title: CD 5

city: Osaka

first: Makoto

last: Matsushita

address: 2-2 Yamadaoka, Suita

department: Urology

institute: Osaka University Graduate School of Medicine

hyb_protocol: After creating the hybridization cocktail, biotinylated cDNA were hybridized with GeneChip Mouse Gene 2.0 ST Array (Affymetrix) for 16 hours.

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: Scanned data were processed using Partek Genomics Suite software.

label: biotin

source_name: Prostate tissue from a mouse model of prostate cancer fed a control diet

label_protocol: Total RNA 1 ug were subjected to cDNA synthesis by Prime Script RT reagent Kit (Takara Bio). Obtained 5.5 μg cDNA were biotinylated and then fragmented by GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: All mice started to feed high-fat diet (HFD-60, Oriental Yeast) or control diet (MF, Oriental Yeast) at 5 weeks of age, and the prostates of the mice were collected at 22 weeks of age.

extract_protocol: Frozen prostates were homogenized using gentle MACS tubes (Miltenyi Biotec), and total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s standard protocol.

treatment_protocol: Prostates were frozen in RNAlater Tissue Collection: RNA Stabilization Solution (Thermo Fisher Scientific) and stored at -20°C until RNA extraction.

value: Pb-Cre+; Pten(fl/fl)

tag: gender

value: male

tag: age

value: 22 weeks of age

value: prostate

tag: diet

value: control diet


title: CD 4

status: Public on Dec 02 2021

type: RNA

country: Japan

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype

tag: tissue


title: CD 1


title: CD 3


title: CD 2


title: S2R+ WT-replicate2

type: SRA

city: Montpellier FRANCE

first: Julie

last: Carnesecchi

address: 1919, route de Mende team JCL team JCL

department: IGMM

country: France

institute: CNRS

library_source: transcriptomic

data_processing:
RNA-Seq analysis was performed by using genome 6 (dm6). The quality of the RNA-Seq reads was quantified via FastQC. Trimming was performed with java script "Trimmomatic 0.36"(Bolger et al., 2014), for the removal of the adapter (TruSeq-SE sequencing adapter), with the following command line: java -jar /path_to_java_script/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 <file.txt> <outputfile.txt> ILLUMINACLIP:TruSeq-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The reads were aligned using STAR (genome generated: STAR --runThreadN 14 --runMode genomeGenerate --genomeFastaFiles Drosophila_melanogaster.BDGP6.dna.toplevel.fa --sjdbGTFfile Drosophila_melanogaster.BDGP6.86.gtf --genomeSAindexNbases 12; running STAR: STAR --runThreadN 14 --genomeDir /STAR/GenomeDir/ --readFilesIn /STAR/<file> --outSAMtype BAM Unsorted) (Dobin et al., 2013). Aligned reads were counted by HTSeq (htseq-count -f bam -r pos -m union -s no -t exon accepted_hits.bam Drosophila_melanogaster.BDGP6.86.gtf > count.txt) for further analysis in DESeq (Anders et al., 2015).
For the analysis in Junction-Seq the aligned reads were counted and the genome flattened with QoRTs by using the available java scripts (counting: java -jar /path/QoRTs.jar QC --singleEnded --minMAPQ 75 --nameSorted sorted.bam Drosophila_melanogaster.BDGP6.86.gtf rawCts/file; flattened: java -jar /path/QoRTs.jar makeFlatGff --stranded Drosophila_melanogaster.BDGP6.86.gtf annoFiles/JunctionSeq.flat.gff.gz) (Hartley and Mullikin, 2015). Differential expression analysis was performed with DESeq2 under standard conditions (Love et al., 2014). Different exon usage and the identification of splicing variants was identified by using the R tool Junction-Seq under standard conditions (Hartley and Mullikin, 2016). All data results were further processed in Excel and False Discovery Rate (FDR) was established at FDR 0.1.
Genome_build: Drosophila_melanogaster.BDGP6.86.gtf
Supplementary_files_format_and_content: Tables with raw gene counts for every gene and each sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: RNAs polyA enriched from Drosophila S2R+ cells

extract_protocol:
Total RNAs were extracted from four independent replicates from Drosophila S2R+ cells expressing GFPnls, myc-UbxWT, or myc-UbxN51A (Gal4-UAS, actin promoter) using Qiagen RNA extraction kit (RNeasy). RNA quality was assessed using BioAnalyzer 2100TM (Agilent Technologies).
Material handling and mRNA-Seq directional libraries were performed with the Deep-Sequencing facility in Heidelberg (Cell Networks), using the true-seq illumina standard protocol

tag: cell type

value: embryonic cells

tag: overexpression

value: overexpressing GFP-Ubx-WT


title: ChIP-Seq WT_2_1_H4K5ac

city: Poznan

first: Piotr

middle: A

last: Ziolkowski

address: Uniwersytetu Poznanskiego 6

department: Institute of Molecular Biology and Biotechnology

country: Poland

institute: Adam Mickiewicz University

library_source: genomic

data_processing:
Quality and adapter trimming as well as (RNA-Seq only) rRNA sequnce removal were performed using BBDuk version 38.57
Gene expression values (Araport11 annotations) were estimated from RNA-Seq data using Salmon version 0.13.1
ChIP-Seq reads were mapped to the reference genome (TAIR10) and spike-in genome (GRCm38) using BWA version 0.7.17
Normalized and smoothed genome coverage profiles were calculated using DANPOS 2.2.2
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files containing expression values of genes (TPM values and raw estimated read counts)
Supplementary_files_format_and_content: Tab-delimited text file containing genome mapping statistics for ChIP-Seq samples, used to correct genome coverage values for plotting
Supplementary_files_format_and_content: Wig files storing normalized and smoothed genome coverage data calculated by DANPOS

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: WT and mutant plants were grown under LD conditions (16 h light and 8 h darkness), under 80-90 µmol/(m2s) of photosynthetically active radiation. Material was collected at the developmental stage of ca. 10 leaves about 5 hours after light onset.

