title: RNA-seq in mouse mature T-cells infected with a plasmid containing an hairpin targeting L3MBTL3, rep 3

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

description:
L3MBTL3_KD_Rep_3
normalized_counts_KD.csv

data_processing:
Quality control of FASTQ files was done using the seeFastq command within systemPipeR.
The fastq files were aligned using TopHat v.2.1.1.
Count tables were generated from BAM files using the summarizeOverlaps function.
Normalization of read counts and the detection of differential expression was done using DESeq2 v.1.24.0 with default parameters.
Criteria for significant deregulated genes are FDR < 0.05 and log2FC > 1 or < -1.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: normalized_counts_*.csv: Count tables of DESeq2 normalized read counts per gene in comma-separated format.

source_name: mouse mature T-cells

growth_protocol: Mouse mature T-cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential amino acids and penicillin/streptomycin.

extract_protocol:
RNeasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and RNase-free DNase (Qiagen #79254).
Library-prep kit: Illumina TruSeq® Stranded Total RNA LT - Ribo-Zero Gold (RS-122-2301/2).

value: hybridoma called E2-10HA

tag: selection

value: puromycin

tag: plasmid

value: pLKO.1-shRNA-L3MBTL3 shRNA_1 Puro


title: Balb-C male mouse liver_DMSO-0 [EPACorton_P01_A04]

status: Public on Dec 01 2022

type: SRA

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

country: USA

institute: US-EPA

library_source: transcriptomic

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user. The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Data normalization was not done
genome build: GRCm38.p5; GCF_000001635.25
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Mus musculus

source_name: Balb-C male mouse liver_DMSO-0

extract_protocol: The liver tissues (~50-100 mg) were preserved in RNAlater (Qiagen, Valencia, CA) and stored at -80°C until RNA extraction. Total RNA was extracted from tissue samples 2-6 months later with Trizol by polytron homogenization. The resultant RNA was further purified using the RNeasy Mini Kit (Qiagen), and RNA integrity was checked with Bioanalyzer RNAnanochip. Samples were submitted to BioSpyder for analysis using the mouse whole genome platform.

treatment_protocol: Balb-C male mice at 10-12 weeks of age were dosed by gavage for 7 consecutive days using 20-gauge stainless steel feeding needles. Doses of 0, 0.03, 0.3, 3.0, and 6.0 mg/kg-day were administered once daily in the afternoon. Control animals were administered an equal volume of deionized water. Four biological replicates consisting of individual animals were included in each dose group. RNA was isolated and gene expression was determined using the mouse TempO-Seq targeted RNA-Seq platform (BioSpyder, Inc; Carlsbad CA).

tag: strain

value: Balb-C

tag: age

value: 10-12 weeks

tag: Sex

value: male

tag: treatment

value: Control

tag: dose

value: 0 mg/kg

tag: tissue

value: liver


title: Tumor 1332-1

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

data_processing:
Alignment-free quantification with salmon (1.5.2)
Normalization with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv matrix of log2(TPM) (genes x samples)

source_name: C3-TAg Tumor 1132

extract_protocol:
Organoid/ECM gels were collected in 15 mL conical tubes, snap frozen and stored in -80 C freezer. For RNA extraction, the gels were thawed on ice and disintegrated in 500 uL Trizol by repeatedly passing the mixture through a 23G needle. RNA was then further purified using the RNeasy Kit (Qiagen, 74104) following the manufacturer's protocol.
TruSeq RNA library prep using manufacturer protocols

treatment_protocol: 1000 C3-TAg tumor organoids or 60,000-80,000 noninvasive cells were embedded in a 500 µl ECM mixture (2.4 mg/ml Collagen I and 2 mg/ml Matrigel or Cultrex) and plated on top of 500 uL base layer of ECM in 6 cm dishes and overlaid with growth media as listed above.

tag: majority phenotype

value: Invasive

tag: growth protocol

value: Digested organoids were embedded in a mixture of collagen I and matrigel and overlaid with DMEM/F-12 media with 1X ITS, 10 ng/ml FGFb, 1X non-essential amino acids. Organoids were grown for 2 days.

value: Tumor


title: ATAC_CR_128

city: Lausanne

first: kevin

last: perez

address: rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

library_source: genomic

data_processing:
Adapter trimming: Trim Galore! version 0.6.6 in paired end mode
Alignment: Bowtie2 version 2.2.5, bowtie2 --very-sensitive -k 10 -X 1000 --dovetail
Filtering: remove multi-mapping, improper pairs Samtools version 1.9, samtools view -f 0x2 -F 0x100
Filtering: remove duplicates, Picard tools version 2.25.6, MarkDuplicates --REMOVE_DUPLICATES true
Peak calling: Genrich version 0.6.1 in atac mode, ignoring ENCODE blacklist, outputting tn5 cut site BED files, q < 0.05
Count matrix: Bedtools version 2.30.0, count the number of tn5 cut sites intersecting (bedtools intersect -c) the union peakset (bedtools merge of individual peaksets)
Alignment: STAR aligner (v2.7.9a) with '--sjdbOverhang 100'.
Counting: featureCounts, Subread package (v2.0.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw matrix table representing the number of tn5 cut sites overlapping each peak for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from whole blood using histopaque.
Omni-ATAC protocol (Corces, 2017) was used to construct the ATAC-seq libraries.

tag: cell type

value: Peripheral blood mononuclear cells

tag: gender

value: F


title: RNA-seq in mouse mature T-cells infected with a plasmid containing a scramble hairpin as control, rep 3

city: Philadelphia

institute: University of Pennsylvania

description:
Control_Rep_3
normalized_counts_KD.csv

tag: cell line

value: pLKO.1-shRNA-scramble Puro


title: Balb-C male mouse liver_DMSO-0 [EPACorton_P01_A03]


title: ATAC_CR_127


title: ATAC_CR_126

value: M


title: RNA-seq in mouse mature T-cells infected with a plasmid containing an hairpin targeting L3MBTL3, rep 2

description:
L3MBTL3_KD_Rep_2
normalized_counts_KD.csv


title: Tumor 1153-1

source_name: C3-TAg Tumor 1153


title: CT26_RECTAS_rep3

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

data_processing:
Basecalling was performed with RTAVersion v3.3.3
The seuqence data was mapped to the genome sequence with HISAT2 ver. 2.2.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

molecule: polyA RNA

source_name: CT26 colorectal adenocarcinoma cells

growth_protocol: Cells were cultured in the following frowth media; B16, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; CT26, RPMI-1640 + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; EG7, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; LLC, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; MC38, RPMI-1640 + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; Pan02, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; WEHI3, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin + 4 µL/L 2-mercaptoethanol. All cell lines were maintained in an incubator at 37oC with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s protocol.
TruSeq stranded mRNA Library kit was used.

treatment_protocol: Cells were treated with 0.1% DMSO or 10 μM RECTAS in 0.1% DMSO for 6 h.

tag: condition

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

tag: derived tissue

value: colorectal adenocarcinoma

value: CT26 colorectal adenocarcinoma cells


title: RNA-seq in mouse mature T-cells infected with a plasmid containing a scramble hairpin as control, rep 2

description:
Control_Rep_2
normalized_counts_KD.csv

value: hybridoma called E2-10HA

value: puromycin


title: RNA-seq in mouse mature T-cells infected with a plasmid containing an hairpin targeting L3MBTL3, rep 1

description:
L3MBTL3_KD_Rep_1
normalized_counts_KD.csv

value: pLKO.1-shRNA-L3MBTL3 shRNA_1 Puro


title: CT26_RECTAS_rep1


title: SC76

city: Jerusalem

first: Tal

last: Michaeli

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

description:
Ser.inj replicate 4
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

data_processing:
Quality control applied with trim_galore V0.6.0 deploying cutadapt V1.18 and fastqc v0.11.7.
Paired-end bisulfite treated FASTQ files were aligned by Bismark V0.13.1 deploying Bowtie2 aligner to mm10 assembly.
Methylation calling performed with bismark_methylation_extractor followed by Bismark cov2cytp and a custom AWK script transforming files to methylKit input format.
Differential methylated regions were obtain with methylKit R-package V1.10.0 and earlier consistent versions.
Genome_build: mm10
Supplementary_files_format_and_content: Tables with methylation levels for each sample (columns) in each relevant tile (rows).

source_name: Hindlimb muscles

extract_protocol:
Hindlimb muscles were dissected from mice following euthanization and kept in wash solution (Ham’s F10 media supplemented with 10% horse serum). The muscles were then finely minced with a surgical scalpel and digested in 2 mg/ml Collagenase II (Worthington, 340 U/mg) for 90 min with agitation. Dissociated fibers were washed and further digested with shaking in 100 U/ml Collagenase II and 2 U/ml Dispase (Invitrogen) for 30 min in a volume of 10 ml, passed 10 times through a 20-G needle to release the associated satellite cells and then washed two more times and filtered through a 45-mm cell strainer. Mononuclear cells from each sample were resuspended in 500 ml wash solution, stained with VCAM1-biotin, CD31-APC, CD45- APC and Sca1-Pacific-Blue antibodies (Biolegend) using a 1:100 dilution at 4°C with gentle agitation for 30 min, washed and resuspended in 500 ml and then stained with Streptavidin-PE-Cy7 (1:100) at 4°C with gentle agitation for 15 min. The resulting preparation contains satellite cells (VCAM1+/CD31-/CD45-/Sca-), which can be separated from remaining cells and debris using flow cytometry. DNA was isolated from purified satellite cells, incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
The methylation profile was checked using the RRBS assay [Boyle, 2012]. Briefly, the DNA was digested with the MspI enzyme to yield CpG enriched fragments. Adapter sequences were ligated at both ends, and DNA fragments were then treated with sodium-bisulfite, allowing for easy distinction between methylated and unmethylated bases. The DNA was then amplified by PCR to produce the final libraries.

treatment_protocol: Muscle injury was carried out on hind-limb muscles (tibialis anterior, gastrocnemius, and quadriceps) from 8.5-9 month old mice by piercing multiple times with a 23-gauge needle.

