title: ATAC-seq KD_HBVneg_rep2

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street

institute: Purdue university

description: HepAD38 -HBV DDX5KD

data_processing:
Data quality control was performed using FastQC v0.11.8. Raw sequencing reads were mapped to hg19 using bowtie2.3.4.3 [2] with “-X 2000”.
All other parameters were kept as default. Duplicate and low quality (MAPQ<30) reads are removed using PicardTools2.21.6
Differential chromatin accessible regions/peaks between DDX5 WT and KD were obtained using MACS2.1.2, peaks overlapped with the hg19 blacklist(wgEncodeDacMapabilityConsensusExcludable.bed) are removed
HOMER4.9.1 was used to annotate the peaks with their adjacent genes that were then subjected to pathway analysis against all biological processes from gene ontology (GO) using Matescape
The IGV tracks were made using bamCoverage from DeepTools3.3.0 with parameter “-p 3 -bs 5 --normalizeUsing CPM -- ignoreDuplicates” and visualized by IGV browser
Genome_build: hg19
Supplementary_files_format_and_content: IGV tracks: bigwig files
Supplementary_files_format_and_content: peak files: .bed files

growth_protocol: Cells were cultured for 10 days. Media was changed every 3 days and passaged if cells were confluent.

extract_protocol:
Cells (5 x 104) were washed in cold PBS and lysed in 50 µl of lysis buffer (10 mM Tris HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Following lysis and centrifugation, nuclei were used for transposition using Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Cat# 20034197) per manufacturer’s protocol. The transposed DNA was cleaned using Qiagen Reaction Cleanup kit (Cat# 28204), eluted in 10 µL elution buffer and stored at -20oC.
Transposed DNA was PCR amplified using primers containing unique adapters. Amplified library was purified using Qiagen MinElute PCR Purification Kit (Cat#28004). Pairedend 2x50 bp sequencing was performed using a HiSeq2500 system (Illumina).

tag: gender

value: male

tag: age

value: 15 yr

tag: passage

value: Liver

tag: genotype/variation

value: KD


title: ATAC-seq KD_HBVneg_rep1

status: Public on Oct 07 2020

type: SRA

country: USA

description: HepAD38 -HBV DDX5KD

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: tissue


title: Pig CiaD input #6

city: Pullman

first: Michael

middle: E

last: Konkel

state: WA

institute: Washington State University

library_source: transcriptomic

data_processing:
MiSeq Instrument Software was used to generate fastq files.
Reads were aligned to the genome using bowtie2 version 2.3.2 using default options.
Reads mapping to each CDS were counted using featureCounts from the subread package, version 1.5.3 using the --largestOverlap option.
Genome_build: Genbank file associated with accession CP006851.1 was used for mapping reads to the C. jejuni genome.
Supplementary_files_format_and_content: Comma delimited text file containing counts of mapped transcripts CDS.

molecule: polyA RNA

organism: Campylobacter jejuni

source_name: Pig CiaD input #6

growth_protocol: C. jejuni were grown in 250 mL MH broth cultures in a microaerobic environment shaking at 220 rpm on an orbital shaker, adjusted to an OD540 of 0.3 in phosphate buffered saline before injection into the intestinal lumen.

extract_protocol:
Bacterial pellets were collected by centrifugation and snap frozen. RNA Extraction was done using the Ambion Ribopure Bacteria kit. rRNA was depleted with 3’ biotinylated oligonucleotides that were designed to hybridize with C. jejuni 16S and 23S rRNAs.
Illumina MiSeq libraries were prepared using the KAPA stranded RNAseq kit

tag: strain/genotype

value: F38011 ∆ciaD

tag: culture time (hours)

tag: culture condition

value: Mueller-Hinton Broth


title: Pig CiaD input #5

source_name: Pig CiaD input #5


title: ATAC-seq WT_HBVneg_rep2

description: HepAD38 -HBV DDX5WT

value: WT


title: Pig CiaD input #11

source_name: Pig CiaD input #11


title: shRNA6

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq data was analyzed by following the procedure described here. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in ≥90% bases, the good quality reads were aligned to the University of California Santa Cruz’s Mus musculus reference genome and transcriptome (build mm10) using the Burrows-Wheeler Aligner.43 The reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were combined to calculate as expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads44 in order to compare transcription levels among samples. The transcripts with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log2 base scale. Principal component analysis was first performed to assess the sample correlations using the expression data of all the genes. The DEGs in diabetic mice versus control mice were identified by the R package DEGseq for sorted GECs, and we selected the genes based on DEGseq adjusted P < 0.05 and 1.5-fold change. The limma test45 was applied for analysis of data in isolated glomeruli with a cutoff of P < 0.05 and 1.5-fold change. The Gene Ontology and pathway analysis for the differentially expressed genes were then performed using INGENUITY IPA (http://www.ingenuity.com/products/ipa) and online tool Enrichr.19 The read coverage of gene functional elements was also visualized by IGV tool (Integrative Genome Viewer; http://www.broadinstitute.org/igv/) from the genome alignment file. Heat map analysis was performed for the top 50 fold-changed DEGs with DEGseq test after median center transformed using Multiple Experiment Viewer (Web MEV) software (mev.tm4.org).46
Supplementary_files_format_and_content: hg38

molecule: total RNA

source_name: podocyte cell line

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RARRES1 shRNA KD

tag: cell type

value: podocyte cell line

tag: treatment

value: TNFa treated


title: shRNA5


title: shRNA4


title: Pig CiaD input #4

source_name: Pig CiaD input #4


title: Pig WT input #8

source_name: Pig WT input #8


title: shRNA2

value: untreated


title: Pig WT input #9

source_name: Pig WT input #9


title: shRNA3


title: Pig WT input #7

source_name: Pig WT input #7


title: shRNA1


title: Pig WT input #6

source_name: Pig WT input #6


title: GIPZ6

value: Scramble shRNA


title: GIPZ5


title: Pig WT input #4

source_name: Pig WT input #4


title: Pig WT input #5

source_name: Pig WT input #5


title: OVE3

value: RARRES1 over-expression


title: CON3

value: Backbone control plasmid


title: Pig WT input #3

source_name: Pig WT input #3


title: Pig CiaD input #10

source_name: Pig CiaD input #10


title: GIPZ1


title: GIPZ4


title: GIPZ3


title: ATAC-seq WT_HBVneg_rep1

description: HepAD38 -HBV DDX5WT


title: Pig CiaD 30 hour Animal #3 Loop #2

source_name: Pig CiaD 30 hour Animal #3 Loop #2

value: Pig ligated intestinal loop


title: Pig WT input #11

source_name: Pig WT input #11


title: CON2


title: GIPZ2


title: CON1


title: Pig WT input #12

source_name: Pig WT input #12


title: Pig CiaD 30 hour Animal #2 Loop #2

source_name: Pig CiaD 30 hour Animal #2 Loop #2


title: Pig CiaD 30 hour Animal #1 Loop #4

source_name: Pig CiaD 30 hour Animal #1 Loop #4


title: Pig WT input #2

source_name: Pig WT input #2


title: Pig CiaD input #1

source_name: Pig CiaD input #1


title: Pig CiaD 30 hour Animal #1 Loop #2

source_name: Pig CiaD 30 hour Animal #1 Loop #2


title: Pig CiaD 30 hour Animal #2 Loop #4

source_name: Pig CiaD 30 hour Animal #2 Loop #4


title: Pig CiaD 12 hour Animal #3 Loop #4

source_name: Pig CiaD 12 hour Animal #3 Loop #4


title: TIB-PKF_S17_L001

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description:
not transfected
PKF118-310-treated
TIB-PKF

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to hg38 using HISAT2 to generate bam files
Counts aligns reads per gene with HTSeq
Differentially expressed gene list was obtained by using DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-normalized read counts; DEseq2-differentially expressed genes

source_name: Owen O’Connor (Columbia University, NY)

growth_protocol: CUTTL1 and TIB153 cells were maintained in RPMI with 10% FBS

extract_protocol:
RNA was extract with Trizol, and purified via Qiagen RNeasy column
Illumina stranded mRNA library prep kit was used
mRNA was enriched by using polyT beads, heat fragmentated, then reverse transcribled to cDNA.  Illumina adapters were ligated to the cDNA and PCR was performed to get the final library.

treatment_protocol: cells were treated with β-Catenin/Tcf Inhibitor II, PKF118-310 at the indicated time/concentrations in the manuscript

value: human T-ALL line


title: TIB-CON_S14_L001

description:
not transfected
control
TIB-CON

value: control


title: TIB-CON_S14_L002

description:
not transfected
control
TIB-CON


title: Pig CiaD 30 hour Animal #3 Loop #4

source_name: Pig CiaD 30 hour Animal #3 Loop #4


title: Pig WT input #10

source_name: Pig WT input #10


title: OVE1

source_name: podocyte cell line


title: OVE2


title: Pig CiaD 12 hour Animal #3 Loop #2

source_name: Pig CiaD 12 hour Animal #3 Loop #2


title: CUTTL-PKF_S7_L002

description:
not transfected
PKF118-310-treated
CUTTL-PKF


title: Pig CiaD 12 hour Animal #2 Loop #2

source_name: Pig CiaD 12 hour Animal #2 Loop #2


title: Pig CiaD 12 hour Animal #2 Loop #4

source_name: Pig CiaD 12 hour Animal #2 Loop #4


title: TIB-PKF_S17_L002


title: CUTTL-PKF_S7_L001


title: Pig CiaD 12 hour Animal #1 Loop #4

source_name: Pig CiaD 12 hour Animal #1 Loop #4


title: CUTTL-CON_S4_L001

description:
not transfected
control
CUTTL-CON


title: Pig CiaD 6 hour Animal #3 Loop #2

source_name: Pig CiaD 6 hour Animal #3 Loop #2


title: Pig CiaD 12 hour Animal #1 Loop #2

source_name: Pig CiaD 12 hour Animal #1 Loop #2


title: Pig CiaD 6 hour Animal #2 Loop #4

source_name: Pig CiaD 6 hour Animal #2 Loop #4


title: Pig CiaD 6 hour Animal #3 Loop #4

source_name: Pig CiaD 6 hour Animal #3 Loop #4


title: SarcTg_R134G_1

city: Farmington

first: Travis

last: Hinson

state: Connecticut

address: 10 Discovery Dr

institute: JAX-GM

description: TNNT2ko iPSC-CMs transduced with R134G TNNT2 lentivirus

data_processing:
Trimmed reads were aligned using STAR
HTSeq was utilized to convert files to raw transcript counts
Counts were analyzed with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: STAR alignment .bam files were converted to .counts using HTSeq (.counts files provided)

source_name: iPSC-CMs (cardiomyocytes)

extract_protocol:
Samples were trizoled and RNA was extracted using standard phenol-chloroform methods
Illumina TruSeq Stranded library preparation

value: iPSC-CMs (cardiomyocytes)