extract_protocol:
RNA for each biological repeat was extracted from 110 mg of rosette leaves number 5-6 (from at least six plants) with TRI Reagent (Merck) and rounds of phenol-chloroform and chloroform extractions followed by isopropanol precipitation. RNA was treated with RQ1 DNase I (Promega), then extracted with phenol-chloroform and precipitated with ethanol. Chromatin was isolated as previously described (Sura et al. Plant Cell 2017), enriched with 2% chromatin isolated from mouse embryonic fibroblasts as spike-in control, and incubated with antibody (α-H3, Abcam ab1791; α-H4K5ac, Millipore 07327; α-H3K9ac Millipore 07352; α-HTA9, Agrisera AS10718; α-H2A.Zac, Diagenode C15410173 pAb-173-050) overnight at 4°C. Dynabeads Protein A (Thermo Fisher Scientific) were added to the samples and incubated for another 2 hours at 4°C. The slurry was washed twice with low salt buffer (with 150 mM NaCl), twice with high salt buffer (with 500 mM NaCl) and once with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, 1 mM PMSF and protease inhibitor cocktail). Chromatin was eluted through incubation in 1% SDS and 0.8 M NaHCO3 at 65°C and the cross-links were reversed by overnight incubation at 65°C. Following Proteinase K treatment and phenol/chloroform extraction, DNA was precipitated and DNA concentration was measured with Qubit dsDNA HS Kit (Thermo Fisher Scientific).
Pure RNA solution was sent to Macrogen Europe (South Korea), where libraries were performed using TruSeq Stranded Total RNA sample preparation with Ribo-Zero Plant. Libraries were sequenced on the Illumina HiSeq 4000, 2x100bp run. 10 ng (H3) or 2 ng (other antibodies) of ChIP-ed DNA was used to prepare DNA libraries with MicroPlex Library Preparation Kit v2 (Diagenode). The library preparation was carried out accoring to the manufacturer (Diagenode) protocol.

value: WT

tag: chip antibody

value: H4K5ac (Millipore 07327)


title: HFD 5

source_name: Prostate tissue from a mouse model of prostate cancer fed a high-fat diet

value: high-fat diet


title: ChIP-Seq WT_2_1_H3K9ac

value: H3K9ac (Millipore 07352)


title: Control_eye_No.1

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

state: Hamburg

address: Martinistr. 52

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: regular eye tissue serves as healthy control reference

hyb_protocol: NanoString standard protocol

scan_protocol: NanoString standard protocol

data_processing: Raw expression data was processed using nSolverAnalysis Software 4.0.70: Background subtraction with geometric mean of negative controls; Normalization with geometric mean of positive controls and standard housekeeping genes; No ratios built.

source_name: orbita

label_protocol: NanoString standard protocol

growth_protocol: Murine Shh-MBs were obtained from 14 day old mice. RBS lesions and control eyes were obtained from E18.5 mouse embryos.

extract_protocol: Each sample represents a single tumor, lesion or eye from an individual animal. RNA was extracted from FF tissue using protocols of the RNeasy® Mini Kit (QIAGEN, 74136).

tag: disease state

value: control

tag: sample

value: FF


title: S2R+ WT-replicate1


title: ChIP-Seq WT_2_1_H3

value: H3 (Abcam ab1971)


title: S2R+ GFP-replicate3

value: overexpressing nlsGFP


title: Tumor-like-lesion_RBS_No.5

description: RBS-lesions occur after E8.5 tamoxifen injection and subtotally replace regular eye structures

value: ocular lesion


title: HFD 4


title: Tumor-like-lesion_RBS_No.4


title: RNA-Seq epl1_4


title: S2R+ GFP-replicate1


title: Tumor-like-lesion_RBS_No.3


title: HFD 3


title: HFD 2


title: Tumor-like-lesion_RBS_No.2


title: RNA-Seq epl1_1


title: HFD 1


title: Tumor-like-lesion_RBS_No.1


title: RNA-Seq WT_8


title: Tumor_Shh-MB_No.3

description: murine counterpart to human SHH-Medulloblastoma

source_name: hindbrain

value: tumor


title: RNA-Seq WT_5


title: mitochondrial enrichment fraction of THP1

city: Montpellier

first: Isabelle

middle: Duroux

last: Richard

address: Hôpital Saint Eloi  80 avenue Augustin Fliche

institute: INSERM

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:expression suite. Target gene signals normalized to the mean of housekeeping genes; deltaCt = (Ct_Target − Ct_mean (Mamm U6, RNU48, RNU44)]

label: FAM

organism: Homo sapiens

label_protocol: Total 500 ng RNA per sample were reverse transcribed to cDNA with Megaplex Human Pool A and B stem loop RT primers (version 3.0) (Thermofisher)and TaqMan MicroRNA RT kit (Invitrogen) as per manufacturer´s instructions for TLDA

growth_protocol: The human monocytic cell line THP-1 monocytes and PMA differenciated macrophages were cultivated  in RPMI 1640 Medium GlutaMAX™ Supplement with 10% FBS at 37°C and 5% CO2.

extract_protocol: The human monocytic cell line THP-1 cells were cultivated in RPMI 1640 Medium GlutaMAX™ Supplement with 10% FBS at 37°C and 5% CO2. The mitochondrial enrichment fractions were prepared at 4 °C using a MACS Mitochondria kit (Miltenyi), and total RNA including miRNAs were extracted using miRNeasy kit (Qiagen). miRNA quantification was performed using the TaqMan® Array Human MicroRNA Card Set v3.0 (Applied Biosystems), according to the manufacturer’s instructions.

treatment_protocol: THP-1 cells were differentiated into THP-1 derived macrophages with 40 ng/mL phorbol 12-myristate 13-acetate (PMA) over-night in RPMI 1640 Medium GlutaMAX™ Supplement with 10% FBS at 37°C and 5% CO2.

