title: H3K27ac-HL-E125-WT-GFPpHigh

data_processing: Single-end reads were mapped to the reference genome NCBI37/mm9 using Bowtie2 version 2.3.4.2 (Langmead and Salzberg 2012), filtered for mapping quality q ≥ 25 and duplicates were removed with SAMtools 1.9. Reads were extended to 250 bp and scaled (1 million/total of unique reads) to produce coverage tracks. BigWig files were visualized in the UCSC genome browser.

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C and supernatant was discarded. Cells for ChIP-seq were resuspended in 10% FCS/PBS and fixed in 1% formaldehyde at room temperature. The fixation was blocked by the addition of 1.25M glycine, cells were isolated by centrifugation (1000g, at 4°C for 8’), resuspended in cold lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, Protease Inhibitor (Roche, 04693159001)) and incubated on ice for 10’ to isolate the cell nuclei. The nuclei were isolated by centrifugation (1000g, at 4°C for 3’), washed in cold 1X PBS, centrifuged again (1000g, at 4°C for 1’) and stored frozen at -80°C after removal of the PBS supernatant.
500000 fixed nuclei were sonicated to a 200-500bp length with the Bioruptor Pico sonicator (Diagenode). H3K27Ac ChIP was (Diagenode C15410174) was performed as previously described (Lee et al. 2006; Paliou et al. 2019) with the addition of 5mM of Na-Butyrate to all buffers. Libraries were then prepared following the Illumina ChIP TruSeq protocol and sequenced as 50bp single-end reads on a illumina HiSeq 4000. Libraries were prepared starting with below <10ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorimeter (Invitrogen – Thermofisher Scientific). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

value: Embryonic Limb Bud

tag: cell population

value: GFP++


title: total RNA-seq from adrenal gland (ENCLB206MJA)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR007NGM/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 2 months_Male 03_ENC4_cDNA458
experiment encode accession: ENCSR007NGM
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB206MJA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J male (2 months) adrenal gland tissue

value: adrenal gland

value: tissue

tag: description

value: B6Cast F1 PND 2 months Male 03 adrenal gland for Wold core

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: unknown

tag: age

value: 2 month

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS110BLI at ENCODE; https://www.encodeproject.org/ENCBS110BLI/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: PBMC, NP5

city: nanchang

first: shulan

last: zhang

state: Jiangxi

address: NO.1 minde Road

country: China

institute: The Second Affiliated Hospital of Nanchang University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM for each Sample

organism: Homo sapiens

source_name: veinal blood

extract_protocol:
After taking venous blood, PBMC was rapidly extracted within 2 hours.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: PBMC

tag: tissue

value: veinal blood

tag: condition

value: control

value: 28 years old

value: F


title: PBMC, NP4

value: 30 years old

value: M


title: total RNA-seq from adrenal gland (ENCLB525HFA)

description:
https://www.encodeproject.org/experiments/ENCSR007NGM/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 2 months_Male 03_ENC4_cDNA458
experiment encode accession: ENCSR007NGM
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB525HFA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: B6Cast F1 PND 2 months Male 04 adrenal gland for Wold core

value: ENCBS886TIW at ENCODE; https://www.encodeproject.org/ENCBS886TIW/


title: R8871

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC 0.11.8
Reads aligned using STAR 2.7.2a
Count table generated using featureCounts 2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file containing a matrix of counts

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
RNA was isolated from 1 mL RBC-lysed whole blood samples stored in RNAlater (500 μl). Globin RNA was removed using the GLOBINCLEAR kit.
Libraries were prepared for samples that passed quality control using the KAPA stranded mRNA kit.

tag: subject id

tag: timepoint

value: Baseline

tag: cmv dnaemia


title: R8473


title: total RNA-seq from adrenal gland (ENCLB688TUY)

description:
https://www.encodeproject.org/experiments/ENCSR158WTT/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND4_Female 03_ENC4_cDNA440
experiment encode accession: ENCSR158WTT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB688TUY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (4 days) adrenal gland tissue

value: tissue

value: B6Cast F1 PND4 Female 03 adrenal gland for Wold core

value: female

value: unknown

value: 4 day

value: ENCBS886BLQ at ENCODE; https://www.encodeproject.org/ENCBS886BLQ/


title: R8757


title: scRNAseq-HL-E125-delPen

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing: No processed data submitted to GEO

source_name: Embryonic Limb Bud

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS.

extract_protocol:
Two replicates of fore and hindlimb buds of E12.5 wildtype embryos and hindlimb buds of mutant embryos (Pitx1Pen-/Pen-, Pitx1-/-) were micro-dissected and incubated for 12 minutes in 400ul trypsin-EDTA 0.25% (Thermo Fischer Scientific, 25300062), supplemented with 40ul of 5% BSA. During incubation tissues were disrupted by pipetting after 6 minutes of incubation and at the end of the 12 minutes. Trypsin was then inactivated by adding 2x volume of 5% BSA and single cell suspension was obtained by passing cells in a 40um cell strainer. Cells were then spun at 250g for 5 minutes at 4° and resuspended in 1%BSA in PBS. Cells were then counted using an automatized cell counter and a 1% BSA 700cells/ul suspension was prepared. 10ul of this solution was used as input for the 10X Genomics library preparation.
Single-cell libraries were prepared using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 following the manufacture’s protocol (10X Genomics, PN-1000075). Briefly, Gel beads in EMulsion (GEMs) are generated by combining Single Cell 3ʹ v3 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Chip B. Incubation of the GEMs produced from the poly-adenylated mRNA barcoded, full-length cDNA. Immediately, gel beads are dissolved and cDNA is amplified via PCR followed by library construction and sequencing. Libraries were paired-end sequenced on a HiSeq 4000. On average, 7000 cells were loaded on the Chromium Chip and between 25000-35000 mean reads were obtained.

value: Embryonic Limb Bud

tag: genotype

value: del(Pen)


title: PBMC, NP3

value: PBMC

value: veinal blood

value: control

value: 25 years old


title: total RNA-seq from gastrocnemius (ENCLB066SMW)

description:
https://www.encodeproject.org/experiments/ENCSR133LMN/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND10 Male
experiment encode accession: ENCSR133LMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB066SMW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (10 days) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 PND10 Male 04 gastrocnemius for Wold core

value: male

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS078GAU at ENCODE; https://www.encodeproject.org/ENCBS078GAU/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: PBMC, NP1

value: 19 years old

value: M


title: total RNA-seq from gastrocnemius (ENCLB961GWJ)

description:
https://www.encodeproject.org/experiments/ENCSR102ZZC/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND4 Male
experiment encode accession: ENCSR102ZZC
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB961GWJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (4 days) gastrocnemius tissue

value: tissue

value: B6Cast F1 PND4 Male 03 gastrocnemius for Wold core

value: unknown

value: 4 day

value: ENCBS895ZIH at ENCODE; https://www.encodeproject.org/ENCBS895ZIH/


title: R8379

value: Baseline


title: H3K27ac-HL-E125-WT-GFPpMild

library_source: genomic

molecule: genomic DNA

value: Embryonic Limb Bud

value: GFP+-


title: OA4

city: Guangzhou

first: Zongrui

last: Jiang

state: Guangdong

address: No.58 of 2nd Zhongshan Road, Yuexiu District, Guangzhou, Guangdong

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
cutadapt software(cutadapt-1.9) used for cutting adaptor with parameters~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100
After removing low-quality sequences and repetitive sequences, clean data is obtained in the format of fastq.gz,then mapped to ensemble-v101 whole genome using hisat2 (hisat2-2.0.4) to obtain the BAM file with parameter ~hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S sample_mapped.sam
The mapped reads of each sample were assembled using StringTie (stringtie-1.3.4d.Linux_x86_64)with default parameters(command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam)
all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam)
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs
Genome_build: ensemble-v101
Supplementary_files_format_and_content: tab-delimited text files include FPKM and raw gene counts for every Sample and every gene

growth_protocol: All samples were then cultured at 37 °C in a humidified atmosphere of 5% CO2 for 48 hours.

extract_protocol:
We used TRIzol (Invitrogen, Carlsbad, USA) to extract total RNA from each meniscus cell, following the manufacturer’s protocol. The RNA quality was checked by an Agilent 2200 and kept at −80 °C, and only samples with a RIN (RNA integrity number) value >7.0 were used for the cDNA library construction.
The cDNA libraries were constructed for each pooled RNA sample using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. We further used Dnase I to eradicate contamination after we wiped off ribosome RNA. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through AMPure XP Beads(beckman coulter) .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeqXTen.