value: Day 25

tag: background

value: PGP1 TNNT2ko

tag: tnnt2 variant


title: SarcTg-R92Q-3

description: TNNT2ko iPSC-CMs transduced with R92Q TNNT2 lentivirus


title: SarcTg_R134G_3


title: Pig CiaD 6 hour Animal #2 Loop #2

source_name: Pig CiaD 6 hour Animal #2 Loop #2


title: SarcTg_R134G_2


title: SarcTg-R92Q-2


title: SarcTg-R92Q-1


title: Pig CiaD 6 hour Animal #1 Loop #2

source_name: Pig CiaD 6 hour Animal #1 Loop #2


title: Pig CiaD 6 hour Animal #1 Loop #4

source_name: Pig CiaD 6 hour Animal #1 Loop #4


title: Pig CiaD 3 hour Animal #3 Loop #4

source_name: Pig CiaD 3 hour Animal #3 Loop #4


title: SarcTg-WT-3

description: TNNT2ko iPSC-CMs transduced with WT TNNT2 lentivirus


title: SarcTg-WT-1


title: Pig CiaD 3 hour Animal #2 Loop #4

source_name: Pig CiaD 3 hour Animal #2 Loop #4


title: SarcTg-WT-2


title: Pig CiaD 3 hour Animal #3 Loop #2

source_name: Pig CiaD 3 hour Animal #3 Loop #2


title: CUTTL-CON_S4_L002

description:
not transfected
control
CUTTL-CON

source_name: Owen O’Connor (Columbia University, NY)


title: MCF7 Input

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

country: Sweden

institute: Scilifelab

data_processing:
ChIP-Seq reads were mapped to the human reference genome assembly hg38(GRCh38) using STAR. Reads with a mapping score of less than 20 and reads which assigned to multiple locations were discarded. ERβ-binding sites were identified by HOMER applying a false dis-covery rate (FDR) less than 0.001 and four-fold enrichment over control (Input) cut-off. Reads which overlap within 200 bp were used to obtain ERβ-binding sites. Only peaks that were present in at least 2 out of 3 replicates were considered for downstream analysis. HOMER was used to perform de novo motif analysis 200bp of identified peaks.
Genome_build: hg38(GRCh38)
Supplementary_files_format_and_content: bedgraph

source_name: Breast

growth_protocol: Cells were cultured in Dulbecco's modified Eagle’s medium (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (P/S) and 1% blasticidine (Sigma Aldrich)

extract_protocol:
Cells were crosslinked with formaldehyde and nuclear chormatin fractions were separted and immunoprecipitated with ERβ anitboides. Magnetic beads were used to pull down the immunoprecipitated DNA and separted by column preparation.
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions

treatment_protocol: All Cells were treated with 10 nM 17β-estradiol (E2, Sigma-Aldrich) dissolved in DMSO for 2h before ChIP experiment.

tag: chip antibody

value: PPZ0506, lot no:A2, mouse monoclonal


title: Pig CiaD 3 hour Animal #1 Loop #4

source_name: Pig CiaD 3 hour Animal #1 Loop #4

value: F38011 ∆ciaD


title: RNA-seq KD_HBVpos_SOR_rep3

description: HepAD38 +HBV DDX5KD +Sorafenib

data_processing:
Data quality control was performed using FastQC v0.11.8
The RNA expression level in each library was estimated by “rsem-calculate-expression” procedure in RSEM v1.3.112 using default parameters except “--bowtie-n 1 –bowtie-m 100 –seed-length 28 --paired-end”.
EdgeR v3.24.013 package was used to normalize gene expression among all libraries and identify differentially expressed genes among samples with following constraints: fold change > 1.5, FDR < 0.05 and TPM > 1
Genome_build: hg19
Supplementary_files_format_and_content: genes.results files

source_name: Hepatocellular carcinoma (HepG2)

growth_protocol: Cells were cultured for 10 days in the presence of tetracycline (no HBV replication) or absence of tetracycline (with HBV replication). Media was changed every 3 days and passaged if cells were confluent.

extract_protocol:
Total RNA was isolated using Purelink mRNA Mini kit (Life Technologies) as per manufacturer's protocol
Libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit, Cat. No. RS-122-2101, RS-122-2102

treatment_protocol: Cells were grown in culture media containing Sorafenib (2.5 μM) for three days prior to harvesting

value: Liver

value: HepG2-derived cell line HepAD38

tag: origin

value: Cancer cell line from 15 yr male

tag: genotype

value: KD

tag: induced hbv replication

value: +HBV

value: Sorafenib


title: RNA-seq KD_HBVpos_rep3

description: HepAD38 +HBV DDX5KD


title: Pig CiaD 3 hour Animal #1 Loop #2

source_name: Pig CiaD 3 hour Animal #1 Loop #2


title: MCF7 ERB ChIP-Seq rep 1


title: RNA-seq KD_HBVneg_rep3

description: HepAD38 -HBV DDX5KD

value: -HBV


title: Pig WT 30 hour Animal #3 Loop #3

source_name: Pig WT 30 hour Animal #3 Loop #3


title: MCF7 ERB ChIP-Seq rep 2


title: HT29 Input

source_name: colon


title: RNA-seq WT_HBVneg_rep3

description: HepAD38 -HBV DDX5WT

value: WT


title: Pig WT input #1

source_name: Pig WT input #1

value: Mueller-Hinton Broth


title: RNA-seq KD_HBVpos_SOR_rep2

description: HepAD38 +HBV DDX5KD +Sorafenib


title: Pig WT 30 hour Animal #3 Loop #1

source_name: Pig WT 30 hour Animal #3 Loop #1

value: Pig ligated intestinal loop


title: HT29 ERB ChIP-Seq rep 3


title: RNA-seq KD_HBVpos_rep2

description: HepAD38 +HBV DDX5KD


title: HT29 ERB ChIP-Seq rep 2


title: Pig WT 30 hour Animal #2 Loop #3

source_name: Pig WT 30 hour Animal #2 Loop #3


title: RNA-seq KD_HBVneg_rep2

description: HepAD38 -HBV DDX5KD


title: Pig WT 30 hour Animal #1 Loop #3

source_name: Pig WT 30 hour Animal #1 Loop #3


title: HT29 ERB ChIP-Seq rep 1


title: Pig WT 30 hour Animal #1 Loop #1

source_name: Pig WT 30 hour Animal #1 Loop #1


title: Pig CiaD 3 hour Animal #2 Loop #2

source_name: Pig CiaD 3 hour Animal #2 Loop #2


title: RNA-seq WT_HBVpos_rep2

description: HepAD38 +HBV DDX5WT


title: SW480 Input


title: RNA-seq WT_HBVneg_rep2

description: HepAD38 -HBV DDX5WT


title: Pig WT 12 hour Animal #3 Loop #3

source_name: Pig WT 12 hour Animal #3 Loop #3


title: Pig WT 12 hour Animal #3 Loop #1

source_name: Pig WT 12 hour Animal #3 Loop #1


title: SW480 ERB ChIP-Seq rep 2


title: RNA-seq WT_HBVpos_rep3

description: HepAD38 +HBV DDX5WT


title: RNA-seq KD_HBVpos_rep1

description: HepAD38 +HBV DDX5KD


title: RNA-seq KD_HBVpos_SOR_rep1

description: HepAD38 +HBV DDX5KD +Sorafenib


title: Pig WT 12 hour Animal #2 Loop #3

source_name: Pig WT 12 hour Animal #2 Loop #3


title: Pig WT 12 hour Animal #2 Loop #1

source_name: Pig WT 12 hour Animal #2 Loop #1


title: NG-Infected 1

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

country: China

institute: institution of microbology

description:
NG_05
gene_count.xls

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gene_count.xls: count matrix, raw counts.

source_name: macrophages under normal gravity, EPEC-infected

extract_protocol:
Macrophages were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit was used with ≧1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: normal gravity

value: EPEC infection


title: Pig WT 12 hour Animal #1 Loop #3

source_name: Pig WT 12 hour Animal #1 Loop #3


title: NG-Infected 2

description:
NG_06
gene_count.xls


title: Pig WT 30 hour Animal #2 Loop #1

source_name: Pig WT 30 hour Animal #2 Loop #1


title: SMG-Infected 2

description:
SMG_06
gene_count.xls

source_name: macrophages under SMG, EPEC-infected

value: simulated microgravity


title: RNA-seq KD_HBVneg_rep1

description: HepAD38 -HBV DDX5KD

source_name: Hepatocellular carcinoma (HepG2)


title: RNA-seq WT_HBVneg_rep1

description: HepAD38 -HBV DDX5WT


title: SMG-Infected 1

description:
SMG_05
gene_count.xls


title: Pig WT 12 hour Animal #1 Loop #1

source_name: Pig WT 12 hour Animal #1 Loop #1


title: Pig WT 6 hour Animal #3 Loop #3

source_name: Pig WT 6 hour Animal #3 Loop #3


title: Ly6C+ SPF 4

city: Tucson

first: Janko

last: Nikolich-Zugich

state: AZ

address: 1656 E. Mabel St.

institute: University of Arizona

data_processing:
Raw sequence reads were first demultiplexed using the SMART-Seq DE3 Demultiplexer software (www.takarabio.com/products/next-generation-sequencing/rna-seq/ultra-low-input-rna-seq/smart-seq-de3-demultiplexer) and read 1 files were used
Sequencing reads were evaluated using FastQC (v0.11.5, www.bioinformatics.babraham.ac.uk/projects/fastqc/) and preprocessed for quality using Trim Galore (v0.6.4, Phred score threshold of 20 and minimum length of 50 bp, www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Quality reads were then uniquely mapped to the mouse reference genome (GRCm38) using Tophat2 (v2.1.1)
Raw read counts for each sample were obtained by mapping reads at the gene-level using HTSeq-count tool from the Python package HTSeq. DESeq2 R-package (v1.26.0) was then used to perform differential expression (DE) and statistical analysis.
Raw read counts for genes over all samples were normalized through a regularized logarithm transformation (rlog) implemented in DESeq2.
Genome_build: GRCm38 (Mus musculus)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Sorted Primary Naïve CD8 T cells

extract_protocol:
RNA was isolated and purified using Macherey-Nagel NucleoSpin RNA XS columns and reagents (#740902.50)
3' differential expression libraries were generated for each sample using a Takara SMART-Seq v4 3' DE Kit (#635040) and an Illumina Nextera XT DNA Library Preparation Kit (#FC-131-1096) per kit protocol

value: Ly6C+ Naive CD8 T cell

tag: strain

tag: housing condition

value: Specific Pathogen Free


title: Pig WT 6 hour Animal #2 Loop #3

source_name: Pig WT 6 hour Animal #2 Loop #3


title: Ly6C+ SPF 2


title: SW480 ERB ChIP-Seq rep 3

source_name: colon

value: PPZ0506, lot no:A2, mouse monoclonal


title: Ly6C+ SPF 3


title: SW480 ERB ChIP-Seq rep 1


title: Pig WT 6 hour Animal #2 Loop #1

source_name: Pig WT 6 hour Animal #2 Loop #1


title: Ly6C+ SPF 1


title: Pig WT 6 hour Animal #1 Loop #3

source_name: Pig WT 6 hour Animal #1 Loop #3


title: Pig WT 6 hour Animal #1 Loop #1

source_name: Pig WT 6 hour Animal #1 Loop #1


title: Pig WT 6 hour Animal #3 Loop #1

source_name: Pig WT 6 hour Animal #3 Loop #1


title: Mut3_Muscle_E15

type: RNA

city: PARIS

first: Pascal

last: Maire

address: 24 Rue du Fg St Jacques

department: Développement Reproduction et Cancer

country: France

institute: Institut Cochin. INSERM U1016, CNRS UMR 8104, U.Paris

hyb_protocol: The cDNA was then hybridized to GeneChip® Mouse Gene 1.0 or 2.0 ST (Affymetrix) at 45 °C for 17 h. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix).