tag: cell line

tag: treatment

value: monocyte

tag: fraction

value: mitochondrial enrichment fraction


title: RNA-Seq WT_7


title: Tumor_Shh-MB_No.2


title: SG2M-size-sort-exp190610_bin4_bio-rep1_tech-rep2

status: Public on Dec 01 2021

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

data_processing:
read alignment, ChIP-seq Bowtie 1.0.1
read alignment, RNA-seq STAR-2.5.3a
custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: cells

extract_protocol:
cell pellets were lysed in 300 µL TRI Reagent (Zymo Research) by bead beating using a Fastprep 24 (4°C, settings: 5.0 m/s, 1 x 30 seconds). Cell debris was pelleted (13 krpm, 5 minutes) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research).
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing

value: HTB2-GFP (Saccharomyces cerevisiae) + 972 (Schizosaccharomyces pombe)


title: SG2M-size-sort-exp190610_bin4_bio-rep2_tech-rep2


title: SG2M-size-sort-exp190610_bin4_bio-rep2_tech-rep1


title: Total cellular of THP1

extract_protocol: The human monocytic cell line THP-1 cells were cultivated in RPMI 1640 Medium GlutaMAX™ Supplement with 10% FBS at 37°C and 5% CO2. Total RNA including miRNAs of total cellular fraction were extracted using miRNeasy kit (Qiagen). miRNA quantification was performed using the TaqMan® Array Human MicroRNA Card Set v3.0 (Applied Biosystems), according to the manufacturer’s instructions.

value: Total cellular


title: Tumor_Shh-MB_No.1


title: S2R+ GFP-replicate2


title: RNA-Seq epl1_3


title: SG2M-size-sort-exp190610_bin4_bio-rep1_tech-rep1


title: SG2M-size-sort-exp190610_bin3_bio-rep1_tech-rep2


title: SG2M-size-sort-exp190610_bin3_bio-rep2_tech-rep1


title: SG2M-size-sort-exp190610_bin2_bio-rep2_tech-rep2


title: SG2M-size-sort-exp190610_bin2_bio-rep1_tech-rep2


title: SG2M-size-sort-exp190610_bin3_bio-rep1_tech-rep1


title: SG2M-size-sort-exp190610_bin2_bio-rep1_tech-rep1


title: SG2M-size-sort-exp190610_bin1_bio-rep2_tech-rep2


title: SG2M-size-sort-exp190610_bin1_bio-rep1_tech-rep2


title: mitochondrial enrichment fraction of PMA-THP1

extract_protocol: The human monocytic cell line THP-1 cells were differentiated into THP-1 derived macrophages with 40 ng/mL phorbol 12-myristate 13-acetate (PMA) over-night in RPMI 1640 Medium GlutaMAX™ Supplement with 10% FBS at 37°C and 5% CO2. The mitochondrial enrichment fractions were prepared at 4 °C using a MACS Mitochondria kit (Miltenyi), and total RNA including miRNAs were extracted using miRNeasy kit (Qiagen). miRNA quantification was performed using the TaqMan® Array Human MicroRNA Card Set v3.0 (Applied Biosystems), according to the manufacturer’s instructions.

value: PMA

value: macrophage


title: SG2M-size-sort-exp190610_bin1_bio-rep2_tech-rep1


title: Input (IN)

city: Douglas

first: Patrick

last: Schaeffer

state: QLD

address: 1 James Cook Drive

department: CPHMVS

country: Australia

institute: James Cook University

description: Sample type contains three biological replicates e.g IN-1 represents biological replicate 1. The processed data is of each replicate combined

data_processing:
Removal of Illumina adapters and leading and tailing nucleotides with a Phred score ≤ 10  was performed with Trimmomatic (v.0.36)
The replicate data for Input and ChIP-Seq Tus-GFP (pos) were pooled into three separate fastqc files and aligned to the KRX E. coli genome using the default settings of Bowtie2
Samtools (version 1.9) was then used to organise each alignment file
Genome_build: krx.fsa (pending GenBank submission)
Supplementary_files_format_and_content: The single base read counts was calculated for ChIP and Input using genomeCoverageBed (Version: v2.26.0).  Columns are as follows Chromosome I.e contig_2_pilon; chromosome position; depth (number) of reads overlapping this chromosome position
Ter coverage text files are averaged read counts over the 23 base Ter sequences. Columns are as follows Chromosome; chromosome position; depth (number) of reads overlapping this chromosome position

organism: Escherichia coli KRX

source_name: KRX E. coli

growth_protocol: Competent E. coli KRX bacteria were transformed with  pPMS1259 (His6-Tus-GFP) and grown overnight at 37°C. Colonies were resuspended and diluted to an OD600 of 0.1 in LB broth supplemented with ampicillin. All cultures were grown for 45 minutes at 37°C before inducing moderate levels of Tus-GFP with Rhamnose 0.02 % Rhamnose (w/v final culture concentration). Bacteria were incubated for 2 hours at 37°C, followed by 2 hours at 16°C.

extract_protocol:
The lysates were passed three times in a French press at 12,000 psi and each lysate was heated for 10 minutes at 50°C to denature free Tus-GFP. Supernatants were immunoprecipitated (excluding input) with goat anti-GFP IgG (Abcam; Ab6673) and Immunocaptured DNA was released by adding elution and de-crosslinking buffer containing proteinase k. Samples were incubated at 95°C to denature proteinase K and residual crosslinked proteins.
Each library was prepared using the NEBNext Ultra DNA library preparation kit for Illumina.Briefly, 55.5 µL of DNA suspensions were end repaired. Due to the low DNA concentrations in the suspensions, the NEB adaptors were diluted 10 fold in water to 1.5 µM for ligation as recommended. The adaptors were cleaved using uracil excision. Size selection was not recommended for sample < 50 ng. DNA was then cleaned up using Sera-Mag beads (ratio of 1.4) and eluted in 28 µL of 0.1xTE. Index primers were added by PCR using 18 cycles.  The samples were pooled in a single library, denatured and loaded for sequencing with an Illumina MiSeq desktop sequencer.

treatment_protocol: Culture aliquots were subject to formaldehyde solution (final concentration of 1%) and the bacterial suspensions were reacted for 20 minutes at room temperature.

tag: plasmid for expression

value: pPMS1259 (encodes Tus-GFP)


title: SG2M-size-sort-exp190610_bin1_bio-rep1_tech-rep1


title: ChIP-Seq Tus-GFP (pos)

description: Sample type contains three biological replicates, consisting of 2-3 technical replicates e.g 1-1 represents biological replicate 1, technical replicate 1. The processed data is of each replicate combined

value: Goat anti-GFP IgG (Abcam; Ab6673)


title: Total cellular of PMA-THP1

extract_protocol: The human monocytic cell line THP-1 cells were differentiated into THP-1 derived macrophages with 40 ng/mL phorbol 12-myristate 13-acetate (PMA) over-night in RPMI 1640 Medium GlutaMAX™ Supplement with 10% FBS at 37°C and 5% CO2. Total RNA including miRNAs of total cellular fraction were extracted using miRNeasy kit (Qiagen). miRNA quantification was performed using the TaqMan® Array Human MicroRNA Card Set v3.0 (Applied Biosystems), according to the manufacturer’s instructions.


