title: duox-/-(T4)

city: Hefei

first: bing

last: hu

address: School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: mm9

organism: Danio rerio

growth_protocol: Zebrafish embryos were obtained by natural cross and fertilized eggs were raised at 28.5°C and maintained on a 14-hours light/10-hours dark cycle

extract_protocol:
Total RNAs from 4-dpf duox-/- and WT zebrafish were extracted, and 3 g of RNA per sample was prepared for constructed a transcriptional library.
Sequencing libraries were generated with an UltraTM RNA Library Prep Kit (NEB, USA) according to the manufacturer’s instructions. Clustering of the index-coded samples was conducted with a cBot Cluster Generation System using a TruSeq PE Cluster Kit (Illumina, USA), per the instructions. After clustering, the library preparations were sequenced on an Illumina Hiseq 2000 platform. Perl scripts were used to remove the adapter for clean reads, calculating the Q20/Q30 duplicate data, and generating the raw reads.

tag: strain background

value: AB

tag: genotype/variation

value: duox-/-

value: whole larvae

tag: developmental stage

value: 4 dpf


title: BSA-2-1: Macrophages 2h after treatment with BSA #1

status: Public on Dec 09 2020

type: SRA

city: Madrid

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

library_source: transcriptomic

data_processing:
BGISEQ-500 platform
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%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 10 ng/ml M-CSF, with cytokine addition every two days.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: At the end of the differentiaton prtocol, macrophages were either untreated (CNT) or treated with 10 ng/ml E. coli 055:B5 lipopolysaccharide (LPS), 100 ng/ml of the TLR7 agonist CL264 (CL264), BSA or 200 mM palmitate (PAL) for 0.5h, 2h, 4h or 12h.

tag: cell type

value: Monocyte-derived M-CSF macrophages

tag: treatment

value: BSA


title: FAN1_scRNAseq

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

description: processed file is combined into single data matrix

data_processing:
Cell Ranger 2 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
“cellranger count” aligned the Read2 to the mouse reference genome (mm10) using STAR
Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (Ensembl GTFs GRCm38.p4)
The output files for 8 samples were aggregated into one gene-cell matrix using “cellranger aggr” with read depth normalization by total number of mapped reads
Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <300 genes detected or with >3,000 unique expressed genes (as they are potentially cell duplets). Only genes expressed in 10 or more cells were used for further analysis. Cells were also discarded if their mitochondrial gene percentages were over 50%.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_kidney_scRNAseq_datamatrix.txt.gz: each row corresponds to genes (first row is the cluster number), and each column corresponds to single cell, number in the matrix is the normalized UMI count data  Mouse_kidney_RNAseq_datamatrix.txt.gz: each row corresponds to genes and each column corresponds to sample, number in the matrix is the normalized count data

molecule: polyA RNA

organism: Mus musculus

source_name: whole kidney tissue

extract_protocol:
10X Genomics Chromium Prep. Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol.

treatment_protocol: Mice were injected with folic acid (FA) (250 mg/kg once, dissolved in 300 mM NaHCO3) intraperitoneally and sacrificed on day 7

tag: strain

tag: tissue

value: adult kidney

tag: age

value: 5-8 weeks

tag: disease

value: folic acid-induced neprophathy


title: duox-/-(T2)

country: China

institute: University of Science and Technology of China


title: BSA-0-5-3: Macrophages 0.5h after treatment with BSA #3


title: Tamm_1552

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

description:
Bulk RNA-seq
Within_Subject_RawCounts.txt
Within_Subject_CPM.txt

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.5.2b to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M24). Uniquely mapped reads were quantified using HTSeq python suite using protein coding genes by gene.
Genome_build: Human hg38
Supplementary_files_format_and_content: CPM and RawCounts included in separate text files.

source_name: Brodmann Area 38

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. Libraries and sequencing were performed at the McDermott Sequencing Core at UTSW.

tag: sample type

value: Post-mortem

tag: diagnosis

value: Healthy

value: Brodmann Area 38

tag: age (years)

tag: Sex

value: F

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

value: L

tag: rin

tag: batch

tag: brainbank

value: CTLab

tag: protocol

value: Protocol 1


title: Lega_45_scRNA

description:
10X single-nuclei RNA-seq
Within_Subject_snRNAseq_Counts.txt.gz

data_processing:
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. UMI-tools were used to match barcode and reads. Single-nuclei RNA-seq reads were aligned with STAR 2.5.2b to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M24). Gene level expression was calculated using featureCounts. Downstream analysis was performed using Seurat.
Genome_build: Human hg38
Supplementary_files_format_and_content: UMI counts

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol. Libraries and sequencing were performed at the McDermott Sequencing Core at UTSW.

value: Resected

value: Protocol 2


title: Chip6

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

description: No infection control experiment 1, FLAG ChIPs

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the rn6 genome assembly using Bowtie version 2.0.1.
Genome binding peaks for SRF or phospho-Ser103 antibodies were identified using the ‘findPeaks’ command in HOMER with setting of ‘-style factor’: 200 bp peaks with 3-fold enrichment and 0.01 FDR significance over local tags.
HOMER-IDR program was employed to format the data for the IDR R package to determine the IDR threshold and identify the top peaks above that threshold.
Genome_build: rn6
Supplementary_files_format_and_content: bigWig files were generated using the ‘makeUCSCfile’ command in HOMER with setting of ‘-fsize 1e50 -o auto’.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Rat adult cardomyocytes

growth_protocol: Cells were cultured in ACCT medium (M199 Medium, Creatine 5 mM, L-carnitine 2 mM, Taurine 5 mM, HEPES 25 mM, 2,3-Butanedione monoxime 10 mM, BSA 0.2% and 1X Insulin-Transferrin-Selenium Supplement) after langendorff perfusion.

extract_protocol:
The cells for RNA Polymerase II (Pol II) and H3K27ac ChIPs were directly incubated with 1% formaldehyde in PBS for 10 minutes, while all other cells were subjected to cross-linking by disuccinimidyl glutarate for 30 minutes prior to 15 minutes 1% formaldehyde fixation. Cells were washed with PBS for three times, lysed in 1% SDS buffer, and then ChIP assay was performed using the EZ-ChIP kit (Millipore, 17-371), performed as recommended by the manufacturer using 1.4 - 2.9 µg antibody for each immunoprecipitation. To sequence ChIP-enriched DNA, library constructions were performed using KAPA HyperPrep Kits for NGS DNA Library Prep (Kapa Biosystems). Inputs ranged from undetectable via the Qubit dsDNA HS Assay (<10pg/µl) to 5 ng/µl. 14 PCR cycles were adjusted according to input. Samples were barcoded to allow for multiplexing and analysis on an Illumina HiSeq 4000. Cluster generation took place on the Illumina cBot according to the manufacturer's recommendations. Sequencing took place on the Illumina HiSeq 4000 using the reagents provided in the Illumina TruSeq PE Cluster and SBS kits. An average of 15 million single-end 75 base pass-filter reads were generated per sample.
To sequence ChIP-enriched DNA, library constructions were performed using KAPA HyperPrep Kits for NGS DNA Library Prep (Kapa Biosystems).

treatment_protocol: 2.4 millions adult rat ventricular myocytes infected with 300 Multiplicity of Infection (MOI) of adenovirus for 24 hours and/or treated with 20 µM phenylephrine for 1 hour were used for each individual ChIP assay.

tag: cell line

value: primary cultured rat adult ventricular cardiomyocytes

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Mouse M2 anti-Flag


title: Chip7

description: Flag-SRF(WT) experiment 2, FLAG ChIPs


title: Tamm_1553

tag: tissue

value: M


title: Lega_42_scRNA

value: R


title: CL-12-3: Macrophages 12h after treatment with CL264 #3

tag: cell type

value: Monocyte-derived M-CSF macrophages

tag: treatment


title: ChIP_55

description: PE experiment 2, p-SRF(s103) ChIPs

value: Rb anti-p-SRF(S103)


title: Tamm_1555

tag: sample type

value: Post-mortem

tag: diagnosis


title: 202831040067_R01C01

type: genomic

city: MEMPHIS

first: Suzanne

middle: J.

last: Baker

state: TENNESSEE

address: 262 Danny Thomas Place

institute: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC or HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
CSV files: Average Beta & Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: SJ-HGGX39 PDX

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated from frozen tumor tissue by SDS/Proteinase K digestion and phenol/chloroform extraction or from FFPE using a QIAamp DNA FFPE Tissue Kit (Qiagen) according to manufacturer's instructions.

tag: line id

tag: methylation classification


title: BSA-0-5-1: Macrophages 0.5h after treatment with BSA #1

value: BSA


title: Chip5

description: Flag-SRF(S103D) experiment 1, FLAG ChIPs


title: ChIP_54

description: No Drug experiment 2, p-SRF(s103) ChIPs


title: 203550300061_R02C01

source_name: SJ-HGGX77 PDX


title: WT(T1)

tag: strain background

value: AB

tag: genotype/variation

value: WT

value: whole larvae

tag: developmental stage

value: 4 dpf


title: WT(T3)


title: Chip9

description: Flag-SRF(S103D) experiment 2, FLAG ChIPs


title: Tamm_1550

value: Healthy

value: Brodmann Area 38

tag: age (years)

tag: Sex

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere


title: Tamm_1551

tag: tissue

tag: rin

tag: batch

tag: brainbank

value: CTLab

tag: protocol

value: Protocol 1


title: Tamm_1548

tag: sample type

tag: diagnosis


title: ChIP_52

description: PE experiment 1, p-SRF(s103) ChIPs

tag: cell line

value: primary cultured rat adult ventricular cardiomyocytes

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: 203497730104_R06C01

source_name: SJ-HGGX77 Primary

tag: line id

tag: methylation classification


title: 203496240089_R01C01

source_name: SJ-HGGX78 Primary


title: BSA-0-5-2: Macrophages 0.5h after treatment with BSA #2

tag: cell type

tag: treatment


title: Tamm_1547

tag: age (years)

tag: Sex

value: M

tag: race

tag: ethnicity

value: L


title: ChIP_51

description: No Drug experiment 1, p-SRF(s103) ChIPs


title: CL-4-3: Macrophages 4h after treatment with CL264 #3

value: Monocyte-derived M-CSF macrophages


title: CL-12-1: Macrophages 12h after treatment with CL264 #1


title: Chip4

description: Flag-SRF(S103A) experiment 1, FLAG ChIPs

value: Mouse M2 anti-Flag


title: Tamm_1546

value: Post-mortem

tag: tissue

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

value: R


title: 203293640080_R06C01

source_name: SJ-HGGX34 Primary


title: CL-4-2: Macrophages 4h after treatment with CL264 #2


title: Tamm_1545

tag: rin

tag: batch

tag: brainbank

tag: protocol


title: CL-4-1: Macrophages 4h after treatment with CL264 #1


title: 203271750101_R07C01

source_name: SU-DIPG-XXI Cell

value: SU-DIPG-XXI


title: CL-12-2: Macrophages 12h after treatment with CL264 #2


title: ChIP_42

description: PE experiment 1, SRF ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Rb anti-SRF