scan_protocol: the ChIPs were  scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for quality controls

data_processing: Normalisation with R, by project  Project 1 :   WT1_Muscle_E15,WT2_Muscle_E15,WT3_Muscle_E15,Mut1_Muscle_E15,Mut2_Muscle_E15,Mut3_Muscle_E15 → mogene20st_Mm_ENTREZG from Brainarray, version 20, Matrix 3  WT1_Muscle_E18,WT2_Muscle_E18,Mut1_Muscle_E18,Mut2_Muscle_E18 →  mogene10st_Mm_ENTREZG from Brainarray, version 20, Matrix 2  Then we conserved only common genes between the two lists.    Project 2 :  WT1_PAX7_E15, WT2_PAX7_E15, WT3_PAX7_E15, Mut1_PAX7_E15, Mut2_PAX7_E15, Mut3_PAX7_E15, WT6_PAX7_E18, WT7_PAX7_E18, WT8_PAX7_E18, Mut6_PAX7_E18,Mut7_PAX7_E18,Mut8_PAX7_E18   mogene20st_Mm_ENTREZG from Brainarray, version 19, Matrix 1    We strictly follow the Brainrray recomandations for the normalisation by using the affy package they provide for each version of their custom CDF files.

label: biotin

source_name: whole back muscle

label_protocol: 50 ng (E18.5 whole back muscles), 2 ng (E15.5 FACS-sorted cells and whole back muscles) or 0.21 ng (E18.5 FACS-sorted cells) of total RNA were reverse-transcribed following the Ovation PicoSL or PicoV2 WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen).

growth_protocol: No growth protocol, the tissue is extracted directly from E15 or E18 embryos

extract_protocol: RNA extraction from Pax7-nGFP+ FACS-sorted cells was performed using the Qiagen RNeasy microkit directly after isolation. Whole back muscles required a tissue lyser lyse step in Trizol solution.

treatment_protocol: no treatment

value: whole back muscle

tag: genotype/variation

value: SIX1/4 mutant


title: Ly6C- SPF 3

value: Ly6C- Naive CD8 T cell


title: Blastocyst_Aging

city: Narita

first: Yuta

last: Kawagoe

state: Chiba

address: 4-3, Kozunomori

department: Advanced reproductive medicine research center

country: Japan

institute: International University of Health and welfare

description:
Gene ecpression in aging blastocyst
Aging_blastocyst.txt:gProcessedSignal(normalized)

hyb_protocol: The Cy3-labeled cDNA was hybridized overnight at 65 ℃ for 17 hours toAgilent Whole Human Genome Microarray 4x44K v2. These platforms were washed with the Agilent Gene Expression Wash Buffer 1 (Agilent Technologies) for 1 minute at room temperature, and then washed with preheated Agilent Gene Expression Wash Buffer 2 (Agilent Technologies) for 1 minute at 37 ℃. Finally, these platforms were washed with acetonitrile (Agilent Technologies).

scan_protocol: The slides were scanned immediately after washing in the Agilent Microarray Scanner system (Agilent Technologies) detecting fluorescence signals. Fluorescence images were read out using the Agilent Feature extraction software (Agilent Technologies).

data_processing: Scanned images were analysed with the Agilent Feature Extraction Software (Agilent Technologies). The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. Further analysis of microarray data was performed by using Genespring GX 10.7 (Agilent Technologies). The intensity of genes were normalized using default normlization algorithm in  Genespring.

source_name: Human Blastocyst, 38-45 years of age

label_protocol: Two hundred fifty ng of each cDNA samples was labelled with Cy3 dye using quickamp labeling kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Five blastocysts in each group were lysed using SuperAmp Lysis Buffer (Milteny biotec) following the manufacturer's instructions. mRNAs were extracted from lysate by using magnetic beads technology (Milteny biotec). Extracted mRNAs were amplified by SuperAmp RNA amplification kit (Milteny biotec) which is based on a single-primer global PCR. Synthesis of cDNA was performed by using AffinityScript QPCR cDNA Synthesis Kit (Agilent Technologies) according to the manufacturer’s instructions. The quantity of amplified mRNA-derived cDNA was measured by the ND-1000 Spectrophotometer (Thermo Fisher scientific). The integrity of the cDNA was checked by the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: Surplus cryopreserved blastocysts of targeted patients were used as samples. Informed consent for using these blastocysts was obtained from the patients. Cryopresearved embryos were thawed by using Thawing medium (KITAZATO corporation) and immidiatry transferred to SuperAmp Lysis Buffer  (Milteny biotec).

tag: source subject age

value: aging group; 38-45yrs

value: preimplantation embryo

tag: developmental stage

value: Blastocyst


title: Pig WT 3 hour Animal #3 Loop #3

source_name: Pig WT 3 hour Animal #3 Loop #3

tag: strain/genotype


title: Ly6C- SPF 4


title: Ly6C- SPF 1


title: RNA-seq WT_HBVpos_rep1

description: HepAD38 +HBV DDX5WT

tag: tissue

value: Liver

tag: cell line

value: HepG2-derived cell line HepAD38

value: Cancer cell line from 15 yr male

tag: passage

value: +HBV


title: Pig WT 3 hour Animal #3 Loop #1

source_name: Pig WT 3 hour Animal #3 Loop #1

tag: culture time (hours)

tag: culture condition

value: Pig ligated intestinal loop


title: Mut1_Muscle_E15


title: Pig WT 3 hour Animal #2 Loop #3

source_name: Pig WT 3 hour Animal #2 Loop #3


title: Ly6C+ CH 4

tag: cell type

value: Cohoused with pet-shop


title: Mut2_Muscle_E15


title: Ly6C- SPF 2


title: Ly6C+ CH 3


title: Pig WT 3 hour Animal #1 Loop #3

source_name: Pig WT 3 hour Animal #1 Loop #3


title: WT1_Muscle_E15

value: WT


title: Blastocyst_Young

description:
Gene expression in young blastocyst
Young_blastopcyst.txt:gProcessedSignal(normalized)

source_name: Human Blastocyst, 25-37 years of age

value: young group; 25-37yrs


title: Pig WT 3 hour Animal #1 Loop #1

source_name: Pig WT 3 hour Animal #1 Loop #1


title: Ly6C+ CH 2

value: Ly6C+ Naive CD8 T cell


title: Ly6C+ CH 1


title: WT3_Muscle_E15


title: WT2_Muscle_E15


title: Ly6C- CH 4


title: Ly6C- CH 3


title: Ly6C- CH 2


title: Ly6C- CH 1


title: ATAC_Mouse_PDGFRab_UUO_Rep2

city: Aachen

first: Mahmoud

middle: M

last: Ibrahim

address: Pauwelsstraße 30

department: Faculty of Medicine

country: Germany

institute: RWTH Aachen University

description: PDGFRa+/PDGFRb+ were FACS sorted, nuclei were isolated and chromatin was tagmented using Tn5 transposase

data_processing:
Fastq files were aligned to mm10 genome build using STAR in end-to-end mode allowing fragment sizes up to 2000 bp and allowing only uniquely mapped reads. Sequencing duplicates were removed using Picard. Bigwig files were generated using JAMM’s SignalGenerator.sh script using both replicates as input and setting the binsize to 10bp and normalization to depth normalization.
Further details and analysis steps are provided In the methods section of the manuscript.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file containing the geometric average of depth normalized counts from both replicates at 10bp resolution.

extract_protocol:
Kidneys were removed and kidney tissue was digested using Liberase TL and DNAse for 30 min 37°C and apllied to GentleMACs program spleen 4 after 15 minutes and after 30 minutes.
ATAC-Seq libraries were generated according to Buenrostro et al. 2013 using custom primers that were compatible with Illumina Tn5 (Next-seq) and Illumina sequencing instrumens

tag: days after uuo

value: kidney (UUO, unilateral urether obstruction)

value: FVBN


title: ATAC_Mouse_PDGFRab_UUO_Rep1


title: Flower_H3K9me2_ChIPseq

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: H3K9me2 ChIPseq of Arabidopsis flower

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie (v1.1.2), allowing only uniquely mapping reads with 0 mismatches.
Duplicated reads were removed by Samtools.
ChIP-seq peaks were called by MACS2 (v2.1.1).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: ChIP-seq profile

organism: Arabidopsis thaliana

source_name: Arabidopsis flowers

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown at 22 °C in a long day (16 hour light, 8 hour dark) growth room. Flowers and leaves were collected from 4-5 week-old plants.

extract_protocol:
For H3K9me2 ChIP-seq in Arabidopsis flowers, 3 grams of Arabidopsis Col-0 wild-type unopened flower buds were collected. The nuclei were isolated from these materials for in vitro cross-linking with 1% formaldehyde. Nuclei were lysed and the chromatin was sheared with Bioruptor Plus (Diagenode). The sheared chromatins were equally separated for two ChIPs. 5 μl of anti-H3K9me2 (ab1220, abcam) and anti-H3 (ab1791, abcam) antibodies were added for chromatin immunoprecipitation, respectively. This experiment was performed by closely following the protocol described in a previous paper (Zhong et al., 2012).
ChIP-seq libraries were prepared from DNA extracted from the ChIP experiment using Ovation Ultra Low System V2 Kit following manufacturer instructions (NuGEN). The libraries were sequenced on a HiSeq 4000 sequencer (Illumina) to obtain single-end 50 bp reads.

value: flowers

value: 4 weeks

tag: antibody


title: Flower_H3_ChIPseq

description: H3 ChIPseq  of Arabidopsis flower


title: Heart of WT_3 with TAC

city: Ube,Yamaguchi

first: Shigeki

last: Kobayashi

institute: Yamaguchi university

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.8.01).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.8.01). Long reads with more than 1000 nucleotides and short reads with fewer than 20 nucleotides were also discarded.
The trimmed reads were mapped to the mouse reference genome mm38 release-92 using CLC Genomics Workbench software (ver.8.01) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.8.01).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample.