title: Q808-2

city: Changchun

first: Wei

last: Li

state: Jilin

address: No 155 Chuangju Street

country: China

institute: Jilin Provincial Academy of Traditional Chinese Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then theclean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene  were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package  functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or  foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical  cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment  and KEGG pathway enrichment analysis of DEGs were respectively performed using R  based on the hypergeometric distribution
If it was transcript-level quantification, FPKM and read counts value of each transcript  (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using  the DESeq(2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and  foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential  expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts  expression pattern. GO enrichment and KEGGpathway enrichment analysis of DEGs were  respectively performed using R based on the hypergeometric distribution
The reads were reassembled using StringTie. Then gene structure extension and novel  transcripts identification were performed by comparing the reference genome and the known  annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was  performed using ASprofile.  SNP and INDEL were called using samtools and bcftools, and the details were shown on  samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates  and predicts the effects of variants on genes.
Genome_build: ronr 6.0
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Total RNA was extracted from hippocampal tissue sample (about 100 mg)  using TRIzol kit (Invitrogen, USA)  according to the manufacturer’s instructions. RNA purity was checked and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA). Samples with an absorbance (260/280) ratio between 1.8 and 2.2 were considered acceptable. Agilent 2100 Bioanalyzer (Agilent Technologies,  USA) was used to assess the RNA integrity.
The sequencing library was generated by using MGIEasy Universal Library Convert Kit (MGI, China), VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, China), and VAHTS® mRNA Capture Beads (Vazyme, China) according to the manufacturer’s protocols.

value: Wistar

value: hippocampus

tag: weight

value: wild type

value: PTZ + Q808


title: Q808-1


title: PTZ-2

value: PTZ + vehicle


title: PTZ-3


title: Con.-3

value: vehicle


title: Con.-2


title: Con.-1


title: MCF7 cells, shControl-H3K27me3-Rep1

city: Madison

first: NGAI TING

last: CHAN

state: WI

address: 4849 Sheboygan Ave

department: Oncology

institute: University of Wisconsin -- Madison

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP sequencing reads that passed quality score were aligned to the human reference genome (hg38) using Bowtie2 (v2.4.1)
Only unique alignments that passed high mapping quality (MAPQ>30) were retained for downstream analysis. Duplicated reads and reads resides in hg38 blacklist regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) were eliminated by sambamba tools (v0.7.1). Sequencing reads were also aligned to the Drosophila genome (dm6) and normalization factors (Rx factor) were calculated after removing multi-mapping and duplicated reads.
Bigwig files were generated at a resolution of 20bp using the bamCoverage utility from the deepTools (v3.4.3) suits and data were subsequently visualized as ChIP-Rx normalized tracks using IGV genome browser (v2.8.9).
Peaks were called using MACS2 (v2.1.4) with FDR<0.01 for narrow beaks and FDR<0.05 for broad peaks. Peaks intersection was performed by bedtools (v2.29.2) and bedops (v2.4.40). Overlapped peaks that shorter than sequencing tag (100bp) will be discarded.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig  (a continous track representing the normalized ChIP-seq signal)

source_name: MCF7-shControl + eGFP

growth_protocol: Cells are maintained in Dulbecco’s modified medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) (VWR) and 1% Penicillin-Streptomycin (P/S) (Gibco) and cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with corresponding antibodies.
Libraries were prepared according to manufacturer’s protocol of  the Ovation Ultralow System V2 1-16 Kit (NuGEN Technologies).  Briefly, the DNA was end-repaired and ligated to Illumina sequencing adaptors. The ligated DNA was purified using Agencourt RNAClean XP beads (Beckman Coulter). A subsequent PCR amplification step (8-15 cycles) was performed to add linker sequence to the purified fragments for annealing to the Genome Analyzer flow-cell. Following PCR amplification, the library was separated on a 2% agarose gel (120 V, 1.5 hours) to select a narrow range of fragment sizes, and bands between 200-500 bp were excised. The library was purified from the excised agarose gel using the Qiagen MiniElute PCR Purification Kit following the manufacturer’s protocol.

value: human luminal breast cancer cells

value: scramble control KD with eGFP expression

value: H3K27me3 (Cell signaling technology, Cat# 9733, RRID:AB_916252)

value: in regular DMEM medium


title: SG2M-size-sort-exp190610_bin3_bio-rep2_tech-rep2


title: PTZ-1


title: SG2M-size-sort-exp190610_bin2_bio-rep2_tech-rep1


title: DBA_mpFC_RCF 1

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: medial prefrontal cortex tissue from DBA_mpFC_RCF mouse

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole mouse genome oligonucleotide microarray (Agilent grid ID 028005), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 10.7  software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09 for FE ver 10.7 ).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using R, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale.  Differentially expressed genes were selected by a combination of fold change and moderated T-test thresholds (with FDR Pvalue correction) by the R-Bioconductor  tool Limma (FDR<0.05; |Log2 fold-change ratio| >1.0 equivalent to 2.0 fold in linear scale).

source_name: medial prefrontal cortex

label_protocol: For each sample 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: C57BL/6J (C57) and DBA2/J (DBA) female mice (Charles River Laboratories, Italy), 9–12-weeks-old at the time of the microarray experiments, were housed with water and food available ad libitum. Room temperature (21 ± 1 °C) and a 12:12 h light–dark cycle (lights on at 07.00 PM) were kept constant. Adequate measures were taken to minimize pain or discomfort of mice. All experiments were carried out in accordance with Italian national law (DL 116/92 and DL 26/2014) on the use of animals for research based on the European Communities Council Directives (86/609/EEC and 2010/63/UE).