title: Tamm_1543

tag: sample type

tag: diagnosis


title: 203271750101_R06C01

source_name: SU-DIPG-XIX Cell

tag: line id

value: SU-DIPG-XIX

tag: methylation classification


title: ChIP_41

description: No Drug experiment 1, SRF ChIPs


title: Chip3

description: Flag-SRF(WT) experiment 1, FLAG ChIPs


title: CL-2-1: Macrophages 2h after treatment with CL264 #1

tag: cell type

tag: treatment


title: Tamm_1544

tag: age (years)

tag: Sex

tag: race

tag: ethnicity


title: EpBB09

value: Epilepsy

tag: tissue

value: Black

tag: pmi (hours)

tag: epilepsy duration (years)

value: unknown

tag: hemisphere

value: UMB BTB


title: CL-0-5-3: Macrophages 0.5h after treatment with CL264 #3


title: CL-2-2: Macrophages 2h after treatment with CL264 #2


title: CL-0-5-2: Macrophages 0.5h after treatment with CL264 #2


title: 203271750101_R05C01

source_name: SU-DIPG-XVII Cell

value: SU-DIPG-XVII


title: 203271750101_R02C01

source_name: SU-DIPG-IV Cell

value: SU-DIPG-IV


title: ChIP_37

description: No Drug experiment 2, H3K27ac ChIPs

value: Rb anti-H3K27AC


title: EpBB06

value: Brodmann Area 38

value: F

value: Non-Hispanic

tag: rin

tag: batch

tag: brainbank

tag: protocol

value: Protocol 1


title: ChIP_45

description: PE experiment 2, SRF ChIPs

tag: cell line

value: primary cultured rat adult ventricular cardiomyocytes

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: ChIP_38

description: PE experiment 2, H3K27ac ChIPs


title: CL-0-5-1: Macrophages 0.5h after treatment with CL264 #1

value: Monocyte-derived M-CSF macrophages


title: 203271750101_R04C01

source_name: SU-DIPG-XIII Cell

tag: line id

value: SU-DIPG-XIII

tag: methylation classification


title: CL-2-3: Macrophages 2h after treatment with CL264 #3

tag: cell type

tag: treatment


title: ChIP_44

description: No Drug experiment 2, SRF ChIPs


title: ChIP_36

description: PE experiment 1, H3K27ac ChIPs


title: 203271750081_R08C01

source_name: SJ-HGGX42 Cell


title: LPS-12-3: Macrophages 12h after treatment with LPS #3

value: LPS


title: 203293640080_R07C01

source_name: SJ-HGGX58 Primary


title: EpBB05

tag: sample type

value: Post-mortem

tag: diagnosis

tag: age (years)

tag: Sex

value: White

value: L


title: ChIP_35

description: No Drug experiment 1, H3K27ac ChIPs


title: EpBB07

value: Epilepsy

tag: tissue

value: M

tag: race

tag: ethnicity

tag: pmi (hours)


title: LPS-12-2: Macrophages 12h after treatment with LPS #2


title: EpBB04

tag: epilepsy duration (years)

value: unknown

tag: hemisphere

tag: rin

tag: batch

value: UMB BTB


title: 203271750101_R03C01

source_name: SU-DIPG-VI Cell

value: SU-DIPG-VI


title: ChIP_34

description: PE experiment 2, PolII ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Mouse anti-PolII


title: EpBB08

value: Brodmann Area 38

tag: brainbank

tag: protocol


title: EpBB03

value: Hispanic


title: 203271750081_R06C01

source_name: SJ-DIPGX37 Cell

tag: line id

tag: methylation classification


title: 203271750081_R05C01

source_name: SJ-DIPGX29 Cell


title: ChIP_33

description: No Drug experiment 2, PolII ChIPs


title: LPS-12-1: Macrophages 12h after treatment with LPS #1

source_name: macrophages

tag: cell type

tag: treatment


title: EpBB02

source_name: Brodmann Area 38

tag: sample type

tag: diagnosis

tag: age (years)

tag: Sex

value: F

value: Black

value: Non-Hispanic


title: ChIP_32

description: PE experiment 1, PolII ChIPs

source_name: Rat adult cardomyocytes

value: primary cultured rat adult ventricular cardiomyocytes


title: 203271750081_R04C01

source_name: SJ-DIPGX9 Cell


title: Lega_47

value: Resected

value: Healthy

tag: tissue

tag: race

tag: ethnicity

tag: pmi (hours)

value: R

value: Protocol 1


title: LPS-4-3: Macrophages 4h after treatment with LPS #3

value: Monocyte-derived M-CSF macrophages

value: LPS


title: ChIP_31

description: No Drug experiment 1, PolII ChIPs


title: 203271750081_R03C01

source_name: SJ-DIPGX7 Cell


title: LPS-4-2: Macrophages 4h after treatment with LPS #2


title: LPS-4-1: Macrophages 4h after treatment with LPS #1


title: Chip2

value: Mouse M2 anti-Flag


title: 203271750081_R02C01

source_name: SJ-HGGX6 Cell


title: LPS-2-3: Macrophages 2h after treatment with LPS #3


title: 203271750081_R07C01

source_name: SJ-HGGX39 Cell


title: ChIP_26

description: Flag-SRF(S103D) experiment 2, H3K27ac ChIPs

value: Rb anti-H3K27AC


title: Lega_42

value: White

tag: epilepsy duration (years)

tag: hemisphere

tag: rin

tag: batch


title: 203271750081_R01C01

source_name: SJ-HGGX2 Cell


title: ChIP_25

description: Flag-SRF(S103A) experiment 2, H3K27ac ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: LPS-2-1: Macrophages 2h after treatment with LPS #1


title: Lega_41

value: M

tag: brainbank

tag: protocol


title: 203135920067_R07C01

source_name: SJ-HGGX75 Primary

tag: line id

tag: methylation classification


title: ChIP_24

description: Flag-SRF(WT) experiment 2, H3K27ac ChIPs


title: 203135920067_R06C01

source_name: SJ-HGGX60 Primary

value: PXA


title: ChIP_23

description: Flag-SRF(S103D) experiment 1, H3K27ac ChIPs


title: LPS-0-5-3: Macrophages 0.5h after treatment with LPS #3

tag: cell type

tag: treatment


title: 203135920067_R05C01

source_name: SJ-HGGX59 Primary

value: No Match


title: 203135920067_R04C01

source_name: SJ-HGGX39 Primary


title: Lega_35

tag: sample type

tag: diagnosis

value: Brodmann Area 38

tag: age (years)

tag: Sex


title: Lega_45

tag: tissue

value: F

tag: race

tag: ethnicity

tag: pmi (hours)

value: L


title: ChIP_22

description: Flag-SRF(S103A) experiment 1, H3K27ac ChIPs


title: LPS-0-5-2: Macrophages 0.5h after treatment with LPS #2


title: Lega_33

value: Hispanic

tag: epilepsy duration (years)

tag: hemisphere

tag: rin

tag: batch


title: LPS-0-5-1: Macrophages 0.5h after treatment with LPS #1


title: 203135920067_R03C01

source_name: SJ-DIPGX37 Primary


title: Lega_31

value: Non-Hispanic

tag: brainbank

tag: protocol


title: CNT-12-3: Untreated macrophages 12h after addition of activation stimuli #3


title: ChIP_21

description: Flag-SRF(WT) experiment 1, H3K27ac ChIPs

tag: cell line

value: primary cultured rat adult ventricular cardiomyocytes

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: 203135920067_R02C01

source_name: SJ-DIPGX29 Primary

tag: line id

tag: methylation classification


title: Lega_30

tag: sample type

value: Resected

tag: diagnosis

value: Healthy


title: Input_1

description: No infection control experiment 1, Input for FLAG ChIPs

value: Input


title: LPS-2-2: Macrophages 2h after treatment with LPS #2

tag: cell type

value: Monocyte-derived M-CSF macrophages

tag: treatment


title: Lega_44

tag: tissue

tag: age (years)

tag: Sex

tag: race

value: Protocol 1


title: 203135920067_R01C01

source_name: SJ-HGGX78 PDX


title: Lega_27

tag: ethnicity

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

value: R


title: ChIP15

description: Flag-SRF(S103A) experiment 2, PolII ChIPs

value: Mouse anti-PolII


title: CNT-12-2: Untreated macrophages 12h after addition of activation stimuli #2


title: Lega_39

value: White

tag: rin

tag: batch

tag: brainbank

tag: protocol


title: Lega_22

value: Black


title: ChIP16

description: Flag-SRF(S103D) experiment 2, PolII ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: CNT-4-3: Untreated macrophages 4h after addition of activation stimuli #3


title: CNT-12-1: Untreated macrophages 12h after addition of activation stimuli #1


title: ChIP14

description: Flag-SRF(WT) experiment 2, PolII ChIPs


title: 203135920065_R07C01

source_name: SJ-HGGX70 PDX

tag: line id

tag: methylation classification


title: CNT-4-2: Untreated macrophages 4h after addition of activation stimuli #2

tag: cell type

tag: treatment


title: Lega_21

tag: sample type

tag: diagnosis

tag: tissue

tag: age (years)

value: M


title: CNT-2-3: Untreated macrophages 2h after addition of activation stimuli #3


title: Lega_19

tag: Sex

tag: race

tag: ethnicity

tag: pmi (hours)


title: CNT-4-1: Untreated macrophages 4h after addition of activation stimuli #1


title: ChIP13

description: Flag-SRF(S103D) experiment 1, PolII ChIPs


title: Lega_20

tag: epilepsy duration (years)

tag: hemisphere

tag: rin

tag: batch


title: 203135920065_R05C01

source_name: SJ-HGGX60 PDX

value: PXA


title: 203135920065_R04C01

source_name: SJ-HGGX59 PDX

value: No Match


title: 203135920065_R03C01

source_name: SJ-HGGX58 PDX


title: Lega_18

source_name: Brodmann Area 38

value: Brodmann Area 38

value: F

tag: brainbank

tag: protocol


title: 203135920065_R02C01

source_name: SJ-HGGX56 PDX

tag: line id

tag: methylation classification


title: CNT-2-2: Untreated macrophages 2h after addition of activation stimuli #2

source_name: macrophages

tag: cell type

tag: treatment


title: ChIP11

description: Flag-SRF(WT) experiment 1, PolII ChIPs

source_name: Rat adult cardomyocytes

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: Input_8

description: Flag-SRF(S103D) experiment 2, Input for FLAG ChIPs


title: ChIP12

description: Flag-SRF(S103A) experiment 1, PolII ChIPs


title: 203135920065_R08C01

source_name: SJ-HGGX75 PDX


title: Lega_17

description:
Bulk RNA-seq
Within_Subject_RawCounts.txt
Within_Subject_CPM.txt

tag: sample type

tag: diagnosis

tag: tissue

tag: age (years)