source_name: Heart

growth_protocol: Chow: normal diet and randomly fed, temprature: 22℃±1℃, Light-dark cycle: 12-hour light and 12-hour dark (lights on at AM8 and lights off at PM8)

extract_protocol:
Hearts were removed, and total RNA was isolated using RNeasy mini kit (Invitrogen). Polyadenylated  mRNA was purified with oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB). Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.
Fragmentation was performed with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After ligation, library fragments were enriched, and index sequences were inserted with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using an Agilent 2200 TapeStation (D1000, Agilent Thermo Fisher). The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina Next-seq DNA sequencer with 75 bp pair-end cycle sequencing kit (Illumina).

value: Heart

tag: age

value: 12 week old

tag: Sex

value: male

tag: genotype

tag: treatment

value: TAC


title: Heart of V3599K_2 without TAC

tag: strain

value: no TAC


title: Heart of V3599K_2 with TAC


title: Heart of WT_2 with TAC


title: Heart of V3599K_1 with TAC


title: Heart of V3599K_3 with TAC


title: Heart of V3599K_3 without TAC


title: Heart of WT_1 with TAC


title: Heart of WT_3 without TAC


title: Heart of WT_1 without TAC


title: Heart of WT_2 without TAC


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out H3K27me3 rep2

status: Public on Oct 06 2020

city: Bethesda

first: Tao

last: Zhen

state: Maryland

address: 9000 Rockville Pike

institute: NIH

data_processing:
Library strategy: ChIC-seq
For RNA-seq: Raw reads were mapped to mouse genome mm10 by STAR (v2.5.1b). The gene expression levels were quantified and normalized by cuffnorm from cufflinks (v2.2.1) package into an FPKM matrix. Genes were filtered if their expressions < 1 FPKM in all samples. The expression matrix was further log2-transformed. The significant differentially expressed genes (DEGs) were called by cuffdiff (v2.2.1) by requiring q-value <0.01, fold change >=2 and genes in the filtered expression matrix. The enriched GO terms were identified by findGO.pl from HOMER package5 for the DEGs. Gene set enrichment analysis was performed using GenePattern 2.0. Ingenuity Pathway Analysis (Ingenuity Systems) was performed to identify upstream regulator of the DEGs.
For ChIC-seq: Paired-end raw reads were mapped to mouse genome mm10 by Bowtie2 (v2.3.5) with key parameters of --no-mixed --no-discordant --local --very-sensitive. For the mapped paired end reads, only MAPQ>=10, non-redundant and fragment size >=140bp were kept for following analysis. The ChIC IgG data for Mx1-CreCbfb+/56M and Runx1f/fMx1-CreCbfb+/56M samples were pooled as control for calling peaks and normalization, the corresponding samples from two batches were pooled together to call peaks. ChIC-seq peaks were call by cLoops2 (https://github.com/YaqiangCao/cLoops2) with key parameters of -minPts 5 -eps 100,200. Briefly, the new peak-calling algorithm for ChIC-seq was based on the similar idea of cLoops, reads were clustered to find candidate peaks, and the candidate peaks were compare to local permutated background and control data to estimate significance. The target genes of peaks were annotated by annotatePeaks.pl from HOMER, motif analysis for Runx1 knockout changed peaks were carried out by findmotifsgenome.pl from HOMER. The aggregated normalized reads per million (RPM) signals for genes TSS were obtained from cLoops2 agg command.
For single cells RNA-sequencing (scRNA-seq): Reads were processed by 10x Cell Ranger (v3.1.0) command count, to the Cell Ranger mouse reference genome mm10-v3.0.0. The raw counts were further normalized by scaling the median counts through all cells, and two batches of data were separated for clustering analysis of UMAP with key parameters n_neighbors=100, n_components=2, min_dist=0, metric="euclidean" and epoch=1000.
Genome_build: mm10

source_name: abnormal myeloid progenitors cell

extract_protocol: AMP cells were fixed with 1% PFA and subjected to ChIC-seq as described.7 Specifically, antibody+PA-MNase complex with 50,000 cells was used for each sample. RUNX1 (Abcam, AB_2184205), CBFβ (Diagenode, C15310002), MYH11 (Diagenode, C15310254), H3K27Ac (Abcam, AB_2118291) and H3K27me3 (Millipore Sigma, AB_310624) antibodies were used to identify the binding sites of the indicated proteins. All libraries were combined in equimolar proportion into one pool for sequencing with a HiSeq 3000 sequencer

treatment_protocol: Mx1-CreCbfb+/56M and Runx1f/fMx1-CreCbfb+/56M mice were injected with pIpC and 2-3 weeks later, the AMP population in the bone marrow cells of these mice were sorted out.

tag: genotype/variation

value: CBFB-SMMHC knock-in Runx1 knock-out

value: abnormal myeloid progenitors cell

value: Bone marrow

value: H3K27me3 (Millipore Sigma, AB_310624)


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out Runx1 rep2


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out IgG rep2

description: IgG.bedpe.gz

value: IgG


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out MYH11 rep2

value: MYH11 (Diagenode, C15310254)


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out Cbfb rep2

value: CBFβ (Diagenode, C15310002)


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out H3K27ac rep2


title: ChIC-seq CBFB-SMMHC knock-in Runx1 rep2

value: CBFB-SMMHC knock-in


title: ChIC-seq CBFB-SMMHC knock-in MYH11 rep2


title: ChIC-seq CBFB-SMMHC knock-in H3K27me3 rep2


title: Heart of V3599K_1 without TAC


title: Aging, blastocyst, suppressed CXCL5-CXCR2 signal

description:
Gene expression in aging mouse blastocyst, suppressed CXCL5 signling
Aging_mouse_CXCL5 signal suppression_ScaleSig

hyb_protocol: Two ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Mouse Blastocyst, 43 - 53 weeks of age, suppressed CXCL5-CXCR2 signal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2.0 ug Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Two age group of female ICR mice (young; 3-6 weeks of age and aging; 43-53 weeks of age) were purchased from SLC Japan (Shizuoka, Japan) and maintained in a standard laboratory animal facility with controlled environment (temperature; 22 ℃, humidity; 55-65 % and light cycle; 12 hours interval). For embryo collection, super-ovulated mice were mated with male mice immediately after hCG treatment. At 18 hours after hCG injection, zygotes were obtained by flashing the oviducts of mated mice. Collected zygotes were cultured in 30 μl drops of KSOM medium without or with anti-CXCL5 neutralizing antibody (10 μg/ml) and CXCR2 selective antagonist (10nM) for suppressing CXCL5-CXCR2 signal. After 96 hours culture, blastocysts were collected for RNA extraction and microarray analysis.

extract_protocol: Thirty blastocysts in each group were lysed using RNA Lysis Buffer (Agilent) following the manufacturer's instructions.

treatment_protocol: Collected zygotes were cultured in 30 μl drops of KSOM medium. Young mouse embryos were cultured without CXCL5 signal suppression. Aging mouse embryos were cultured without or with anti-CXCL5 neutralizing antibody (10 μg/ml, R&D systems, Abcam) and CXCR2 selective antagonist (10nM, Tocris) for suppressing CXCL5-CXCR2 signal. After 96 hours culture, expanded blastocysts were collected for RNA extraction and microarray analysis.

value: ICR

value: 43-53 weeks

value: mouse preimplantatin embryo

value: Blastocyst

tag: tratment

value: anti-CXCL5 neutralizing antibody (10 μg/ml) and CXCR2 selective antagonist (10nM) during embryo culture


title: ChIC-seq CBFB-SMMHC knock-in H3K27ac rep2


title: Young, blastocyst, without treatment

description:
Gene expression in young mouse blastocyst
Young_mouse_control_ScaleSig

source_name: Mouse Blastocyst, 3 - 6 weeks of age

value: 3-6 weeks

tag: developmental stage


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out Runx1 rep1


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out MYH11 rep1


title: ChIC-seq CBFB-SMMHC knock-in Cbfb rep2


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out IgG rep1

description: IgG.bedpe.gz


title: ChIC-seq CBFB-SMMHC knock-in MYH11 rep1


title: ChIC-seq CBFB-SMMHC knock-in IgG rep1

description: IgG.bedpe.gz


title: ChIC-seq CBFB-SMMHC knock-in H3K27ac rep1


title: Aging, blastocyst, without treatment

description:
Gene expression in aging mouse blastocyst
Aging_mouse_control_ScaleSig

source_name: Mouse Blastocyst, 43 - 53 weeks of age


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out Cbfb rep1


title: Pig WT 3 hour Animal #2 Loop #1

source_name: Pig WT 3 hour Animal #2 Loop #1

tag: strain/genotype

value: Pig ligated intestinal loop


title: ChIC-seq CBFB-SMMHC knock-in Cbfb rep1

tag: tissue


title: ChIC-seq CBFB-SMMHC knock-in H3K27me3 rep1


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out H3K27me3 rep1


title: ChIC-seq CBFB-SMMHC knock-in Runx1 rep1


title: ChIC-seq CBFB-SMMHC knock-in Runx1 knock-out H3K27ac rep1


title: P6S_rep3

city: Tokyo

first: Masayuki

last: Miya

state: Tokyo

address: Bunkyo, Yayoi 1-1-1

institute: The University of Tokyo

description: Gene expression of P6 leaf sheath

hyb_protocol: At least 1,100 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB (Agilent; G2519F#15241) at 65℃ for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed raw signal intensities of all probes were transformed to log2 scale, and normalization procedures were performed, including 75th-percentile normalization for inter-array comparison and baseline correlation to the median value within each dataset, using GeneSpring GX12 software (Agilent Technologies).

organism: Oryza sativa Japonica Group

source_name: Leaf

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen) and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice (Oryza sativa L. ssp. japonica cv. Nipponbare) seeds were sown in germinatinggermination boxes, and the seedlings were grown in a growth chamber (14 -h light period at 30℃ °C and 10 -h dark period at 25℃). °C). At 14–15 days after germination, the seedlings in which the tip of the fifth leaf hashad just emerged from the fourth leaf were collected and used for samplinganalysis. The seedlings were dissected under a dissecting microscope to separate the tissues at different developmental stages and different partslocations along the longitudinal axis of the leaves.