value: Hindlimb muscles

value: Muscle stem cell

value: satellite cells isolated after serum injection


title: heart

description:
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls
Figure_5s_.xls

source_name: Heart

value: Heart tissue

value: NORMAL

value: 1 week old


title: ATAC_CR_124


title: RNA-seq in mouse mature T-cells infected with a plasmid containing a scramble hairpin as control, rep 1

description:
Control_Rep_1
normalized_counts_KD.csv


title: ATAC_CR_125


title: CT26_DMSO_rep3

value: Treatment with 0.1% DMSO  for 6 h


title: EG7_DMSO_rep2

source_name: EG7 lymphoma cells

value: lymphoma

value: EG7 lymphoma cells


title: ATAC_CR_121

value: Peripheral blood mononuclear cells

value: F


title: CT26_DMSO_rep2


title: ATAC_CR_122

value: M


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ WT, rep 4

description:
RBPJ_WT_Rep_4
normalized_counts_rescue.csv

value: Blasticidin

value: pMY-Bio-Flag-mRBPJ WT CRr IRES Blasticidin


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ F261A/A284V mutant, rep 4

description:
RBPJ_F261A/A284V_Rep_4
normalized_counts_rescue.csv

value: hybridoma called E2-10HA

value: pMY-Bio-Flag-mRBPJ F261A/A284V CRr IRES Blasticidin


title: EG7_DMSO_rep1


title: CT26_DMSO_rep1

value: colorectal adenocarcinoma

value: CT26 colorectal adenocarcinoma cells


title: SC74

description:
Ser.inj replicate 2
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: Hindlimb muscles

value: Muscle stem cell


title: SC73

description:
Ser.inj replicate 1
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: satellite cells isolated after serum injection


title: SC75

description:
Ser.inj replicate 3
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with an empty vector control, rep 4

description:
eV_Rep_4
normalized_counts_rescue.csv

value: pMY-Bio IRES Blasticidin


title: Balb-C male mouse liver_DMSO-0 [EPACorton_P01_A02]

value: Balb-C

value: 10-12 weeks

value: male

value: Control

value: 0 mg/kg

value: liver


title: B16_RECTAS_rep3

source_name: B16 melanoma cells

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

value: melanoma

value: B16 melanoma cells


title: ATAC_CR_120

value: Peripheral blood mononuclear cells

value: M


title: CT26_RECTAS_rep2

value: colorectal adenocarcinoma


title: ATAC_CR_119


title: SC55

description:
MuSCP 2 months after injury replicate 3
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: satellite cells isolated from pregnant mouse 2 months after injury


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ F261A/A284V mutant, rep 3

description:
RBPJ_F261A/A284V_Rep_3
normalized_counts_rescue.csv

value: hybridoma called E2-10HA

value: Blasticidin

value: pMY-Bio-Flag-mRBPJ F261A/A284V CRr IRES Blasticidin


title: SC56

description:
MuSCP 2 months after injury replicate 4
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: Hindlimb muscles

value: Muscle stem cell


title: B16_RECTAS_rep2


title: ATAC_CR_118


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ WT, rep 3

description:
RBPJ_WT_Rep_3
normalized_counts_rescue.csv

value: pMY-Bio-Flag-mRBPJ WT CRr IRES Blasticidin


title: SC54

description:
MuSCP 2 months after injury replicate 2
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls


title: ATAC_CR_117


title: B16_DMSO_rep3

value: Treatment with 0.1% DMSO  for 6 h


title: SC53

description:
MuSCP 2 months after injury replicate 1
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ F261A/A284V mutant, rep 2

description:
RBPJ_F261A/A284V_Rep_2
normalized_counts_rescue.csv


title: ATAC_CR_116


title: SC66

description:
MuSCP replicate 5
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls
Figure_5s_.xls

value: non activated satellite cells isolated from pregnant mouse


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ WT, rep 2

description:
RBPJ_WT_Rep_2
normalized_counts_rescue.csv


title: B16_DMSO_rep1


title: ATAC_CR_114


title: ATAC_CR_115


title: SC64

description:
MuSCP replicate 4
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls
Figure_5s_.xls


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with an empty vector control, rep 2

description:
eV_Rep_2
normalized_counts_rescue.csv

value: pMY-Bio IRES Blasticidin


title: Enthesis WT P56

city: New York

first: Fei

last: Fang

state: New York

address: 650 W 168th Street, Blacking Building 1408

department: Orthopedic Surgery

institute: Columbia University

data_processing:
Raw sequencing output were processed through 10X genomics Cell Rnager software suite using default setting.
Reads were mapped to the mm10 transcriptome. Read counts were normalized to log2 reads per million mapped (rpm) and a cutoff of log2 rpm >= 1 was used to determine whether a given gene was expressed in a cell.
Cells with genes expressed less than 2 cells, cells<1000 UMIs with >20% UMIs mapped to mitochondrial genes, and <200 genes were removed.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files describe barcode, features, and mattrix for each sample
Supplementary_files_format_and_content: comma-separated text files include features and matrix for each sample

source_name: Supraspinatus tendon enthesis

extract_protocol:
Tendon entheses from P11, P18, and P56 C57BL/6J mice were dissected under surgical microscope and pooled together. They were digested in HBSS solution with 300 mg/ml liberase, 20 ng/ml Dnase, 5% FBS, and 100 mg/ml HEPES for 1.5 hours at 37 celsius degree. The samples were filtered through a 40 μm strain, resuspended in the RBC lysis buffer for 5 minutes at room temperature and stained with Cd45 in 200 μl PBS with 5% FBS for 45 minutes at 4°C. Then, the samples were washed with PBS three times, resuspended in 500 μl PBS with 1 ug/ml DAPI and 5% FBS, and filtered into polypropylene FACS tubes. Single cells without Cd45 and DAPI staining were index sorted by a BD influx Sorter and collected into a microcentrifuge tube for scRNA-seq 10 Genomics experiments. For dissociation of Gli1-lineage cells, tendon enthesesof GliCreERT;Ai14 mice of P7, P11, P18, P21, P28, and P42 were dissected, pooled together, and digested in the aforementioned solution under the same condition discussed above. All cells were stained with 1 ug/ml DAPI and were index sorted by a BD influx Sorter. Single cells without DAPI staining and red fluorescence were collected into 96-well plates, prefilled with lysis buffer for scRNA-Seq analysis.
For all enthesis cells, resulting pooled, 3’-end libraries was sequenced on Illumina® NovaSeq™ 6000; For Gli1-lineage cells, Pooled 3’-end sequencing libraries were prepared and finally sequenced on an IIlumina NextSeq 500

value: Tendon enthesis

value: post natal day 56


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ F261A/A284V mutant, rep 1

description:
RBPJ_F261A/A284V_Rep_1
normalized_counts_rescue.csv


title: Enthesis WT P18

value: post natal day 18


title: SC63

description:
MuSCP replicate 3
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls
Figure_5s_.xls


title: SC29

description:
MuSCP replicate 2
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls
Figure_5s_.xls


title: ATAC_CR_112


title: B16_RECTAS_rep1

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

value: melanoma

value: B16 melanoma cells


title: SC27

description:
MuSCP replicate 1
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls
Figure_5s_.xls


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with a plasmid encoding RBPJ WT, rep 1

description:
RBPJ_WT_Rep_1
normalized_counts_rescue.csv


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with an empty vector control, rep 3

description:
eV_Rep_3
normalized_counts_rescue.csv


title: ATAC_CR_111

value: Peripheral blood mononuclear cells

value: M


title: Enthesis WT P11

value: post natal day 11


title: RNA-seq in mouse mature T-cells depleted of RBPJ and infected with an empty vector control, rep 1

description:
eV_Rep_1
normalized_counts_rescue.csv

value: hybridoma called E2-10HA

value: Blasticidin


title: B16_DMSO_rep2


title: rve5_29_2

city: hangzhou

first: wei

last: li

address: Yuhangtang Road 866 ,Zijingang Campus, Zhejiang University

country: China

institute: zhejiang univeisity

data_processing:
RNA-Seq: Cutadapt software (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination.
RNA-Seq: After removed the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) to map reads to the tair10 genome. The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version: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). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8.Linux_x86_64).
RNA-Seq: 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).
Genome_build: TAIR10
Supplementary_files_format_and_content: genes_fpkm_expression.txt: Tab-delimited text file includes count and FPKM values for every gene and every sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings grow under long day (LD) conditions (16/8 h light / dark cycle at 22˚C).

extract_protocol:
Total RNA was extracted using Trizol reagent, Illumina TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings grow under long day (LD) conditions (16/8 h light / dark cycle at 29˚C).

value: seedlings

value: 5 days

value: 29C for 12h

tag: genotype

value: rve5-2 T-DNA mutant


title: ATAC_CR_109


title: rve5_29_3


title: ATAC_CR_113


title: SC69

description:
MuSC 2 months after injury replicate 2
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls

value: Hindlimb muscles

value: Muscle stem cell

value: satellite cells 2 months after injury


title: SC71

description:
MuSC 2 months after injury replicate 4
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: SC70

description:
MuSC 2 months after injury replicate 3
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: rve5_22_3

value: 22C for 12h


title: ATAC_CR_107

value: F


title: ATAC_CR_106


title: SC26

description:
MuSC replicate 5
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls

value: non activated satellite cells


title: SC67

description:
MuSC 2 months after injury replicate 1
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: rve5_22_2


title: ATAC_CR_110


title: SC25

description:
MuSC replicate 4
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: ATAC_CR_105


title: rve5_22_1


title: WT_29_3

value: wild type


title: SC24

description:
MuSC replicate 3
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: rve5_29_1


title: WT_29_2


title: Brain_DA_treated_168_hour_rep3

type: RNA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health.

data_processing: Bioconductor oligo package, RMA normalization. Comparisons were made using the Bioconductor limma package, fitting an ANOVA model as well as an ANCOVA model with a 3 degree of freedom spline.

label: biotin

organism: Danio rerio

source_name: Brain, DA treated, 168 hour

label_protocol: RNA was processed for hybridization to Affymetrix Zebrafish Genome array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Analysis was done on three RNA replicates per time point, each consisting of RNA from 3-4 pooled brains. Total RNA was isolated from zebrafish brains using the miRNeasy Mini Kit (Qiagen Inc., Valencia, CA) following manufacturer’s instructions, and stored at -70°C. RNA quantity and quality (OD260/280 and OD260/230 ratios) were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA integrity was characterized using the Agilent RNA 6000 Nano Kit with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Brain


title: ATAC_CR_104

value: Peripheral blood mononuclear cells


title: ATAC_CR_103


title: Brain_control_168_hour_rep2

source_name: Brain, control, 168 hour


title: ATAC_CR_108

value: M


title: Brain_control_168_hour_rep3


title: Brain_control_168_hour_rep1


title: SC23

description:
MuSC replicate 2
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: Brain_DA_treated_168_hour_rep1


title: WT_29_1


title: ATAC_CR_102


title: Brain_DA_treated_168_hour_rep2


title: Brain_DA_treated_48_hour_rep1

source_name: Brain, DA treated, 48 hour


title: Brain_DA_treated_48_hour_rep2


title: Brain_DA_treated_48_hour_rep3


title: WT_22_2


title: ATAC_CR_100


title: ATAC_CR_099


title: Brain_control_48_hour_rep2

source_name: Brain, control, 48 hour


title: M35

description:
muscle tissue replicate 2
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls

value: muscle tissue


title: Brain_control_48_hour_rep1


title: SC22

description:
MuSC replicate 1
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: ATAC_CR_098


title: HiC_dis3-54_mt_30c_2

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description:
HiC_1kb_abs.bed
HiC_2.5kb_abs.bed
dis3-54c-30c_1kb.iced.matrix
dis3-54c-30c_2.5kb.iced.matrix

data_processing:
ChIP-seq samples were sequenced on either Hiseq2500 with single-end method (50-bp reads) or Novaseq6000 with pair-end method (150-bp reads). S.pombe Hi-C samples were sequenced on Hiseq4000 with pair-end method (100-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (V3.04.04, Novocraft technologies) with default parameters. Aligned reads were converted into BAM and replicates were merged using samtools (v1.10). Significantly enriched peaks were identified using MACS2 (v.2.1.4) and mapped reads were quantified using Deeptools (v3.1.3) and bwtool (v1.0).
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner. Strand-specific signal tracks of RNA-seq were generated by using bam2wig.py from RseQC (v3.0.1).
Hi-C data were aligned to the S.pombe genome (ASM294v2) using bowtie2 and normalized using HiC-Pro (v2.11.0-beta). The raw and ICE-normalized matrix was generated at 1-kb and 2.5-kb bin resolution using valid interaction pairs.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: ChIP-seq: Yeast ChIP-seq bigwig files were created using deeptools bamCoverage (RPM normalization). In case of calibrated bigWigs for set4 experiments, samtools flagstat was used to count reads that were mapped to s.pombe and s.cerevisiae respectively. The occupancy ratio (OR) was calculated according to the previous publication (Hu, B. et al 2015). Then the calibrated s.pombe ChP (Rad21-5FLAGand notag) bigwigs were created using bamCoverage –scaleFactor option; Hi-C: ICE normalized HiC matrix text files and abs files (in HiC-Pro format); RNA-seq: bigwig files and normalized forward/reverser RPKM test files. The number of mapped reads was further analyzed using HOMER and DESeq.

