PC replicate 2


title: Col-0, 1d IDL, rep2


title: SF6

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

data_processing:
We used Snakemake (Koster and Rahmann, 2012) to manage the bioinformatics workflow in a reproducible manner.
We used FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample. We used TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) to trim low-quality bases (quality score lower than 20), adapter sequences (required overlap of 6bp), and end-repair bases from the 3’ end of reads. Reads shorter than 20bp after trimming are discarded. We aligned trimmed reads to hg19 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) with the ATAC specific parameters -X 2000 --no-mixed --no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads are marked with Picard (Picard) (v2.20.2). Alignments to autosomes are kept (i.e. sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard were removed, and alignments below a MAPQ threshold were removed (< 10). These filtering steps are performed with samtools (Li et al., 2009) (v1.2). Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) were removed with bedtools (Quinlan and Hall, 2010) (v2.28.0). Sample-wise peaks were called with macs2 (Zhang et al., 2008) (v2.1.2) with the ATAC specific flags -f BAM --nomodel --shift -100 --extsize 200. Peaks over all samples were then merged with bedops (Neph et al., 2012) (v2.4.36).
Finally, MultiQC (Ewels et al., 2016) (v1.7) generated a report combining FastQC, trimming, alignment, and duplicate calling over all the samples. For ATAQ specific QC metrics we used ataqv (Ataqv) (v1.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Sample-wise narrowPeak files were generated with macs2 (Zhang et al., 2008) (v2.1.2) with the ATAC specific flags -f BAM --nomodel --shift -100 --extsize 200.

source_name: Dermal fibroblasts

growth_protocol: Two 4 mm punch biopsies from the distal forearm of healthy volunteers and SSc patients were obtained for cell isolation. After skin digestion, cells were grown to 75% confluency on collagen-coated plates before purification. ECs were purified through positive selection using the CD31 MicroBead Kit (Miltenyi Biotech) while negatively selected cells eluted were fibroblasts. A portion of the collected fibroblasts (passage 0) were lysed and underwent tagmentation. Purified ECs were grown on collagen-coated plates maintained in EBM-2 media supplemented with EGM-2 MV Microvascular Endothelial SingleQuots Kit from Lonza. These cells underwent several rounds of purification during expansion and cells with passages between 2 and 6 were used for ATAC-seq library preparation.

extract_protocol:
To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
We followed the steps decribed in "Nature Methods volume 10, pages1213–1218(2013)". For both fibroblasts and ECs (from 6 patients and 6 controls), 50,000 cells were used for the Tn5 transposition reaction, and DNA libraries were prepared.

value: Skin

value: Fibroblasts

tag: subject

value: diffuse cutaneous systemic sclerosis patient


title: RNAseq_DN67_AAVS1_unstim

source_name: primary T cells


title: SF5


title: Col-0, 1d IDL, rep1

value: 1 day


title: Col-0, 6h IDL, rep3


title: Group 3_H1_GFP_Sox2_2

description: 12793_10099_147165_HGHM3BGXK_H1_GFP_Sox2_2_ATGTCAGA

source_name: Human H1 ESC GFP Overexpressing 2

value: GFP Overexpression

tag: group


title: ZT 0 IgA+ PC replicate 1

value: Wild Type


title: Col-0, 1d IDL, rep3

value: Leaf


title: Group 3_H1_hTFAP2A_Sox2_1

description: 12793_10099_147166_HGHM3BGXK_H1_hTFAP2A_Sox2_1_CCGTCCGC

source_name: Human H1 ESC TFAP2A Overexpressing 1


title: SF3


title: Group 3_H1_GFP_Sox2_1

description: 12793_10099_147164_HGHM3BGXK_H1_GFP_Sox2_1_AGTTCCGT

source_name: Human H1 ESC GFP Overexpressing 1


title: SF4


title: Group 2_H1_Ap2A_ATAC2

description: 12793_10099_147159_HGHM3BGXK_H1_Ap2A_ATAC2_TCCTGAGC

data_processing:
Demultiplexing, bcl2fastq
Trimming, Group #1 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0, Groups #2-4 CutAdapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0
Group #1 Alignment 'hisat2  --phred33 --rna-strandness RF --dta --no-unal' , Group #2 -4 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000'
Groups #2-4 Marking Duplicates, Picard MarkDuplicates
Filtering, samtools view, sort, index
Peak calling, MACS2 Group #2 callpeak -f BAMPE -g 2913022398  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73, Group #3, callpeak -f BAMPE -g 2913022398 -q 0.05 --call-summits Group #4, callpeak -f BAMPE -g 1218492533  -q 0.05 --call-summits --nomodel --shift 37 --extsize 73
RNA-Seq Quantification Group #1 featureCounts -t exon -s 2 -g gene_id
Assembly: Group #1,2,3 UCSC hg38 Group #4 ENSEMBL galGal6
Supplementary files format and content: .narrowPeak, MACS2 peaks
Supplementary files format and content: .txt, FeatureCounts quantification file
Supplementary files format and content: .bam, alignment files


title: Col-0, 6h IDL, rep2

value: 6 hours


title: SF2


title: CCD-18Co cells, ZNF281 siRNA, biol rep 1

value: Colon fibroblast cell line

value: ZNF281 siRNA

value: control


title: Group 2_H1_Ap2A_ATAC1

description: 12793_10099_147158_HGHM3BGXK_H1_Ap2A_ATAC1_AGGCAGAA


title: NF6

value: Healthy


title: Group 2_H1_GFP_ATAC1

description: 12793_10099_147156_HGHM3BGXK_H1_GFP_ATAC1_TAAGGCGA