extract_protocol: Total RNA was extracted from the each sample using a RNeasy Mini Kit (QIAGEN). The quantity and quality of the obtained RNAs were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

value: Nipponbare

value: Leaf

value: P6 leaf sheath


title: SA_rep1

description: Gene expression of shoot apex containing the SAM and P1 and P2 leaf primordia

source_name: Shoot apex

value: Shoot apex

value: Shoot apex containing the SAM and P1 and P2 leaf primordia


title: P6B_rep1

description: Gene expression of P6 leaf blade

value: P6 leaf blade


title: P6S_rep2

description: Gene expression of P6 leaf sheath


title: SA_rep2


title: SA_rep3


title: P6B_rep3

description: Gene expression of P6 leaf blade


title: P5S_rep2

description: Gene expression of P5 leaf sheath

value: P5 leaf sheath


title: P6BS_rep1

description: Gene expression of blade-sheath boundary region of P6 leaf

value: Blade-sheath boundary region of P6 leaf


title: P5BS_rep2

description: Gene expression of blade-sheath boundary region of P5 leaf

value: Blade-sheath boundary region of P5 leaf


title: P6B_rep2

description: Gene expression of P6 leaf blade


title: P6S_rep1

description: Gene expression of P6 leaf sheath


title: P5BS_rep1


title: P5S_rep3

description: Gene expression of P5 leaf sheath


title: P4S_rep3

description: Gene expression of P4 leaf sheath

value: P4 leaf sheath


title: P5S_rep1

description: Gene expression of P5 leaf sheath


title: P4Bm_rep2

description: Gene expression of middle parts of P4 leaf blade

value: Middle parts of P4 leaf blade


title: P5BS_rep3


title: P4S_rep1

description: Gene expression of P4 leaf sheath


title: P4Bm_rep3


title: P5B_rep1

description: Gene expression of P5 leaf blade

value: P5 leaf blade


title: P6BS_rep2


title: P5B_rep2

description: Gene expression of P5 leaf blade


title: P5B_rep3

description: Gene expression of P5 leaf blade


title: P6BS_rep3


title: P4Bb_rep1

description: Gene expression of basal parts of P4 leaf blade

value: Basal parts of P4 leaf blade


title: P4Bb_rep3


title: P4Bm_rep1


title: P4S_rep2

description: Gene expression of P4 leaf sheath


title: P4Bb_rep2


title: P4Ba_rep2

description: Gene expression of apical parts of P4 leaf blade

value: Apical parts of P4 leaf blade


title: F.mosseae-inoculated-Rep2

city: Bellaterra

first: Blanca

last: San Segundo

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Raw reads were checked for quality by using FastQC v0.11.3
Trimming and removal of adapters involved using Trimmomatic v0.33 (minimum quality score 35, minimum length 25).
The obtained reads were mapped against the Oryza sativa Japonica (IRGSP-1.0) by using STAR (v2.4.0j)
Alignment files were filtered to remove reads with mapping quality (MAPQ) <30. FeatureCounts (v1.4.5-p1)
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: FPKM

organism:
Oryza sativa
Funneliformis mosseae

source_name: Wildtype Rice (cv. Loto) root-inoculated with F. mosseae

growth_protocol: Non-inoculated and F-mosseae-inoculated transplantes seedlings were grown at the greenhouse under a 14h/10h day/night cycle, 28ºC/25ºC and 60% humidity

extract_protocol:
Total RNA was extracted with the Maxwell 16 LEV Plant RNA Kit (Promega) following manufacturer's instructions.
Indexed libraries prepared from 1ug purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples pooled; each index-tagged sample present in equimolar amounts (final concentration of pooled samples at 2nm). Pooled samples subjected to cluster generation and sequencing using Illumina Hseq 2500. 2x100 paired-ennd at final concentration of 8pmol.

treatment_protocol: Rice Loto seeds were dehusked, surface-sterilized twice with 5% sodium hypochlorite for 15 min, and washed extensively with sterile water. Seeds were germinated on petri dishes with sterile water for 7 days and then transplanted to 150ml-cones (20.5 cm; 2 plants/cone) containing a mix of 63.3% quartz sand (0.3-0.8 mm), 31.6% soil (turface and vermiculite 2:1), and 5% of granular inoculum of Funneliformis mosseae. No inoculum was added to the substrate for the non-inoculated, control plants.

value: leaf

tag: rice cultivar

value: Loto (japonica)

tag: f. mosseae strain


title: F.mosseae-inoculated-Rep1


title: Untreated sample 1

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
fastp was used to observe read quality
fastp was used to trim data
HISAT2  (v2.1)  to align reads to the reference genome
FeatureCounts  (v2.1) was used to count reads mapping to genes
edgeR Bioconductor package (v3.16.5) to identify differentially expressed genes
Genome_build: Candida auris NCBI reference genome version B11221
Supplementary_files_format_and_content: counts

organism: Candidozyma auris

source_name: whole cell

growth_protocol: Candida aurus (AR0390) cells

extract_protocol:
Ambion Ribopure yeast kit
Illumina TruSeq kit
2x150 on a NovaSeq 6000

treatment_protocol: Exponential-phase cultures of C. auris AR0390 were treated with either DMSO (1%), lopinavir (10 µg/ml), itraconazole (1 µg/ml), or a combination of both drugs.

tag: drug treatment

value: no treatment


title: F.mosseae-inoculated-Rep3


title: ITC + LPV sample 1

value: lopinavir+itraconazole


title: ITC sample 1

value: itraconazole


title: immature Sertoli cells, V3

city: Jingzhou

first: Liang

last: Hao

state: Hubei

address: JingMi road

institute: Yangtze University

data_processing:
illumina bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa11.1 whole genome using Hisat2 v2.0.5 with parameters --rna-strandness RF --dta -t -p 4.
Fragments per Kilobase per Million Mapped Fragments of(FPKM) were calculated using a protocol from Trapnell, C. et al, 2010.FPKM method can eliminate the influence of gene length and sequencing amount on the calculated gene expression.
Genome_build: Sus scrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Testis

growth_protocol: iSCs were cultured in Minimum Essential Medium (MEM) with Eagle's balanced salt solution (HyClone, USA), supplementing with 10% fetal bovine serum (Clark, Australia) and 1% penicillin-streptomycin (Gibco, USA), in a 5% CO2 incubator at 37°C.

extract_protocol:
Trizol reagent (Sigma) was used to isolate the total RNA of samples collected from three controls (C1, C2 and C3) and three AA2P-treated (V1, V2 and V3) iSC cells.
The libraries were constructed and sequenced on an Illumina Hiseq X-Ten (Illumina, San Diego, CA, USA) in a single lane.

treatment_protocol: The cells were seeded at a density of approximately 1×10e5 cells/mL, and cultured for 6h, before treated with the L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P, Sigma, USA) at 250μM.

tag: cell type

value: immature Sertoli cells

value: 80 to 90 days gestation

value: VC-treated group of immature Sertoli cells


title: immature Sertoli cells, C3

value: control group of immature Sertoli cells


title: immature Sertoli cells, V1


title: LPV sample 1

city: West Lafayette

value: lopinavir


title: immature Sertoli cells, V2


title: P4Ba_rep1

value: Nipponbare

value: Leaf


title: P3_rep1

description: Gene expression of entire P3 leaf primordium

value: Entire P3 leaf primordium


title: immature Sertoli cells, C1


title: immature Sertoli cells, C2


title: P3_rep3


title: P4Ba_rep3


title: Tax1BP1 knock-out 4

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) were hybridized with 2.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Mouse Gene 1.0 ST Array CDF Files
meta-probeset file: MoGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (7.8 MB, 10/7/11)

source_name: Tax1BP1 knock-out

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Mice were housed under 12 h day/night cycles, were fed standard rodent chow and had access to drinking water ad libitum.

extract_protocol: RNA was extracted with the RNeasy Mini Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA

tag: strain background

value: Tax1BP1 knock-out

value: 12 weeks

value: male

value: liver


title: Tax1BP1 wildtype 1

source_name: Tax1BP1 wildtype

value: Tax1BP1 wildtype


title: Tax1BP1 wildtype 4


title: DVL3_RAD_8

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Libraries were pooled and sequenced on the NextSeq 500 using the FMHLS genomics CTU, yielding an average of 10M reads per sample.
FASTQ files were aligned to the mm10 genomic reference using STAR aligner and counts quantified at a gene level with HTseq-Counts to yield 5-8M mapped reads per sample.
Genome_build: mm10
Supplementary_files_format_and_content: read count

source_name: Allograft Prostate Cancer Tumour

extract_protocol:
2-4 (10uM) sections were transferred into RNAase free microcentrifuge tube. The paraffin was removed by incubating in xylene and ethanol. For lysate and total RNA purification, digestion buffer and proteinase-K was added to the samples as per manufacturer’s instructions (Norgen kit).
RNA libraries preparations were generated using the Quant-seq 3’ mRNA-Seq FWD kit (Lexogen PART NO k15.96) according to manufacturer’s instructions, with 500ng input RNA. FFPE-derived RNA was prepared using the suggested manufacturer's instructions. Libraries were pooled and sequenced on the NextSeq 500 using the FMHLS genomics CTU, yielding an average of 10M reads per sample.

treatment_protocol: Mice were inoculated subcutaneously with 1x10^6 DVL3 cells

tag: background strain

value: Allograft Prostate Cancer Tumour

tag: cell line

tag: radiation treatement


title: Tax1BP1 wildtype 2

tag: age

tag: Sex


title: DVL3_RAD_4

tag: genotype


title: P3_rep2


title: Tax1BP1 wildtype 3

tag: genotype/variation


title: DVL3_RAD_3


title: Tax1BP1 knock-out 1


title: DVL3_RAD_5


title: Tax1BP1 knock-out 2


title: Tax1BP1 knock-out 3


title: DVL3_RAD_2


title: WT_MPP4

city: Guangzhou

first: Juan

last: Du

state: Guangdong

address: 190 Kaiyuan Avenue

department: South China Institutue of Stem Cell & Regneration Medicine

institute: Guangzhou Institutes od Biomedicine and Health

data_processing:
Bcl2fastq convert .bcl files into fastq files
Alignment, normalization of genes expression and differential expression genes (DEGs) analysis were performed by RSEM and DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw counts was generated as a csv file

source_name: Multipotent progenitor cells

extract_protocol:
cDNA of sorted 1000 MPP aliquots were generated, amplified as in ref (Tang et al., 2010)
Sequencing libraries were generated with illumina Nextera XT DNA Sample Preparation Kit.

treatment_protocol: 1000 sorted MPP cells were used for sequencing.

tag: strain

value: WT

value: bone marrow

value: Multipotent progenitor cells

tag: surface markers


title: TS16-21

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

country: South Korea

institute: The Catholic University of Korea

description: IDH1 wildtype

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance stabilizing transformed and quantile normalized using the R/Bioconductor lumi package

label: Biotin

source_name: GBM TS

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: TS complete media, composed of DMEM/F-12, 1x B27, 20 ng/mL bFGF, and 20 ng/mL EGF

extract_protocol: Total RNA was extracted from the GBM TSs using a Qiagen RNeasy Plus Mini kit.