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: S. pombe: 1) For Hi-C experiments, yeast cells were grown to mid-log phases at 32 degrees, unless indicated otherwise. 2) For ChIP-seq in tetracycline-regulated system, cells were grown to mid-log phase at 30 degress in YES medium supplied with 2.5 ug/ml of anhydrotetracycline (ahTet). Depletion of rrp6+ was achieved by culturing cells in YES medium that lacks ahTet at indicated times (8, 12hr). Recovery of rrp6+ was achieved by culturing cells at fresh YES medium containing 2.5ug/ml of ahTet. 3) for ChIP-seq experiments, yeast cells were grown to mid-log phases at 30 degrees, unless indicated otherwise.

extract_protocol:
S. pombe (ChIP) : Fixed cells were sonicated twelve times (15 sec on, 180 sec off) using a Fisher Scientific sonic Dismembrator Model 500 sonicator at 30% output. The immunoprecipitated DNA was eluted using SigmaPrep™ spin column and then subjected to protease treatment and cross-linking reversal. Subsequently, the DNA was purified using Qiaquick PCR purification kit (Qiagen).
S. pombe (RNA isolation): DNase-treated mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.
S.pombe (in situ Hi-C): formaldehyde-fixed cells (1.6 x 10^7 cells) were digested with zymolyase. Restriction enzyme digestion (MboI – 4 cutter), filling-in, ligation, crosslink reversal, DNA shearing and library construction were done according to previous publications (Rao, SSP et al 2014) with minor modifications.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT). mRNA-seq libraries were made using NEXTflex™ Rapid Directional mRNA-Seq kit (5138-10, BIOO) from purified mRNA.


title: M42

description:
muscle tissue replicate 4
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: ATAC_CR_096


title: M34

description:
muscle tissue replicate 1
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: ATAC_CR_101


title: Brain_DA_treated_24_hour_rep3

source_name: Brain, DA treated, 24 hour


title: M36

description:
muscle tissue replicate 3
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: SC86

description:
CSC 2 months after injury replicate 3
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: contralateral satellite cells 2 months after injury


title: SC85

description:
CSC 2 months after injury replicate 2
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls


title: ATAC_CR_097


title: HiC_dis3-54_mt_30c_1


title: HiC_dis3-54_wt_34c_2

description:
HiC_1kb_abs.bed
HiC_2.5kb_abs.bed
dis3-54c-34c_1kb.iced.matrix
dis3-54c-34c_2.5kb.iced.matrix


title: WT_22_3


title: SC83

description:
CSC 2 months after injury replicate 1
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls


title: ATAC_CR_095


title: SC48

description:
CSC replicate 3
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: contralateral satellite cells


title: ATAC_CR_094


title: WT_22_1

value: seedlings


title: HiC_dis3-54_wt_34c_1


title: SC47

description:
CSC replicate 2
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls


title: 34L

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

country: United Kingdom

institute: UCL Ear Institute

data_processing:
Run data were demultiplexed and converted into fastq files using Illumina’s bcl2fastq Conversion Software v2.19
Kallisto package was used to map reads to a chicken reference genome (Gallus_gallus-GRCg6a) and to quantifying abundances of transcripts using default settings
Genome_build: Gallus_gallus-GRCg6a

organism: Gallus gallus

source_name: otocyst

extract_protocol:
Total RNA was extracted from each individual otocysts using the RNAqueous™-Micro Total RNA Isolation Kit (Ambion) according to the manufacturers protocol. The quality of isolated RNA was tested using Agilent 2200 Tapestation and only samples with RIN of at least 9 were used for library
Libraries were made using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech): cDNA was generated using the SMART (Switching Mechanism at 5' End of RNA Template) technology during 10 cycles of PCR. cDNA integrity and quantity was checked on the Agilent Bioanalyser using the High Sensitivity DNA kit, and 200pg of cDNA was then converted to sequencing library using the Nextera XT DNA protocol (Illumina
Samples were sequenced 43bp paired-end read and high output - 400 million reads per run on NextSeq 500 instrument (Illumina)

treatment_protocol: The E2 chicken right otic placodes were in ovo electroporated with pCAB-NICD1-IRES-mRFP1 or control pCAB-IRES-mRFP1. Both left untransfected and the right transfected otocysts were collected 6h or 24h later and cleaned from the surrounding mesenchyme. For the tissue culture, both left and right otocyst were dissected from chicken embryos aged E2.5, cleaned from the surrounding mesenchyme and individually incubated free floating in LY411575-enriched (10µM, right otocyst) or control (DMSO, left otocyst) media for 6h or 24h.

value: White Leghorn

value: embryonic day 2.5

value: DMSO

tag: duration of treatment


title: 33L


title: HiC_pfs2-11_32c_2

description:
HiC_1kb_abs.bed
HiC_2.5kb_abs.bed
pfs2-11_1kb.iced.matrix
pfs2-11_2.5kb.iced.matrix


title: ATAC_CR_092


title: ATAC_CR_093


title: SC46

description:
CSC replicate 1
denovo_methylation_Figure_4.xls
demethylation_Figure_4_.xls

value: Hindlimb muscles


title: 32L


title: 34R


title: SC6

description:
ACTP replicate 3
Figure_5s_.xls

value: Muscle stem cell

value: activated satellite cells isolated from pregnant mouse


title: HiC_rrp6d_32c_2

description:
HiC_1kb_abs.bed
HiC_2.5kb_abs.bed
rrp6D_1kb.iced.matrix
rrp6D_2.5kb.iced.matrix


title: HiC_pfs2-11_32c_1


title: Brain_DA_treated_24_hour_rep2


title: SC7

description:
ACTP replicate 4
Figure_5s_.xls


title: Brain_control_24_hour_rep3

source_name: Brain, control, 24 hour


title: ATAC_CR_091

source_name: Peripheral blood mononuclear cells


title: ATAC_CR_090


title: 33R


title: SC5

description:
ACTP replicate 2
Figure_5s_.xls


title: HiC_rrp6d_32c_1


title: 32R


title: HiC_Rad21K1_32c_2

description:
HiC_1kb_abs.bed
HiC_2.5kb_abs.bed
rad21K1_1kb.iced.matrix
rad21K1_2.5kb.iced.matrix


title: Brain_control_24_hour_rep2


title: HiC_Rad21K1_32c_1


title: ATAC_CR_088


title: HiC_972_32c_2

description:
HiC_1kb_abs.bed
HiC_2.5kb_abs.bed
wt_1kb.iced.matrix
wt_2.5kb.iced.matrix

value: wt


title: SC4

description:
ACTP replicate 1
Figure_5s_.xls


title: Brain_control_24_hour_rep1


title: Brain_DA_treated_24_hour_rep1


title: SC14

description:
ACT replicate 5
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls

value: activated satellite cells


title: ATAC_CR_087


title: ATAC_CR_086

value: F


title: HiC_972_32c_1


title: 3L


title: 1L


title: SC11

description:
ACT replicate 3
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: SC10

description:
ACT replicate 2
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: SC13

description:
ACT replicate 4
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: ATAC_CR_085


title: 5R


title: ATAC_CR_089


title: 3R


title: ATAC_CR_083


title: ATAC_CR_084


title: 5L


title: 1R


title: ACTP5

data_processing:
Raw reads were quality (threshold 32) and adapter trimmed, with cutadapt (version 1.12), discarding reads shorter than 15nt. Samples prepared with the SMARTer kit were also trimmed off their first 5 bases prior to that. The remaining reads were filtered by quality with FASTX (version 0.0.14), using parameters -q 20 and -p 90.
Alignment was done with TopHat (version 2.0.14), against the mouse GRCm38 genome assembly, with the following parameters: -N 3, --read-gap-length 5, --read-edit-dist 8, --read-realign-edit-dist 3, --no-coverage-search, and --segment-length 20 for the TruSeq samples or --segment-length 18 and --library-type fr-secondstrand for the SMARTer samples. Both types were run with gene annotations from Ensembl release 84 (-G parameter).
Quantification was done with htseq-count (version 0.6.0. TruSeq samples, with the parameter -s 'no', while SMARTer samples with -s ‘yes’ and -t 'transcript'. An annotation file that lacked information for genes of type IG, TR, Mt, rRNA, tRNA, miRNA, misc_RNA, scRNA, snRNA, snoRNA, sRNA, scaRNA, piRNA, vaultRNA, ribozyme, artifact and LRG_gene, was used for both types.
Mature quadriceps muscle samples were taken from the project "An RNASeq normal tissue atlas for mouse and rat", by the Boehringer Ingelheim Pharma GmbH & Co. KG Target Discovery Research center, and added as additional samples in the system. Accession numbers for those samples were SAMEA104310458, SAMEA104310459 and SAMEA104310460, of the project PRJEB22693 (ENA database, https://www.ebi.ac.uk/ena/browser/view/PRJEB22693).
Differential expression was done with the DESeq2 package (version 1.22.1). First, only protein coding genes, with an average of at least 3 counts in each condition, that do not overlap other genes (either on the same or the opposite strand), were taken for the analysis (10792 genes). Normalization and differential expression analysis were performed with default parameters, except not using the independent filtering algorithm and setting the significance threshold to padj<0.05. Genes with a significant change in expression were further filtered to consider only genes with a baseMean above 5, and an absolute log2FoldChange greater than 5/sqrt(baseMean) + 0.6.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file. The first row is a header row. Columns include general gene details, raw counts, normalized counts, the baseMean, differential expression results from DESeq2 for each comparison, and columns for easy filtering of the genes chosen in the analysis. A "?" denotes missing data. Missing raw counts (and all columns thereafter), are due to initial filtering for expressed protein coding genes.