value: meniscus

value: human primary meniscus cells

tag: subject status

value: Osteoarthritis


title: H3K27ac-HL-E125-WT-GFPp

tag: cell population

value: GFP+


title: WGBS from thymus (ENCLB830DLD)

description:
https://www.encodeproject.org/experiments/ENCSR001MFH/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse thymus
experiment encode accession: ENCSR001MFH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB830DLD
fragmentation methods: shearing (Covaris S2)
size range: 180-500

source_name: Mus musculus strain B6NCrl mixed sex adult (54-61 days) thymus tissue

value: thymus

tag: description

value: Thymus tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

tag: health state

value: healthy

value: ENCBS234DBQ at ENCODE; https://www.encodeproject.org/ENCBS234DBQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: H3K27ac-HL-E125-WT-GFPn

value: GFP-


title: R8362

value: Baseline


title: PBMC, NP2

value: PBMC

value: veinal blood

value: control

value: 29 years old

tag: Sex

value: F


title: H3K27ac-HL-E125-delPen-GFPp

value: Embryonic Limb Bud

value: GFP+


title: R8450


title: R8365


title: WGBS from thymus (ENCLB178OCW)

description:
https://www.encodeproject.org/experiments/ENCSR001MFH/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse thymus
experiment encode accession: ENCSR001MFH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB178OCW
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: thymus

value: tissue

value: Thymus tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River

tag: biosample encode accession

tag: dev stage


title: scRNAseq-FL-E125-WT

tag: age

value: wildtype


title: WGBS from thymus (ENCLB563PXZ)

description:
https://www.encodeproject.org/experiments/ENCSR001MFH/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse thymus
experiment encode accession: ENCSR001MFH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB563PXZ
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: pooled male and female

value: adult

tag: lab

value: Len Pennacchio, LBNL

tag: source

value: Len Pennacchio

value: ENCBS932EVQ at ENCODE; https://www.encodeproject.org/ENCBS932EVQ/


title: WGBS from thymus (ENCLB868EWM)

description:
https://www.encodeproject.org/experiments/ENCSR001MFH/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse thymus
experiment encode accession: ENCSR001MFH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB868EWM
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: healthy

tag: link

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from small intestine (ENCLB689TYA)

description:
https://www.encodeproject.org/experiments/ENCSR211VXF/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse small intestine
experiment encode accession: ENCSR211VXF
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB689TYA
fragmentation methods: shearing (Covaris S2)
size range: 180-500

source_name: Mus musculus strain B6NCrl mixed sex adult (54-61 days) small intestine tissue

value: small intestine

value: Small intestine tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: ENCBS718BAQ at ENCODE; https://www.encodeproject.org/ENCBS718BAQ/


title: RNAseq-HL-E125-WT-GFPp

data_processing: Single-end reads were mapped to the mm9 reference genome using STAR mapper version 2.5.2a with default settings. Further processing was done according to (Paliou et al. 2019). BigWig files were visualized in the UCSC genome browser. Counting was done using R version 3.6.2 and differential expression was analyzed through the “DEseq2” R package. The DEseq2 R package was also used to produce heatmaps by subtracting from each gene value per condition, given by vst, the mean value of all conditions. Genes were picked according to adjusted p-value, all being significantly differentially expressed between conditions. Pitx1 fold enrichment between WT GFP+ and GFP- populations was calculated normalizing the total normalized read count per million. Significance in the fold enrichment was calculated using a Student’s t.test (type 2, 1 tail), inputting the normalized counts from each condition (2 normalized counts per genetic background). Expression heatmaps were generated for satellite and mesenchymal markers as defined in Supplementary table S1. Moreover, genes with expression less or equal to 1 RPKM in all 8 samples (GFP+ wildtype: replicate 1 and 2; GFP- wildtype: replicate 1 and 2, GFP+ mutant: replicate 1 and 2; GFP- mutant: replicate 1 and 2) were removed from the analysis. For the GFP- specific heatmap, we additionally removed all genes with less or equal to 1 RPKM in all 4 GFP- samples. The colour of the expression heatmap corresponds to the z-score transformed RPKM values, using the mean and standard deviation per gene based on all 8 samples. Log2FC was calculated by averaging replicates RPKM for each datasets and dividing Pitx1GFP and Pitx1GFP;ΔPen values.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA from 1,5 x10^5 cells was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: tissue


title: total RNA-seq from gastrocnemius (ENCLB877YIZ)

description:
https://www.encodeproject.org/experiments/ENCSR133LMN/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND10 Male
experiment encode accession: ENCSR133LMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB877YIZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: B6Cast F1 PND10 Male 03 gastrocnemius for Wold core

value: male

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS766LFK at ENCODE; https://www.encodeproject.org/ENCBS766LFK/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: OA2

value: meniscus

tag: cell type

value: human primary meniscus cells

value: Osteoarthritis


title: WGBS from small intestine (ENCLB406BIW)

description:
https://www.encodeproject.org/experiments/ENCSR211VXF/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse small intestine
experiment encode accession: ENCSR211VXF
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB406BIW
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: tissue

value: pooled male and female

value: healthy

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS933VLA at ENCODE; https://www.encodeproject.org/ENCBS933VLA/


title: R8213

tag: subject id

value: Baseline


title: R8335

tag: timepoint


title: OA3


title: WGBS from small intestine (ENCLB096RHE)

description:
https://www.encodeproject.org/experiments/ENCSR211VXF/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse small intestine
experiment encode accession: ENCSR211VXF
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB096RHE
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: small intestine

value: Small intestine tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: R7774

tag: cmv dnaemia


title: RNAseq-HL-E125-WT-GFPn

value: Embryonic Limb Bud

value: GFP-

tag: genotype


title: R7651


title: NA4

tag: subject status

value: Healthy


title: H3K27ac-HL-E125-delPen-GFPn

tag: cell population


title: RNAseq-HL-E125-delPen-GFPp

value: GFP+


title: NA3

value: meniscus

value: human primary meniscus cells


title: R7631


title: NA2


title: WGBS from small intestine (ENCLB479QNY)

description:
https://www.encodeproject.org/experiments/ENCSR211VXF/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse small intestine
experiment encode accession: ENCSR211VXF
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB479QNY
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: tissue

tag: description

value: ENCBS718BAQ at ENCODE; https://www.encodeproject.org/ENCBS718BAQ/


title: R7607


title: R7435


title: OA1

value: Osteoarthritis


title: NA1


title: R7302


title: RNAseq-HL-E125-delPen-GFPn


title: R6700


title: total RNA-seq from layer of hippocampus (ENCLB427GHO)

description:
https://www.encodeproject.org/experiments/ENCSR330DDD/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6Cast F1 2 months male
experiment encode accession: ENCSR330DDD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB427GHO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (2 months) layer of hippocampus tissue

value: layer of hippocampus

value: male

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS762CAG at ENCODE; https://www.encodeproject.org/ENCBS762CAG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from layer of hippocampus (ENCLB763FGI)

description:
https://www.encodeproject.org/experiments/ENCSR128FBT/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6CastF1 PND14 3x female
experiment encode accession: ENCSR128FBT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB763FGI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (14 days) layer of hippocampus tissue

value: female

value: 14 day

value: ENCBS708FHL at ENCODE; https://www.encodeproject.org/ENCBS708FHL/


title: Gene-corrected AOs_2

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequenced reads of the NaPi2Bhigh cells were trimmed using fastp, and aligned to the GRCh38 using STAR 2.7.3a.
RSEM was used to calculate tanscripts per million (TPM) values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values.

source_name: NaPi2Bhigh cells isolated from alveolar organoids, P3 day14

growth_protocol: Human iPSC-derived NaPi2B positive cells were isolated by FACS. Sorted NaPi2B positive cells were mixed with human fetal lung fibroblasts in 200 μL of Matrigel diluted to 1/2 with DCIK medium (Ham's F12 containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA, 15 mM HEPES, 0.8 mM CaCl2, 0.1% ITS premix and 50 U/mL penicillin–streptomycin) supplemented with 10 μM Y-27632, and placed on a 12-well cell culture insert. 1 mL of DCIK medium supplemented with 10 μM Y-27632 was added to the lower chamber. The medium in the lower chamber was replaced with DCIK medium every 2-3 days.

extract_protocol:
Total RNA of NaPi2B high cells isolated by FACS was extracted using RNeasy micro (Qiagen).
Sequence libraries were prepared using the TruSeq Stranded mRNA (illumina).

treatment_protocol: The cells were passaged 3 times using NaPi2B as a surface antigen and NaPi2Bhigh cells were isolated.

value: iPSC derived NaPi2Bhigh cells

value: wild type


title: HPS1 patient-specific AOs_3

value: c.1472_1487dup16 variant in HPS1


title: total RNA-seq from layer of hippocampus (ENCLB354XHU)

description:
https://www.encodeproject.org/experiments/ENCSR128FBT/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6CastF1 PND14 3x female
experiment encode accession: ENCSR128FBT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB354XHU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: ENCBS229LCL at ENCODE; https://www.encodeproject.org/ENCBS229LCL/


title: Gene-corrected AOs_3


title: runx2b-/- bulk RNA-seq rep3

city: wuhan

first: yulong

last: chen

state: hubei

address: shizishan street  hongshan district

institute: huazhong agricultural university

description:
MUT_3_60dpf
All_reads_counts.txt

data_processing:
Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling.
Using Cell Ranger to identify and count the barcode sequence for scRNA-seq
6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Genome_build: GRCz11
Supplementary_files_format_and_content: [scRNA-seq samples]  Cell Ranger ouput files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary_files_format_and_content: [bulkRNA-seq samples]  Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: muscle and IB

extract_protocol:
tail muscles with IBs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit (Illumina, USA) was used with 1 ug of total RNA for the construction of sequencing libraries. The single-cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for  the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.