value: Brain

value: M


title: TS16-27

description: IDH1 wildtype


title: DVL3_RAD_1


title: TS16-139

description: IDH1 wildtype


title: TS15-87

description: IDH1 wildtype

value: F


title: WT_MPP3


title: TS16-23

description: IDH1 wildtype


title: TS16-117

description: IDH1 wildtype


title: TS14-30

description: IDH1 wildtype


title: TS15-88

description: IDH1 wildtype


title: TS14-08_3

description: IDH1 wildtype


title: WT_MPP1


title: TS14-15

description: IDH1 wildtype


title: TS14-48

description: IDH1 wildtype


title: TS14-08_2

description: IDH1 wildtype


title: NA_MPP3

value: Nup98-Hoxa10hd fusion gene (NA)


title: WT_MPP2


title: TS14-08_4

description: IDH1 wildtype


title: NA_MPP2


title: NA_MPP1


title: TS14-12

description: IDH1 wildtype


title: WT_MP_rep4

source_name: Myeloid progenitor cells

extract_protocol:
Total RNA of each sorted myeloid progenitor sample was extracted with RNeasy micro kit (QIAGEN).
Sequencing library were prepared with illumina Truseq RNA Sample Preparation Kit.

treatment_protocol: 0.1 million myeloid progenitor cells (Lin-ckit+Sca1-) were sorted as one sample from bone marrow nucleated cells of respective recipient mice. Donor-derived NA MP cells (Tdtomato+) were sorted from NA MPP recipient mice 3 months post transplantation, while WT MP cells(CD45.2+) were obtained from control group received WT MPP transplantation at the same time point.

value: Myeloid progenitor cells


title: WT_MP_rep5


title: TS14-08_1

description: IDH1 wildtype


title: TS14-05_2

description: IDH1 wildtype


title: TS14-05_3

description: IDH1 wildtype


title: NA_MPP4


title: WT_MP_rep2


title: TS14-05_1

description: IDH1 wildtype


title: TS13-79

description: IDH1 wildtype


title: TS13-71_2

description: IDH1 wildtype


title: TS13-71_3

description: IDH1 wildtype


title: WT_MP_rep1


title: TS13-64_2

description: IDH1 wildtype


title: NA_MP_rep4


title: TS13-71_1

description: IDH1 wildtype


title: TS13-64_1

description: IDH1 wildtype


title: TS13-68

description: IDH1 wildtype


title: TS13-30_2

description: IDH1 wildtype


title: NA_MP_rep3


title: NA_MP_rep2


title: NA_MP_rep1


title: TS13-20_2

description: IDH1 wildtype


title: zebrafish embryo Aldh3a1-KO-rep5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: zebrafish embryo RNA

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: danRer11
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without PTU (2.5 ml in 25 ml) to suppress pigmentation

extract_protocol:
Total RNA was isolated from TG(fli1:EGFP) zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol (Qiagen).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Not applicable

value: embryo

value: 48 hours after post fertilization


title: zebrafish embryo Aldh3a1-KO-rep4

description: zebrafish embryo RNA


title: zebrafish embryo Aldh3a1-KO-rep6

description: zebrafish embryo RNA


title: WT_MP_rep3


title: SHR, female, pre-estrus, biological rep 8

city: Aurora

first: Laura

middle: Maren

last: Saba

state: CO

address: 12850 East Montview Blvd.

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description:
SHR-201066-8-PreE
201066-8-brain-b35

data_processing:
Reads were trimmed to remove adapters and low-quality base calls using cutadapt
Individual isoforms and genes from the Ensembl Transcriptome (v96) were quantitated using RSEM.
Genome_build: RN6
Supplementary_files_format_and_content: tab-delimited text files include estimated read counts, TPM, and FPKM values for each Sample (standard RSEM output)
Supplementary_files_format_and_content: estimated count matrices with genes as rows and Samples as columns

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from whole brain of three alcohol-naïve male rats using the RNeasy Midi Kit with additional cleanup performed using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Sequencing libraries were constructed using the Illumina TruSeq Stranded RNA Library Prep Kit with Ribo-Zero (Illumina, San Diego, CA, USA), in accordance with the manufacturers protocol.
Library quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Samples were sequenced (2x100 paired-end reads) on the Illumina HiSeq2500 (Illumina, San Diego, CA, USA) with 4 libraries multiplexed per lane.

value: SHR/OlaIpcv

value: female

tag: estruc cycle stage

value: pre-estrus

value: brain


title: zebrafish embryo Aldh3a1-KO-rep1

description: zebrafish embryo RNA

tag: tissue


title: SHR, female, pre-estrus, biological rep 11

description:
SHR-201066-11-PreE
SHR-201066-11-PreE-brain-b37


title: zebrafish embryo wildtype-rep5

description: zebrafish embryo RNA


title: zebrafish embryo wildtype-rep4

description: zebrafish embryo RNA


title: SHR, female, pre-estrus, biological rep 12

description:
SHR-201066-12-PreE
SHR-201066-12-PreE-brain-b37


title: zebrafish embryo Aldh3a1-KO-rep3

description: zebrafish embryo RNA


title: zebrafish embryo Aldh3a1-KO-rep2

description: zebrafish embryo RNA


title: zebrafish embryo wildtype-rep1

description: zebrafish embryo RNA


title: TS13-30_1

description: IDH1 wildtype


title: SHR, female, pre-estrus, biological rep 10

description:
SHR-201066-10-PreE
201066-10-brain-b35


title: SHR, female, post-estrus, biological rep 13

description:
SHR-201066-13-PostE
201066-13-brain-b35

value: post-estrus


title: SHR, female, post-estrus, biological rep 8

description:
SHR-200317-8-PostE
200317-8-brain-b35


title: SHR, female, post-estrus, biological rep 6

description:
SHR-200317-6-PostE
200317-6-brain-b35


title: zebrafish embryo wildtype-rep2

description: zebrafish embryo RNA


title: SHR, female, post-estrus, biological rep 12

description:
SHR-201376-12-PostE
SHR-201376-12-PostE-brain-b37


title: TS13-41

description: IDH1 wildtype


title: TS13-14_1

description: IDH1 wildtype


title: TS13-20_1

description: IDH1 wildtype


title: TS13-18

description: IDH1 wildtype


title: TS13-03

description: IDH1 wildtype


title: TS13-14_2

description: IDH1 wildtype


title: SHR, male, biological rep 1

description:
SHR-199890-1-M
SHR-199890-1-M-brain-b37

value: male

value: not applicable


title: SHR, male, biological rep 2

description:
SHR-199890-2-M
199890-2-brain-b35


title: zebrafish embryo wildtype-rep3

description: zebrafish embryo RNA

value: WT


title: SHR, female, estrus, biological rep 5

description:
SHR-200317-5-E
200317-5-brain-b35

value: estrus


title: SHR, female, estrus, biological rep 6

description:
SHR-201066-6-E
SHR-201066-6-E-brain-b37


title: SHR, female, estrus, biological rep 9

description:
SHR-200317-9-E
200317-9-brain-b35


title: SHR, female, estrus, biological rep 11

description:
SHR-199890-11-E
SHR-199890-11-E-brain-b37


title: BN-Lx, female, pre-estrus, biological rep 5

description:
BNLx-202386-5-PreE
BNLx-202386-5-PreE-brain-b37

value: BN-Lx/Cub


title: BN-Lx, female, post-estrus, biological rep 6

description:
BNLx-202386-6-PostE
BNLx-2020386-6-PostE-brain-b37


title: BN-Lx, female, pre-estrus, biological rep 3

description:
BNLx-200537-3-PreE
200537-3-brain-b35


title: BN-Lx, male, biological rep 2

description:
BNLx-200537-2-M
200537-2-brain-b35


title: BN-Lx, female, post-estrus, biological rep 5

description:
BNLx-200537-5-PostE
200537-5-brain-b35


title: BN-Lx, male, biological rep 1

description:
BNLx-200537-1-M
200537-1-brain-b35


title: BN-Lx, female, pre-estrus, biological rep 7b

description:
BNLx-202386-7-PreE
BNLx-202386-7-PreE-brain-b37


title: BN-Lx, female, pre-estrus, biological rep 7a

description:
BNLx-200538-7-PreE
200538-7-brain-b35


title: BN-Lx, female, estrus, biological rep 9

description:
BNLx-200538-9-E
200538-9-brain-b35


title: BN-Lx, female, post-estrus, biological rep 3

description:
BNLx-204114-3-PostE
BNLx-204114-3-PostE-brain-b37


title: BN-Lx, female, post-estrus, biological rep 4

description:
BNLx-200537-4-PostE
BNLx-200537-4-PostE-brain-b37


title: BN-Lx, female, estrus, biological rep 2

description:
BNLx-202829-2-E
BNLx-202829-2-E-brain-b37


title: BN-Lx, female, estrus, biological rep 4

description:
BNLx-202386-4-E
BNLx-202386-4-E-brain-b37


title: Osteoclast-Cited2-KO-bulkRNAseq-1

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

data_processing:
Single-cell RNA-seq was performed on cells on Day 0, Day 1 and Day3 of the osteoclast culture system with a target output of 3,000 cells/ per time point.  Single cells were captured with the 10x Genomics Chromium system.  The sequencing library was generated using the 10x Genomics Single Cell 3′ Solution (version 2) kit and subjected to Illumina sequencing (HiSeq 4000).  Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.). For bulk-RNA-seq, cDNA and sequencing libraries were processed using FastQC (v0.1.1.8), TrimGalore (v0.6.4) and Kallisto (v0.46.0) with the mouse transcriptome index (mus musculus GRCm38.96), and analyzed by DESeq2 (v1.26) to quantify gene expression with PCA, hierarchical clustering and differential expression analysis (using log fold change shrinkage and adjusted p-value <0.05).
Supplementary_files_format_and_content: Excel files include expression values for each sample

source_name: osteoclasts

extract_protocol:
This osteoclast culture was performed on collagen-coated dishes, which permitted a harvesting of the adherent cells by enzymatic treatment and then a preparation of the single-cell suspensions.  Murine bone marrow cells were cultured with M-CSF for 2 days, and these cells were further cultured for 3 days with RANKL in the presence of M-CSF.  scRNA-seq, bulk RNA-seq and proteome analyses were performed at the following time points: Day 0 (before RANKL stimulation), Day 1 (1 day after RANKL stimulation) and Day 3 (3 days after RANKL stimulation). Bulk-RNA seq analysis was also performed using control and Cited2-KO cells on Day 3 of the osteoclastogenic culture system to investigate the role and point of action of Cited2 in the trajectory of osteoclastogenesis.
RNA libraries were prepared for sequencing using standard Ion Torrent Proton protocols

value: In vitro cultured osteoclasts (72h after RANKL stimulation)


title: Osteoclast-Cited2-control-bulkRNAseq-3


title: Osteoclast-Day3-bulkRNAseq-1

value: 8 weeks old


title: Osteoclast-Day1-bulkRNAseq-3

value: In vitro cultured osteoclasts (24h after RANKL stimulation)


title: Osteoclast-Day0-bulkRNAseq-1

value: In vitro cultured osteoclasts (before RANKL stimulation)


title: Osteoclast-Cited2-control-bulkRNAseq-2


title: Osteoclast-Day3-bulkRNAseq-2


title: Osteoclast-Day1-bulkRNAseq-1


title: Osteoclast-Day0-bulkRNAseq-2


title: Osteoclast-Day0-bulkRNAseq-3


title: Osteoclast-Cited2-KO-bulkRNAseq-2


title: Osteoclast-Cited2-control-bulkRNAseq-1


title: BN-Lx, female, estrus, biological rep 8

description:
BNLx-200538-8-E
200538-8-brain-b35


title: Osteoclast-Day3-bulkRNAseq-3


title: Nari3

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: blood

value: adult

tag: treatment

value: Naringenin treatment 30 days


title: Osteoclast-Day1-bulkRNAseq-2


title: Reanalysis PCa_Z59

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: Prostate adenocarcinoma from Caucasian men