value: L


title: Input_7

description: Flag-SRF(S103A) experiment 2, Input for FLAG ChIPs


title: CNT-2-1: Untreated macrophages 2h after addition of activation stimuli #1


title: 203135920065_R01C01

source_name: SJ-DIPGX9 PDX


title: 202835130001_R08C01

source_name: SJ-HGGX70 Primary


title: Lega_16

tag: Sex

tag: race

tag: ethnicity

value: Hispanic

tag: pmi (hours)


title: CNT-0-5-3: Untreated macrophages 0.5h after addition of activation stimuli #3


title: Lega_15

value: Non-Hispanic

tag: epilepsy duration (years)

tag: hemisphere

tag: rin

tag: batch


title: Input_6

description: Flag-SRF(WT) experiment 2, Input for FLAG ChIPs

value: primary cultured rat adult ventricular cardiomyocytes


title: Input_5

description: No infection control experiment 2, Input for FLAG ChIPs


title: CNT-0-5-2: Untreated macrophages 0.5h after addition of activation stimuli #2


title: 202835130001_R06C01

source_name: SJ-HGGX56 Primary

tag: line id

tag: methylation classification


title: Lega_14

value: Resected

value: Healthy

tag: brainbank

tag: protocol


title: Input_4

description: Flag-SRF(S103D) experiment 1, Input for FLAG ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Input


title: 202835130001_R05C01

source_name: SJ-HGGX2 Primary


title: Lega_13

tag: sample type

tag: diagnosis

value: Protocol 1


title: 202831040048_R07C01

source_name: SJ-DIPGX37 PDX


title: Input_46

description: SRF siRNA transfection+PE experiment 2, Input for both SRF and p-SRF(S103) ChIPs


title: CNT-0-3: macrophages before addition of activation stimuli #3

tag: cell type

value: Monocyte-derived M-CSF macrophages

tag: treatment


title: Lega_12

tag: tissue

tag: age (years)

tag: Sex

tag: race

value: R


title: 202831040048_R06C01

source_name: SJ-HGGX34 PDX


title: Lega_11

value: White

tag: ethnicity

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere


title: Lega_10

tag: rin

tag: batch


title: 202831040048_R05C01

source_name: SJ-DIPGX29 PDX

tag: line id

tag: methylation classification


title: CNT-0-1: macrophages before addition of activation stimuli #1


title: Lega_09

tag: brainbank

tag: protocol


title: siRNA MAF donor #3

data_processing:
BGISEQ-500 platform
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%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using HISAT2 with default parameters.
Read counts for each gene were calculated using htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with raw gene counts for every gene (denoted as Ensemble gene ID) and every sample

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

treatment_protocol: Macrophages were transfected with either Control siRNA or MAFB-specific siRNA or MAF-specific siRNA for 24h

tag: cell

tag: sirna

value: siMAF


title: 202831040048_R02C01

source_name: SJ-DIPGX7 PDX


title: 202831040047_R05C01

source_name: SJ-DIPGX53 Primary


title: Input_43

description: SRF siRNA transfection+PE experiment 1, Input for both SRF and p-SRF(S103) ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: Input_44

description: No Drug experiment 2, Input for both SRF and p-SRF(S103) ChIPs


title: Lega_07

tag: sample type

tag: diagnosis

tag: tissue

tag: age (years)


title: CNT-0-5-1: Untreated macrophages 0.5h after addition of activation stimuli #1

tag: cell type

tag: treatment


title: siRNA MAF donor #2


title: 202234360017_R07C01

source_name: SJ-HGGX42 PDX


title: Lega_06

tag: Sex

tag: race

tag: ethnicity

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere


title: siRNA MAFB donor #3

value: siMAFB


title: siRNA MAF donor #1


title: Input_41

description: No Drug experiment 1, Input for both SRF and p-SRF(S103) ChIPs


title: Input_3

description: Flag-SRF(S103A) experiment 1, Input for FLAG ChIPs


title: CNT-0-2: macrophages before addition of activation stimuli #2


title: 202234360017_R06C01

source_name: SJ-HGGX42 Primary

tag: line id

tag: methylation classification


title: Input_45

description: PE experiment 2, Input for both SRF and p-SRF(S103) ChIPs


title: Input_34

description: PE experiment 2, Input for both PolII and H3K27ac ChIPs


title: G401_T2

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description:
14 day growth PR20 treated, replicate 2
G401_UT2_vs_G401_T2_results.csv
combo.csv
DNA - integrated sgRNA sequence

data_processing:
Library strategy: CRISPR screen
CRISPR screen analysis
illumina basecalling
casTLE normalization and analyzis
MAGeCK normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_CRISPR.sh
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements and differential representation (output from casTLE)

source_name: G401 cells

growth_protocol: G401-cas9 cells were infected with the epigenetic sgRNA sublibrary were grown in separate spinner flasks. Cells were maintained for 14 days at 1000× coverage (~1000 cells containing each sgRNA) at a concentration of 500,000 cells/mL, t

extract_protocol:
Genomic DNA was extracted for all screen populations separately according to the protocol included with QIAGEN Blood Maxi Kit.
sgRNA sequences were amplified and prepared for deep-sequencing by two sequential PCR reactions as described previously (Morgens et al., 2016).

treatment_protocol: ~50 million G401 cells in four 15 cm tissue culture dishes were treated with PR20 peptide in three pulses at 1.5 uM. After 24 hours, PR20 was removed and culture was allowed to recover for 2 days. Then, cells were trypsinized, pooled together across plates, and replated in fresh media lacking PR20 at equivalent concentrations. After three rounds of this treatment, the screen was concluded.

value: G401 cells

value: PR20 treated


title: G401_T1

description:
14 day growth PR20 treated, replicate 1
G401_UT1_vs_G401_T1_results.csv
combo.csv
DNA - integrated sgRNA sequence


title: siRNA MAFB donor #2

tag: cell

tag: sirna


title: 202234360017_R04C01

source_name: SJ-DMGX40 Primary


title: Input_33

description: No Drug experiment 2, Input for both PolII and H3K27ac ChIPs

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)


title: siRNA control donor #3

value: siRNA control


title: Input_42

description: PE experiment 1, Input for both SRF and p-SRF(S103) ChIPs


title: 201525200072_R08C01

source_name: SJ-DIPGX53 PDX


title: Input_32

description: PE experiment 1, Input for both PolII and H3K27ac ChIPs


title: G401_UT1

description:
14 day growth untreated, replicate 1
G401_UT1_vs_G401_T1_results.csv
combo.csv
DNA - integrated sgRNA sequence

value: untreated


title: siRNA control donor #2

source_name: macrophages


title: 201525200072_R07C01

source_name: SJ-HGGX51 PDX


title: Input_31

description: No Drug experiment 1, Input for both PolII and H3K27ac ChIPs

source_name: Rat adult cardomyocytes


title: ChIP-seq of KLF5 in TT

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

description: ChIP enriched DNA

data_processing:
Read alignment: Bowtie2
Peak calling and signal normalizaiton: MACS2
UCSC tool bedgraphtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Cancer cell line

extract_protocol:
ChIP-enriched DNA
NEB Ultra II DNA library prep kit

tag: antibody

value: KLF5, abcam ab137676

value: TT

tag: genotype

value: wildtype


title: Input_2

description: Flag-SRF(WT) experiment 1, Input for FLAG ChIPs

value: primary cultured rat adult ventricular cardiomyocytes


title: siRNA control donor #1


title: 201525200072_R06C01

source_name: SJ-HGGX49 PDX

value: PXA


title: Input_16

description: Flag-SRF(S103D) experiment 2, Input for both PolII and H3K27ac ChIPs


title: ChIP-seq of KLF5 in KYSE70

description: ChIP enriched DNA


title: 202234360017_R05C01

source_name: SJ-DMGX40 PDX


title: siRNA MAFB donor #1


title: 201525200072_R02C01

source_name: SJ-HGGX49 Primary


title: Clarias macrocephalus 24dpf_rep1

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description:
Illumina mRNA-seq
Clarias24-1

data_processing:
Illumina CASAVA 1.9.1 software was used for basecalling. Fastqc software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v 0.36, and masked for low-complexity or low-quality sequence.
Remaining high-quality reads of the seven libraries were assemblied into unique sequences of transcripts in Inchworm via greedy K-mer extension (K-mer 25). After mapping of reads to Inchworm contigs, Chrysalis incorporated reads into de Bruijn graphs. Butterfly ultimately generated full-length transcripts.
The assembled transcriptome was passed to CD-HIT (version 4.7) to reduce redundancy with 95% identity
The merged transcriptome assembly served as the reference transcriptome. The high-quality reads from each sample were mapped back to it and detected using RSEM software. Differential expression analysis was performed between two adjacent time points using an R package DESeq2
Genome_build: N.A. De novo transcript contig assemby was used for mapping.
Supplementary_files_format_and_content: Gzipped, tab-delimiited text file inlcuding raw reads counts for every gene in every sample

organism: Clarias macrocephalus

source_name: whole fry

extract_protocol:
RNA extraction was conducted using the Qiagen RNeasy Plus Kit following the manufacture protocols.
The RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Ribosomal RNA depletion was conducted using Ribozero rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA sequencing library preparation was performed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA). Enriched RNAs were fragmented for 15 minutes at 94 °C. The first strand and second strand cDNA were subsequently synthesized. The cDNA fragments were end-repaired and adenylated at 3'ends, and a universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA) and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).

tag: age

value: 24 days post fertilization

tag: tissue

value: whole-body

value: Unknown


title: Input_15

description: Flag-SRF(S103A) experiment 2, Input for both PolII and H3K27ac ChIPs

value: Input


title: Clarias macrocephalus 17dpf_rep2

description:
Illumina mRNA-seq
Clarias17-2

value: 17 days post fertilization


title: ChIP-seq of KLF5 in KNS62

description: ChIP enriched DNA


title: ChIP-seq of KLF5 in HT55, replicate 2

description: ChIP enriched DNA


title: Input_14

description: Flag-SRF(WT) experiment 2, Input for both PolII and H3K27ac ChIPs


title: Input_13

description: Flag-SRF(S103D) experiment 1, Input for both PolII and H3K27ac ChIPs


title: Clarias macrocephalus 17dpf_rep1

description:
Illumina mRNA-seq
Clarias17-1


title: Normal lung, bronchus cells-BEAS-2B-input DNA [CSE_input]

city: Chengdu

first: Yongchun

last: Shen

address: Medical clinic 37 Guoxue Alley

institute: West China Hospital of Sichuan University

description:
CSE_input
CSE_peaks.txt

data_processing:
RNA-seq:
Illumina Casava1.7 software used for basecalling.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed with parameters ILLUMINACLIP:{adaptor.fa}:2:30:10 -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Homo_sapiens.GRCh38 using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
ChIP-seq:
Illumina Casava1.7 software used for basecalling.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed with parameters ILLUMINACLIP:{adaptor.fa}:2:30:10 -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Homo_sapiens.GRCh38 using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for reads distribution analysis.
The MACS2 software (Version 2.1.1) was used for peak calling. The bedtools (Version 2.25.0) was used for peaks annotation and peak distribution analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: All_samples_rpkm.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: CSE_peaks.txt: Tab-delimited peak text file.