tag: strain

value: Tg (sp7/eGFP) transgenic line

value: muscle and IB

value: 60 dpf


title: total RNA-seq from left cerebral cortex (ENCLB759XQX)

description:
https://www.encodeproject.org/experiments/ENCSR321WYK/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND10 Female L. cortex
experiment encode accession: ENCSR321WYK
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB759XQX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (10 days) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 PND10 Female 03 left cerebral cortex for Wold biobank

tag: Sex

value: unknown

value: 10 day

value: ENCBS056HYO at ENCODE; https://www.encodeproject.org/ENCBS056HYO/


title: R6578

value: Baseline


title: HPS1 patient-specific AOs_2


title: total RNA-seq from layer of hippocampus (ENCLB372FSM)

description:
https://www.encodeproject.org/experiments/ENCSR330DDD/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6Cast F1 2 months male
experiment encode accession: ENCSR330DDD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB372FSM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

tag: biosample encode accession

value: male

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS379YDE at ENCODE; https://www.encodeproject.org/ENCBS379YDE/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: runx2b-/- bulk RNA-seq rep1

description:
All_reads_counts.txt
MUT_1_60dpf


title: Gene-corrected AOs_1

value: iPSC derived NaPi2Bhigh cells

value: wild type


title: runx2b+/+ bulk RNA-seq rep2

description:
All_reads_counts.txt
WT_2_60dpf

value: Tg (sp7/eGFP) transgenic line

value: muscle and IB


title: runx2b-/- bulk RNA-seq rep2

description:
All_reads_counts.txt
MUT_2_60dpf

value: 60 dpf


title: R6271


title: prelep

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Sequences of samples were aligned to the UCSC musculus reference genome (mm10) using TopHat with default settings. RefSeq-annotated gene expression was calculated using Cuffdiff software. Genes with FPKM below 0.5 in all samples were filtered, and only genes with a fold change (FC) larger than 1.5 were counted as up- or downregulated genes.
Genome_build: mm10
Supplementary_files_format_and_content: cuffdiff_RPKM

source_name: prelep

growth_protocol: Mice (C57BL/6, male) were maintained in an animal room with 12-hr light/12-hr dark cycles and free access to food and water at the laboratory animal center of Xiamen University. All experimental procedures were performed according to the approved guidelines from the Animal Care and Use Committee of Xiamen University (201507), and all mice were handled following the “Guide for the Care and Use of Laboratory Animals” and the “Principles for the Utilization and Care of Vertebrate Animals.”

extract_protocol:
Spermatogonia were obtained from the testes of thirty 7-day-old mice. Preleptotene, leptotene/zygotene, and pachytene spermatocytes were obtained from the testes of five 17-day-old mice. The germ cell mixture was isolated by a two-step enzymatic digestion protocol as described previously. In brief, the testes were decapsulated and then incubated with approximately 10 volumes of HBSS solution containing 1 mg/ml collagenase IV (17104–019, Gibco, USA) and 1 mg/ml DNase I (DN25, Sigma, USA) at 37 °C with gentle shaking. After washing, the testes were incubated in HBSS containing 1 mM EDTA, 0.25% trypsin, and 500 mg/ml DNase I at 37 °C. When most cells were dispersed, the action of trypsin was terminated by adding a 10% volume of fetal bovine serum (FBS). Then, the cell suspension was filtered through nylon mesh with a 40-μm pore size to remove large clumps of cells. The filtrate was centrifuged at 1000 g for 5 min. After removing the supernatant, cells in the pellet were resuspended and cultured in F12/DMEM with 5% fetal bovine serum for 4–6 hours for Sertoli cell adherence. Then, the supernatant cells were collected and centrifuged at 1000 g for 5 min to obtain the germ cell mixture sediment. Next, the purified germ cells were isolated using gravity sedimentation with an STA-PUT device based on cytological classification and morphological analysis, as described previously[35]. The purity of the four types of germ cells was assessed by observing cell diameters and morphology under a microscope bright field and the levels of marker genes and proteins.
Total RNA was isolated from separated spermatogonia, preleptotene spermatocytes, leptotene/zygotene spermatocytes, and pachytene spermatocytes using an RNeasy Mini Kit (74104, Qiagen, Germany) following the manufacturer’s protocol. DNase I in column digestion was performed to remove genomic DNA. Ribosomal RNA was eliminated by an Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA) according to the manufacturer's instructions. Then, sequencing libraries were generated using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s instructions. RNA-seq was performed with Illumina’s HiSeq 2500 system at RiboBio Co., Ltd. (Guangzhou, China).

value: preleptotene


title: lep-zygo

source_name: lep-zygo

value: leptotene/zygotene


title: type_A_spermatogonia

value: spermatogonia


title: R6554


title: HPS1 patient-specific AOs_1

value: c.1472_1487dup16 variant in HPS1


title: Spen_CLAP_Input_Replicate_A

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

description:
RNA
Male ES cells (pSM33 ES cell line)
KCNQ1OT1MM10.out.neg.bedgraph

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and assessed with Fastqc v0.11.9. Subsequently, the DPM (GATCGGAAGAG) and RPM (ATCAGCACTTA) sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1 along with the 3’ end DPM sequences that result from short reads being read through into the barcode (GGTGGTCTTT, GCCTCTTGTT, CCAGGTATTT, TAAGAGAGTT, TTCTCCTCTT, ACCCTCGATT). The additional trimming helps improve read mapping in the end-to-end alignment mode. The SPRITE barcodes of trimmed reads are identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with an RPM or a DPM barcode are split into two separate files, to process RNA and DNA reads individually downstream, respectively.
RNA reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping --sp 1000,1000. Unmapped and reads with a low MapQ score (samtools view -bq 20) were filtered out for downstream realignment. Mapped reads were annotated for gene exons and introns with the featureCounts tool from the subread package v1.6.4 using Ensembl GRCm38 v95 gene model annotation and the Repeat and Transposable element annotation from the Hammel lab. Filtered reads were subsequently realigned to our custom collection of repeat sequences using Bowtie v2.3.5, only keeping mapped and primary alignment reads.
DNA reads were aligned to GRCm38.p6 using Bowtie2 v2.3.5, filtering out unmapped and reads with a low MapQ score (samtools view -bq 20). Data generated in F1 hybrid cells (pSM33: C57BL/6 × 129SV-Jae or pSM44: 129 × castaneous) were assigned the allele of origin using SNPsplit v0.3.4. RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0.
RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Genome_build: mm10
Supplementary_files_format_and_content: RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments.

source_name: Mouse Embryonic Stem cells

extract_protocol:
Cells were lifted using trypsinization and were crosslinked in suspension at room temperature with 2mM disuccinimidyl glutarate (DSG) for 45 minutes followed by 3% Formaldehyde for 10 minutes to preserve RNA and DNA interactions in situ.
After lysis of cells, nuclei were lightly sonicated. DNA was DNAse digested to an average size of approximately 150-1000 bp in length. Crosslinked complexes of interacting DNA, RNA, and protein were isolated on NHS beads, RNA and DNA ends were repaired, DNA was dA-tailed to generate a protruding 3’ A-base for ligation of barcodes, RNA was ligated with a partially ssRNA-dsDNA adaptor for ligation of barcodes, and were then split-pool tagged with a series of barcodes over multiple rounds of split-and-pool tagging. A distinct RNA adaptor was ligated to RNA to flag a molecule as RNA rather than DNA. This adaptor contains a shared overhang that allows for simultaneous tagging of RNA and DNA during the split-and-pool tagging process. Reverse transcription was performed to convert RNA into cDNA. After split-and-pool tagging, crosslinks were reversed, the DNA/RNA was isolated, was amplified 8-12 cycles using standard Illumina library prep (dual index), and purified using SPRI beads and gel cut. Libraries were sequenced on a NovaSeq S4 chip (150x150 read length).

tag: cell line

value: Male ES cells

tag: protocol

value: CLAP

tag: treatment

value: 16hr doxycycline for Xist induction


title: runx2b+/+ bulk RNA-seq rep3

description:
All_reads_counts.txt
WT_3_60dpf

tag: age


title: total RNA-seq from left cerebral cortex (ENCLB678QZW)

description:
https://www.encodeproject.org/experiments/ENCSR321WYK/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND10 Female L. cortex
experiment encode accession: ENCSR321WYK
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB678QZW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND10 Female 04 left cerebral cortex for Wold biobank

value: female

tag: dev stage

value: unknown

value: 10 day

tag: lab

tag: source

tag: link

value: ENCBS716XOP at ENCODE; https://www.encodeproject.org/ENCBS716XOP/


title: R6607

tag: subject id

tag: timepoint

value: Baseline


title: T_8_rep3: Tha-infected 8hr post-infection replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11 . Only sequences at least 25 nucleotides (nt) in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment against the reference genome (Human (GRCh38) from ENSEMBL version 98).
Genes were counted using featureCounts version 1.4.6-p3  from the Subreads package (parameters: -t gene -g gene_id -s 2 -p).
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.24.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameter and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with both an absolute log2FC > 1 and an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Human (GRCh38) from ENSEMBL version 98
Supplementary_files_format_and_content: Matrix from DESeq2

source_name: Neuronal progenitor cell-derived neurons

growth_protocol: iPSC-derived NPCs were maintained in DMEM/F12 medium with N-2 and B27 supplements, and bFGF on PLO and Laminin-coated plate until differentiation. The medium was changed to Neurobasal medium with B27 and Glutamax and refreshed every 2~3 days for 14 days for neuron differentiation.

extract_protocol:
Total RNAs were prepared after Trizol extraction, DNase I treatment, second Trizol extraction and ethanol precipitation.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA library kit.

treatment_protocol: Neurons treated with viruses or mock-medium were harvested at 0, 8, 24, and 40hrs post-infection.