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for 866 human and 89 human viral miRNAs from the Sanger miRBase (release 12.0) (Human miRNA Microarray V3, Agilent Technologies). After 20 hours slides were washed and scanned.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505B

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze miRNA expression profiles in normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = subtract with an offset of 20) and normalized using the quantile method. Duplicated probes were averaged.

source_name: Prostate Cancer

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following the manufacturers protocol (Agilent Technologies). Briefly, 100 ng of totRNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed.

extract_protocol: TotRNA was isolated following standard TriReagent protocol (Sigma-Aldrich) and DNAse treatment was performed (TURBO Dnase Free, Life Technologies). totRNA quality and quantity were checked by means of bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific) respectively.

value: Tumor


title: Reanalysis PCa_L16


title: Reanalysis PCa_M26


title: Reanalysis PCa_Y48


title: Nari1


title: Reanalysis PCa_L12


title: Reanalysis PCa_Z56


title: Reanalysis PCa_P57


title: Reanalysis PCa_Z55


title: Reanalysis PCa_P55


title: Ctrl3

value: PBS treatment 30 days


title: INS-1_non-treated_rep2

city: Taiyuan

first: Lijuan

last: Cui

state: Shanxi

address: Xinjian south road

department: School of basic medicine

institute: Shanxi Medical University

description: lncRNAs and mRNAs expression in non-treated INS-1 cells

hyb_protocol: Each slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

data_processing:
Data was extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data was normalized by Quantile algorithm, limma packages in R. The significant differentially expressed lncRNAs and mRNAs between the two groups were selected if the fold changes of the Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data was extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data was normalized by Quantile algorithm, limma packages in R.
The significant defferentially expressed lncRNAs and mRNAs between the two groups were selected if the fold changes of the threshold values were ≥1.5 and p≤0.05

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol:
Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
The initial sample of the chip experiment was total RNA, and the total RNA was subjected to quality inspection by NanoDrop ND-2000 spectrophotometer and Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US), and the quality-qualified RNA was subjected to subsequent chip experiments.

value: islet

tag: agent


title: INS-1_non-treated_rep3

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.


title: ATAC-seq - ASEL/R (delta150) #2

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: ASE delta150 #2 - MLC1310 (delta150 - no tbx binding site)

data_processing:
For ChIP-seq, the single-end raw reads of ChIP-seq dataset were mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). Uniquely mapped reads were retained and duplicated reads were marked and discarded using SAMtools (v0.1.18). For visualization, the coverage tracks (i.e. bigWig files) were generated from bam files using kent-ucsc (v2.79). Sharp peaks were identified with macs2 (v2.1.0) against the pooled control samples with default parameters.
For ATAC-seq, the paired-end raw reads of ATAC-seq data were trimmed with Cutadapt (v1.18) and mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). For all samples, multi-mapped reads were filtered with SAMtools (v0.1.20) and duplicate reads were marked and discarded with Picard-tools (v2.18.27; Broad Institute). For visualization, the normalized coverage tracks (i.e. bigWig files) were generated from bam files using with R packages GenomicRanges (v1.38.0) and rtracklayer (v1.46.0) with paired-end option.
Genome_build: ce11
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million

organism: Caenorhabditis elegans

source_name: ASEL/R (delta150)

extract_protocol:
ChIP assays were performed as previously described in (Askjaer et al., 2014) with minor modifications. ATAC-seq libraries were prepared as described in (Corces et al., 2017) with minor modifications.
ChIP-seq: NEBNext® Ultra II DNA Library Prep Kit. ATAC-seq: Nextera DNA Library Prep Kit

tag: developmental stage

value: Embryo - 350 minutes

value: ASEL/R


title: INS-1_non-treated_rep1


title: Ctrl1


title: ATAC-seq - ABp 350 minutes (delta150) #2

description: 350min ABp delta150 #2 - MLC2309 - no tbx binding site

source_name: Embryo (ABp) - 350 minutes (delta150)

value: lucIs39[tbx-37p::mNeonGreen::2xNLS::tbx-37 3'UTR; pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR; med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR)]; lsy-6(luc160[lsy-6::d150]) V

value: ABp


title: Reanalysis PCa_Y50


title: Reanalysis PCa_K6


title: ATAC-seq - ABa 350 minutes (delta150) #2

description: 350min ABa delta150 #2 - MLC2309 - no tbx binding site

source_name: Embryo (ABa) - 350 minutes (delta150)

value: ABa


title: ATAC-seq - ABa 350 minutes (delta150) #1

description: 350min ABa delta150 #1 - MLC2309 - no tbx binding site


title: ATAC-seq - ABp 350 minutes (delta150) #1

description: 350min ABp delta150 #1 - MLC2309 - no tbx binding site


title: INS-1_Geniposide_rep3

description: lncRNAs and mRNAs expression after 24hrs Geniposide treated INS-1 cells

value: GLP-1RA Geniposide


title: ATAC-seq - ASEL/R (delta150) #1

description: ASE delta150 #1 - MLC1310 (delta150 - no tbx binding site)


title: Pancreas_STARTinput1

city: La Jolla

first: Nathan

last: Lewis

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: UCSD

description:
normalized_TSS_counts.tsv
eTSS_NCBI_picr.bed.gz
eTSS_NCBI_picr.meta.tsv.gz
eTSS_syn20999279_picr.bed.gz
eTSS_syn20999279_picr.meta.tsv.gz
peaks_location.tsv

data_processing:
5' and control processing: cutadapt (Martin, 2011) was used to trim adapter sequences and low quality bases from the reads. Reads were aligned to the Chinese Hamster genome assembly PICR (Rupp et al., 2018) and annotation GCF_003668045.1, part of the NCBI Annotation Release 103. Sequence alignment was accomplished using the STAR aligner v2.5.3a. Reads mapped to multiple locations were removed from analysis. Tags were then made using Homer v4.11 command "makeTagDirectory {o_dir} -genome {g} -checkGC -single {bam}"
5' and control processing: Peaks for 5'GRO-seq csRNA-seq was done using Homer v4.11 with input GRO-Seq, using "findPeaks {tss_tag_file} -style tss -i {control_tag_file} -norm 1000000"
5' and control processing: Peaks were then merged using homer command "mergePeaks -d 150 -strand {in_files} > {out}"
Ribosome-depleted RNA: Alignment performed using STAR v2.5.3a with default parameters and removing reads mapped to multiple locations. Quantification performed using htseq-count, with the command "htseq-count -f bam -s reverse -t exon -i gene {bam_f} {annotation} > {out)}"
ATAC-seq: ATAC-seq was processed using the pipeline here: https://github.com/kundajelab/atac_dnase_pipelines . Briefly, the reads were trimmed using cutadapt v1.9.1. Reads were aligned using Bowtie v2.2.4. Peaks were called using Macs2 v2.1.3 with a p-value of 0.01, and replicates were merged using irreproducible discovery rate (IDR) (Li et al., 2011) of 0.1. The fold-change value is the number of normalized counts over the local background, taken as 10,000 kb surrounding.
TSS called using custom Python scripts and thresholding based on distance to NCBI annotation.
Bedgraph were generated by constructing single-nucleotide resolution bedGraph files based on 5' read positions using HOMER. TSS peak files contain TSS cluster positions defined using HOMER's findPeaks.pl command (tab-delimited text files). Normalized to 1e7 uniquely aligned reads.
RNA bedgraph files, which was strand agnostic, created first by making the tag directory , with command  "makeTagDirectory {tag_dir} {bam_file} -read2 -single". Then, bedgraph file was made using "makeUCSCfile {tag_dir} -o {bedgraph_file} -style rnaseq". Normalized to 1e7 uniquely aligned reads.
Genome_build: PICR GCF_003668045.1
Genome_build: [genome annotation]  PICR NCBI Annotation 103
Genome_build: [genome annotation]  picr_proteogenomics.gff (https://www.synapse.org/#!Synapse:syn20999279)
[normalized_TSS_counts.tsv]  Counts-per-million (CPM) matrix, n-by-m matrix, where n is the number of TSS, and m is the number of samples. Each column has a header that names after the title column above, and there is an ID column which gives an ID for each peak.
[peaks_location.tsv]  tsv file of locations of the peaks, along with average CPM.
[eTSS_NCBI_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by NCBI Refseq.
[eTSS_NCBI_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[eTSS_syn20999279_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by Synapse.org ID syn20999279.
[eTSS_syn20999279_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[ATAC_peaks.bed.gz]  A tsv file outputted from Homer mergePeaks on bed files outputted from macs2 using the aforementioned pipeline. The Stat column is the averaged 10*log10qvalue over the samples that contained the peak. This is a modified bed file with a header and a column that indicates which samples contained the open-chromatin position.

organism: Cricetulus griseus

source_name: Pancreas

growth_protocol: See paper for complete protocol details. Female Chinese hamsters (Cricetulus griseus) were generously provided by George Yerganian (Cytogen Research and Development, Inc) and housed at the University of California San Diego animal facility on a 12h/12h light/dark cycle with free access to normal chow food and water. All animal procedures were approved by the University of California San Diego Institutional Animal Care and Use Committee in accordance with University of California San Diego research guidelines for the care and use of laboratory animals. None of the used Hamsters were subject to any previous procedures and all of them were used naive without any previous exposure to drugs. Euthanized hamsters were quickly chilled in a wet ice/ethanol mixture (~50/50), organs were isolated, placed into Trizol LS, flash frozen in liquid nitrogen and stored at -80C for later use. CHO-K1 cells were grown on F-K12 media at 37 Â°C with 5 % CO2 (GIBCO-Invitrogen, carlsbad, CA, USA). Hamster bone marrow-derived macrophages (BMDMs) were generated as detailed previously (Link et al., 2018). Hamster bone marrow-derived macrophages (BMDMs) were generated as detailed previously (Link et al., 2018).