extract_protocol:
Hindlimb muscles were dissected from mice following euthanization and kept in wash solution (Ham’s F10 media supplemented with 10% horse serum). The muscles were then finely minced with a surgical scalpel and digested in 2 mg/ml Collagenase II (Worthington, 340 U/mg) for 90 min with agitation. Dissociated fibers were washed and further digested with shaking in 100 U/ml Collagenase II and 2 U/ml Dispase (Invitrogen) for 30 min in a volume of 10 ml, passed 10 times through a 20-G needle to release the associated satellite cells and then washed two more times and filtered through a 45-mm cell strainer. Mononuclear cells from each sample were resuspended in 500 ml wash solution, stained with VCAM1-biotin, CD31-APC, CD45- APC and Sca1-Pacific-Blue antibodies (Biolegend) using a 1:100 dilution at 4°C with gentle agitation for 30 min, washed and resuspended in 500 ml and then stained with Streptavidin-PE-Cy7 (1:100) at 4°C with gentle agitation for 15 min. The resulting preparation contains satellite cells (VCAM1+/CD31-/CD45-/Sca-), which can be separated from remaining cells and debris using flow cytometry. RNA was extracted with the Qiagen kit.
Libraries for non-injured animals were prepared with the SMARTer stranded total RNA sample prep kit - low input mammalian, with ribosomal RNA depletion; libraries for injured animals were made with the TruSeq RNA library prep kit, after poly-A selection.


title: 24L

value: embryonic day 3

value: non-transfected


title: 23L


title: ATAC_CR_080

value: Peripheral blood mononuclear cells


title: ACTP6


title: ATAC_CR_081

value: M


title: ATAC_CR_082


title: ACTP3


title: ACTP4


title: L03_127, KO_PARP1, OL9, biol rep 4

city: Novosibirsk

first: Maxim

last: Ri

address: Lavrenteva st. 6

country: Russia

institute: LLC AcademGene

data_processing:
Quality control of raw reads were performed using FastQC  v0.11.9
Sequence reads were aligned to hg38 human genome using STAR v 2.7.8.
Quantification of reads was also performed using STAR, option –quantMode GeneCounts
Quality control of aligment were performed using module infer_experiment.py of RSeQC v4.0.0, module CollectRnaSeqMetrics from Picard v2.26.6
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: Cells were grown in DMEM/F12 medium supplemented with 1×GlutaMAX, 100 c.u./ml penicillin and 100 mg/ml streptomycin, in the presence of 10% fetal bovine serum in a 5% CO2 atmosphere.

extract_protocol:
RNA was isolated with the Trizol according to the manufacturer instructions.
RNA were enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module, libraries were prepared with MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd., China)

treatment_protocol: Cells were treated for 5-5,5 hours with following agents: 1) No treatment, 2) 0.1% DMSO, 3) 100 nM (for WT HEK293) or 50 nM (for PARP1-KO HEK293) Tpc + 0.1% DMSO, 4) 5 μM OL9-119 solved in 0.1% DMSO, 5) 100 nM (for WT HEK293) or 50 nM (for PARP1-KO HEK293) Tpc + 5 μM OL9-119.

value: human embryonic kidney cells

value: PARP1 knockdown


title: L03_126, KO_PARP1, TPC_OL9, biol rep 4


title: L03_128, KO_PARP1, TPC, biol rep 4

value: TPC


title: ATAC_CR_078


title: L03_34, WT, TPC, biol rep 4

value: WT


title: ATAC_CR_079


title: 4L

value: White Leghorn


title: ATAC_CR_077


title: SC9

description:
ACT replicate 1
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls


title: L03_33, WT, OL9, biol rep 4


title: ACTP2


title: 24R


title: 23R


title: ACTP1


title: MuSCP3

value: non activated satellite cells isolated from pregnant mouse


title: L03_32, WT, TPC_OL9, biol rep 4


title: MuSCP2


title: ATAC_CR_074


title: 4R


title: LB_versus_human serum Exp_1

city: Chicago

first: Hyunwoo

last: Lee

state: IL

address: 900 S. Ashland Ave., MBRB #3020

department: Center for Biomolecular Sciences

institute: University of Illinois at Chicago

description: Comparison of control RNA samples prepared from cells grown in LB to the experimental RNA samples from cells grown in heat-inactivated human serum.

hyb_protocol: Hybridization was performed according to the protocol provided by JCVI/PFGRC. Microarray slides were prehybridized in 5x SSC, 0.1% SDS, and 1% bovine serum albumin at 42°C for 1 h. Slides were then washed at room temperature with distilled water, and allowed to dry. About 5-6 µg of dye-labeled cDNA probes, with 100 pmoles of dye incorporation and corresponding to each growth condition, was mixed together, dried, and resuspended in a solution of 40%formamide, 5xSSC, and 0.1% SDS. Resuspended probes were heated to 95°C before hybridization. The probe mixture was then added to the microarray slide and allowed to hybridize overnight at 42°C.

scan_protocol: Microarrays were scanned using a Perkin Elmer confocal dual-laser microarray scanner equipped with ScanArray Lite software (Perkin Elmer, Boston, MA).

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder. Microarray data were normalized by LOWESS in TIGR MIDAS software (available at http://www.jcvi.org/software/tm4). The 'IA' and 'IB' channels in the *.mev files correspond to Cy3 (Ch1) and Cy5 (Ch2).

organism: Bacillus anthracis str. Sterne

source_name: Wild type cells grown in LB

label_protocol: cDNA was generated according the protocol from PFGRC (http://pfgrc.tigr.org/protocols/protocols.shtml). Random hexameric primers were allowed to anneal to the RNA and Superscript II DNA polymerase (Invitrogen) was used for reverse transcription overnight at 42°C. The reaction mix contained a 3:2 ratio of aminollyl-dUTP to dTTP. Subsequently the RNA was hydrolyzed by heating at 65°C for 15 min in the presence of 0.2 M NaOH and 0.1 M EDTA and cDNA was purified using the Wizard SV-gel and PCR clean-up kit (Promega).  The purified aminoallyl-cDNA was allowed to react with AlexaFluor dyes 555 (Cy3) and 647 (Cy5) (Invitrogen) for 1 h at room temperature. The labeled cDNA was purified using Qiagen QIAquick PCR purification kit (Valencia, CA), precipitated and dissolved in 10 µl water.

growth_protocol: An overnight culture of B. anthracis in LB medium was diluted 1:50 in fresh LB and grown to OD600 0.5. The cells were harvested, washed once with Phosphate buffered saline (PBS) and inoculated at OD600 0.02 into either 25 ml LB or 25 ml heat-inactivated human serum. After approximately 4 generations of growth, which corresponds to 2.5 h in LB and 5 h in serum.

extract_protocol: Total RNA was isolated using Ambion’s Ribopure microbial RNA isolation kit according to the manufacturer’s instructions.

treatment_protocol: At the time of cell harvest, Two volumes of RNAprotect Bacteria Reagent were added to bacterial culture.

value: Sterne

source_name: Wild type cells grown in human serum


title: 22L


title: 19L


title: L03_30, WT, DMSO, biol rep 4

value: DMSO


title: ATAC_CR_076


title: ATAC_CR_075


title: 21L


title: 22R


title: ACT5

source_name: Hindlimb muscles

value: Hindlimb muscles

value: Muscle stem cell


title: ACT6


title: L03_29, WT, no, biol rep 4

value: no


title: ATAC_CR_072


title: MuSCP1


title: 21R


title: LB_versus_human serum Exp_4


title: ATAC_CR_071


title: L03_124, KO_PARP1, DMSO, biol rep 4


title: LB_versus_human serum Exp_2


title: ATAC_CR_073


title: LB_versus_human serum Exp_3


title: L03_26, WT, OL9, biol rep 3


title: L03_28, WT, TPC, biol rep 3


title: ACT3

value: activated satellite cells


title: L03_25, WT, TPC_OL9, biol rep 3


title: ACT4


title: 19R


title: ATAC_CR_070

value: F


title: L03_117, WT, DMSO, biol rep 3


title: ATAC_CR_069


title: 15L

value: embryonic day 2.5


title: L03_116, WT, no, biol rep 3


title: 13L

value: non-transfected


title: ACT2


title: ACT1


title: ATAC_CR_068

value: Peripheral blood mononuclear cells


title: ATAC_CR_067

value: M


title: L02_128, KO_PARP1, no, biol rep 4

value: human embryonic kidney cells


title: L02_127, KO_PARP1, TPC, biol rep 3

value: PARP1 knockdown


title: MuSC2

value: non activated satellite cells


title: 12L


title: MuSC3


title: 15R


title: ATAC_CR_066


title: MuSC1


title: L02_126, KO_PARP1, OL9, biol rep 3


title: ATAC_CR_065


title: 13R


title: L02_125, KO_PARP1, TPC_OL9, biol rep 3


title: Bdi21_Input DNA

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
Raw reads from ChIP-seq data were mapped to the different Brachypodium genomes using bwa mem with the default parameters.
The mapped reads with MAPQ values >= 20 as uniquely mapping for further analysis.
RPM values were calculated with 1 kb windows along the genome to make it comparable between different samples.
Genome_build: Bdistachyon_314_v3.0; Bhybridum_463_v1.0; Bstacei_316_v1.0
Supplementary_files_format_and_content: BED files contains the positions of mapped reads of the ChIP-seq.

organism: Brachypodium distachyon

growth_protocol: Suitable materials were planted in the greenhouse ChIP-seq experiments.

extract_protocol:
Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the maize CENH3 antibody.The ChIP-enriched DNAs of different lines of  Brachypodium species were performed Illumina sequencing. The  CENH3 antibody is a rabbit polyclonal antiserum and was raised against the peptides: KDIQLARRISGHRGY. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits.
ChIP libraries were prepared according to standard Illumina's instructions.180-400 bp fragments (contained the joint) were selected by gel extraction.