tag: cell type

value: NPC-derived neuron

tag: infection

value: Tha-infected

tag: harvest time

value: 8hr post-infection


title: R6191

tag: cmv dnaemia


title: T_8_rep2: Tha-infected 8hr post-infection replicate 2


title: runx2b+/+ bulk RNA-seq rep1

description:
All_reads_counts.txt
WT_1_60dpf

tag: strain

value: Tg (sp7/eGFP) transgenic line

tag: tissue

value: muscle and IB

value: 60 dpf

tag: genotype

value: wild type


title: R5992


title: Healty donor derived AOs_3

data_processing:
Sequenced reads of the SPC-GFP+ cells were trimmed using fastp, and aligned to the GRCh38 using STAR 2.7.3a.
RSEM was used to calculate tanscripts per million (TPM) values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values.

source_name: SPC+ cells isolated from alveolar organoids, P3 day14

growth_protocol: Human iPSC-derived SPC+ cells were isolated by FACS. Sorted SPC+ cells were mixed with human fetal lung fibroblasts in 200 μL of Matrigel diluted to 1/2 with DCIK medium (Ham's F12 containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA, 15 mM HEPES, 0.8 mM CaCl2, 0.1% ITS premix, 0.1% DMSO and 50 U/mL penicillin–streptomycin) supplemented with 10 μM Y-27632, and placed on a 12-well cell culture insert. 1 mL of DCIK medium supplemented with 10 μM Y-27632 was added to the lower chamber. The medium in the lower chamber was replaced with DCIK medium every 2-3 days.

extract_protocol:
Total RNA of SPC-GFP+ cells isolated by FACS was extracted using RNeasy micro (Qiagen).
10 ng of total RNA was reverse-transcribed and amplified with 7 cycles using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Nextera XT DNA Library Preparation Kit (illumina) was used to prepare sequence libraries.

treatment_protocol: The cells were passaged 2-3 times, depending on SPC-GFP expression.

value: iPSC derived SPC+

value: healty


title: T_8_rep1: Tha-infected 8hr post-infection replicate 1


title: R6126

source_name: Whole Blood


title: Spen_CLAP_Capture_Replicate_A

tag: cell line

value: Male ES cells

value: CLAP

value: 16hr doxycycline for Xist induction


title: MT inf (replicate 3)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. A quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Read alignment was performed using STAR v2.3.0.
Data were converted and sorted by samtools 1.2 and reads per gene were counted via htseq version 0.6.
Data analysis was performed using R (3.2.1) and differential gene expression was analyzed using DESeq2 (v1.8.1).
Candidate genes were filtered to a minimum of a 2-fold change and a FDR-corrected p < 0.05 (padjusted).
Genome_build: mm10
Supplementary_files_format_and_content: read counts

source_name: C2C12 skeletal muscle cell

extract_protocol:
RNA was isolated using GenElute Total RNA Miniprep kit (Sigma-Aldrich) according to instructions
Library preparation for RNA sequencing was performed using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, USA; Cat. N°RS-122-2002), starting from 1,000 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega, Mannheim, Germany). The size range of the final cDNA libraries (average 350 bp) was determined in DNA 1000 chips using the Bioanalyzer 2100. CDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina.

tag: developmental stage

value: myotube

tag: differentiation protocol

value: DMEM, 2% horse serum, 144 hours

tag: infection status

value: Toxoplasma gondii, strain NTE, MOI 5:1

tag: duration

value: 24 hours post infection


title: MT inf (replicate 2)


title: T4M_8_rep1: Th4M-infected 8hr post-infection replicate 1


title: Healty donor derived AOs_2

source_name: SPC+ cells isolated from alveolar organoids, P2 day14


title: T4M_40_rep2: Th4M-infected 40hr post-infection replicate 2

value: 40hr post-infection


title: MT inf (replicate 1)


title: runx2b-/- scRNA-seq

tag: age


title: Healty donor derived AOs_1


title: T4M_40_rep1: Th4M-infected 40hr post-infection replicate 1

value: NPC-derived neuron


title: MT ni (replicate 1)

value: non-infected


title: Spen_CLAP_Input_Replicate_B

tag: protocol

tag: treatment


title: R6040

tag: subject id

value: Baseline


title: T4M_24_rep2: Th4M-infected 24hr post-infection replicate 2

value: 24hr post-infection


title: pach

source_name: pach

value: pachytene spermatocytes


title: R8517

tag: timepoint


title: runx2b+/+ scRNA-seq

value: Tg (sp7/eGFP) transgenic line

value: muscle and IB

value: 60 dpf


title: T4M_24_rep1: Th4M-infected 24hr post-infection replicate 1

tag: cell type


title: Spen_CLAP_Capture_Replicate_B


title: T4M_8_rep3: Th4M-infected 8hr post-infection replicate 3

tag: infection

value: 8hr post-infection


title: R8263


title: R5662


title: R5572


title: T4M_0_rep1: Th4M-infected 0hr post-infection replicate 1

tag: harvest time

value: 0hr post-infection


title: T4M_8_rep2: Th4M-infected 8hr post-infection replicate 2


title: R6013

tag: cmv dnaemia


title: R9278


title: R7702


title: R9148


title: R7633


title: R8882


title: T4M_40_rep3: Th4M-infected 40hr post-infection replicate 3


title: T_40_rep2: Tha-infected 40hr post-infection replicate 2

value: Tha-infected


title: R8765


title: ST3 - uninfected

city: NANJING

first: LIUYANG

last: Du

state: JIANGSU

address: WEIGANG NO.1

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description: control

data_processing:
Sequencing libraries were generated us-ing NEBNext® Multiplex. The   sRNA molecules were ligated to a 5′adaptor and a 3′ adaptor using T4 RNA   ligase 1.
Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix.
At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
After cluster generation the  library reparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.
Expression level of miRNAs was normalized by TPM (transcript per million) through the following criteria: Normalized expression = (mapped reads) / (total reads) * 1000000
Genome_build: Sus scrofa ensembl 76
Supplementary_files_format_and_content: tab-delimited excel files include normalized values for each Sample

organism: Sus scrofa

source_name: swine testicular cells

extract_protocol:
Total RNA was isolated from uninfected or infected ST cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
Sequencing libraries were generated using Small RNA Sample Pre Kit according to the manufacture.

treatment_protocol: ST cells were uninfected or infected with PDCoV at a multiplicity of infection (MOI) of 10 and harvested at 11 hour post infection or without, respectively.

value: swine testicular cells

value: uninfected


title: MT ni (replicate 2)

tag: strain

value: myotube

value: DMEM, 2% horse serum, 144 hours


title: R7559


title: R8680


title: R8704


title: MB inf (replicate 3)

value: myoblast

value: Toxoplasma gondii, strain NTE, MOI 5:1

value: 24 hours post infection


title: R6856


title: MB inf (replicate 2)


title: MT ni (replicate 3)

value: non-infected


title: T4M_0_rep3: Th4M-infected 0hr post-infection replicate 3

value: NPC-derived neuron


title: MB inf (replicate 1)


title: R8516

value: Baseline


title: MB ni (replicate 3)


title: T4M_0_rep2: Th4M-infected 0hr post-infection replicate 2


title: R6824


title: T_0_rep3: Tha-infected 0hr post-infection replicate 3


title: MB ni (replicate 2)


title: T_40_rep3: Tha-infected 40hr post-infection replicate 3

value: 40hr post-infection


title: T_40_rep1: Tha-infected 40hr post-infection replicate 1


title: PS1 - infected

description: infected at MOI=10 and harvested at 11 hour post infection

value: infected by PDCoV PDCoV-CH-HA3-2017(MK040455)


title: T_24_rep3: Tha-infected 24hr post-infection replicate 3

value: 24hr post-infection


title: R7002


title: ST2 - uninfected

description: control


title: T_24_rep1: Tha-infected 24hr post-infection replicate 1


title: ST1 - uninfected

description: control


title: miRNA-Seq OA004_IL.1b rep3

description: miRNA

data_processing:
RNA-Seq: Reads filtering under criteria removing reads with 20% of the base quality lower than 13
RNA-Seq: HISAT2.1.0 mapping to reference genome
RNA-Seq: count counting
miRNA-Seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)base quality >15 b) 17bp < read length < 26bp.
miRNA-Seq: Utilizing the BWA software, we mapped the clean data to miRBase 22.0 human miRNA database and GRCh38 genome.
miRNA-Seq: count counting
Genome_build: GRCh38

source_name: meniscus

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the meniscus cells fully adhered to the plate, three samples were treated with 5 ng/ml IL-1β to simulate OA inflammatory pathology (OA004_IL-1B, OA006_IL-1B, OA008_IL-1B), while the other three samples were replaced with refreshed medium instead((OA004_NC, OA006_NC, OA008_NC).

tag: tissues

value: meniscus


title: R6184


title: miRNA-Seq OA004_IL.1b rep1

description: miRNA


title: MB ni (replicate 1)


title: PS3 - infected


title: miRNA-Seq OA004_NC rep3

description: miRNA


title: PS2 - infected


title: R5933


title: R6602


title: NI_8_rep1: non-infected 8hr post-infection replicate 1

value: 8hr post-infection


title: miRNA-Seq OA004_NC rep2

description: miRNA


title: T_0_rep2: Tha-infected 0hr post-infection replicate 2

value: 0hr post-infection


title: T_0_rep1: Tha-infected 0hr post-infection replicate 1

value: Tha-infected


title: CNOT66L-KO-GCs-P44h-Rep2

city: Hangzhou

first: Xingxing

last: Dai

address: YuHangTang 866

institute: Life Sciences Institute

description:
ko2-44h
Cnot66l-FPKM.txt

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the 1Cell-stage embryo sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Cnot66l-FPKM.txt: Tab-delimited text file includes FPKM values of all RNA-seq samples.