source_name: Normal lung, bronchus cells

growth_protocol: BEAS-2B cells obtained from the American Type Culture Collections (Manassas, VA, USA) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin G sodium and 50 μ g/ml streptomycin sulfate (Invitrogen, Carlsbad, CA, USA).

extract_protocol:
Nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA. The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-JunD antibody (Thermo Fisher, 710701) and named “IP”.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: For ChIP-seq, 2 × 10e7 Beas-2B cells exposed to 8% CSE for 24h.

tag: cell type

value: Epithelial virus-transformed bronchus cells

tag: treatment

value: CSE for 24h

tag: chip antibody


title: Normal lung, bronchus cells-BEAS-2B-JunD [CSE_IP]

description:
CSE_IP
CSE_peaks.txt

value: JunD (Thermo, 710701)


title: ChIP-seq of KLF5 in HT55, replicate 1

description: ChIP enriched DNA


title: Clarias macrocephalus 16dpf_rep2

description:
Illumina mRNA-seq
Clarias16-2

value: 16 days post fertilization

tag: Sex


title: Normal lung, bronchus cells-BEAS-2B rep3 [EV_CSE_3]

description:
EV_CSE_3
All_samples_rpkm.txt

extract_protocol:
The total RNA was extracted using the Total RNA Kit I (Omega Bio-tek, Norcross, GA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For RNA-seq, BEAS-2B cells were transfected with pcDNA3.1-JunD construct or empty vector for 12 hours using Lipofectamine 2000. After transfection, cells were exposed to CSE for 24h.

tag: transfection

value: Empty vector for 12 hours


title: G401_UT2

description:
14 day growth untreated, replicate 2
G401_UT2_vs_G401_T2_results.csv
combo.csv
DNA - integrated sgRNA sequence

value: G401 cells


title: ChIP-seq of KLF5 in HT29

description: ChIP enriched DNA


title: Clarias macrocephalus 24dpf_rep2

description:
Illumina mRNA-seq
Clarias24-2


title: ChIP-seq of KLF5 in TE10

description: ChIP enriched DNA


title: Normal lung, bronchus cells-BEAS-2B rep2 [EV_CSE_2]

description:
EV_CSE_2
All_samples_rpkm.txt


title: 201525200072_R03C01

source_name: SJ-HGGX51 Primary


title: Clarias macrocephalus 16dpf_rep1

description:
Illumina mRNA-seq
Clarias16-1


title: ChIP-seq of KLF5 in HARA, replicate 2

description: ChIP enriched DNA

value: HARA


title: Input_11

description: Flag-SRF(WT) experiment 1, Input for both PolII and H3K27ac ChIPs


title: Clarias macrocephalus 14dpf_rep2

description:
Illumina mRNA-seq
Clarias14-2

value: 14 days post fertilization


title: Input_12

description: Flag-SRF(S103A) experiment 1, Input for both PolII and H3K27ac ChIPs


title: OA.H11

city: Urbana

first: Ann

middle: Marie

last: Kemper

state: IL

address: 1008 W Hazelwood Dr

institute: University of Illinois

data_processing:
Quality control on all 28 samples (56 paired-end files) was performed using fastp (version 0.19.5) and summarized using MultiQC (version 1.6)
All fastq files were trimmed using Trimmomatic(version 0.38) in paired end mode to trim any remaining adaptors, then trim leading or trailing bases with quality scores below 28, then discarding a read pair if either read was shorter than 30 bases
Salmon (version 0.11.3) was used to quasi-map to the EquCab3.0 genome assembly (NCBI Annotation Release 103) with --validateMappings --rangeFactorizationBins 4 --gcbias --seqbias options enabled.
R package tximport was used to estimate gene-level counts from transcript-level quantification
Reads were filtered and normalized (TMM) using edgeR, surrogate variables were calculated and counts were corrected using sva, and DE analysis performed using limma-trend
Genome_build: EquCab3.0
Supplementary_files_format_and_content: tab-delimited files with normalized log2(cpm) values for each sample, genes with <1 cpm in 6 samples removed

organism: Equus caballus

source_name: synovium

extract_protocol:
Synovial tissue samples were collected arthroscopically from the MCPJ of eleven adult horses before (pre-OA) and 16 weeks after (OA) experimental induction of OA as well as from the sham-operated joints (sham). Synovium samples were placed in RNAlater (Qiagen, Valencia, CA) and stored at -80°C until further processing.  Frozen samples were crushed to powder with a mortar and pestle and placed in tubes containing ceramic beads (Precellys® 2ml Hard Tissue Homogenizing Ceramic Beads CK28, Cayman Chemical, Ann Arbor, MI) and TRIzol reagent (Invitrogen, Carlsbad, CA). Mechanical homogenization was performed for cell lysis (Precellys® Minilys, Bertin Corp., Rockville, MD) prior to RNA extraction on spin columns using the RNeasy Micro Kit (Qiagen, Valencia, CA) per manufacturer instructions. Samples were subjected to standard library preparation and sequencing (100 base-pair, paired-end) on an Illumina HiSeq4000 at the University of Illinois Roy J Carver Biotechnology Center.
Libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' and sequenced on an Illumina HiSeq4000. Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

value: synovium

tag: status

value: OA

tag: disease state

value: Osteoarthritis


title: Clarias macrocephalus 14dpf_rep1

description:
Illumina mRNA-seq
Clarias14-1


title: Normal lung, bronchus cells-BEAS-2B rep1 [EV_CSE_1]

description:
EV_CSE_1
All_samples_rpkm.txt


title: Normal lung, bronchus cells-BEAS-2B rep3 [J_D_CSE_3]

description:
J_D_CSE_3
All_samples_rpkm.txt

value: pcDNA3.1-JunD for 12 hours


title: ChIP-seq of KLF5 in HARA, replicate 1

description: ChIP enriched DNA

value: KLF5, abcam ab137676

value: wildtype


title: Clarias macrocephalus 13dpf_rep2

description:
Illumina mRNA-seq
Clarias13-2

value: 13 days post fertilization

value: whole-body

value: Unknown


title: Normal lung, bronchus cells-BEAS-2B rep2 [J_D_CSE_2]

description:
J_D_CSE_2
All_samples_rpkm.txt

value: Epithelial virus-transformed bronchus cells


title: preOA.H11

value: preOA

value: Not affected


title: Clarias macrocephalus 13dpf_rep1

description:
Illumina mRNA-seq
Clarias13-1


title: Sham.H10

value: Sham


title: Normal lung, bronchus cells-BEAS-2B rep1 [J_D_CSE_1]

description:
J_D_CSE_1
All_samples_rpkm.txt

value: CSE for 24h


title: Clarias macrocephalus 5dpf_rep2

description:
Illumina mRNA-seq
Clarias5-2

value: 5 days post fertilization


title: G1E-ER4 ZNF410_differentiated rep2 (ChIP-seq)

city: Philadelphia

first: xianjiang

last: lan

state: Pennsylvania

address: 315A Abramson Research Center 3615 Civic Center Blvd

department: Hematology

institute: children's hospital of philadelphia

data_processing:
Reads were aligned against reference genome hg38 or mm9 using Bowtie2 (v2.2.9) and the default parameters.
Alignments with MAPQ score lower than 10 and PCR duplicates were removed using Samtools (v0.1.19). Reads aligned to mitochondria, random contigs and ENCODE blacklisted regions were also removed for downstream analysis.
Data were filtered using the following specifications…
Genome coverage files were generated and normalized to 1 million reads per library using bedtools (v2.25.0), and then converted to bigwig format for visualization using the UCSC Toolkit.
Peaks were called using MACS2 (v2.1.0) and a 0.05 q-value cutoff. The final peaks were those overlapped by both ZNF410 replicates but not in control replicates (empty vector and knock-out samples), then manually filtered to exclude peaks near centromere/telomere regions that did not look like peaks on genome browser
Genome_build: hg38 for human and mm9 for mouse
Supplementary_files_format_and_content: bigwig files

growth_protocol: HUDEP-2 cells were cultured and differentiated accrooding to standard protocol (Grevet et al., Science 2018). In vitro primary CD34+ cells were cultured with a three-phase human CD34+ hematopoietic stem and progenitor cells (HSPCs) culture system (Grevet et al., Science, 2018). G1E-ER4 cells were cultured in IMDM supplemented with 15% FBS, 1% penicillin/streptomycin, Kit ligand, monothioglycerol and epoetin alpha.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to standard Illumina protocols

treatment_protocol: 100 nM estradiol was added to induce G1E-ER4 cell differentiation for 24 hours

value: G1E-ER4 immortalized erythroid cell line

value: ZNF410 (proteintech, 14529-1-AP)

value: G1E-ER4 cells at 24 hours of differentiation


title: OA.H10

value: synovium

value: OA


title: G1E-ER4 ZNF410_differentiated rep1 (ChIP-seq)


title: Clarias macrocephalus 5dpf_rep1

description:
Illumina mRNA-seq
Clarias5-1


title: parental_D56

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0), and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: parental D56 hESC-derived lung cells

growth_protocol: hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.