tag: genotype/variation

value: young leaves

tag: chip antibody


title: ATAC_CR_064


title: ENNB_Lo_Intestine2

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
TrimGalore 0.4.2 wrapper tool (https://github.com/FelixKrueger/TrimGalore) was used for removing adaptors and quality trimming, applying the default parameters. Library quality was investigated using fastQC included in the TrimGalore wrapper.
libraries were mapped to the Atlantic salmon genome (RefSeq Assembly ICSASG_v2) using the Hisat2 short read aligner version 2.0.4
Transcript levels for the individual libraries were estimated using FeatureCounts (Liao et al., 2014) of the Subread package (http://subread.sourceforge.net/).
Read counts were further normalized using Bioconductor R package (version 3.4.4) DESeq2 (version 1.18.1) (Love et al., 2014).
DESeq2 was further used for analysis of differentially expressed genes (DEGs) in a pair-wise comparison of each contrast (Ctrl vs BEA-low, Ctrl vs BEA-high, Ctrl vs ENNB-low, Ctrl vs ENNB-high)
Assembly: ICSASG_v2
Supplementary files format and content: Comma delimited text file containing normalized read counts

organism: Salmo salar

source_name: Intestine

extract_protocol:
Total RNA was extracted from the distal intestine and liver tissues sampled using QIAzol® Lysis Reagent and the EZ1® RNA Tissue Mini Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol.
Total RNA samples were sent to Novogene Europe, Cambridge, UK, for cDNA library preparation and sequencing using the Illumina NovaSeq 6000 platform for 150 bp paired end reads. Enriched mRNA was prepared using Oligo(dT beads). cDNA libraries were prepared following manufacturer’s instructions per the Novogen pipeline (Novogene Europe, Cambridge, UK)

value: Intestine


title: L02_124, KO_PARP1, DMSO, biol rep 3


title: L02_123, KO_PARP1, no, biol rep 3


title: ATAC_CR_063


title: Adi-3_Input DNA


title: ATAC_CR_062


title: ENNB_Lo_Intestine1


title: L02_122, KO_PARP1, TPC, biol rep 2

value: TPC


title: ATAC_CR_061


title: L02_121, KO_PARP1, OL9, biol rep 2


title: Ctrl_Intestine6

value: Ctrl


title: PeakMicroglia_RNAseq

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: MicrogliaRnaSeqCounts.csv

data_processing:
For MiGS data, reads were aligned to mm10 with bowtie2 (options: -N 1 -L 20 --phred33). Reads with mapping quality (MAPQ) < 10 were discarded. Average coverage in non-overlapping 50bp bins was counted genome-wide using the preprocessing functions of MethylAction (Bhasin, et al., 2015). Chromosomes X and Y were excluded, because the samples are a pool of mice from both sexes.
For RNA-seq data, reads were aligned to mm10 using TopHat (Trapnell, et al., 2009) (options: --library-type fr-firststrand). Read counts were quantified for ENSEMBL mouse genes using featureCounts (Liao, et al., 2014) (options: -F GTF -s 2 -Q 30 -T 20 -p -B -C). FPKM values were computed using edgeR (Robinson, et al., 2010). Chromosomes X and Y were excluded, because the samples are a pool of mice from both sexes.
Genome_build: mm10
Supplementary_files_format_and_content: For MiGS data, a text file has been provided for each sample that contains normalized read counts within the non-overlapping 50bp windows genome wide. Windows with all zero values or all values below a noise cutoff have been removed, so only windows considered to have signal remain. Each row represents one 50bp window. The genomic coordinates (mm10) are provided in the first three columns. The remaining column contains the average coverage of MiGS reads for the window in the sample. For RNA-seq data, reads were counted for ENSEMBL transcription units using featureCounts. The provided CSV file contains one row for each gene, one column containing the raw read counts (no normalization for library size) for each sample, and one column containing the FPKM-normalized read counts for each sample.

source_name: microglia

growth_protocol: C57Bl/6 mice were obtained from the National Cancer Institute. Ccr2rfp/+::Cx3cr1gfp/+ mice were generated by cross breeding Ccr2rfp/rfp::C57Bl/6 mice (Saederup et al., 2010) with Cx3cr1gfp/gfp::C57Bl/6 mice (Jung et al., 2000). Animal experiments were performed according to the protocols approved by the Institutional Animal Care and Use Committee at the Cleveland Clinic following the National Institute of Health guidelines for animal care.

extract_protocol:
Illumina TruSeq Stranded Total RNA with Ribo-zero Gold
Brains and spinal cords were removed and homogenized. Mononuclear cells were separated with a 30% / 70% Percoll (GE Healthcare, NJ, USA) gradient as previously reported (Pino and Cardona, 2011). Single cell suspensions from CNS were stained with anti-F4/80-APC (BM8; eBioscience, CA, USA) and anti-CD45-PerCP (30-F11; BioLegend). Cells were sorted on a BD FACSAria II (BD Biosciences). Data were analyzed with FlowJo software (TreesStar, OR, USA).  Genomic DNA and RNA were extracted from the same samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).

treatment_protocol: EAE was induced in Ccr2rfp/+::Cx3cr1gfp/+ mice of 24-28 weeks of age using myelin-oligodendrocyte-glycoprotein peptide 35-55 (MOG) as described (Huang et al., 2006). All mice were weighed and graded daily for clinical stages as previously reported (Saederup et al., 2010). We defined clinical stage of EAE as follows: onset was the day EAE signs appeared; peak was the second day score didn’t increase after sustained daily worsening; and recovery was the second day score didn’t decrease after a period of sustained daily improvement.

tag: activation

value: peak

tag: background mouse strain


title: BEA_Hi_Intestine6


title: 12R

tag: strain

value: White Leghorn

tag: age


title: L02_115, WT, TPC, biol rep 2

value: WT

tag: treatment


title: L02_114, WT, OL9, biol rep 2


title: L02_16, WT, TPC_OL9, biol rep 2


title: Macrophage_TDGKO_PBseq_site1_site2_rep3

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

description: target coordinates:chr6:122870051-122870267;chr6:108445115-108445343

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
Assembly: hg19 for human, mm10 for mourse.
Library strategy: PB-seq

source_name: iMacrophage

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol:
Genomic DNA was extracted from day 7 i3Neurons and day 2 C/EBPα-induced Macrophages using DNeasy® Blood & Tissue (QIAGEN; Cat. #69504) following manufacturer’s instructions.
100 ng genomic DNA was used in a 50-μl reaction containing 600 mM sodium acetate solution (3M, pH = 4.3) (Quality Biological, 351-309-101) and 1 M pyridine borane (Alfa Aesar, L13178-09),  and incubated for 16 h at 37°C in a Eppendorf ThermoMixer shaking at 850 rpm. The product was purified by QIAquick Nucleotide Removal Kit (QIAGEN; Cat. # 28306). 4 primer pairs, covering 26 CpGs within neuronal enhancer regions were designed using BiSearch Web (http://bisearch.enzim.hu). Amplicons were between 200-250 base pairs. We also designed 3 primer pairs, which cover 19 CpGs within macrophage enhancer regions. The PCR amplicons were generated using the PyroMark PCR kit (QIAGEN; Cat. # 978703) and quantified using Qubit assays (Invitrogen). PCR amplicons were pooled, then library preparation steps were performed as described (PMID: 33767446). The final libraries were quantified using the KAPA library quantification kit for Illumina (KAPA Biosystems) and sequenced on Illumina Miseq (150 bp, paired end).

tag: harvested day

value: TDG-/-

value: NT


title: ATAC_CR_059


title: L02_15, WT, DMSO, biol rep 2

value: DMSO


title: ATAC_CR_058


title: BEA_Hi_Intestine4

tag: tissue


title: BEA_Hi_Intestine3


title: ATAC_CR_057


title: BEA_Lo_Intestine3


title: Macrophage_TDGKO_PBseq_site1_site2_rep1

institute: Center for Excellence in Molecular Cell Science


title: Adi-3_CENH3_ChIPSeq

tag: molecule type

value: ChIPed DNA


title: ATAC_CR_056

tag: cell type

value: F


title: L02_14, WT, no, biol rep 2

value: no


title: ENNB_Hi_Intestine4


title: Bdi21_CENH3_ChIPSeq


title: ENNB_Hi_Intestine1


title: iMacrophage_WT_PBseq_site1_site2_rep3


title: NaiveMicroglia_RNAseq

description: MicrogliaRnaSeqCounts.csv

value: naïve


title: ATAC_CR_055

value: Peripheral blood mononuclear cells

tag: gender

value: M


title: iMacrophage_WT_PBseq_site1_site2_rep2


title: ATAC_CR_060


title: ATAC_CR_054


title: BEA_Lo_Intestine5


title: Ctrl_Intestine1


title: ATAC_CR_053


title: iMacrophage_WT_PBseq_site1_site2_rep1


title: L01_102, KO_PARP1, no, biol rep 2

tag: cell line

value: human embryonic kidney cells

value: PARP1 knockdown


title: Macrophage_TDGKO_PBseq_site1_site2_rep2


title: L01_101, KO_PARP1, TPC, biol rep 1


title: iMacrophage_TDGKO_PBseq_site3_rep3

description: target coordinates:chr4:89354094-89354300


title: BEA_Hi_Liver3

source_name: Liver

value: Liver


title: iMacrophage_TDGKO_PBseq_site3_rep2


title: ATAC_CR_052


title: BEA_Lo_Liver3


title: BEA_Lo_Liver2


title: ATAC_CR_051


title: L01_100, KO_PARP1, OL9, biol rep 1


title: BEA_Lo_Liver1


title: iMacrophage_TDGKO_PBseq_site3_rep1


title: L01_99, KO_PARP1, TPC_OL9, biol rep 1


title: ATAC_CR_050


title: L01_104, KO_PARP1, TPC_OL9, biol rep 2


title: iMacrophage_WT_PBseq_site3_rep3


title: L01_103, KO_PARP1, DMSO, biol rep 2


title: ATAC_CR_049


title: L01_98, KO_PARP1, DMSO, biol rep 1


title: L01_97, KO_PARP1, no, biol rep 1


title: ENNB_Lo_Liver6


title: IN nuclear profiling

city: Hsinchu

first: Joye

last: Li

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

description: nuclear RNA

data_processing:
The raw reads of fastq were preprocessed with the adapter trimmer PEAT (https://github.com/jhhung/PEAT)
Processed reads aligned with the ad hoc NTA aligner Tailor (https://github.com/jhhung/Tailor); We configured Tailor by setting the minimum sequence alignment length to 18 nt and maximum hit occurrence to at most 10 positions.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: Embryoid bodies

growth_protocol: ESCs were cultured and differentiated into spinal MNs/INs as previously described (Wichterle et al., 2002; Wichterle et al., 2009). Two dosages of SAG treatment (500 nM SAG for MNs; 5 nM for INs, respectively) in addition to RA were applied during the differentiation process. Cells were collected followed by the subcellular fractionation on day 7 for miRNA-seq.

extract_protocol:
Subcellular fractioned RNA were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq Small RNA Library Prep Kit-Set A.

tag: developmental stage

value: day 7

tag: biological replicates


title: ENNB_Lo_Liver4


title: ATAC_CR_048


title: L01_4, WT, OL9, biol rep 1

tag: genotype


title: ATAC_CR_047


title: L01_13, WT, TPC, biol rep 1

value: TPC


title: ATAC_CR_045


title: L01_3, WT, TPC_OL9, biol rep 1


title: ATAC_CR_046


title: ENNB_Lo_Liver5


title: iMacrophage_WT_PBseq_site3_rep2


title: ENNB_Lo_Liver2


title: iMacrophage_WT_PBseq_site3_rep1


title: MN nuclear profiling

description: nuclear RNA


title: ESC-derived IN Day 7 replicate 2

growth_protocol: ESCs were cultured and differentiated into spinal MNs as previously described (Wichterle et al., 2002; Wichterle et al., 2009). Cells were trypsinized and collected for FACS at day 7 to purify GFPon and GFPoff neurons for miRNA-seq.

extract_protocol:
FACS sorted cells were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq Small RNA Library Prep Kit-Set A.

value: replicate 2


title: L01_2, WT, DMSO, biol rep 1


title: ESC-derived MN Day 7 replicate 1

value: replicate 1


title: ESC-derived MN Day 7 replicate 2


title: Ctrl_Intestine5

value: Intestine

value: Ctrl


title: L01_1, WT, no, biol rep 1

value: WT


title: Ctrl_Liver5


title: ATAC_CR_043

extract_protocol:
PBMCs were isolated from whole blood using histopaque.
Omni-ATAC protocol (Corces, 2017) was used to construct the ATAC-seq libraries.