source_name: Cnot66l DKO Mouse Ovarian Granulosa Cells (PMSG 44h)

extract_protocol:
Mouse Ovarian Granulosa Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads.

tag: genotype

value: CNOT6/6L KO

tag: Sex

value: Female

value: Ovarian granulosa cells

value: PMSG, 44h


title: RNA-Seq OA004_IL.1b rep3


title: NI_8_rep2: non-infected 8hr post-infection replicate 2


title: CNOT66L-KO-GCs-0h-Rep1

description:
ko1-0h
Cnot66l-FPKM.txt

source_name: Cnot66l DKO Mouse Ovarian Granulosa Cells


title: NI_8_rep3: non-infected 8hr post-infection replicate 3


title: RNA-Seq OA004_NC rep3


title: NI_0_rep3: non-infected 0hr post-infection replicate 3


title: RNA-Seq OA004_NC rep2


title: WT-GCs-0h-Rep1

description:
WT1-0h
Cnot66l-FPKM.txt

source_name: Mouse Ovarian Granulosa Cells

value: WT


title: R6151


title: R6095


title: NI_40_rep2: non-infected 40hr post-infection replicate 2


title: NI_40_rep3: non-infected 40hr post-infection replicate 3


title: miRNA-Seq OA004_NC rep1

description: miRNA


title: R6305


title: miRNA-Seq OA004_IL.1b rep2

description: miRNA


title: CNOT66L-KO-GCs-P44h-Rep1

description:
ko1-44h
Cnot66l-FPKM.txt


title: NI_24_rep3: non-infected 24hr post-infection replicate 3


title: NI_40_rep1: non-infected 40hr post-infection replicate 1


title: RNA-Seq OA004_IL.1b rep2


title: WT-GCs-P44h-Rep2

description:
WT2-44h
Cnot66l-FPKM.txt

source_name: Mouse Ovarian Granulosa Cells (PMSG 44h)


title: RNA-Seq OA004_IL.1b rep1


title: NI_24_rep1: non-infected 24hr post-infection replicate 1


title: WT-GCs-P44h-Rep1

description:
WT1-44h
Cnot66l-FPKM.txt


title: RNA-Seq OA004_NC rep1


title: NI_0_rep1: non-infected 0hr post-infection replicate 1


title: NI_0_rep2: non-infected 0hr post-infection replicate 2


title: NI_24_rep2: non-infected 24hr post-infection replicate 2


title: CNOT66L-KO-GCs-0h-Rep2

description:
ko2-0h
Cnot66l-FPKM.txt


title: WT-GCs-0h-Rep2

description:
WT2-0h
Cnot66l-FPKM.txt


title: MP3

status: Public on Nov 03 2021

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from ob/ob Mouse liver with PM2.5 exposure and drinking metformin

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: ob/ob Mouse with PM2.5 exposure and drinking metformin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: ob/ob male mice were kept at 2 wks at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: Mice were euthanized after two weeks PM2.5 exposure. Total RNA was isolated with TRIzol (Invitrogen) from liver organs (n=5 per group) at each time point according to manufacturer’s instructions.

treatment_protocol: Mice were exposed to atmospheric particulate matter exposure chamber for 6 hours a day for two weeks; the drug intervention group was treated with metformin in drinking water, and the dose was calculated based on body weight.

value: ob/ob

tag: gender

value: Male

tag: tissue

value: Liver


title: MP4


title: P12

description: Gene expression data from ob/ob Mouse liver with PM2.5 exposure

source_name: ob/ob Mouse with PM2.5 exposure


title: M33

description: Gene expression data from ob/ob Mouse liver with drinking metformin

source_name: ob/ob Mouse with drinking metformin


title: Area C: Ctrl-Cy5 vs NEFAs-Cy3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicates 3 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.

source_name: Granulosa cells from control

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).

value: Granulosa cells

source_name: Granulosa cells exposed to high NEFAs during IVM


title: MP8


title: P10


title: Freshwater stickleback in freshwater, individual 2

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

data_processing:
Basecalling with CASAVA 1.8.2 software
Reads were mapped to gasAcu1 genome with tophat2 software (version 2.1.0)
Genome_build: gasAcu1
Supplementary_files_format_and_content: Raw read counts in individual samples are proveded as a csv table

organism: Gasterosteus aculeatus

source_name: gills

growth_protocol: Ten freshwater three-spined sticklebacks were collected in the Mashinnoye Lake, Republic of Karelia, Russia, in June-July 2014. The same number of marine three-spined sticklebacks were collected in the Kandalaksha Gulf Coast (15 km from the railway station Poyakonda, Republic of Karelia, Russia) during the same time frame. To equal physiological state of the fish, only males in breeding dress were collected.

extract_protocol:
For RNA-seq, we used the same sample collection and treatment procedure as described for bisulfite sequencing. Four fish from each of the four experimental groups were taken for transcriptome analysis. Gills were isolated and fixed with IntactRNA® reagent (Evrogen). Total RNA was extracted from the samples with Trisol reagent according to the manufacturer’s instructions (Invitrogen).
Quality was checked with the BioAnalyser and RNA 6000 Nano Kit (Agilent). PolyA RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). An Illumina library was made from polyA RNA with NEBNext® mRNA Library Prep Reagent Set (NEB) according to the manual.

treatment_protocol: To explore immediate epigenetic response of a stickleback to changes in osmotic conditions of the environment, five marine fish were kept for 4 days in fresh water (M@F) and, vice versa, five freshwater fish were kept for 4 days in marine water (F@M). Control samples were kept in their native habitats (marine samples in marine water (M@M), freshwater samples in fresh water (F@F)) to equal captivity stress influence.

tag: original population

value: Freshwater

value: gills


title: M31


title: Freshwater stickleback in freshwater, individual 5


title: Freshwater stickleback in marine water, individual 4

value: fish kept for 4 days in marine water


title: M34


title: Freshwater stickleback in freshwater, individual 1


title: M35


title: Area D: Ctrl-Cy5 vs NEFAs-Cy3

description: Biological replicates 4 of 4


title: C20

description: Gene expression data from ob/ob Mouse liver with filter air

source_name: ob/ob Mouse with filter air


title: MP1


title: P17


title: P15


title: Freshwater stickleback in freshwater, individual 4


title: MP2


title: Area B: Ctrl-Cy3 vs NEFAs-Cy5

description: Biological replicates 2 of 4


title: Freshwater stickleback in marine water, individual 3


title: Marine stickleback in freshwater, individual 5

value: Marine

value: fish kept for 4 days in freshwater


title: Marine stickleback in freshwater, individual 3


title: Marine stickleback in freshwater, individual 1


title: Marine stickleback in marine water, individual 4


title: M28


title: Freshwater stickleback in marine water, individual 2


title: P14


title: C21


title: C24


title: C25


title: At-Cs_1_4426.A

city: Cologne

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

institute: Max Planck Institute for Plant Breeding Research

description:
Pair of genomes mapped: Cs+At
Cs_fungalTranscriptome.csv
Cs_plantTranscriptome.csv

data_processing:
Raw-RNASeq reads were trimmed with Trimmomatic and parameters TRAILING:20 AVGQUAL:20 HEADCROP:10 MINLEN:100
Trimmed reads were mapped onto pairs of reference genomes using HiSat2
Per-gene read counts were retrieved from HiSat2 alignments using FeatureCounts
RPKM values were calculated from FeatureCounts data
Differential gene expression analyses were conducted with DESeq2, independently for plant and fungal transcriptomes
Genome_build: TAIR10.1
Genome_build: https://mycocosm.jgi.doe.gov/Chame1/Chame1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Parch1/Parch1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Phapo1/Phapo1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Truan1/Truan1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Macpha1/Macpha1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Zalva1/Zalva1.home.html
Supplementary_files_format_and_content: Files '_fungalTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of fungal genes in planta vs. on medium. This file also provide RPKM values in control (mycelium grown on medium) and test (fungus in planta) conditions
Supplementary_files_format_and_content: Files '_plantTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of  A. thaliana genes mock-inoculated vs. inoculated with mycelium. This file also provide RPKM values in control (mock-treated plants) and test (plant inoculated with mycelium) conditions

organism:
Arabidopsis thaliana
Chaetomium sp.

source_name: roots,mycelium

growth_protocol: Seven A. thaliana seeds (or 16 drops of 10µL crushed mycelium solution) were grown in a sterile plate gnotobiotic system filled with an agar medium (described in Gruber et al. 201 - 100µM inorganic Phosphate). Culture was carried out in growth cabinets for 28 days at 21 °C for 10 hours with light (intensity 4), and at 19 °C and 14 hours in the dark.

extract_protocol:
Total RNA was extracted from plant roots or mycelium grown on medium using Qiagen RNEasy Plant Mini Kit
An RNAseq library was prepared with the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and then sequenced in single read mode on a HiSeq 3000 system

treatment_protocol: Prior to growth, plant seeds were inoculated with fungal mycelium or mock solution. For the control conditions, fungal inoculum were grown on the same agar-based culture medium.

tag: developmental stage

value: 28 days post seed inoculation

tag: culture medium

value: 100µM Pi MS-Agar

tag: inoculation

value: Mycelium-inoculated seeds


title: Freshwater stickleback in marine water, individual 1

tag: treatment


title: C19


title: Marine stickleback in freshwater, individual 4


title: Marine stickleback in freshwater, individual 2


title: Normoxia 2 EV

city: Boston

first: Guoping

last: Li

state: MA

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

description: Long RNAs

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2
DESeq2 v1.30.1 was used to generate normalized read counts for each of the transcripts across each sample.
Genome_build: Homo Sapiens GRCh38/hg38
Supplementary_files_format_and_content: Processed data files are csv files containing DESeq2 normalized read counts.