extract_protocol: Total RNA was extracted from nucleus accumbens (NAc) and medial prefrontal cortex (mpFC) , with n=4 samples per treatment group (RCF C57, Control C57, RCF DBA, Control DBA). Total RNA was extracted  using Trizol (Life Technologies, Inc, USA), according to the manufacturer's instructions, and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: As  described in (D'Amato et al., 2011; Di Segni et al., 2016; Ventura et al., 2013), pups from the same litter spent the first postnatal day (PND0) with their biological mother. On PND1, litters were randomly assigned to experimental (RCF) or Control (Cont) treatment. RCF pups were fostered by introducing the entire litter into the home cage of a different dam whose pups had just been removed and moved to a different adoptive mother. This procedure was repeated daily (4 times, from PND1 up to PND4) until the fourth adoptive mother was reached. Pups were left with the last adoptive mother until weaning. Control litters were only picked up daily and reintroduced in their home cage, for the same period, and had their mothers returned within 30 s. Animals were weaned at PND28, separated by sex and housed in groups of 4 littermates. All experiments were performed on 3-month-old adult female mice. To prevent potential estrous cycle group synchronization, experimental subjects for cross-fostered and control female groups were sorted by collecting not >2 individuals per cage/litter (Ventura et al., 2013; Di Segni et al., 2016; 2017). Four treatment groups were used for this experiment: RCF C57, Control C57, RCF DBA, Control DBA.

value: neuronal tissue

tag: transgenic

value: DBA2/J (DBA)

tag: Sex

value: female

value: 12 weeks

value: Repeated cross-fostering (RCF)

tag: age of treatment

value: 9-12 weeks


title: DBA_Nac_RCF 2

description: Nucleus Accumbens tissue from DBA_Nac_RCF mouse

source_name: Nucleus Accumbens

tag: age


title: DBA_mpFC_ctr 1

description: medial prefrontal cortex tissue from DBA_mpFC_ctr mouse

tag: strain


title: DBA_Nac_ctr 1

description: Nucleus Accumbens tissue from DBA_Nac_ctr mouse


title: DBA_mpFC_RCF 2


title: DBA_Nac_ctr 2


title: DBA_Nac_RCF 1


title: DBA_Nac_ctr 3


title: DBA_mpFC_ctr 3


title: DBA_Nac_RCF 4


title: DBA_Nac_ctr 4


title: C57_Nac_ctr 3

description: Nucleus Accumbens tissue from C57_Nac_ctr mouse


title: DBA_mpFC_ctr 2


title: C57_Nac_RCF 2

description: Nucleus Accumbens tissue from C57_Nac_RCF mouse


title: DBA_mpFC_ctr 4


title: C57_Nac_RCF 3


title: C57_Nac_RCF 4


title: C57_mpFC_RCF 2

description: medial prefrontal cortex tissue from C57_mpFC_RCF mouse


title: DBA_mpFC_RCF 3


title: DBA_mpFC_RCF 4


title: C57_Nac_RCF 1


title: DBA_Nac_RCF 3


title: C57_Nac_ctr 4


title: C57_Nac_ctr 2


title: NB4 DMSO 24h rep 2

city: Milan

first: Fabio

last: Bedin

address: Via Olgettina 60

institute: SR-TIGET

data_processing:
Basecalls was performed using bcl2fastq software v2 and quality check performed with fastqc version 0.11.5
Sequenced reads were mapped to hg38 using STAR v2.7
Reads counts and differential expressed genes were calculated using rsem and DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 output

source_name: NB4 cell line

growth_protocol: NB4 cells were grown in RPMI plus 10% of fetal bovine serum (FBS), 2mM glutamine (Glu) and 1% Penicillin/Streptomycin (P/S). They were grown in cell culture flasks and maintained at a concentration of around 3-5 x 105/ml.

extract_protocol:
Total RNA was extracted by using the RNeasy Mini kit (Qiagen, 74104).
mRNA-sequencing (mRNA-seq) libraries were prepared with the TruSeq RNA Sample Preparation v2 kit (RS-122-2002, Illumina) according to the manufacturer’s protocol, starting from 500 ng of total RNA per sample.

treatment_protocol: NB4 cells were plated at a concentration of 1 x 106, subjected to two cycles of infection with the lentivirus and harvested 48 hours after transduction. Regarding the treatment with the LSD1 inhibitor, NB4 cells were plated at a concentration of 4 x 105 and treated for 24 hours with MC2580 (2 µM) or DMSO as control.

value: treated for 24h with DMSO (control)


title: NB4 MC280 24h rep 1

value: treated for 24h with the LSD1 inhibitor MC2580


title: NB4 MC280 24h rep 2


title: NB4 DMSO 24h rep 1


title: NB4 shB2 rep 2

value: NB4 transduced with the lentiviral pLKO.1 puro (EV) vector containing the shB2 targeting GSE1

value: 48h transduction


title: NB4 shB2 rep 1


title: NB4 shA1 rep 2

value: NB4 transduced with the lentiviral pLKO.1 puro (EV) vector containing the shA1 targeting GSE1


title: NB4 shA1 rep 1


title: Input EV

data_processing:
Basecalls was performed using bcl2fastq software v2 and quality check performed with fastqc version 0.11.5
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie v4.8.2 with the option (-m 1 –v 2)
peaks were called using MACS version macs 1.4.2 with threshold of 10-5
Genome_build: hg38
Supplementary_files_format_and_content: bed file containing chromosome coordinates of peaks and MACS score

extract_protocol:
Cells were lysed with SDS buffer and chromatin was subjected to 35 cycles of sonication prior to the incubation with the anti-V5 antibody.
DNA libraries were prepared with 10 ng of DNA through an in-house protocol (modified from Blecher-Gonen et al., DOI: 10.1038/nprot.2013.023) by the IEO genomic facility and sequenced on a NovaSeq 6000 (Illumina) instrument.

treatment_protocol: NB4 cells were plated at a concentration of 4 x 105 and treated for 24 hours with MC2580 (2 µM) or DMSO as control.