extract_protocol: Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v2

treatment_protocol: hPSC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of DMEM/F12 (3:1) (Life Technologies) supplemented with 1×N2 (Life Technologies), 1×B27 (Life Technologies), 50 μg/ml ascorbic acid, 2 mM Glutamax (Gibco), 0.4 μM monothioglycerol, 0.05% BSA at 37 °C in a 5% CO2/5% O2/95% N2 environment. hPSCs were treated with Accutase and plated onto low attachment 6-well plates (Corning), re-suspended in endoderm induction medium containing 10 μM Y-27632, 0.5 ng/ml human BMP4 (R&D Systems), 2.5 ng/ml human bFGF, 100 ng/ml human Activin A (R&D Systems), for 72-76 hours dependent on the formation rates of endoderm cells. On day 3 or 3.5, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,000–150,000 cells/well). For induction of anterior foregut endoderm, the endoderm cells were cultured in SFD medium supplemented with 1.5 μM dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 36 hours, and then switched to 36 hours of 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 6–15), the resulting anterior foregut endoderm was treated with 3 μM CHIR99021 (CHIR, Stem-RD), 10 ng/ml human FGF10, 10 ng/ml human KGF, 10 ng/ml human BMP4 and 50-60 nM all-trans retinoic acid (ATRA), in SFD medium for day 8–10. The day 10–15 culture was maintained in a 5% CO2/air environment. On days 15 and 16, the lung field progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, 10 ng/ml human BMP4, and 50 nM ATRA. Day 16–25 cultures of late stage lung progenitor cells were maintained in SFD media containing 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55) in 3D culture, cultures were re-plated and embedded in 90% Matrigel after brief trypsinization in SFD media containing maturation components containing 3 μM CHIR99021, 10 ng/ml human FGF10; 10 ng/ml human KGF, 50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione, Sigma Aldrich).

value: RUES2 embryonic stem cell line

value: lung cells derived from hESC


title: parental_D46

source_name: parental D46 hESC-derived lung cells


title: G1E-ER4 IgG_differentiated  (ChIP-seq)

value: Rabbit IgG(Sigma, I5006-10MG)


title: SK_VD24_REP3

city: Chicago

first: Sonia

last: Kupfer

address: 900 East 57th Street, MB#9

department: Department of Medicine

institute: University of Chicago

data_processing:
ATAC-seq fastq reads aligned with bwa mem (v 0.7.17)
ATAC-seq read filtering performed with samtools (v 1.10)
ATAC-seq peak calling performed with MACS2 (v 2.1.0)
ATAC-seq differential peak calling performed with R packages DiffBind and edgeR
ATAC-seq motif enrichment and peak annotation performed with HOMER (v 4.11.1)
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2
Genome_build: ATAC-seq and RNA-seq reads were aligned to reference sequence hs37d5
Supplementary_files_format_and_content: peak files are MACS2 outputted narrowPeak files for treated and untreated ATAC-seq samples at the two timepoints

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. ATAC-seq: cells were  treated using the Omni-ATAC protocol with some modifications. Briefly, the cells were treated with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then suspended in the transposition reaction mix (50% TD Tagment DNA buffer, 5% TDE1 Tagment DNA Enzyme,33% PBS) for 30 minutes.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina. ATAC-seq ibraries were prepared using the Nextera Index kit (Illumina #15055289).

treatment_protocol: After 24 hours of culturing in the basal media, organoids were treated with either 100nM 1α,25(OH)2D3 or vehicle control (ethanol) for 4 and 18 hours (for ATAC-seq), or 6 or 24 hours (for RNA-seq).

value: organoid

value: rectosigmoid mucosa

value: vitamin D 24 hrs


title: OA.H09

value: Osteoarthritis


title: Clarias macrocephalus 3dpf_rep2

description:
Illumina mRNA-seq
Clarias3-2

value: 3 days post fertilization

value: whole-body

value: Unknown


title: SK_VD24_REP2


title: G1E-ER4 input_differentiated  (ChIP-seq)


title: ChIP-seq of KLF5 in NCI-H508

description: ChIP enriched DNA

value: KLF5, abcam ab137676

value: wildtype


title: Clarias macrocephalus 3dpf_rep1

description:
Illumina mRNA-seq
Clarias3-1


title: preOA.H09

value: preOA

value: Not affected


title: Sample 8_1967_ALK5PRcre

city: COLLEGE STATION

first: Qinglei

last: Li

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
After generating a list of read counts, the data reads were filtered by removing the genes that the sums of reads of entire row were less than three
Data were normalized using the effective library sizes and a trimmed mean-M correction factor based on standard edgeR model (PMID: 20196867). The common dispersion and tagwise dispersions were estimated as recommended in the edgeR manual
Pairwise comparison was performed in egdeR to determine differential gene expression.
Genome_build: GRCm38.94_mouse
Supplementary_files_format_and_content: logFC, logCPM, Pvalue, and FDR values for each gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tgfbr1 Pgr-Cre knockout mouse decidual

extract_protocol:
Decidual tissues from E6.5 were prepared by clearing away maternal myometrial and embryonic materials under a dissecting microscope. Samples were stored at -80 °C for subsequent RNA and/or protein isolation. Total RNA was isolated from mouse decidual tissues using RNeasy Mini Kit (Qiagen) based on manufacturer’s protocol. Briefly, mouse decidual tissues were collected and homogenized in lysis buffer (Qiagen) that contains β-mercaptoethanol prior to RNA extraction. Total RNA was eluted with nuclease-free water and concentration measured using a NanoDrop Spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: embryonic day 6.5 (E6.5)

value: Mouse Decidual


title: Sham.H09

value: synovium

value: Sham


title: SK_ETH24_REP3

value: ethanol control 24 hrs


title: Sham.H08


title: ChIP-seq of KLF5 in BICR31

description: ChIP enriched DNA


title: SK_VD24_REP1


title: Sample 6_1915_ALK5PRcre


title: OGT KO-3

city: Shinjuku-ku

first: Koichi

last: Murakami

state: Tokyo

address: Shinanomachi 35

country: Japan

institute: Keio University School of Medicine

data_processing:
TopHat (version 2.0.13; with default parameters) was used to mapped to the reference genome (UCSC/mm10) with annotation data from iGenomes (Illumina).
The levels of gene expression were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters).
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: bedGraph files include FPKM  values for each Sample

source_name: Ogt ∆/Y_Bone Marrow LSK cells

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (QIAGEN) from sorted Lin- Sca-1+ c-Kit+ (LSK) cells cDNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, Palo Alto, CA, USA). The ds-cDNA was fragmented using S220 Focused- ultrasonicator (Covaris)
cDNA libraries were generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA).

tag: genotype/variation

value: Ogt KO

value: bone marrow

value: LSK cells


title: Sample 7_1965_ALK5PRcre


title: OGT KO-2


title: OGT KO-1


title: SK_ETH24_REP2

value: organoid

value: rectosigmoid mucosa


title: preOA.H10


title: Sample 5_1865_ALK5PRcre


title: WT-3

source_name: wild type_Bone Marrow LSK cells

value: wild type


title: OA.H08

value: OA

value: Osteoarthritis


title: Sample 4_1973_control

source_name: WT mouse decidual


title: OA.H07


title: SK_ETH24_REP1


title: WT-2


title: preOA.H07


title: Sham.H07


title: WT-1


title: SK_VD6_REP1

value: vitamin D 6 hrs


title: SK_VD6_REP3


title: Sample 2_1968_control


title: SK_VD6_REP2


title: Sham.H11


title: Sham.H06


title: Sample 3_1969_control


title: OA.H06


title: 9274651025_R05C02

source_name: SJ-HGGX6 PDX

tag: line id

tag: methylation classification


title: SK_ETH6_REP3

value: ethanol control 6 hrs


title: Sample 1_1909_control


title: SK_ETH6_REP2


title: 9274651025_R04C02

source_name: SJ-HGGX6 Primary


title: OA.H05


title: D8_10X

city: Guangzhou

first: Tianyu

last: WANG

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
10X Genomics software cellranger version 2.1.1 was used for mapping of the 10x single cell RNA-seq data. The read1 data of pooled cells were split into single-cell data using the barcode sequences contained in the first 16 bp. The next 10 bp were recorded as unique molecular identifiers (UMIs). Read2 with 98 bp were aligned to the hg38 genome.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: human embryonic cells

extract_protocol:
Cells in each sample were isolated using 10X Genomics
The libraries were constructed using Chromium™ Single Cell 3' Reagent Kits v2. R2 is biological. R1 includes cell barcode and UMI sequence. In R1, the first 16bp is cell barcode and the next 10bp is UMI.

value: hematopoietic stem/progenitor cells


title: preOA.H05

value: preOA

value: Not affected


title: SK_ETH6_REP1


title: zfishRibo0wt_7h

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description:
RNA-seq wild type
ribo-zero-profile.csv

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
Reads were aligned to UCSC genome danRer11 with STAR aligner (version 2.7.3a ), using Ensembl 98 gene models.
TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: danRer11
Supplementary_files_format_and_content: comma-delimited csv files include TPM values for each Sample

source_name: zebrafish early embryo

growth_protocol: Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.

extract_protocol:
poly (A) capture and ribo depletion
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For treated embryos: α-amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription (200ng/ul).

tag: developmental stage

value: early embryo

tag: time post fertilization in hrs

tag: rna extraction protocol

value: ribosomal depletion


title: Sham.H04

value: synovium

value: Sham


title: KKU-213A-EBF1 vector-rep1

city: Nai-Muang, Muang District

first: Napat

last: Armartmuntree

state: Khon Kaen

address: Mittapap Rd.

department: Biochemistry, Faculty of Medicine

country: Thailand

institute: Khon Kaen University

data_processing:
Genedata Profiler Genome software was used for basecalling.
STAR (v. 2.5.3a) was used to align RNA sequencing reads to reference genome.
Genome_build: hg18
Supplementary_files_format_and_content: Matrix table include FPKM values for each Sample

source_name: Human cholangiocarcinoma

growth_protocol: KKU-213A cell line was cultured in Ham’s F12 medium supplemented with 10% fetal calf serum, 100 U/mL of penicillin, and 100 µg/mL of streptomycin at 37 °C in a humidified incubator maintained in an atmosphere of 5% CO2.

extract_protocol:
The total RNA was extracted using NucleoSpin® RNA kit from KKU-213A cells treated with Empty vector (control cells; n=2) or EBF1 plasmid vector (EBF1-overexpressing cells; n=2).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KKU-213A cell line was transiently transfected with 1 µg of Empty vector or EBF1 vector using Lipofectamine 2000. Cells transfected with empty vector served as control cells.

tag: cell line

value: Human mixed (papillary and non-papillary cholangiocarcinoma cell line), KKU-213A

tag: tissue sampling

value: biliary tract

value: treated with EBF1 vector for 24 hours

tag: genotype

value: EBF1 overexpression


title: zfishRibo0wt_6h

description:
RNA-seq wild type
ribo-zero-profile.csv


title: A549 cells with PRMT1 knockdown

type: RNA

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

description: Gene expression data from A549 cells with knockdown of PRMT1

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45°C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

label: biotin

source_name: A549 cells infected with lentivirus carrying shRNA against PRMT1 (shPRMT1), and cultured for 8 days

label_protocol: Biotin-labeled cRNA were prepared using MessageAmp™ Premier RNA Amplification Kit (Ambion) and the protocol of the kit manufacturer from 100 ng total RNA.