source_name: HEK293 cells

growth_protocol: HEK293 cells were grown in DMEM(Gibco,New York, USA) supplemented with 10% FBS(Gibco,New York, USA) on tissue culture plates cultured to about 80% confluency

extract_protocol:
Cellular RNA was extracted using theTRIzol™ (Thermo Fisher, Waltham, USA) after treatment and extracellular RNA was isolated using ExoRNeasy midi kit (Qiagen, Hilden, Germany) by following the manufacturer's protocol
Long RNA libraries were contructed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio USA, Cat # - 634413) by following the manufacturer's instructions

treatment_protocol: HEK293 cells were transfected with 4EC1 plasmid using Lipofectamine 3000 (ThermoFisher, Waltham, USA) for 48 hours and transferred to Hypoxia chamber for 24 hrs for RNA collection.

tag: cell line

tag: sample type

value: Extracellular Vesicles

value: Normoxia

value: Human Embryonic Kidney Cell line


title: Normoxia 1 EV

description: Long RNAs

tag: cell type


title: Hypoxia 1 EV

description: Long RNAs

value: Hypoxia


title: Hypoxia 3 EV

description: Long RNAs


title: Normoxia 3EV

description: Long RNAs


title: Hypoxia 2 EV

description: Long RNAs


title: Marine stickleback in marine water, individual 5


title: At-Cs_2_4426.I


title: At-Cs_3_4426.Q


title: Marine stickleback in marine water, individual 3


title: Marine stickleback in marine water, individual 2


title: Normoxia 3 Cell

description: Long RNAs

value: Cells


title: Hypoxia 1 Cell

description: Long RNAs


title: Normoxia 2 Cell

description: Long RNAs


title: Hypoxia 2 Cell

description: Long RNAs


title: Hypoxia 3 Cell

description: Long RNAs


title: At_1_4426.H

description: Pair of genomes mapped: all, in each respective analysis

organism: Arabidopsis thaliana

source_name: roots

value: Mock-inoculated seeds


title: Normoxia 1 Cell

description: Long RNAs


title: mCC_rep2

first: Juliet

last: Girard

address: 610 Charles E Young Dr E

description:
mCC biological replicate 2
lzHmlGhi2_S2

data_processing:
Illumina software for basecalling
Sequencing data was analyzed using Partek Flow, a web-based software platform. Sequences were aligned to the Drosophila melanogaster reference genome r6.22 (Flybase) using STAR aligner with default parameters. Read counts were normalized by counts per million (CPM). Differential genes expression analysis was performed using ANOVA with a fold change cutoff of 2 and FDR<0.05 (see Supplementary file 3 Tables 1 and 2).
Genome_build: r6.22
Supplementary_files_format_and_content: normalized counts

organism: Drosophila melanogaster

source_name: lz-GAL4, UAS-mGFP; HmlΔ-DsRed.nls lz>mGFP_mCC

growth_protocol: 20 virgin females and 10 males were mated in each vial at 25 degrees C. Eggs were laid in the vials for a 6 hour and then adults were transferred to a new vial. Vials were placed back at 25 degrees for 90-96 hours until larvae reached early thrid instar. Larvae were thoroughly washed in DEPC-treated water prior to dissection.

extract_protocol:
Lymph glands were dissected out of early 3rd instar larvae, their anterior lobes were removed, and the primary lobes were transferred to a watchglass filled with dissecting buffer on ice. After dissection, the lymph glands were dissociated as previously described with some modifications (Harzer et al. 2013; Khan et al. 2016). After being washed with MDS buffer twice, these tissues were transferred to 1.5 mL DNA LoBind tubes (Eppendorf) and incubated with 200 µL of dissociation solution containing 1 mg/mL of papain (Sigma, P4762) and 1 mg/mL of collagenase (Sigma, C2674) in Schneider’s medium. They were dissociated for 15 minutes in a shaking incubator at 25°C, 300 rpm. Next, 500 µL of cold Schneider’s medium was added and the suspension was gently pipetted up and down using a low-binding 1000 µL tip (Olympus Plastics) 20 times for mechanical dissociation. After centrifugation at 3000 rpm for 5 minutes, cells were resuspended and washed with 500 µL of 1X PBS (Corning, MT21040CV) containing 0.04% of UltraPure BSA (Invitrogen, AM2616) and then passed through a 35 micrometer cell strainer (Falcon 352235). , Dissociated, live lymph gland cells were sorted using the BD FACSARIA-H. Gates and compensation were based on single color controls. Cells were sorted into 300 µL of DNA/RNA Shield (Zymo) in DNA LoBind tubes and frozen at -80°C prior to RNA extraction. Total RNA was extracted from each sample using the Quick-RNA Microprep Kit (Zymo). RNA quality control was performed using the Agilent 4150 TapeStation system.
3' mRNA capture; cDNA libraries were prepared using KAPA Stranded mRNA-seq kit (KAPA Biosystems)

treatment_protocol: Experiment was done on untreated wild-type larvae.

tag: line

value: lz-GAL4, UAS-mGFP; Hml{delta}-DsRed.nls lz>mGFP

tag: age

value: 93-117 hours after egg lay (25 degrees C)

tag: tissue/cell type

value: lymph gland blood cells

tag: cell population

value: mCC


title: mCC_rep1

description:
mCC biological replicate 1
lzHmlGhi1_S1


title: iCC_rep4

description:
iCC biological replicate 4
lzHmlGlo4_S8

source_name: lz-GAL4, UAS-mGFP; HmlΔ-DsRed.nls lz>mGFP_iCC

value: iCC


title: mCC_rep3

description:
mCC biological replicate 3
lzHmlGhi3_S3


title: iCC_rep3

description:
iCC biological replicate 3
lzHmlGlo3_S7


title: mCC_rep4

description:
mCC biological replicate 4
lzHmlGhi4_S4


title: iCC_rep1

description:
iCC biological replicate 1
lzHmlGlo1_S5


title: PL_rep3

description:
PL biological replicate 3
lzHmlR3_S11

source_name: lz-GAL4, UAS-mGFP; HmlΔ-DsRed.nls lz>mGFP_PL

value: PL


title: iCC_rep2

description:
iCC biological replicate 2
lzHmlGlo2_S6


title: PL_rep4

description:
PL biological replicate 4
lzHmlR4_S12


title: dissociated lymph gland blood cells_rep1

description: biological replicate 1

data_processing:
Illumina software for basecalling
Each paired read was trimmed for adapter sequences according to 10x Genomics Chromium™ Single Cell 3' v3 specifications using Partek Flow software. Trimmed reads were aligned to the Drosophila melanogaster reference genome r6.22 (Flybase) using STAR aligner with default parameters.
After alignment, UMIs were deduplicated and barcodes were then filtered and quantified to generate a single cell count matrix. Genes with fewer than 30 total reads across three samples were excluded. Low-quality cells and potential doublets were filtered out by selecting out cells with high read counts (>85,000), an especially low (<1500) or high (>4500) number of genes detected, or a high percentage of mitochondrial reads (>6%).
Read counts were normalized with the following order: (1) CPM; (2) Add 1; (3) Log2 transformation. Genes that were not expressed in any cells were excluded and a total of 9,458 genes were detected. Data was then corrected for batch effects between samples. All rRNA and three sex-related lncRNA (lncRNA:roX1, lncRNA:roX2, and lncRNA:CR40469) were filtered out. The data was imputed using the MAGIC algorithm (van Dijk et al. 2018) with the number of nearest neighbors =50.
Genome_build: r6.22
Supplementary_files_format_and_content: Matrix table with raw gene counts (UMI) for every gene for each sample

source_name: domeMESO-GFP.nls HmlΔ-DsRed.nls_lymph gland blood cells

growth_protocol: 20 virgin females and 10 males were mated in each vial at 25 degrees C. Eggs were laid in the vials for a 3 hour and then adults were transferred to a new vial. Vials were placed back at 25 degrees for 90-93 hours until larvae reached early thrid instar. Larvae were thoroughly washed in DEPC-treated water prior to dissection.

extract_protocol:
Lymph glands were dissected out of early 3rd instar larvae,  their anterior lobes were removed, and the primary lobes were transferred to a watchglass filled with dissecting buffer on ice. After dissection, the lymph glands were dissociated as previously described with some modifications (Harzer et al. 2013; Khan et al. 2016). After being washed with MDS buffer twice, these tissues were transferred to 1.5 mL DNA LoBind tubes (Eppendorf) and incubated with 200 µL of dissociation solution containing 1 mg/mL of papain (Sigma, P4762) and 1 mg/mL of collagenase (Sigma, C2674) in Schneider’s medium. They were dissociated for 15 minutes in a shaking incubator at 25°C, 300 rpm. Next, 500 µL of cold Schneider’s medium was added and the suspension was gently pipetted up and down using a low-binding 1000 µL tip (Olympus Plastics) 20 times for mechanical dissociation. After centrifugation at 3000 rpm for 5 minutes, cells were resuspended and washed with 500 µL of 1X PBS (Corning, MT21040CV) containing 0.04% of UltraPure BSA (Invitrogen, AM2616) and then passed through a 35 micrometer cell strainer (Falcon 352235). For preparation of the single cell RNA-Seq sample, the cell suspension was concentrated by centrifuging and resuspending in a lower volume of PBS containing 0.04% BSA (30 µL). Cell concentration and viability were assessed using the Countess II automated cell counter (Applied Biosystems). The samples with final concentration of more than 650 cells/µL and viability of more than 85% were used for single cell RNA-Seq.
3' mRNA capture: Libraries were prepared using the instructions for 10X Genomics Single Cell 3' GEX version 3. 5,000 cells were targeted for each sample.