title: ENNB_Lo_Intestine3


title: ATAC_CR_040


title: ENNB_Lo_Liver1


title: ESC-derived MN Day 4 replicate 2

value: day 4


title: ESC-derived MN Day 4 replicate 1


title: ATAC_CR_042


title: h3.3ko_MS_3 [Strand-specific RNA-seq]

city: Beijing

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using CPM
Assembly: TAIR10
Supplementary files format and content: *.bw, normlized transcripts coverage files

source_name: mature seeds

growth_protocol: Mature seeds

extract_protocol:
Seeds were collected and total RNA was extracted with Minibest plant RNA extraction kit (Takara)
Sequencing libraries were prepared with MGIEasy RNA directional library preparation kit according to the manufacture’s instruction

value: mature seeds


title: ESC-derived IN Day 7 replicate 1


title: ESC-derived MN Day 3 replicate 2

value: day 3


title: ATAC_CR_041

city: Lausanne

institute: University of Lausanne

data_processing:
Adapter trimming: Trim Galore! version 0.6.6 in paired end mode
Alignment: Bowtie2 version 2.2.5, bowtie2 --very-sensitive -k 10 -X 1000 --dovetail
Filtering: remove multi-mapping, improper pairs Samtools version 1.9, samtools view -f 0x2 -F 0x100
Filtering: remove duplicates, Picard tools version 2.25.6, MarkDuplicates --REMOVE_DUPLICATES true
Peak calling: Genrich version 0.6.1 in atac mode, ignoring ENCODE blacklist, outputting tn5 cut site BED files, q < 0.05
Count matrix: Bedtools version 2.30.0, count the number of tn5 cut sites intersecting (bedtools intersect -c) the union peakset (bedtools merge of individual peaksets)
Alignment: STAR aligner (v2.7.9a) with '--sjdbOverhang 100'.
Counting: featureCounts, Subread package (v2.0.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw matrix table representing the number of tn5 cut sites overlapping each peak for each sample


title: Ctrl_Intestine4


title: BEA_Hi_Intestine5


title: h3.3ko_MS_2 [Strand-specific RNA-seq]


title: h3.3ko_MS_1 [Strand-specific RNA-seq]


title: ATAC_CR_039


title: ESC-derived MN Day 2 replicate 2

value: day 2


title: Col_MS_3 [Strand-specific RNA-seq]

value: Col


title: ATAC_CR_036

value: Peripheral blood mononuclear cells

value: F


title: ATAC_CR_035

value: M


title: ATAC_CR_044


title: Col_MS_2 [Strand-specific RNA-seq]


title: BEA_Lo_Intestine2


title: h3.3ko_G24h_3 [h3.3ko_G24h_3]

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
Reads per gene were counted by HTseq version 0.11.2
Transcripts per million (TPM) values were generated using R
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Assembly: TAIR10
Supplementary files format and content: *.txt, TPM values for all samples

source_name: imbibed seeds

growth_protocol: Mature seeds, seeds imbibed for different time periods

extract_protocol:
Seeds were collected and total RNA was extracted with Minibest plant RNA extraction kit (Takara)
Sequencing libraries were prepared with BGISEQ-500 RNA-seq library preparation kit according to the manufacturer’s instruction

value: imbibed seeds

value: seeds subject to germination for 24 hours


title: Ctrl_Intestine3


title: h3.3ko_G24h_2 [h3.3ko_G24h_2]


title: BEA_Lo_Intestine1


title: ESC-derived MN Day 2 replicate 1


title: Col_MS_1 [Strand-specific RNA-seq]


title: BEA_Lo_Intestine4


title: ATAC_CR_032


title: h3.3ko_G24h_1 [h3.3ko_G24h_1]


title: BEA_Hi_Intestine1


title: Ctrl_Intestine2


title: ATAC_CR_031


title: ESC-derived MN Day 3 replicate 1


title: h3.3ko_G12h_2 [h3.3ko_G12h_2]

value: seeds subject to germination for 12 hours


title: HT-1197_BAY-4931_rep_2

city: Boston

first: Andrew

last: Cherniack

state: Mass

address: 450 Brookline Ave

department: Molecular Oncology

institute: Dana Farber Cancer Institute

data_processing:
Star was use to map reads per gene using --quantMode
Assembly: HG19
Supplementary files format and content: 3 column table:  column 1: gene ID column  2: counts for unstranded RNA-seq column 3: counts for the 1st read strand aligned with RNA column 4: counts for the 2nd read strand aligned with RNA

growth_protocol: HT-1197 cells were grown in MEMalpha with 10% fetal bovine serum in a 6-well plate and incubated in a humidifed chamber with 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Library was constructed and sample were sequenced using standard RNA sequencing procedures at Genewiz (Plainfield, NJ

treatment_protocol: At approximately 70% cell confluency, compounds were added. 24 hours after compound addition, RNA was harvested. Treatment conditions; vehicle (DMSO), rosiglitazone 500nM, SR10221 500nM, T0070907 500nM, BAY-4931 200nM

value: Urinary Bladder Carcinoma

tag: time

value: 24 hours


title: HT-1197_BAY-4931_rep_3


title: ATAC_CR_037

first: kevin

last: perez

address: rue du Bugnon 27


title: ENNB_Hi_Intestine6


title: ATAC_CR_030


title: ESC

source_name: Embryonic stem cell

value: ESC


title: ATAC_CR_034


title: h3.3ko_G12h_1 [h3.3ko_G12h_1]


title: HT-1197_BAY-4931_rep_1


title: ENNB_Hi_Intestine5

value: Intestine


title: HT-1197_T0070907_rep_3


title: HT-1197_T0070907_rep_2


title: h3.3ko_G12h_3 [h3.3ko_G12h_3]


title: ATAC_CR_028


title: h3.3ko_S48h_3 [h3.3ko_S48h_3]

value: seeds stratified for 48 hours


title: h3.3ko_S48h_2 [h3.3ko_S48h_2]


title: BEA_Hi_Intestine2


title: ATAC_CR_038


title: ATAC_CR_029


title: HT-1197_T0070907_rep_1


title: ENNB_Hi_Intestine2


title: ATAC_CR_027


title: h3.3ko_S48h_1 [h3.3ko_S48h_1]


title: ENNB_Lo_Intestine6


title: HT-1197_SR10221_rep_3


title: h3.3ko_S24h_3 [h3.3ko_S24h_3]

value: seeds stratified for 24 hours


title: ENNB_Lo_Intestine5


title: R21105190LR01-KYSE450-NC-2

city: beijing

first: shaobo

last: zhang

address: 北京市朝阳区潘家园南里17号

institute: 北京协和医学院

data_processing:
RSEM (V1.2.29) (Li B, et al. 2011) can accurately quantify gene or transcript expression levels from RNA-seq data.
EdgeR (Robinson, M.D., McCarthy et al. 2010) used the overdispersed Poisson model and empirical Bayes model to estimate the dispersion of all gene expression levels.
Supplementary_files_format_and_content: counts and RPKM values of each gene

source_name: ESCC cells

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols.RNA purification, reverse transcription, library construction and sequencing were performed in Mingma Technologies Co., Ltd at Shanghai according to the manufacturer's instructions (Illumina). The mRNA-focused sequencing libraries from total RNA were prepared using VAHTS mRNA-seq v3 Library Prep Kit (Vazyme). PolyA mRNA was purified from total RNA using oligo-dT-attached magnetic beads and then fragmented by fragmentation buffer. Taking these short fragments as templates, first strand cDNA was synthesized using reverse transcriptase and random primers, followed by second strand cDNA synthesis. Then the synthesized cDNA was subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. Then Illumina sequencing adapters were added to both size of the cDNA fragments. After PCR amplification for DNA enrichment, the AMPure XP Beads (Beckmen) were used to clean up the target fragments of 200–300 bp. After library construction, Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific) was used to quantify concentration of the resulting sequencing libraries, while the size distribution was analyzed using Agilent BioAnalyzer (Agilent). Sequencing was performed using an Illumina Novaseq 6000 following Illumina-provided protocols for 2x150 paired-end sequencing in Mingma Technologies Co., Ltd at Shanghai.

value: Human ESCC cell lines

tag: genotype/variation

value: control


title: HT-1197_SR10221_rep_2


title: R21105189LR01-KYSE450-NC-1

address: 北京市朝阳区潘家园南里17号


title: h3.3ko_S24h_2 [h3.3ko_S24h_2]


title: ENNB_Lo_Intestine4


title: HT-1197_SR10221_rep_1


title: BEA_Hi_Liver6

value: Liver


title: h3.3ko_S24h_1 [h3.3ko_S24h_1]


title: HT-1197_Rosiglitazone_rep_3

value: rosiglitazone 500nM


title: ENNB_Hi_Intestine3


title: R21105187LR01-KYSE450-4-1

address: 北京市朝阳区潘家园南里17号

value: knockdown MAFB


title: h3.3ko_S12h_3 [h3.3ko_S12h_3]

value: seeds stratified for 12 hours


title: R21105186LR01-KYSE450-1-2

address: 北京市朝阳区潘家园南里17号


title: BEA_Hi_Liver5


title: BEA_Hi_Liver4


title: HT-1197_Rosiglitazone_rep_1


title: h3.3ko_S12h_1 [h3.3ko_S12h_1]


title: R21105185LR01-KYSE450-1-1

address: 北京市朝阳区潘家园南里17号


title: BEA_Hi_Liver2


title: h3.3ko_MS_3 [h3.3ko_MS_3]

value: mature seeds


title: BEA_Hi_Liver1


title: HT-1197_DMSO_rep_2

value: DMSO (Vehicle)


title: HT29_NC2

first: Haoyan

last: Chen

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg38) using HISAT2 version 2.1.0   with the default options with a TopHat transcript index built from Ensembl_GRCh38.
Count files of the aligned sequencing reads were generated by the featurecount
Genome_build: hg38
Supplementary_files_format_and_content: count file

source_name: HT29 cell line

extract_protocol:
Total RNA of HT29 cells with different treatments was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human colorectal cancer cells

tag: passage

value: medium control


title: h3.3ko_MS_2 [h3.3ko_MS_2]


title: h3.3ko_MS_1 [h3.3ko_MS_1]


title: HT29_NC1


title: BEA_Lo_Liver4


title: R21105188LR01-KYSE450-4-2

address: 北京市朝阳区潘家园南里17号


title: HT-1197_DMSO_rep_1


title: HT29_FN3

value: cocultured with F. nucleatum


title: ENNB_Hi_Liver6


title: Col_G24h_3 [Col_G24h_3]

value: imbibed seeds

value: Col

value: seeds subject to germination for 24 hours


title: Col_G24h_2 [Col_G24h_2]


title: C4-2-ENZ rep2

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (GRCh38/hg38) using STAR (2.5.2b)
HTSeq was used to calculate gene expression
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data file is in TSV format: geneID <TAB> raw_count