growth_protocol: A549 cells were cultured in F-12K medium (Thermo Fisher Scientific) supplemented with 10% bovine fetal serum (Gibco). Cells were grown at 37°C with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A549 cells were infected with lentivirus carrying shRNA against PRMT1 for 8 days after puromycin selection. In parallel, cells were infected with lentivirus carrying empty vector as a control. Afterwards, cells were trypsinized and washed twice with PBS, and subjected to total RNA extraction.

tag: cell type

value: Lung carcinoma cell line

value: PRMT1 knockdown

tag: cell line source

value: 58 year old Caucasian male


title: 9274651025_R03C02

source_name: SJ-HGGX2 PDX


title: PB_10X

source_name: peripheral blood


title: OA.H04

tag: tissue

value: OA

value: Osteoarthritis


title: Sham.H03


title: KKU-213A-Empty vector-rep2

tag: treatment

value: treated with Empty vector for 24 hours

value: control


title: Sham.H05


title: zfishRibo0wt_5h

description:
RNA-seq wild type
ribo-zero-profile.csv


title: MeV F 3rd library after passage at mini-scale passage 1

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

data_processing:
Illumina Control software was used for basecalling
BBTools for mergingpaired-end reads
bowtie2 for alignment
IGVtools for exporting wig file.
Genome_build: Measles F gene sequence (6316-7968bps of LC420351.1) were used for alignment.
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

organism: Measles morbillivirus

source_name: baby hamster kidney cells

growth_protocol: Measles virus were rescued in Bsr-T7 cells

extract_protocol:
Trizol
Total cytosolic RNA were reverse transcribed by F gene specific primer. Then amplicons were amplified by PCR targeting 1st quarter, 2nd quarter, 3rd quarter, and 4th quarter of F gene. Cytosolic RNAs were extracted by Trizol, then RNA were reverse transcribed by superscript III (invitrogen) with a primer set of  'forward; ACTCATCCAGTGTCCATCATG' and 'reverse; TGTTTCAAGAGTTGTAGAGGATCA' to amplify entire F gene.   Using 1st amplicon as a template, we amplified part of F gene (1st, 2nd, 3rd, 4th quarter) by using cloneamp (takara bio).   Using 1st amplicon as a template, we amplified part of F gene (1st, 2nd, 3rd, 4th quarter) by using cloneamp (takara bio).  1st-f; CCAGTGTCCATCATG, 1st-r; CTTGAGAGTTCAGCA, 2nd-f; CACTTCACCAGTCCA, 2nd-r; TAGGCTATACTGAGT,  3rd-f; GACACAGAGTCCTACTTCATTGT, 3rd-r; GCAGTGATCGGCAGCAATG, 4th-f; GACAAGATCCTAACATA, 4th-r; AAGAGTTGTAGAGGATCA.  DNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, Inc. (South Plainfield, NJ, USA). DNA Library Preparation, clustering, and sequencing reagents were used throughout the process using NEBNext Ultra DNA Library Prep kit following the manufacturer s recommendations (Illumina, San Diego, CA, USA). End repaired adapters were ligated after adenylation of the 3 ends. The pooled DNA libraries were loaded on the Illumina instrument according to manufacturer s instructions.  The samples were sequenced by MiSeq on a 2x 250 paired-end (PE) configuration. Base calling was conducted by the Illumina Control Software (HCS) on the Illumina instrument.

value: Bsr-T7 cells

tag: passages

value: 1 passage

tag: molecule

value: cytosolic RNA


title: zfishRibo0wt_4h

description:
RNA-seq wild type
ribo-zero-profile.csv

value: early embryo

value: ribosomal depletion


title: KKU-213A-Empty vector-rep1


title: A549 cells (control)

description: Gene expression data from A549 cells (control)

source_name: A549 cells infected with lentivirus carrying empty shRNA knockdown vector pLKO.1, and cultured for 8 days


title: OA.H02

source_name: synovium

value: synovium

tag: status

tag: disease state


title: MeV F 4th library after passage replicate 3


title: Lega_41_scRNA

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Within_Subject_snRNAseq_Counts_NewBatch.txt.gz

data_processing:
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. UMI-tools were used to match barcode and reads. Single-nuclei RNA-seq reads were aligned with STAR 2.5.2b to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M24). Gene level expression was calculated using featureCounts. Downstream analysis was performed using Seurat.
Human hg38
Input tables are included as tab separated files.

source_name: Brodmann Area 38

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3 according to the manufacturer’s protocol. Libraries and sequencing were performed at the McDermott Sequencing Core at UTSW.

value: Resected

tag: diagnosis

value: Healthy

value: Brodmann Area 38

tag: library type

value: 10X single-nuclei RNA-seq

tag: age (years)

tag: Sex

value: M

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

value: R

tag: rin

tag: batch

tag: brainbank

tag: protocol

value: Protocol 2


title: Lega_33_scRNA

tag: genotype

tag: tissue

value: Hispanic


title: MeV F 4th library after passage replicate 2

tag: cell type

tag: passages

tag: molecule


title: zfishRibo0wt_3h

description:
RNA-seq wild type
ribo-zero-profile.csv

tag: developmental stage

tag: time post fertilization in hrs

tag: treatment

tag: rna extraction protocol


title: zfishRibo0wt_8h

description:
RNA-seq wild type
ribo-zero-profile.csv


title: KKU-213A-EBF1 vector-rep2

tag: cell line

value: Human mixed (papillary and non-papillary cholangiocarcinoma cell line), KKU-213A

tag: tissue sampling

value: biliary tract

value: treated with EBF1 vector for 24 hours

value: EBF1 overexpression


title: Sham.H02

tag: status

value: Sham

tag: disease state

value: Not affected


title: zfishRibo0wt_2h

description:
RNA-seq wild type
ribo-zero-profile.csv

value: early embryo

value: ribosomal depletion


title: MeV F 3rd library after passage at mini-scale passage 2

value: Bsr-T7 cells

value: 2 passage

value: cytosolic RNA


title: Lega_30_scRNA

value: Resected

tag: diagnosis

value: Healthy

value: Brodmann Area 38

tag: library type

value: 10X single-nuclei RNA-seq

tag: age (years)

tag: Sex

value: F

tag: race

tag: ethnicity

tag: pmi (hours)

tag: epilepsy duration (years)

tag: hemisphere

tag: rin


title: zfishRibo0wt_1h

description:
RNA-seq wild type
ribo-zero-profile.csv

tag: developmental stage

tag: time post fertilization in hrs


title: MeV F 3rd library after passage replicate 3

tag: cell type

tag: passages

value: 1 passage

tag: molecule


title: OA.H03

tag: tissue

value: synovium

tag: status

value: OA

value: Osteoarthritis


title: preOA.H01

value: preOA

tag: disease state


title: OA.H01


title: Sham.H01

value: Sham


title: ChIP-seq of POL2S5 in HARA sgKLF5#2

description: ChIP enriched DNA

source_name: Cancer cell line

tag: antibody

value: Ser5-Phosphorylated POL2, Cell signaling s13523

tag: cell line

value: HARA

tag: genotype

value: KLF5 KO


title: ChIP-seq of POL2S2 in HARA sgKLF5#2

description: ChIP enriched DNA

value: Ser2-Phosphorylated POL2, Cell signaling s13499


title: MeV F 3rd library after passage replicate 1

value: Bsr-T7 cells


title: zfishPolyAwt_8h

description:
RNA-seq wild type
polyA-profile.csv

value: early embryo

tag: treatment

tag: rna extraction protocol

value: poly (A) capture


title: zfishRibo0wt_0h

description:
RNA-seq wild type
ribo-zero-profile.csv

value: ribosomal depletion


title: ChIP-seq of BRD4 in HARA sgKLF5#2

description: ChIP enriched DNA

value: BRD4, Bethyl laboratories A301-985A100


title: zfishPolyAwt_7h

description:
RNA-seq wild type
polyA-profile.csv


title: MeV F 3rd library after passage replicate 2

value: cytosolic RNA


title: MeV F 4th library after passage replicate 1


title: ChIP-seq of POL2S5 in HARA sgAAVS1

description: ChIP enriched DNA

value: negative control


title: zfishPolyAwt_5h

description:
RNA-seq wild type
polyA-profile.csv


title: MeV F 2nd library after passage replicate 2

value: 1 passage


title: MeV F 2nd library after passage replicate 3


title: zfishPolyAwt_6h

description:
RNA-seq wild type
polyA-profile.csv


title: RNA_Va_SD-rep2

city: beijing

first: Liangyu

last: Liu

address: 105, North Road of Western 3rd Ring

institute: Capital Normal University

data_processing:
ATAC-seq: Raw reads were mapped to Arabidopsis thaliana TAIR10 genome, with the following parameters: bowtie2 -p 4 -X 1000; aligned reads with MAPQ>10 were used and duplicated reads were remove..
RNA-seq: Raw reads were mapped to Arabidopsis thaliana TAIR10 genomeby HISAT2. Expression value were geneated by DEseq2. DEG were identified by DEseq2.
Genome_build: TAIR 10
Supplementary_files_format_and_content: narrowPeak format; TSV format; BIGWIG format

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: Vascular cell nuclei in Short days

growth_protocol: Two wild-type accessions Col-0 and Ler and two INTACT transgenic lines GAS1p:NTF/ACT2p:BirA  and FDHp:NTF/ACT2p:BirA were used in this study. Plants were cultivated on soil in short days (SDs) with a photoperiod cycle of 8 hours light / 22℃ and 16 hours darkness / 20℃ in greenhouse.

extract_protocol: ATAC-seq: Prepare 50,000 fresh isolated beads conjured nuclei for the consequent ATAC-Seq tagmentation. Convert the buffer from NPBt into tagmentation reaction (Vazyme TD501) using magnet rack. Incubate the beads conjured nuclei 37℃ for 30 min. Extract DNA by a CTAB-chloroform based method and finally store the DNA water solution at -20℃. Follow the Vazyme TD501 manual to set up ATAC-Seq library. 12 cycles are applied to the PCR step. All these steps above, from material collection until DNA extraction must be executive continuously to ensure the chromatin fresh. RNA-seq: Total nuclei RNA was extracted from about 100,000 isolated nuclei using the RNeasy Micro Kit (Qiagen, 74004). cDNA was amplified using the Single Cell Full Length mRNA Amplication Kit (Vazyme, N712) according to the user manual. The RNA-seq library of each sample was prepared using TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, TD501). The library was purified by the VAHTS DNA Clean Beads (Vazyme, N411) and quantified using Qubit and Agilent 2100 before sequencing by the Illumina HiSeq XTen.

treatment_protocol: Half of the 14SD plants were moved to long-day-greenhouse (16 hours light / 22℃ and 8 hours darkness / 20℃) and the other half were kept in SD condition. After extra 3LDs or 3SDs treatment, the plants were collected for INTACT nuclei isolation.