value: domeMESO-GFP.nls Hml{delta}-DsRed.nls

value: 90-93 hours after egg lay (25 degrees C)

value: lymph gland


title: PL_rep2

description:
PL biological replicate 2
lzHmlR2_S10


title: At_3_4426.X

value: 28 days post seed inoculation

tag: strain

value: 100µM Pi MS-Agar


title: PL_rep1

description:
PL biological replicate 1
lzHmlR1_S9


title: dissociated lymph gland blood cells_rep3

description: biological replicate 3


title: dissociated lymph gland blood cells_rep2

description: biological replicate 2


title: At_2_4426.P


title: High fat diet_P. gingivalis_rep3

city: Niigata

first: Kazuhisa

last: Yamazaki

address: 2-110-1 Gakkocho-dori, Chu-o-ku

institute: Niigata University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Liver High fat diet_P. gingivalis_rep3

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA from liver samples was extracted using a RNeasy Mini kit, treated with DNase I (Qiagen, Germantown, MD).

value: 10 weeks old

value: Male


title: High fat diet_P. gingivalis_rep4

source_name: Liver High fat diet_P. gingivalis_rep4


title: HealthyDonor_Tcell_21hrStim_rep4

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped using STAR_2.6.1d aligner.
FeatureCounts v2.0.0 was used to generate the raw counts.
Genome_build: human genome GRCh37.p13 (Genome Reference Consortium 622 Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009
Supplementary_files_format_and_content: raw read count .txt file

source_name: Primary T cells

growth_protocol: Primary T cells that were expanded by activation with antibodies to CD3 and CD28 for 3 days then cultured and maintained in cRPMI plus IL-2 (100 U/mL) supplementation

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen)
Reverse transcription and cDNA pre-amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech/Takara). Libraries were prepared using the Nextera XT DNA Sample Preparation Kit and the Nextera Index Kit (Illumina).
mRNA libraries were pooled and paired-end 150-bp sequencing was performed on the Illumina HiSeqX platform.

treatment_protocol: Expanded primary T cells from healthy controls and patients were stimulated with 20 ng/mL PMA and 450 ug/mL ionomycin in cRPMI. Cells were harvested at 3 hours and 6 hours post-stimulation and immediately frozen at -80°C. After the 6-hour time point, the remaining cells were washed twice to remove residual PMA/ionomycin. Culturing was then continued, and cells were harvested at 12 hours and 21 hours post-stimulation and immediately frozen.

tag: disease state

value: Healthy donor 4

value: Primary T cells

tag: pma stimulation

value: 21 hours


title: High fat diet_no bacteria_rep4

source_name: Liver High fat diet_no bacteria_rep4

tag: gender


title: Patient_Tcell_21hrStim_rep2

value: Patient 2


title: Patient_Tcell_21hrStim_rep3

value: Patient 3


title: Patient_Tcell_21hrStim_rep1

value: Patient 1


title: High fat diet_P. intermedia_rep2

source_name: Liver High fat diet_P. intermedia_rep2


title: HealthyDonor_Tcell_12hrStim_rep4

value: 12 hours


title: Patient_Tcell_21hrStim_rep4

value: Patient 4


title: High fat diet_P. intermedia_rep4

source_name: Liver High fat diet_P. intermedia_rep4


title: High fat diet_P. gingivalis_rep5

source_name: Liver High fat diet_P. gingivalis_rep5


title: HealthyDonor_Tcell_21hrStim_rep1

value: Healthy donor 1


title: High fat diet_no bacteria_rep2

source_name: Liver High fat diet_no bacteria_rep2


title: High fat diet_P. gingivalis_rep2

source_name: Liver High fat diet_P. gingivalis_rep2


title: High fat diet_P. gingivalis_rep1

source_name: Liver High fat diet_P. gingivalis_rep1


title: Patient_Tcell_12hrStim_rep1


title: Regular chow_no bacteria_rep2

source_name: Liver Regular chow_no bacteria_rep2


title: HealthyDonor_Tcell_21hrStim_rep3

value: Healthy donor 3


title: High fat diet_P. intermedia_rep3

source_name: Liver High fat diet_P. intermedia_rep3


title: High fat diet_P. intermedia_rep1

source_name: Liver High fat diet_P. intermedia_rep1


title: High fat diet_no bacteria_rep3

source_name: Liver High fat diet_no bacteria_rep3


title: High fat diet_no bacteria_rep1

source_name: Liver High fat diet_no bacteria_rep1


title: Regular chow_no bacteria_rep3

source_name: Liver Regular chow_no bacteria_rep3


title: Regular chow_no bacteria_rep1

source_name: Liver Regular chow_no bacteria_rep1


title: Patient_Tcell_12hrStim_rep4


title: HealthyDonor_Tcell_21hrStim_rep2

value: Healthy donor 2


title: Area A: Ctrl-Cy3 vs NEFAs-Cy5

description: Biological replicates 1 of 4

source_name: Granulosa cells exposed to high NEFAs during IVM

tag: tissue

value: Granulosa cells

source_name: Granulosa cells from control


title: Patient_Tcell_6hrStim_rep3

source_name: Primary T cells

value: 6 hours


title: HealthyDonor_Tcell_12hrStim_rep2


title: HealthyDonor_Tcell_12hrStim_rep1


title: HealthyDonor_Tcell_12hrStim_rep3


title: HealthyDonor_Tcell_3hrStim_rep4

value: 3 hours


title: HealthyDonor_Tcell_6hrStim_rep3


title: Patient_Tcell_6hrStim_rep2


title: HealthyDonor_Tcell_3hrStim_rep2


title: HealthyDonor_Tcell_3hrStim_rep3


title: HealthyDonor_Tcell_3hrStim_rep1


title: Patient_Tcell_12hrStim_rep3


title: HealthyDonor_Tcell_6hrStim_rep1


title: Patient_Tcell_3hrStim_rep1


title: Patient_Tcell_unstim_rep4

value: Unstimulated


title: HealthyDonor_Tcell_6hrStim_rep4


title: Patient_Tcell_12hrStim_rep2


title: HealthyDonor_Tcell_unstim_rep4


title: Patient_Tcell_3hrStim_rep4


title: Patient_Tcell_unstim_rep1


title: Patient_Tcell_unstim_rep3


title: HealthyDonor_Tcell_unstim_rep2


title: Patient_Tcell_unstim_rep2


title: Patient_Tcell_3hrStim_rep3


title: SMAD-2KQ_1

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

description: MDA-MB-231 cells transducted with SMAD3 K20/117Q  (2KQ) mutant

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: breast cancer cells

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

treatment_protocol: serum starvation for 24 hours

value: breast cancer cells

tag: smad3 genotype


title: SMAD-WT_3

description: MDA-MB-231 cells transducted with SMAD3 wild type (WT)

value: WT


title: SMAD-WT_1


title: BRx142_day112_ovary_input

first: Gabriel

middle: Alejandro

last: Golczer Gatti

address: 55 Fruit St

department: MGH Cancer Center

institute: Harvard Medical School

description: Ovary metastasis.

data_processing:
Reads trimmed for adapter pollutions and low quality using Trimgalore (v0.4.3).
Aligned to the human genome (hg19 assembly) using BWA (v0.7.15).
PCR duplicates were removed using sambamba13 and potential mouse reads were further removed using a custom Java script with the criteria of (1) more than 2 mismatches; (2) human genome alignment score ratio less than 0.67 and mapping quality less than 30.
BigWig files for visualization were created using deeptools with CPM function.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig or bedGraph

source_name: Breast cancer circulating tumor cells

growth_protocol: BRx82 and BRx142 CTC cell lines were established from primary CTCs, viably isolated from blood specimen of patients with metastatic hormone-receptor positive breast cancer, following microfluidic enrichment using the CTC-iChip. CTC cultures were maintained as anchorage independent clusters under hypoxia, in tumor sphere medium.

extract_protocol:
Cell lines cultured in vitro, or tumor xenograft-derived and FACS-sorted single cell suspension were washed with ice-cold PBS, and crosslinked with 1% formaldehyde (Sigma) for 10 minutes (for histone modifications and RNA pol II) or 15 minutes (for transcription factors) at room temperature and quenched with glycine. ChIP was performed using EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore) following the recommended protocol. Briefly, nuclei were isolated with cold nuclei isolation buffer and sheared with Covaris S2 instrument with an optimized program (Duty Cycle: 5%; Intensity: 4; Cycles/Burst: 200; treatment time: 360s) to yield an average fragment size of approximately 300 bp. Chromatin was incubated with Protein A/G Dynabeads (ThermoFisher) together with 5 μg ChIP-grade antibody overnight at 4°C with rotation. The beads were then collected and washed extensively with high- and low-salt buffers. DNA was de-crosslinked and purified through ethanol precipitation. Before immunoprecipitation with Dynabeads and antibody, 10% of chromatin was saved as input control.
Immunoprecipitated DNA from ChIP experiment, together with input DNA were all subjected to end repair, dA-tailing and ligation of Illumina sequencing adapters according to the instructions from KAPA Hyper Prep Kits (Kapa Biosystems). After ligation, the final PCR amplification was performed with KAPA Hifi Hotstart Readymix (2x, Kapa Biosystems), Illumina universal primer and Illumina index primer. Barcoded libraries were pooled and sequenced on Illumina HiSeq X platform with 150 bp paired-end reads.