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol:
Total RNA were extracted using standard RNA extraction method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C4-2 cells were treated with/without enzalutamide for 1 month.

tag: disease state

value: prostate cancer

value: prostate cancer cell

tag: phenotype

value: enzalutamide-resistant


title: HT-1197_Rosiglitazone_rep_2

value: Urinary Bladder Carcinoma

value: 24 hours


title: HT29_FN2


title: h3.3ko_S12h_2 [h3.3ko_S12h_2]


title: C4-2-ENZ rep1


title: ENNB_Hi_Liver5

value: Liver


title: HT29_NC3


title: Col_G24h_1 [Col_G24h_1]


title: C4-2-CON rep2

value: control


title: C4-2-CON rep1


title: Col_G12h_3 [Col_G12h_3]

value: seeds subject to germination for 12 hours


title: ENNB_Hi_Liver4


title: HT29_FN1


title: ENNB_Hi_Liver3


title: Control knockdown-2

city: Hamilton

first: Ava

last: Keyvani Chahi

state: ON

address: 1280 Main Street West

country: Canada

institute: McMaster University

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 24) using STAR version 2.5.1b
Gene expression were obtained as readcount directly from STAR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file of gene-level counts
Supplementary_files_format_and_content: raw counts

source_name: Human Cord Blood

growth_protocol: Mononucleated cells (MNC) from cord blood samples were isolated by density gradient centrifugation with Ficoll-Paque (GE Healthcare). Stem and progenitor cells were enriched by lineage depletion using the StemSep Human Progenitor Cell Enrichment Kit according to the manufacturer’s protocol (StemCell Technologies) and viably frozen in FBS-10% DMSO. Ex vivo suspension culture of Lin-CD34+ cells was in StemSpan Serum Free Expansion Medium (Stem Cell Technologies) supplemented with growth factors Thrombopoietin (TPO; 20 ng/ml, Peprotech), Stem cell factor (SCF; 100 ng/ml, R&D Systems), Flt3 ligand (FLT3-L; 100 ng/ml, R&D Systems) and Interleukin 6 (IL-6; 20 ng/ml, Peprotech) at 37oC 5% CO2.

extract_protocol:
RNA was isolated by TRIzol-LS following manufacturer’s protocol (ThermoFisher Scientific), and then further purified using RNeasy Micro columns (Qiagen) and quantified by QuBit (ABI). Quality of total RNA was assessed with BioAnalyzer Nano (Agilent) and all samples had a RIN above 8.
250 ng of total RNA was used for library preparation. Libraries were constructed using the KAPA RNA PolyA Stranded kit

treatment_protocol: Lin-CD34+ cells were isolated by FACS and cultured for 6-12 hours prior to lentiviral introduction at multiplicity of infection (MOI) of 50-100 lentiviral particles per cell. 72 hours following lentiviral administration when transgene expression is maximal, transduction-marker-positive cells were isolated by FACS.

value: Lin-CD34+ HSPCs

tag: shRNA

value: Control knockdown


title: MCF10A, TGFb3, rep3

city: Seoul

first: Jungmin

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

institute: Korea University College of Medicine

data_processing:
Sequencing reads were trimmed for bases with base quality score less than 20
Trimmed sequencing reads were aligned to mouse transcriptome hg38 using HISAT2
Transcript abundances were estimated by StringTie2
Genome_build: hg38
Supplementary_files_format_and_content: tpm-values-all-samples.txt

source_name: MCF10A, TGFb3

growth_protocol: MCF10A cells were cultured in DMEM/F12 (Gibco-Life Technologies) containing 5% horse serum, EGF (100ng/ml), hydrocortisone (1mg/ml), cholera toxin (1mg/ml), insulin (10mg/ml), and pen/strep (Gibco-Life Technologies) at 37˚C in 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent.
RNA sequencing was performed using the Illumina NovaSeq 6000 system, with paired-end 2 x 101 bp read length

treatment_protocol: MCF10A cells were cultured under high calcium conditions (10 mM calcium + 1 mM ionomycin) for 16 hrs, or treated with TGFb1, 2, or 3 (10 nM) for 16 hrs.

value: Breast

value: 16 hrs with TGFb3


title: HT-1197_DMSO_rep_3

value: DMSO (Vehicle)


title: BEA_Lo_Liver5


title: MCF10A, TGFb3, rep2


title: Control knockdown-1


title: MCF10A, TGFb3, rep1


title: Col_G12h_1 [Col_G12h_1]


title: Col_G12h_2 [Col_G12h_2]


title: MCF10A, high calcium, rep3

source_name: MCF10A, high calcium

value: 16 hrs with high calcium (10mM calcium with ionomycin)


title: ENNB_Hi_Liver1


title: PLAG1 knockdown-2

value: PLAG1 knockdown


title: MCF10A, high calcium, rep1


title: ENNB_Lo_Liver3


title: Ctrl_Liver6

value: Ctrl


title: Col_S48h_2 [Col_S48h_2]

value: imbibed seeds

value: Col

value: seeds stratified for 48 hours


title: MCF10A, high calcium, rep2


title: Luciferase overexpression-2

tag: transduction

value: Luciferase overexpression


title: PLAG1 knockdown-1


title: Col_S48h_3 [Col_S48h_3]

tag: treatment


title: Col_S48h_1 [Col_S48h_1]


title: Ctrl_Liver4


title: Col_S24h_3 [Col_S24h_3]

value: seeds stratified for 24 hours


title: Luciferase overexpression-1


title: PLAG1-S overexpression-2

value: PLAG1-S overexpression


title: MCF10A, control, rep3

source_name: MCF10A, control

value: untreated


title: MCF10A, control, rep2


title: Ctrl_Liver2

value: Liver


title: PLAG1-S overexpression-1


title: ENNB_Hi_Liver2


title: Col_S24h_1 [Col_S24h_1]


title: Ctrl_Liver3


title: MCF10A, control, rep1


title: ATACseq_Treg_Foxp3_KO_rep3

city: Aachen

first: Zhijian

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

data_processing:
ATAC-seq libraries were trimmed with Trim Galore (parameters -q 30 –paired –trim1) and aligned to mouse genome (mm9) using Bowtie2  (parameters -X2000 –no-mixed –no-discordant)
Duplicates fragments were removed, and reads were filtered for alignment quality of >Q30 using samtools
Next, we use MAC2 to perform peak calling (parameters –nomodel –nolambda –keep-dup auto –call-summits)
Transcription factor footprinting and differential activity was performed using HINT-ATAC
Genome_build: mm9

source_name: splenic Treg cells

extract_protocol: Omni-ATAC-seq was performed according to  with minor modifications. Prior to transposition dead cells were removed by centrifugation (800 rpm, 4 min, 4°C). The transposition reaction was with 7.5 μL Tagment DNA Enzyme 1 (TDE1) for 60 ‘min at 37°C. Pre-amplification was with NEBNext Ultra II Q5 Master Mix and Nextera PCR Primers (5 cycles). Quantitative PCR amplification was with NEBNext Ultra II Q5 Master Mix, Nextera PCR Primer and SYBR Gold to determine the number of additional cycles. PCR amplification of additional cycles was as for pre-amplification. PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined by Agilent High Sensitive DNA Kit and TapeStation, respectively. ATACseq libraries were sequenced on the Illumina NextSeq 500 Platform with 75 bps paired-end reads in duplicates.

value: splenic Treg cells


title: FLAG-PLAG1-S-3

data_processing:
Library strategy: CUT&RUN
CUT&RUN sequencing was trimmed using fastp v. 0.19.5 and aligned to GRCh38 and S. cerevisiae yeast genome (sacCer3) for the spike-in normalization using bowtie2 v. 2.3.5.
Bam files were sorted and indexed based on the genomic coordinates using samtools v.1.9. Bam files of the replicates were pooled, and peaks were called from the pooled replicates by MACS2 v. 2.2.5 based on FLAG vs IgG with the spike-in control normalization and q-value cutoff <0.05. Peaks that overlap with the Encode black list have been removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed file of spike-in-normalized peaks

extract_protocol:
Following CUT&RUN protocol, DNA was extracted with the MinElute PCR Purification kit (Qiagen 28004)
DNA libraries were prepared with ThruPLEX® DNA-Seq Kit (Takara R400675) and DNA Unique Dual Index Kit (Takara R400666) according to manufacturer’s instructions.

tag: antibody

value: Lin-CD34+ HSPCs


title: Col_S12h_3 [Col_S12h_3]

tag: tissue

value: seeds stratified for 12 hours


title: ATACseq_Treg_Foxp3_KO_rep2


title: FLAG-PLAG1-S-2


title: Col_S12h_2 [Col_S12h_2]


title: ATACseq_Treg_Foxp3_KO_rep1


title: FLAG-PLAG1-S-1


title: Col_S12h_1 [Col_S12h_1]


title: ATACseq_Treg_WT_rep3


title: IgG-3

value: IgG


title: Col_S24h_2 [Col_S24h_2]


title: Col_MS_3 [Col_MS_3]

value: mature seeds


title: ATACseq_Treg_WT_rep2


title: Ctrl_Liver1


title: IgG-1


title: Control, WDSW, 4 Weeks, Mouse 1

city: Richmond

first: Huiping

last: Zhou

state: VA

address: 1220 East Broad Street

department: Department of Microbiology and Immunology

institute: Virginia Commonwealth University

data_processing:
BBDuk
Sequencing reads were trimmed and filtered using bbduk to remove adapters and low-quality reads.
Reads from mouse samples were mapped to Ensembl GRCm38 transcripts annotation (release 82), using RSEM.
Assembly: GRCm38
Supplementary files format and content: one tab-delimited matrix file including count values for all samples

extract_protocol:
Total liver RNA of HuRhKO mice fed with WDSW for 4 weeks was isolated using Chemagic Prepito®-D Nucleic Acid Extractor (PerkinElmer, USA) with a Prepito RNA kit (PerkinElmer, USA).
RNA libraries for RNA-seq were prepared using NGS platforms following Genewiz's protocols.