tag: cultivar

tag: photoperiod

value: Short Day(8h/16h)

value: vascular cells


title: ChIP-seq of POL2S2 in HARA sgAAVS1

description: ChIP enriched DNA

extract_protocol:
ChIP-enriched DNA
NEB Ultra II DNA library prep kit


title: ECs_scRNA-seq

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

data_processing:
cellranger V3
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited text files for genes and cell barcodes, mtx files for cell-gene expression counts

organism: Drosophila melanogaster

source_name: FACS sorted escort cell

growth_protocol: Flies were cultured on standard media with yeast paste added to the food surface, and the culture temperature was 25 C

extract_protocol:
RNA and library was prepared by following the manufacturer’s instructions of 10X genomics scRNA-seq
Libraries were prepared for sequencing using standard Illumina protocols; 10X genomics single cell RNA-sequencing

value: ovary

tag: age

value: adult stage 5-7 days old


title: RNA_Va_SD-rep1


title: zfishPolyAwt_4h

description:
RNA-seq wild type
polyA-profile.csv


title: MeV F 2nd library after passage replicate 1


title: MeV F 1st library after passage replicate 3


title: ChIP-seq of BRD4 in HARA sgAAVS1

city: Salt Lake City

first: Xiaoyang

institute: University of Utah

description: ChIP enriched DNA

data_processing:
Read alignment: Bowtie2
Peak calling and signal normalizaiton: MACS2
UCSC tool bedgraphtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig


title: RNA_Va_LD-rep3

source_name: Vascular cell nuclei in shifted Long days

value: Long Day(16h/8h)


title: 9274651001_R06C02

city: MEMPHIS

first: Suzanne

last: Baker

address: 262 Danny Thomas Place

institute: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
BeadStudio software v3.2
CSV files: Average Beta & Unmethylated and methylated signal intensities

source_name: SJ-DIPGX7 Primary

extract_protocol: genomic DNA was isolated from frozen tumor tissue by SDS/Proteinase K digestion and phenol/chloroform extraction or from FFPE using a QIAamp DNA FFPE Tissue Kit (Qiagen) according to manufacturer's instructions.

tag: line id

tag: methylation classification


title: zfishPolyAwt_3h

description:
RNA-seq wild type
polyA-profile.csv

tag: developmental stage

tag: time post fertilization in hrs


title: MeV F 1st library after passage replicate 2

tag: cell type

tag: passages


title: zfishPolyAwt_2h

description:
RNA-seq wild type
polyA-profile.csv


title: ChIP-seq of BRD4 in HARA sgKLF5#1

last: Zhang

address: 1950 CIrcle of Hope

description: ChIP enriched DNA


title: MeV F 1st library after passage replicate 1

tag: molecule


title: RNA_Va_LD-rep1

tag: tissue


title: nsun1_polysomes_1

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description:
polysomal RNA
replicate 1

data_processing:
FASTQ Trimmer by column (Galaxy Version 1.0.0) was used to remove the first 12 bases from the 5’ end of each read due to an obvious base bias in this region, as detected by FastQC (Galaxy Version 0.69)
Filter by quality (Galaxy Version 1.0.0) was performed using a cut-off value of 20 and only reads with a maximum number of 8 bases with quality lower than the cut-off value were retained.
RNA STAR (Galaxy Version 2.6.0b-1) was used to align reads to the WBcel235 reference genome using the default options.
Aligned reads with a minimum alignment quality of 10 were counted using htseq-count (Galaxy Version 0.9.1).
Genome_build: WBcel235
Supplementary_files_format_and_content: HTseqCOUNT output (*.tabular)

organism: Caenorhabditis elegans

source_name: polysome fraction of sucrose gradient

growth_protocol: The N2 strain was synchronized by timed egg lay and grown on NGM agar plates seeded with RNAi control bacteria (HT115) until reaching adulthood. Three independent biological replicates were analyzed.

extract_protocol:
Nematodes were washed off the plates, lysed on ice using a pellet pestle and cleared by centrifugation. Lysates were separated on a sucrose gradient, polysomal RNA and RNA from lysate was isolated using Trizol LS using the manufacturer's protocol. RNA concentration and quality was analysed with a Bioanalyzer 2100 using the RNA 6000 Nano Kit (Agilent Technologies) before the samples were sent for next generation sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols by GATC Biotech (Konstanz, Germany).

treatment_protocol: Young adult nematodes were exposed to either RNAi control or nsun-1 RNAi for three days.

tag: RNAi

value: nsun-1 RNAi

tag: strain


title: RNA_Ep_SD-rep3

source_name: Epidermis cell nuclei in Short days

value: epidermis cells


title: zfishPolyAwt_0h

description:
RNA-seq wild type
polyA-profile.csv


title: MeV F 4th library in pEMC (genome coding plasmid) with high mutation rate

source_name: PCR amplicon

value: no passage

value: PCR amplicon from plasmid


title: MeV F 2nd library in pEMC (genome coding plasmid) with high mutation rate


title: RNA_Ep_SD-rep2


title: MeV F 1st library in pEMC (genome coding plasmid) with high mutation rate


title: TreatedAamanitin_zfishPolyAalpha_7h

description:
RNA-seq alpha amanitin
alpha-amanitin-prolife.csv

source_name: zebrafish early embryo

value: alpha-amanitin injected


title: MeV F 3rd library in pEMC (genome coding plasmid) with high mutation rate


title: TreatedAamanitin_zfishPolyAalpha_7.5h

value: early embryo


title: control_polysomes_2

description:
polysomal RNA
replicate 2

value: RNAi control


title: RNA_Ep_SD-rep1


title: RNA_Ep_LD-rep3

source_name: Epidermis cell nuclei in shifted Long days


title: RNA_Ep_LD-rep2


title: control_polysomes_1

description:
polysomal RNA
replicate 1


title: MeV F 4th library in pCDNA3 with high mutation rate


title: TreatedAamanitin_zfishPolyAalpha_6h

value: poly (A) capture


title: nsun1_polysomes_3

description:
polysomal RNA
replicate 3


title: nsun1_total_3

description: replicate 3

source_name: whole lysate


title: RNA_Va_LD-rep2


title: nsun1_polysomes_2

description:
polysomal RNA
replicate 2


title: zfishPolyAwt_1h

description:
RNA-seq wild type
polyA-profile.csv


title: MeV F 2nd library in pCDNA3 with high mutation rate


title: nsun1_total_2

description: replicate 2


title: TreatedAamanitin_zfishPolyAalpha_6.5h


title: RNA_Ep_LD-rep1


title: TreatedAamanitin_zfishPolyAalpha_5h


title: control_polysomes_3

description:
polysomal RNA
replicate 3


title: ATAC_Va_SD-rep2

description:
ATAC_Va_SD.pks.bed
ATAC_Va_SD.bw

value: vascular nuclei


title: TreatedAamanitin_zfishPolyAalpha_5.5h


title: MeV F 3rd library in pCDNA3 with high mutation rate


title: TreatedAamanitin_zfishPolyAalpha_4h


title: ATAC_Va_SD-rep1

description:
ATAC_Va_SD.pks.bed
ATAC_Va_SD.bw


title: control_total_2

description: replicate 2


title: nsun1_total_1

description: replicate 1


title: ATAC_Va_LD-rep2

description:
ATAC_Va_LD.pks.bed
ATAC_Va_LD.bw


title: TreatedAamanitin_zfishPolyAalpha_4.5h


title: MeV F 3rd library in pCDNA3 with middle mutation rate


title: control_total_1

description: replicate 1


title: MeV F 3rd library in pCDNA3 with low mutation rate


title: ATAC_Va_LD-rep1

description:
ATAC_Va_LD.pks.bed
ATAC_Va_LD.bw


title: ATAC_Ep_SD-rep1

description:
ATAC_Ep_SD.pks.bed
ATAC_Ep_SD.bw

value: epidermis nuclei


title: ATAC_Ep_SD-rep2

description:
ATAC_Ep_SD.pks.bed
ATAC_Ep_SD.bw


title: ciHHV-6A_vp_onp

city: Burlington

first: Seth

last: Frietze

state: Vermont

address: 106 Carrigan Drive

department: Biomedical and Health Sciences

institute: University of Vermont

description:
ciHHV-6A_vp2_onp
ciHHV-6A_vp1_onp

data_processing:
Library strategy: 4C-Seq
Demultiplexing (Demux) Illumina reads with HiSeq2000 software, MinION reads with oxford nanopore and minibar software.
4C-Seq trimming and alignment with R.4Cker software scripts and STAR aligner for RNA-Seq, RNA counts files generation with featureCounts software.
trans interactions identification and plotting with R.4Cker software and custom bioinformatics, statistical analysis, and plotting scripts using R.
cis interactions identiification with peakC software
read simulation for telomere content analysis with ART software
Visualization: BigWig tracks generation and visualization with Seqsetvis R package and custom scripts using R, as well as IGB.  Circos plots generated with circlize R package and custom R scripts. Ideogram karyotype plots with KareotypeR R package and custom R scripts, as well as IGB.
Genome_build: Human:GRCh38.p1: NC_000012.1 ; HHV6A: NC_001664.4 (iciHHV6A cells) and NC_001664.2 + recombinant elements (293-HHV-6A cells)
Supplementary_files_format_and_content: 4C-Seq peak regions: Bed and BedGraph; 4C-Seq and RNA-Seq signal tracks: BedGraph and BigWig; RNA-Seq transcript counts: RNA-seq counts .

organism:
Homo sapiens
Human betaherpesvirus 6A

source_name: SMC cells

growth_protocol: Human smooth muscles cells (SMCs) were isolated from the from the umbilical veins of an iciHHV6A+ subject.  SMCs were immortalized following transduction with a lentiviral vector (pLenti CMV/TO SV40 small + large T (W612-1), a gift form Eric Campeau and obtained from Addgene (plasmid #22298)) and expressing the SV40 T antigens. SMCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum (FBS), 1% penicillin streptomycin (Pen/Strep), and 1% L-Glutamine. Human epithelial kidney 293 T (293 T, ATCC CRL-11268) cells were cultured in the same medium but supplemented with 10% FBS. All cells were maintained in 10 cm2 flasks as a monolayer culture in a humidified 5% CO2 air incubator at 37°C. Bacterial artificial chromosome (BAC)-derived HHV6A (strain U1102) expressing green fluorescent protein (GFP) under the control of the HCMV major immediate early (IE) promoter (293-HHV-6A) was propagated in JJHan cells as described previously [13]. 293 T cells were infected with 293-HHV-6A and GFP positive cells were isolated using a FACS AriaIII cell sorter (BD Biosciences). Clones harboring the integrated 293-HHV-6A genome were identified by quantitative PCR (qPCR) and HHV-6A integration was confirmed by fluorescent in situ hybridization (FISH).