value: NB4 transduced with the empty lentiviral pLEX_307 vector


title: Input GSE1 DMSO

value: NB4 transduced with the lentiviral pLEX_307-GSE1 construct, which contains the GSE1 transcript variant 2 (NM_001134473.3)


title: Input GSE1 MC2580


title: V5 EV ChIP

value: V5 antibody (Abcam, ab9116)


title: C57_mpFC_RCF 3


title: NB4 EV rep 1

value: NB4 transduced with the empty lentiviral pLKO.1 puro (EV) vector


title: C57_Nac_ctr 1


title: C57_mpFC_RCF 1


title: C57_mpFC_ctr 3

description: medial prefrontal cortex tissue from C57_mpFC_ctr mouse


title: C57_mpFC_RCF 4


title: NB4 EV rep 2


title: V5 GSE1 MC2580 ChIP


title: RNAseq_07307

city: Boston

first: Peter

last: Castaldi

state: MA

address: 181 Longwood Ave

institute: Harvard Medical School

description:
gene_counts.tsv
exon_counts.tsv
isoform_counts.tsv

data_processing:
alignment: STAR, 2-pass
gene and exon counts: Rsubread v1.32.2
isoform counts: Salmon v0.12.0 and tximport v1.10.0
Genome_build: Ensembl Genes release 94, GRCh38.p12 assembly
Supplementary_files_format_and_content: count matrices

source_name: blood

growth_protocol: X

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

treatment_protocol: X

tag: current smoker

tag: pack years

tag: race (1=white, 2=black)

tag: gender (1=male, 2=female)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: monocyte percent