treatment_protocol:
HuRflox/flox mice (C57BL/6 J) were from the Jackson Laboratory (Bar Harbor, ME). Hepatocyte-specific HuR knockout (HuRhKO) mice were generated by tail-vein injection of HuRflox/flox mice with AAV8-thyroxine-binding globulin promoter (TBGP)-Cre recombinase from Addgene (Watertown, MA).
Control mice were injected with the same amount of AAV8-TBGP-GFP from Vector Biolabs (Malvern, PA). Age and gender-matched HuRhKO and control mice were fed ad libitum a Western diet, with 42% kcal from fat and containing 0.1% cholesterol from Envigo (Cat#: TD.88137, Indianapolis, IN) with a high fructose-glucose solution (23.1 g/L d-fructose +18.9 g/L d-glucose) (Western diet plus sugar water, WDSW) for 4 weeks

value: Control

tag: diet

value: WDSW

value: 4 weeks

tag: Sex

value: male


title: 4M, ovoid cells

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M.smegmatis MC2 155 genome using bowtie2 with parameters -p 4 (and --local --dovetail in case paired-end sample)
Reads counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of reads (or fragments) overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped reads were used in a subsequent analysis. The files "Counts_XX.txt" represent these counts (File "Counts_all.txt" contains values for all samples).
Assembly: NC_008596.1

organism: Mycolicibacterium smegmatis MC2 155

source_name: bacterial culture

growth_protocol: Cells were first grown in Nutrient broth (“Himedia”, India) in the presence of 0.05 % Tween-80 at 37 °C and 200 rpm for 24 h. The resulting culture was added at a concentration of 105–106 cells/ml to 250 ml of Sauton (pH 7.0, for “active” cultures) or modified Sauton (pH 6.0-6.2, for “dormant” cultures) medium. The modified Sauton medium contained (per litre): 0.5 g KH2PO4; 1.4 g MgSO4·7H2O; 4 g L-asparagine; 60 ml glycerol; 0.05 g ferric ammonium citrate; 2 g sodium citrate, and 0.1 ml 1% ZnSO4·7H2O, supplemented with 0.05% Tween-80. The modification included a decrease of the initial pH to 6.0–6.2 (no titration with NaOH) (Kudykina et al., 2011). Cultures were incubated at 37°C under constant shaking for 10–20 days, and pH values were periodically measured. Active control cultures were harvested at late exponential/pre-stationary phase. Dormant cells were harvested when cultures entered the post-stationary phase, changing the color and reaching pH 6.0–6.2 (after 13–15 days of cultivation). Cultures were transferred to plastic-capped tubes (50 ml) and maintained under static conditions without agitation at room temperature for up to 30 days post inoculation.

extract_protocol:
Active and dormant (ovoid) cultures were harvested by centrifugation at 7000 rpm for 15 min and washed 3 times with an ice-cold PBSm buffer containing (per liter) 8 g NaCl, 0.2 g MgCl2, and 0.24 g Na2HPO4 (pH 7.0). The bacterial pellet was re-suspended in the same buffer containing phenylmethanesulfonyl fluoride (PMSF) then lysed by using zirconium beads on a bead beater homogenizer (MP Biomedicals FastPrep-24) for 30 sec, three times. The bacterial lysate was centrifuged at 13000 rpm for 10 min at 4 °C. The supernatant was separated into membrane and cytosolic fractions using ultracentrifugation at 105000g and 4 °C for 2 h. The membrane fraction was washed with PBSm using ultracentrifugation. For RNA isolation the pellet was re-suspended in ice-cold 100 mM HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) buffer (pH 8.0) containing 5 mM EDTA and the zwitterionic detergent CHAPS (3-(3-cholamidopropyl) dimethylammonio-1-propanesulfonate hydrate (2%) (w/v)).
Total RNA waw isolated by phenol-chloroform extraction as described previously [Rustad TR, Roberts DM, Liao RP, Sherman DR. Isolation of mycobacterial RNA. Methods Mol Biol. 2009;465:13–21.]
After isolation RNA was treated with Turbo DNase (Life Technologies, USA) to remove traces of genomic DNA. Amounts and purity of RNA were determined spectrophotometrically; integrity of RNA was assessed in 1% agarose gel. Sequencing libraries were generated using the resulting RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, USA) according to the manufacturers' protocol.

tag: cell type

value: bacterial culture

tag: strain

tag: state

value: dormant (ovoid)


title: Control, WDSW, 4 Weeks, Mouse 2


title: HuR hKO, WDSW, 4 Weeks, Mouse 3

value: Hepatocyte-specific HuR knockout


title: Col_MS_1 [Col_MS_1]

value: Col


title: ATACseq_Treg_WT_rep1


title: IgG-2


title: Col_MS_2 [Col_MS_2]


title: Skin Tissue,white,S07

status: Public on Nov 30 2022

city: Guiyang

first: wei

last: yuan

state: Guizhou Province

address: Huaxi District

department: College of Animal Science

institute: Guizhou University

description: miRNA

data_processing:
The raw image data files obtained from Illumina X-ten platform sequencing are converted into raw sequencing sequences (Raw Data or Raw Reads) by Base Calling and the results are stored in FASTQ file format
Sequence alignment of Unannotated reads with the reference genome using Bowtie software to obtain position information on the reference genome
Sequences of reads from the reference genome on the alignment were compared with mature miRNA sequences from the known miRNA database miRBase (v21)
miRDeep2 is mainly used for animal miRNA prediction
The expression of miRNAs in each sample was counted and the expression was normalized by TPM algorithm
Assembly: Sscrofa11.1

organism: Sus scrofa

source_name: Skin Tissue

extract_protocol:
The skin tissues were disinfected with alcohol and the hairs were removed, and the skin tissues were placed in RNAwait and stored at -80 ℃. The RNA was extracted using the NEB Next Ultra small RNA Sample Library Prep Kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin Tissue

value: Xiang

tag: skin color

value: white


title: 3M, active cells

value: active


title: Skin Tissue,white,S06

description: miRNA


title: Skin Tissue,white,S02

description: miRNA


title: Skin Tissue,black,S04

description: miRNA

value: black


title: HuR hKO, WDSW, 4 Weeks, Mouse 4

value: Liver

tag: genotype


title: Skin Tissue,black,S03

description: miRNA


title: 85_tumor

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

hyb_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA) equipped with extended dynamic range (XDR) software, according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual. Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol

data_processing: signal intensities were extracted by Agilent Feature Extraction 10.7.3.1 software. The arrays were normalized by dividing by the mean intensity only using the 25th and 75th percentile range of the data. Intensity level of each miRNA was scaled by the median of the distribution of the miRNA for samples processed in the first chip version and by the median of the distribution of the miRNA for samples processed in the second chip version, and all values multiplied for the mean value between the two medians. Data were log2-trasformed. For the analyses we consider just miRNAs common at the two platforms and miRs that were absent across all samples were removed. miRNAs not expressed were excluded

source_name: Oral Cavity

extract_protocol: Total RNA extraction was performed using the RNeasy kit (Qiagen) following the manufacturer's instructions.

tag: gender

value: Female

tag: g

tag: t

tag: n

tag: hpv

value: HPV-

value: Oral Cavity


title: 84_tumor

label_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

value: Male


title: 85_peritumor


title: 86_normal

source_name: Pharynx

value: N+

value: Pharynx


title: 85_normal


title: 5_tumor

source_name: Larynx

value: Larynx


title: 86_peritumor


title: 84_peritumor


title: 82_tumor


title: 84_normal


title: 82_normal


title: Skin Tissue,black,S05

description: miRNA


title: 82_peritumoral


title: 81_tumor


title: 81_normal


title: 80_normal


title: 76_tumor


title: 74_tumor


title: 76_normal


title: 86_tumor


title: 80_peritumor


title: 74_peritumoral


title: 81_peritumor


title: 80_tumor


title: 74_normal


title: 76_peritumoral


title: 73_peritumor

value: HPV+


title: 73_normal


title: 73_tumor


title: 71_tumor


title: 71_normal


title: 71_peritumor


title: 70_tumor


title: 70_peritumor


title: 69_tumor


title: 69_peritumor


title: 70_normal


title: 69_normal


title: 67_normal


title: 68_peritumor


title: 68_tumor


title: 65_normal


title: 65_peritumor


title: 68_normal


title: 67_tumor


title: 67_peritumor


title: 65_tumor


title: 62_tumor


title: 62_normal


title: 59_tumor


title: 62_peritumor


title: 59_peritumor


title: 59_normal


title: 58_normal


title: 58_tumor


title: 57_tumor


title: 56_normal


title: 55_tumor


title: 57_normal


title: 58_peritumor


title: 57_peritumor


title: 55_normal


title: 54_tumor


title: 53_peritumor


title: 53_tumor


title: 56_tumor


title: 56_peritumor


title: 52_tumor


title: 51_peritumor


title: 49_tumor


title: 49_peritumor


title: 54_peritumor


title: 54_normal


title: 48_tumor


title: 48_peritumor


title: 53_normal


title: 55_peritumor


title: 51_tumor


title: 46_tumor


title: 47_tumor


title: 46_peritumor


title: 52_normal


title: 47_normal


title: 51_normal


title: 45_tumor


title: 47_peritumor


title: 52_peritumor


title: 45_normal


title: 45_peritumor


title: 44_tumor


title: 44_normal


title: 44_peritumor


title: 41_tumor


title: 42_normal


title: 42_peritumor


title: 49_normal


title: 41_peritumor


title: 41_normal


title: 40_tumor


title: 48_normal


title: 39_tumor


title: 39_peritumor


title: 40_normal


title: 46_normal


title: 39_normal


title: 37_tumor


title: 36_peritumor


title: 36_normal


title: 36_tumor


title: 37_normal


title: 37_peritumor


title: 35_normal


title: 34_tumor


title: 34_peritumor


title: 34_normal


title: 33_tumor


title: 33_peritumor


title: 33_normal


title: 35_peritumor


title: 32_tumor


title: 42_tumor


title: 32_peritumor


title: 40_peritumor


title: 32_normal


title: 31_peritumor


title: 31_tumor


title: 31_normal


title: 30_normal


title: 30_peritumor


title: 29_tumor


title: 28_tumor


title: 30_tumor


title: 29_normal


title: 35_tumor


title: 28_peritumor


title: 27_tumor


title: 28_normal


title: 26_normal


title: 26_peritumor


title: 27_peritumor


title: 25_normal


title: 25_peritumor


title: 26_tumor


title: 24_normal


title: 24_peritumor


title: 23_peritumor


title: 23_normal


title: 23_tumor


title: 22_tumor


title: 22_peritumor


title: 22_normal


title: 21_tumor


title: 29_peritumor


title: 21_peritumor


title: 20_peritumor


title: 20_tumor


title: 21_normal


title: 20_normal


title: 19_tumor


title: 27_normal


title: 25_tumor


title: 24_tumor


title: 19_peritumor


title: 18_normal


title: 18_peritumor


title: 12_normal


title: 12_peritumor


title: 19_normal


title: 17_peritumor


title: 14_peritumor


title: 13_peritumor


title: 14_normal


title: 18_tumor


title: 12_tumor


title: 17_tumor


title: 15_peritumor


title: 13_normal


title: 17_normal


title: 14_tumor


title: 15_tumor


title: 10_tumor


title: 10_peritumor


title: 9_tumor


title: 15_normal


title: 13_tumor


title: 8_tumor


title: 7_tumor


title: 7_normal


title: 6_normal


title: 6_peritumoral


title: 8_peritumor


title: 8_normal


title: 9_peritumor


title: 4_tumor


title: 10_normal


title: 126_tumor


title: 133_tumor


title: 124_tumor


title: 123_tumor


title: 121_tumor


title: 120_tumor


title: 119_tumor


title: 4_peritumor


title: 117_tumor


title: 118_tumor


title: 114_tumor


title: 115_tumor


title: 113_tumor


title: WAT_Pnpla7_WT_4W

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression in WT WATs at 4 weeks

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Mouse GE 4x44K v2 Microarray  for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.0.1.1) with set to default for all parameters.

source_name: WT WAT at 4 weeks

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted from livers was purified using a RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

value: WAT

value: WT

tag: age

value: 4 weeks


title: 111_tumor