extract_protocol:
RNA-Seq: RNA was extracted from an HHV-6A infected 293T cell line using Trizol Reagent (Life Technologies) and purified using Direct-zol RNA MicroPrep Kit (Zymo Research #R2060) following the manufacturer’s instructions. 4C-Seq: In order to identify the higher order chromatin structure and virus-host DNA contacts, 4C-seq libraries were prepared using both HHV-6A and iciHHV-6A samples as described previously by Krijger et al. 2020.
RNA-Seq: Libraries were quantified using Qubit (Life Technologies), and quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit (Agilent Technologies). Barcoded libraries were pooled and sequenced on an Illumina HiSeq 2000 to obtain 100-bp paired-end reads. 4C-Seq: Library indexing was performed using the DNA HT Dual Index Kit (Illumina) or with custom dual indexing primers with an additional 8 cycles of PCR. Indexing of nanopore libraries was performed with custom 12-nucleotide dual index primers with 8 additional PCR cycles. Libraries were pooled and sequenced with either HiSeq2000 or minION platforms.

treatment_protocol: 293-HHV-6A cells were infected with recombinant HHV6A virus, iciHHV6A+ cells and Lymphocytes were derived from patients samples

value: Umbilical Artery Smooth Muscle Cells


title: MeV F 1st library in pCDNA3 with high mutation rate


title: TreatedAamanitin_zfishPolyAalpha_3.5h


title: MeV F 3rd library in pCDNA3 with no mutation


title: ciHHV-6A_rna_days1-7

description:
ciHHV-6A_rna_day1
ciHHV-6A_rna_day2
ciHHV-6A_rna_day3
ciHHV-6A_rna_day4
ciHHV-6A_rna_day5
ciHHV-6A_rna_day6
ciHHV-6A_rna_day7

data_processing:
Demultiplexing (Demux) Illumina reads with HiSeq2000 software, MinION reads with oxford nanopore and minibar software.
4C-Seq trimming and alignment with R.4Cker software scripts and STAR aligner for RNA-Seq, RNA counts files generation with featureCounts software.
trans interactions identification and plotting with R.4Cker software and custom bioinformatics, statistical analysis, and plotting scripts using R.
cis interactions identiification with peakC software
read simulation for telomere content analysis with ART software
Visualization: BigWig tracks generation and visualization with Seqsetvis R package and custom scripts using R, as well as IGB.  Circos plots generated with circlize R package and custom R scripts. Ideogram karyotype plots with KareotypeR R package and custom R scripts, as well as IGB.
Genome_build: Human:GRCh38.p1: NC_000012.1 ; HHV6A: NC_001664.4 (iciHHV6A cells) and NC_001664.2 + recombinant elements (293-HHV-6A cells)
Supplementary_files_format_and_content: 4C-Seq peak regions: Bed and BedGraph; 4C-Seq and RNA-Seq signal tracks: BedGraph and BigWig; RNA-Seq transcript counts: RNA-seq counts .

source_name: HEK293T cells

tag: cell line

value: Human Embryonic Kidney Cells 293T

tag: time

value: days 1-7


title: TreatedAamanitin_zfishPolyAalpha_2h

tag: treatment


title: ATAC_Ep_LD-rep2

description:
ATAC_Ep_LD.pks.bed
ATAC_Ep_LD.bw


title: TreatedAamanitin_zfishPolyAalpha_3h

tag: rna extraction protocol


title: TreatedAamanitin_zfishPolyAalpha_2.5h


title: control_total_3

description: replicate 3


title: iciHHV-6A_vp_onp

description:
iciHHV-6A_vp2_onp
iciHHV-6A_vp1_onp


title: iciHHV-6A_vp

description:
iciHHV-6A_vp1_rep1
iciHHV-6A_vp2_rep1
iciHHV-6A_vp1_rep2
iciHHV-6A_vp2_rep2


title: BJOSKM96HS2

status: Public on Dec 08 2020

city: Birmingham

first: Kejin

last: Hu

address: 1825 University Blvd.

department: Department of Biochemistry and Molecular Genetics

institute: UAB School of Medicine

description: Transduced with the four reprogramming factors OSKM lentiviral preparation, RNA extracted 96 hours post transduction

data_processing:
Pre-alignment quality assessments of the raw fastq sequences were carried out using FastQC (version 0.11.7) (Andrews, 2010). The raw fastq sequences were aligned to the human hg38 reference genome (GenBank assembly accession: GCA_000001405.28). The alignments were carried out using STAR (version 2.7.1a) (Dobin et al 2013) with default parameters. Post-alignment quality assessments were carried out with RSeQC (version 2.6.3) (Wang et al 2012) and MultiQC (version 1.4) (Ewels et al 2016). Samtools (version 0.0.19) (Li et al 2009) and IGV (version 2.6.2) (Thorvaldsdóttir et al 2013) were used for indexing and viewing the alignments respectively. Gene expression was quantified as gene level counts using the htseq-count function (version 0.12.3) (Anders et al 2015); the Ensembl gene annotations for the human genome were used (genebuild-last-updated 2019-06). The htseq-count default parameters were used. Differentially expressed genes were identified using DESeq2 (version 1.28) (Love et al 2014). DESeq2 was run with default parameters (Love et al 2014).
Genome_build: The human hg38 reference genome (GenBank assembly accession: GCA_000001405.28).
Supplementary_files_format_and_content: excel file containing deseq2 normalized gene expression for each gene in each sample

source_name: newborn foreskin

growth_protocol: human ESCs were grown in feeder-free/serum-free chemically defined E8 meium: E8 medium (pH 7.4) for iPSC maintenance: DMEM/nutrient mixture F-12 (F-12) (DMEM/F-12), 1.74 g/L NaHCO3, 1 g/L sodium chloride, 64 mg/L L-ascorbic acid 2-phosphate sesquimagnesium (see Note 6), 13.6 µg/L sodium selenium, 4 ng/mL FGF2, 20 μg/mL insulin, 10 μg/mL transferrin, and 2 μg/L TGFβ1 . Human fibroblasts were grown in fibroblast medium: Fibroblast growth medium: Dulbecco's Modified Eagle Medium (DMEM) with high glucose, supplemented with 10% heat-inactivated fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 1x penicillin-streptomycin (100 U/mL penicillin and 100 ug/mL streptomycin), 0.1 mM Minimum Essential Medium (MEM) Non-Essential Amino Acids (NEAA), and 4 ng/mL human basic fibroblast growth factor (bFGF, also known as FGF2)

extract_protocol:
RNA was isolated using TRIzol™ Reagent (Invitrogen, Cat. 15596026) followed by DNA digestion with DNAseI (Thermo Fisher Scientific, Cat. AM2222) and a cleanup step using Quick-RNA Miniprep (Zymo Research, Cat. R1054). RNA concentration was determined using Nanodrop spectrophotometer (Thermo Fisher Scientific).
Sequencing library was constructed by BGI using its protocol (Document #, SOP-SS-027; Version #, A0, Effective date: 2018-06-11)PolyA mRNA was purified from total RNA using the oligo(T) attached to magentic beads. The mRNA was then fragmented.  cDNA was then generated using random hexamer-primerd reverse transcription followed by the second-strand cDNA synthesis. The synthesized cDNA was then subject to end-repair, and 3' adenylated. Adapters were then ligated to the ends of these 3' adenylated cDNA fragments. The cDNA was further PCR amplified. The amplified cDNA was purified with Ampure XP Beads. The library was validated on the Agilent 2100 bioanalyzer. The double strand PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circular DNA were formated as the final library.
RNA-seq using nanoball technology, sequening was conducted by BGI

treatment_protocol: fibroblasts were transduced with the reprogramming factors OCT4, SOX2, KLF4 and MYC. RNA was extracted at  the indicated time post transduction (48 hours, 72 hours, and 96 hours). Lentiviral titers used were OCT4, 8; SOX2, 5; KLF4, 5; MYC, 3.

value: BJ, ATCC cat# is CRL-2522

value: 96 hours post transduction

tag: growth protocol

value: grown in fibroblast media


title: ATAC_Ep_LD-rep1

description:
ATAC_Ep_LD.pks.bed
ATAC_Ep_LD.bw

tag: cultivar

tag: photoperiod

value: Long Day(16h/8h)


title: BJOSKM96HS3

value: Transduced with the four reprogramming factors OSKM lentiviral preparation


title: BJOSKM96HS1


title: CRLOSKM72HS1

description: Transduced with the four reprogramming factors OSKM lentiviral preparation, RNA extracted 72 hours post transduction

source_name: newborn skin, male

value: CCD-1079Sk, ATCC Cat# is CRL-209

value: 72 hours post transduction


title: CRL72HS2

description: RNA harvested 72 hours post seeding, no treatment

value: no treatment

value: 72 hours post seeding


title: CRLOSKM48HS2

description: Transduced with the four reprogramming factors OSKM lentiviral preparation, RNA extracted 48 hours post transduction

value: 48 hours post transduction


title: CRL72HS1


title: CRL48HS2

description: RNA harvested 48 hours post seeding, no treatment

value: 48 hours post seeding


title: CRL48HS1


title: ciHHV-6A_vp

description:
ciHHV-6A_vp1_rep1
ciHHV-6A_vp2_rep1
ciHHV-6A_vp1_rep2
ciHHV-6A_vp2_rep2


title: BJ72HS3


title: iciHHV-6A_vp_titration

description:
iciHHV-6A_vp2_titration_1 (10e7 starting cells, 35 PCR cycles)
iciHHV-6A_vp2_titration_2 (10e7 starting cells, 25 PCR cycles)
iciHHV-6A_vp2_titration_3 (10e6 starting cells)
iciHHV-6A_vp2_titration_4 (10e5 starting cells)
iciHHV-6A_vp2_titration_5 (10e4 starting cells)
iciHHV-6A_vp1_titration_1 (10e7 starting cells, 35 PCR cycles)
iciHHV-6A_vp1_titration_2 (10e7 starting cells, 25 PCR cycles)
iciHHV-6A_vp2_titration_3 (10e6 starting cells)
iciHHV-6A_vp2_titration_4 (10e5 starting cells)
iciHHV-6A_vp2_titration_5 (10e4 starting cells)

value: Titrations (titrations refer to the number of cells that were used as input to the assay; see "Description" field)


title: BJ48HS3


title: BJ48hS2


title: H1P43

description: at passage 43, no treatment

source_name: preimplantation embryo

value: human ESC line H1 originally derived by James Thomson

value: at passage 43

value: ESC were grown in the feeder-free, serum-free chemically defined medium (E8 medium)


title: BJ48hS1


title: hESH9

description: no treatment

value: human ESC line H9 originally derived by James Thomson


title: CRLOSKM48HS1


title: hESH1

description: no treatment


title: H9P69S2

description: at passage 69, no modification

value: no modification

value: at passage 69