extract_protocol:
[RNA-seq]  RNA was extracted from organs that were homogenized in Trizol LS using an Omni Tissue homogenizer. After incubation at RT for 5 minutes, samples were spun at 21.000g for 3 minutes, supernatant transferred to a new tube and RNA extracted following manufacturerâs instructions. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) according to the manufacturer-supplied protocol.
[csRNA-seq]  Capped small RNA-sequencing was performed identically as described by (S. H. Duttke et al., 2019). Briefly, total RNA was size selected on 15% acrylamide, 7M UREA and 1x TBE gel (Invitrogen EC6885BOX), eluted and precipitated over night at -80Â°C. Given that the RIN of the tissue RNA was often as low as 2, essential input libraries were generated to facilitate accurate peak calling. csRNA libraries were twice cap selected prior to decapping, adapter ligation and sequencing. Input libraries were decapped prior to adapter ligation and sequencing to represent the whole repertoire of small RNAs with 3â-OH.
[sRNA-seq]  Similar to csRNA-seq, without the decapping.
[5'GRO-seq and GRO-seq]  Global nuclear run-on sequencing (GRO-seq (Core et al., 2008) and 5âGRO-seq (Core et al., 2008; Lam et al., 2013)) were performed as described below. Nuclei from hamster tissues were isolated as described in (Hetzel et al., 2016). Hamster BMDM nuclei were isolated using hypotonic lysis [10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2; 0.1% IGEPAL] and flash frozen in GRO-freezing buffer [50 mM Tris-HCl pH 7.8, 5 mM MgCl2, 40% Glycerol]. 0,5-1 x 106 BMDM nuclei were run-on with BrUTP-labelled NTPs as described (S. H. C. Duttke et al., 2015) with 3x NRO buffer [15mM Tris-Cl pH 8.0, 7.5 mM MgCl2, 1.5 mM DTT, 450 mM KCl, 0.3 U/Âµl of SUPERase In, 1.5% Sarkosyl, 366 ÂµM ATP, GTP (Roche) and Br-UTP (Sigma Aldrich) and 1.2 ÂµM CTP (Roche, to limit run-on length to ~40 nt)]. Reactions were stopped after five minutes by addition of 750 Âµl Trizol LS reagent (Invitrogen), vortexed for 5 minutes and RNA extracted and precipitated as described by the manufacturer.
[GRO-seq]  RNA pellets were fully resuspended in 18 Âµl ddH2O + 0.05% Tween (dH2O+T). Subsequently, 2 Âµl fragmentation mix [100 mM ZnCl2, 10 mM Tris-HCl pH 7.5] was added and the samples incubated at 70Â°C for 15 minutes. RNA fragmentation was stopped by placing samples on ice and addition of 2.5 Âµl 100 mM EDTA p.H. 8.0 and 500 Î¼l cold GRO binding buffer [GRO-BB; 0.25Ãsaline-sodium-phosphate-EDTA buffer (SSPE), 0.05% (vol/vol) Tween, 37.5 mM NaCl, 1 mM EDTA p.H. 8.0]. BrU enrichment was performed using a BrdU Antibody (Sigma B8434-200 Âµl Mouse monoclonal BU-33) coupled to Protein G (Dynal 1004D) beads. Per run on reaction, 3x 20 Âµl of Protein G beads were washed twice in DPBS+0.05% Tween 20 (DPBS+T) and then the antibody coupled in a total volume of 1 ml DPBS+%T under gentle rotation. 1 Âµl of antibody was used per 8 Âµl of beads. After one hour at RT, the beads were collected using a magnet and the supernatant saved for future coupling reactions. Coupled beads were washed twice with GRO-BB prior to use. It is recommended to pre-chill beads to 4áµC prior to the IP as traces of RNase may be observed. RNase activity can be monitored e.g. using IDTâs RNaseAlertÂ®. No crosslinking is required and worked best in our hands followed by DMP >>> Bs3. To each reaction of fragmented NRO-RNA with added GRO-BB, 20 Î¼l equilibrated Î±BrdU beads were added and the samples slowly rotated at 4 Â°C for 80 minutes. Beads were subsequently collected on a magnet and the IP reaction washed twice with 500 Î¼l GRO binding buffer before RNA was eluted by incubation of the beads in 500 Î¼l Trizol LS (Thermo Fisher) under medium agitation for 5 minutes. 120 Î¼l of TET [10 mM Tris-HCl pH 7.5, 1 mM EDTA p.H. 8.0, 0.05 % Tween20] was added to increase the supernatant and RNA extracted as described by the manufacturer. For end-repair and decapping, RNA pellets were dissolved in 8 Âµl TET by vigorous vortexing, heated to 70Â°C for 2 minutes and placed on ice. After a quick spin, 22 Âµl Repair MM [3 Âµl 10x PNK buffer, 15.5 Âµl dH2O+T, 0.5 Âµl SUPERase-In RNase Inhibitor (10 U, Ambion), 2 Âµl PNK (20U, Enzymatics Y904L), 1 Âµl RppH (5U, NEB)] was added, mixed by flicking and incubated at 37Â°C for 1 hour. To phosphorylate the 5âend, 1 Âµl 10 mM ATP was subsequently added and the reactions were incubated for another 45 minutes at 37Â°C (the high ATP concentration is advised to quench RppH activity). Following end repair, 2.5 Âµl 50 mM EDTA was added, reactions mixed and then heated to 70Â°C for 2 minutes before being placed on ice. A second BrdU enrichment was performed as detailed above. For library preparation, RNA pellets were dissolved in 2.75 Âµl TET + 0.25 Âµl Illumina TruSeq 3âAdapter (10 mM), heated to 70Â°C for 2 minutes and placed on ice. 7 Âµl of 3âMM [4.75 Âµl 50% PEG8000, 1 Âµl 10x T4 RNA ligase buffer (NEB), 0.25 Âµl SUPERase-In, 1 Âµl T4 RNA Ligase 2 truncated (200U; NEB)] was added, mixed well by flicking and reactions incubated at 20Â°C for 1 hour. Reactions were diluted by addition of 10 Âµl TET + 2 Âµl 50 mM EDTA, heated to 70Â°C for 2 minutes, placed on ice and a third round of BdUTP enrichment was performed. RNA was transferred as a pellet to PCR strips during the 75% ethanol wash and dried. Samples were dissolved in 4 Âµl TET [10 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 0.05% Tween 20] + 1 Âµl 10 mM reverse transcription (RT) primer. To anneal the RT-primer, the mixture was incubated at 75Â°C for 5 minutes, 37Â°C for 15 minutes and 25Â°C for ~10 minutes.  To ligate the 5â Illumina TruSeq adapter, 10 Âµl 5âMM [1.5 Âµl ddH2O + 0.2% Tween20, 0.25 Âµl denaturated 5âTruSeq adapter (10 mM), 1.5 Âµl 10x T4 RNA ligase buffer, 0.25 Âµl SUPERase-In, 0.2 Âµl 10 mM ATP, 5.8 Âµl 50% PEG8000, 0.5 Âµl T4 RNA ligase 1 (5U; NEB)] was added and reactions were incubated at 25Â°C for 1 hour. Reverse transcription was performed using Protoscript II (NEB) [4 Âµl 5x NEB FirstStrand buffer (NEB; E7421AA), 0.25 Âµl SUPERase-In, 0.75 Âµl Protoscript II (150U; NEB)] at 50Â°C for 1 hour. After addition of 30 Âµl PCR MM [25 Âµl 2x LongAmp Taq 2X Master Mix (NEB), 0.2 Âµl 100 mM forward primer, 2.8 Âµl 5 M Betaine and 2 Âµl 10 mM individual barcoding primer], mixtures were amplified for 13 cycles. PCR reactions were cleaned up using 1.5 volumes of SpeedBeadsâ¢ (GE Healthcare) in 2.5 M NaCl/20%PEG8000 and the libraries size selected on a PAGE/TBE gels to 150â225 bp. Gel slices were shredded by spinning through a 0.5 ml perforated PCR tube placed on top of a 1.5 ml tube. 150 Âµl Gel EB [0.1% LDS, 1M LiCl, 10 mM Tris-HCl pH 7.8] was added and the slurry incubated under agitation overnight. To purify the eluted DNA, 800 Âµl Zymogen ChIP DNA binding buffer (D5205) was added into the 1.5 ml tube containing the shredded gel slice and the Gel EB, mixed by pipetting and the slurry transferred to a ZymoMiniElute column. Samples were first spun at 1000g for 3 minutes, then 10k g for 30 seconds. Flow through was removed, and samples washed with 200 Âµl Zymo WashBuffer (with EtOH). Gel remainders were removed by flicking and columns washed by addition on another 200 Âµl Zymo WashBuffer. Flow through was removed, columns spun dry by centrifugation at 14k g for 1 minute and DNA eluted by addition of 20 Âµl pre-warmed Sequencing TET [10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 0.05% Tween 20]. Libraries were sequenced on an Illumina NextSeq 500 at using 75 cycles single end.
[5' GRO-seq]  RNA pellets were resuspendend in 10 Âµl TET, heated to 70Â°C for 2 minutes and placed on ice. 10 Âµl of dephosporylation MM [2 Âµl 10x CutSmart, 6.75 Âµl dH2O+T, 1 Âµl Calf Intestinal alkaline Pho

value: Female

value: Pancreas

tag: assay

value: total short RNA (20-65nt)

tag: molecule


title: Spleen_STARTinput1

value: Spleen; blood


title: INS-1_Geniposide_rep2


title: Reanalysis PCa_G70


title: INS-1_Geniposide_rep1


title: ATAC-seq - ABa 200 minutes (delta150) #1

description: 200min ABa delta150 #1 - MLC2309 - no tbx binding site

source_name: Embryo (ABa) - 200 minutes (delta150)

value: Embryo - 200 minutes

tag: cell type


title: ATAC-seq - ABa 200 minutes (delta150) #2

description: 200min ABa delta150 #2 - MLC2309 - no tbx binding site


title: Muscle_STARTinput1

source_name: Muscle

value: Muscle


title: ATAC-seq - ABp 200 minutes (delta150) #1

description: 200min ABp delta150 #1 - MLC2309 - no tbx binding site

source_name: Embryo (ABp) - 200 minutes (delta150)


title: ATAC-seq - ABp 200 minutes (delta150) #2

description: 200min ABp delta150 #2 - MLC2309 - no tbx binding site


title: ATAC-seq - ABa 90 minutes (delta150) #2

description: 90min ABa delta150 #2 - MLC2309 - no tbx binding site

source_name: Embryo (ABa) - 90 minutes (delta150)

value: Embryo - 90 minutes


title: ATAC-seq - ABp 90 minutes (delta150) #1

description: 90min ABp delta150 #1 - MLC2309 - no tbx binding site

source_name: Embryo (ABp) - 90 minutes (delta150)


title: Lung_STARTinput1

source_name: Lung

value: Lung


title: MiscOrgans_STARTinput1

source_name: Whole Organism

value: Whole Organism


title: Reanalysis PCa_F51

value: Tumor


title: Liver_STARTinput1

source_name: Liver

value: Liver


title: ATAC-seq - ASER #3

description: Batch 2 ASER 1.5k cells

source_name: ASER

value: otIs252[lsy-6::YFP (fosmid); rol-6(su1006)] II;  otIs235[che-1p::mChopti; rol-6(su1006)] V

value: Embryo - 350 minutes

value: ASER


title: Reanalysis PCa_Y44