tag: eosinophil percent

tag: batch


title: RNAseq_29213


title: C57_mpFC_ctr 1

tag: tissue

tag: treatment


title: C57_mpFC_ctr 2

tag: transgenic


title: RNAseq_89907


title: RNAseq_47210


title: V5 GSE1 DMSO ChIP

tag: cell type

tag: chip antibody


title: RNAseq_53643

tag: age


title: RNAseq_97477


title: RNAseq_96138


title: RNAseq_83819


title: RNAseq_03525


title: RNAseq_47388


title: RNAseq_03262


title: RNAseq_62882


title: RNAseq_76940


title: RNAseq_31807


title: RNAseq_18695


title: RNAseq_50373


title: RNAseq_60971


title: RNAseq_52395


title: RNAseq_04838


title: RNAseq_89470


title: RNAseq_42243


title: RNAseq_08496


title: RNAseq_25862


title: RNAseq_20149


title: RNAseq_96464


title: RNAseq_80264


title: RNAseq_10503


title: RNAseq_30536


title: RNAseq_98616


title: RNAseq_79490


title: RNAseq_23751


title: RNAseq_64436


title: RNAseq_78179


title: RNAseq_26571


title: RNAseq_80418


title: RNAseq_08500


title: RNAseq_68434


title: RNAseq_75949


title: RNAseq_20465


title: RNAseq_95505


title: RNAseq_30331


title: RNAseq_72775


title: RNAseq_34556


title: RNAseq_94126


title: RNAseq_68492


title: RNAseq_09294


title: RNAseq_02252


title: RNAseq_71182


title: RNAseq_03162


title: RNAseq_21142


title: RNAseq_96267


title: RNAseq_47134


title: RNAseq_76642


title: RNAseq_52041


title: RNAseq_29212


title: RNAseq_89439


title: RNAseq_26001


title: RNAseq_44331


title: RNAseq_07933


title: RNAseq_73407


title: RNAseq_42242


title: RNAseq_62005


title: RNAseq_50441


title: RNAseq_98801


title: RNAseq_47511


title: RNAseq_72179


title: RNAseq_08866


title: RNAseq_22308


title: RNAseq_96228


title: RNAseq_72569


title: RNAseq_70840


title: RNAseq_05260


title: RNAseq_79772


title: RNAseq_08895


title: RNAseq_72877


title: RNAseq_24332


title: RNAseq_63660


title: RNAseq_49711


title: RNAseq_43704


title: RNAseq_01689


title: RNAseq_68114


title: RNAseq_23183


title: RNAseq_45628


title: RNAseq_69340


title: RNAseq_81946


title: RNAseq_45232


title: RNAseq_24721


title: RNAseq_16246


title: RNAseq_77991


title: RNAseq_38368


title: RNAseq_65462


title: RNAseq_26707


title: RNAseq_54391


title: RNAseq_48884


title: RNAseq_81393


title: RNAseq_26175


title: RNAseq_68776


title: RNAseq_46586


title: RNAseq_43111


title: RNAseq_53787


title: RNAseq_04646


title: RNAseq_73850


title: RNAseq_23154


title: RNAseq_96445


title: RNAseq_62614


title: RNAseq_85901


title: RNAseq_76452


title: RNAseq_46093


title: RNAseq_39726


title: RNAseq_47812


title: RNAseq_25700


title: RNAseq_71063


title: RNAseq_89071


title: RNAseq_53223


title: RNAseq_18936


title: RNAseq_81769


title: RNAseq_53540


title: RNAseq_69677


title: RNAseq_59001


title: RNAseq_37586


title: RNAseq_86640


title: RNAseq_53537


title: RNAseq_12772


title: RNAseq_97702


title: RNAseq_08523


title: RNAseq_04240


title: RNAseq_60502


title: RNAseq_57382


title: RNAseq_17313


title: RNAseq_14993


title: RNAseq_58115


title: RNAseq_61499


title: RNAseq_18587


title: RNAseq_10376


title: RNAseq_92636


title: RNAseq_56674


title: RNAseq_06255


title: RNAseq_74143


title: RNAseq_57411


title: RNAseq_29158


title: RNAseq_05564


title: RNAseq_87064


title: RNAseq_25171


title: RNAseq_50675


title: RNAseq_95538


title: RNAseq_13133


title: RNAseq_62861


title: RNAseq_76538


title: RNAseq_04197


title: RNAseq_50749


title: RNAseq_29993


title: RNAseq_32222


title: RNAseq_16294


title: RNAseq_31247


title: RNAseq_85684


title: RNAseq_86953


title: RNAseq_24653


title: RNAseq_88708


title: RNAseq_99564


title: RNAseq_34467


title: RNAseq_59610


title: RNAseq_50727


title: RNAseq_71143


title: RNAseq_48032


title: RNAseq_12964


title: RNAseq_43213


title: RNAseq_01520


title: RNAseq_28085


title: RNAseq_27273


title: RNAseq_74489


title: RNAseq_58009


title: RNAseq_09990


title: RNAseq_26895


title: RNAseq_67475


title: RNAseq_96190


title: RNAseq_15515


title: RNAseq_85605


title: RNAseq_99437


title: RNAseq_57322


title: RNAseq_31049


title: RNAseq_64732


title: RNAseq_20092


title: RNAseq_17907


title: RNAseq_75332


title: RNAseq_31693


title: RNAseq_24493


title: RNAseq_67330


title: RNAseq_78195


title: RNAseq_62022


title: RNAseq_26192


title: RNAseq_39249


title: RNAseq_62008


title: RNAseq_54944


title: RNAseq_08149


title: RNAseq_78590


title: RNAseq_53074


title: RNAseq_75185


title: RNAseq_78449


title: RNAseq_84732


title: RNAseq_17620


title: RNAseq_76835


title: RNAseq_08560


title: RNAseq_41282


title: RNAseq_91002


title: RNAseq_02087


title: RNAseq_11833


title: RNAseq_32017


title: RNAseq_17957


title: RNAseq_79949


title: RNAseq_78938


title: RNAseq_96965


title: RNAseq_07596


title: RNAseq_60493


title: RNAseq_10634


title: RNAseq_86005


title: RNAseq_57513


title: RNAseq_24815


title: RNAseq_09428


title: RNAseq_25413


title: RNAseq_48181


title: RNAseq_44265


title: RNAseq_37381


title: RNAseq_01932


title: RNAseq_68781


title: RNAseq_51061


title: RNAseq_47050


title: RNAseq_40664


title: RNAseq_96656


title: RNAseq_91069


title: RNAseq_89577


title: RNAseq_09631


title: RNAseq_02513


title: RNAseq_62171


title: RNAseq_65246


title: RNAseq_67453


title: RNAseq_81704


title: RNAseq_39667


title: RNAseq_39968


title: RNAseq_86070


title: RNAseq_25287


title: RNAseq_27504


title: RNAseq_71125


title: RNAseq_29877


title: RNAseq_01697


title: RNAseq_61447


title: RNAseq_21500


title: RNAseq_47021


title: RNAseq_02083


title: RNAseq_74030


title: RNAseq_36609


title: RNAseq_46966


title: RNAseq_52228


title: RNAseq_08348


title: RNAseq_83952


title: RNAseq_82205


title: RNAseq_34064


title: RNAseq_97440


title: RNAseq_11605


title: RNAseq_29729


title: RNAseq_47575


title: RNAseq_37564


title: RNAseq_33307


title: RNAseq_21989


title: RNAseq_90164


title: RNAseq_27981


title: RNAseq_16365


title: RNAseq_99899


title: RNAseq_04565


title: RNAseq_52204


title: RNAseq_60600


title: RNAseq_95515


title: RNAseq_34882


title: RNAseq_24887


title: RNAseq_10762


title: RNAseq_04377


title: RNAseq_76582


title: RNAseq_47281


title: RNAseq_35763


title: RNAseq_75925


title: RNAseq_00325


title: RNAseq_20033


title: RNAseq_63275


title: RNAseq_33493


title: RNAseq_63493


title: RNAseq_96587


title: RNAseq_25973


title: RNAseq_93810


title: RNAseq_46555


title: RNAseq_37350


title: RNAseq_48703


title: RNAseq_51365


title: RNAseq_37370


title: RNAseq_56211


title: RNAseq_57295


title: RNAseq_86131


title: RNAseq_63854


title: RNAseq_89426


title: RNAseq_31553


title: RNAseq_17874


title: RNAseq_42128


title: RNAseq_26830


title: RNAseq_72996


title: RNAseq_99284


title: RNAseq_75507


title: RNAseq_86917


title: RNAseq_75326


title: RNAseq_58757


title: RNAseq_66588


title: RNAseq_78392


title: RNAseq_90498


title: RNAseq_73274


title: RNAseq_97590


title: RNAseq_08607


title: RNAseq_75029


title: RNAseq_89179


title: RNAseq_49458


title: RNAseq_83899


title: RNAseq_75039