treatment_protocol: All the animal experiments were performed according to the animal protocol reviewed and approved by MGH Subcommittee on Research Animal Care (IACUC). 6-8 week-old female immunodeficient NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice (Jackson Laboratory) were used for mammary fat pad injections and intracardiac injections. Mice were anaesthetized with isoflurane prior to tumor cell injections. For intracardiac injections, the left side of the mouse chest was opened to expose the rib cage and 500,000 BRx142, BRx82 or M231 cells suspended in 100 μl PBS were gently injected into the left ventricle of the heart. The skin was closed and sutured and a 90-day estrogen release pellet (Innovative Research of America) was placed subcutaneously behind the neck of each mouse. Mice were routinely monitored under the IVIS Lumina II imaging system (PerkinElmer) after intraperitoneal injections of D-luciferin substrate (Sigma), and tumor derived bioluminescent signal was measured. Tumors tissue was dissected immediately after sacrificing the mice. Tissues were washed with PBS to remove excessive blood and stromal tissue and were minced with a scalpel. Tissue digestion was performed with collagenase/hyaluronidase cocktail (Stemcell) in DMEM medium at 37°C on a rocker for 2-4 hours. Samples were vortexed every 30 minutes to enhance tissue dissociation/digestion. After digestion, the tissue solution was passed through a 70 μm filter to obtain a single cell suspension, which was then stained with PE-anti-human CD298 antibody (Biolegend) together with DAPI for 30 minutes at 4°C in the dark. Unbound antibody and DAPI were removed by washing with DMEM medium. In addition to the anti-human antibody CD298, CTCs were also tagged with endogenous GFP, and human CTC-derived cells recovered from mouse tissues were identified by double staining for both PE and GFP, as well as being low for DAPI staining (indicating cell viability). Cells were sorted using a FACS Fusion Cell Sorter (BD) into an 1.5 ml Eppendorf tube for bulk ChIP-seq experiments.

tag: patient id

value: xenograft ovary metastasis

tag: timepoint

value: day 112

value: breast cancer circulating tumor cells

value: female

tag: chip antibody


title: SMAD-WT_2


title: PolII_BRx142_preinjection_181227_input

description: Culture under serum-free medium.

tag: culture condition

value: Serum-free


title: NR4A1_BRx82_day220_ovary_input

description: Ovary metastasis.

value: day 220


title: PolII_BRx82_preinjection_181227_input

description: Culture under serum-free medium.


title: NR4A1_BRx82_day240_breast_input

description: Breast metastasis.

value: xenograft breast metastasis

value: day 240


title: SMAD-2KQ_3

tag: cell line


title: FOS_BRx82_day100_ovary_input

description: Ovary metastasis.

value: day 100


title: NR4A1_BRx142_day260_ovary_input

description: Ovary metastasis.

value: day 260


title: NR4A1_BRx82_day220_brain_input

description: Brain metastasis.

value: xenograft brain metastasis


title: BRx142_day112_ovary_polII

description: Ovary metastasis.

value: total RNA polII (Diagenode; Cat#C15200004)


title: BRx82_day220_brain_polII

description: Brain metastasis.


title: NR4A1_BRx142_day270_ovary_input

description: Ovary metastasis.

value: day 270


title: SMAD-2KQ_2


title: NR4A1_BRx142_day260_ovary

description: Ovary metastasis.

value: NR4A1 (Novus Biologicals; Cat#NB100-56745)


title: PolII_BRx142_preinjection_181227

description: Culture under serum-free medium.


title: NR4A1_BRx82_day240_breast

description: Breast metastasis.

value: NR4A1 (Abcam; Cat#ab13851)


title: Input_PolIIS2S5_MCF10a_serumWD24h

description: Serum starve for 24h

source_name: MCF10A breast epithelial cells

value: breast epithelial cell line

value: Serum starvation (24h)


title: NR4A1_BRx142_day270_ovary

description: Ovary metastasis.

value: xenograft ovary metastasis


title: NR4A1_BRx82_day220_ovary

description: Ovary metastasis.


title: FOS_BRx82_day100_ovary

description: Ovary metastasis.

value: FOS (Santa Cruz Biotechnology; Cat#sc-271243X)


title: Input_PolIIS2S5_MCF10a_serumback6h

description: Serum replenish for 6h

value: Serum refeeding (6h)


title: PolII_BRx82_preinjection_181227

description: Culture under serum-free medium.

value: breast cancer circulating tumor cells

value: female


title: NR4A1_BRx82_day220_brain

description: Brain metastasis.

value: day 220


title: Input_PolIIS2S5_MCF10a_serumback1h

description: Serum replenish for 1h

value: Serum refeeding (1h)


title: PolIIS5_MCF10a_serumback_30min

description: Serum replenish for 30min

value: Serum refeeding (30min)

value: phospho RNA polymerase II S5 (Abcam; Cat#ab5131)


title: PolIIS5_MCF10a_serumback_1h

description: Serum replenish for 1h


title: PolIIS5_MCF10a_in_serum

description: Culture under serum medium.

value: Serum


title: Patient_Tcell_6hrStim_rep1

value: Patient 1

value: Primary T cells

value: 6 hours


title: PolIIS2_MCF10a_serumWD24h

description: Serum starve for 24h

value: phospho RNA polymerase II S2 (Abcam; Cat#ab5095)


title: PolIIS2_MCF10a_serumback3h

description: Serum replenish for 3h

value: Serum refeeding (3h)


title: PolIIS2_MCF10a_serumback30min

description: Serum replenish for 30min

value: breast epithelial cell line


title: HealthyDonor_Tcell_6hrStim_rep2

value: Healthy donor 2


title: Input_NR4A1_RNApolII_MCF10a_serumWD_back6h

description: Serum replenish for 6h


title: Input_NR4A1_RNApolII_MCF10a_serumWD_back3h

description: Serum replenish for 3h


title: Input_PolIIS2S5_MCF10a_serumback3h

description: Serum replenish for 3h


title: PolIIS2_MCF10a_in_serum

description: Culture under serum medium.


title: PolIIS2_MCF10a_serumback1h

description: Serum replenish for 1h


title: Input_NR4A1_RNApolII_MCF10a_in_serum

description: Culture under serum medium.


title: Input_NR4A1_RNApolII_MCF10a_serumWD_24h

description: Serum starve for 24h

value: Serum starvation (24h)


title: Input_PolIIS2S5_MCF10a_serumback30min

description: Serum replenish for 30min


title: RNApolII_MCF10a_serumWD_back6h

description: Serum replenish for 6h

value: total RNA polII (Diagenode; Cat#C15200004)


title: RNApolII_MCF10a_serumWD_back30m

description: Serum replenish for 30min


title: RNApolII_MCF10a_serumWD_back3h

description: Serum replenish for 3h


title: RNApolII_MCF10a_serumWD_back1h

description: Serum replenish for 1h


title: Input_PolIIS2S5_MCF10a_in_serum

description: Culture under serum medium.


title: PolIIS5_MCF10a_serumWD_24h

description: Serum starve for 24h


title: PolIIS5_MCF10a_serumback_6h

description: Serum replenish for 6h

value: Serum refeeding (6h)


title: PolIIS5_MCF10a_serumback_3h

description: Serum replenish for 3h


title: RNApolII_MCF10a_serumWD_24h

description: Serum starve for 24h


title: RNApolII_MCF10a_in_serum

description: Culture under serum medium.


title: NR4A1_MCF10a_serumWD_back6h

description: Serum replenish for 6h

value: NR4A1 (Novus Biologicals; Cat#NB100-56745)


title: Input_NR4A1_RNApolII_MCF10a_serumWD_back1h

description: Serum replenish for 1h

value: female


title: NR4A1_MCF10a_serumWD_back3h

description: Serum replenish for 3h


title: Input_NR4A1_RNApolII_MCF10a_serumWD_back30min

description: Serum replenish for 30min


title: NR4A1_MCF10a_serumWD_back1h

description: Serum replenish for 1h


title: NR4A1_MCF10a_serumWD_back30m

description: Serum replenish for 30min


title: Input_H3K27ac_MCF10a_serumWD_back6h

description: Serum replenish for 6h


title: Input_H3K27ac_MCF10a_serumWD_back30min

description: Serum replenish for 30min


title: NR4A1_MCF10a_serumWD_24h

description: Serum starve for 24h


title: Input_H3K27ac_MCF10a_serumWD_back3h

description: Serum replenish for 3h


title: Input_H3K27ac_MCF10a_serumWD_24h

description: Serum starve for 24h


title: Input_H3K27ac_MCF10a_in_serum

description: Culture under serum medium.


title: H3K27ac_MCF10a_serumWD_back6h

description: Serum replenish for 6h

value: H3K27ac (Active motif; Cat#39133)


title: H3K27ac_MCF10a_in_serum

description: Culture under serum medium.


title: H3K27ac_MCF10a_serumWD_back1h

description: Serum replenish for 1h

value: Serum refeeding (1h)


title: H3K27ac_MCF10a_serumWD_back3h

description: Serum replenish for 3h


title: NR4A1_MCF10a_in_serum

description: Culture under serum medium.


title: H3K27ac_MCF10a_serumWD_back30min

description: Serum replenish for 30min

value: Serum refeeding (30min)