title: RNAseq_59578


title: RNAseq_14539


title: RNAseq_07214


title: RNAseq_22167


title: RNAseq_12631


title: RNAseq_16251


title: RNAseq_18364


title: RNAseq_08231


title: RNAseq_03657


title: RNAseq_30901


title: RNAseq_49371


title: RNAseq_05844


title: RNAseq_00227


title: RNAseq_35248


title: RNAseq_62856


title: RNAseq_77488


title: RNAseq_44439


title: RNAseq_95704


title: RNAseq_64238


title: RNAseq_11169


title: RNAseq_79676


title: RNAseq_03157


title: RNAseq_33958


title: RNAseq_16743


title: RNAseq_86221


title: RNAseq_86607


title: RNAseq_52661


title: RNAseq_87155


title: RNAseq_39508


title: RNAseq_06484


title: RNAseq_40827


title: RNAseq_00219


title: RNAseq_22679


title: RNAseq_32082


title: RNAseq_86663


title: RNAseq_01214


title: RNAseq_09756


title: RNAseq_96131


title: RNAseq_73340


title: RNAseq_72631


title: RNAseq_98542


title: RNAseq_72834


title: RNAseq_82081


title: RNAseq_02996


title: RNAseq_07078


title: RNAseq_71948


title: RNAseq_39032


title: RNAseq_59731


title: RNAseq_01869


title: RNAseq_44819


title: RNAseq_30192


title: RNAseq_00792


title: RNAseq_18560


title: RNAseq_59764


title: RNAseq_51274


title: RNAseq_60052


title: RNAseq_44077


title: RNAseq_02502


title: RNAseq_87137


title: RNAseq_10864


title: RNAseq_96360


title: RNAseq_10826


title: RNAseq_80293


title: RNAseq_91369


title: RNAseq_13631


title: RNAseq_92233


title: RNAseq_33041


title: RNAseq_10259


title: RNAseq_29759


title: RNAseq_53694


title: RNAseq_20884


title: RNAseq_62237


title: RNAseq_76595


title: RNAseq_71084


title: RNAseq_51813


title: RNAseq_63100


title: RNAseq_16388


title: RNAseq_57395


title: RNAseq_05988


title: RNAseq_50190


title: RNAseq_71559


title: RNAseq_95874


title: RNAseq_23462


title: RNAseq_71427


title: RNAseq_32274


title: RNAseq_64209


title: RNAseq_80754


title: RNAseq_31133


title: RNAseq_58258


title: RNAseq_40763


title: RNAseq_65520


title: RNAseq_61425


title: RNAseq_51304


title: RNAseq_68769


title: RNAseq_93918


title: RNAseq_79978


title: RNAseq_93357


title: RNAseq_38831


title: RNAseq_20926


title: RNAseq_29292


title: RNAseq_79177


title: RNAseq_01851


title: RNAseq_82258


title: RNAseq_53586


title: RNAseq_79756


title: RNAseq_13943


title: RNAseq_03886


title: RNAseq_27997


title: RNAseq_83388


title: RNAseq_14318


title: RNAseq_66940


title: RNAseq_79683


title: RNAseq_43786


title: RNAseq_23255


title: RNAseq_85348


title: RNAseq_13586


title: RNAseq_57174


title: RNAseq_65417


title: RNAseq_62191


title: RNAseq_82655


title: RNAseq_27823


title: RNAseq_91991


title: RNAseq_83587


title: RNAseq_57046


title: RNAseq_95520


title: RNAseq_99527


title: RNAseq_41945


title: RNAseq_62367


title: RNAseq_46386


title: RNAseq_19871


title: RNAseq_79644


title: RNAseq_00776


title: RNAseq_87411


title: RNAseq_44744


title: RNAseq_96571


title: RNAseq_51466


title: RNAseq_87015


title: RNAseq_84423


title: RNAseq_15460


title: RNAseq_82405


title: RNAseq_47652


title: RNAseq_13430


title: RNAseq_50442


title: RNAseq_20976


title: RNAseq_72206


title: RNAseq_57635


title: RNAseq_69006


title: RNAseq_24999


title: RNAseq_77445


title: RNAseq_71524


title: RNAseq_79852


title: RNAseq_04650


title: RNAseq_50897


title: RNAseq_10551


title: RNAseq_80345


title: RNAseq_85318


title: RNAseq_29715


title: RNAseq_33246


title: RNAseq_16236


title: RNAseq_55701


title: RNAseq_77456


title: RNAseq_06848


title: RNAseq_16956


title: RNAseq_49574


title: RNAseq_92340


title: RNAseq_01802


title: RNAseq_86319


title: RNAseq_29860


title: RNAseq_16965


title: RNAseq_42247


title: RNAseq_72430


title: RNAseq_50204


title: RNAseq_05561


title: RNAseq_08904


title: RNAseq_21651


title: RNAseq_83230


title: RNAseq_98809


title: RNAseq_53674


title: RNAseq_56459


title: RNAseq_16058


title: RNAseq_77378


title: RNAseq_66866


title: RNAseq_50102


title: RNAseq_68219


title: RNAseq_71012


title: RNAseq_67062


title: RNAseq_17020


title: RNAseq_98771


title: RNAseq_02742


title: RNAseq_48561


title: RNAseq_90160


title: RNAseq_80521


title: RNAseq_74278


title: RNAseq_46661


title: RNAseq_31238


title: RNAseq_27677


title: RNAseq_28115


title: RNAseq_28010


title: RNAseq_38530


title: RNAseq_36996


title: RNAseq_72709


title: RNAseq_02516


title: RNAseq_69472


title: RNAseq_29905


title: RNAseq_21627


title: RNAseq_18324


title: RNAseq_34413


title: RNAseq_40336


title: RNAseq_51632


title: RNAseq_25382


title: RNAseq_09040


title: RNAseq_64516


title: RNAseq_18646


title: RNAseq_27494


title: RNAseq_50712


title: RNAseq_83077


title: RNAseq_76700


title: RNAseq_78276


title: RNAseq_28450


title: RNAseq_07134


title: RNAseq_96211


title: RNAseq_95601


title: RNAseq_10283


title: RNAseq_08576


title: RNAseq_95450


title: RNAseq_73058


title: RNAseq_93120


title: RNAseq_76698


title: RNAseq_26783


title: RNAseq_67846


title: RNAseq_42790


title: RNAseq_18998


title: RNAseq_54576


title: RNAseq_03890


title: RNAseq_40380


title: RNAseq_99534


title: RNAseq_09538


title: RNAseq_36170


title: RNAseq_93718


title: RNAseq_03210


title: RNAseq_09554


title: RNAseq_43578


title: RNAseq_33526


title: RNAseq_30634


title: RNAseq_06215


title: RNAseq_46112


title: RNAseq_58292


title: RNAseq_31723


title: RNAseq_33613


title: RNAseq_37769


title: RNAseq_60336


title: RNAseq_57473


title: RNAseq_82357


title: RNAseq_54569


title: RNAseq_59124


title: RNAseq_91929


title: RNAseq_78865


title: RNAseq_64717


title: RNAseq_04552


title: RNAseq_10618


title: RNAseq_28898


title: RNAseq_96002


title: RNAseq_98241


title: RNAseq_69180


title: RNAseq_57448


title: RNAseq_83933


title: RNAseq_24910


title: RNAseq_04036


title: RNAseq_16461


title: RNAseq_26708


title: RNAseq_32624


title: RNAseq_94127


title: RNAseq_62945


title: RNAseq_87340


title: RNAseq_46358


title: RNAseq_09533


title: RNAseq_70615


title: RNAseq_44346


title: RNAseq_65787


title: RNAseq_67056


title: RNAseq_45829


title: RNAseq_26143


title: RNAseq_29290


title: RNAseq_60199


title: RNAseq_75099


title: RNAseq_14816


title: RNAseq_72625


title: RNAseq_83881


title: RNAseq_23972


title: RNAseq_09485


title: RNAseq_45273


title: RNAseq_98492


title: RNAseq_13966


title: RNAseq_46115


title: RNAseq_08392


title: RNAseq_41132


title: RNAseq_44611


title: RNAseq_35036


title: RNAseq_50361


title: RNAseq_42800


title: RNAseq_86461


title: RNAseq_32137


title: RNAseq_93567


title: RNAseq_60688


title: RNAseq_53604


title: RNAseq_28876


title: RNAseq_68006


title: RNAseq_66736


title: RNAseq_21593


title: RNAseq_56964


title: RNAseq_07209


title: RNAseq_03145


title: RNAseq_73867


title: RNAseq_51376


title: RNAseq_14724


title: RNAseq_29552


title: RNAseq_11775


title: RNAseq_01707


title: RNAseq_66906


title: RNAseq_30424


title: RNAseq_26668


title: RNAseq_96985


title: RNAseq_98081


title: RNAseq_87577


title: RNAseq_14625


title: RNAseq_17208


title: RNAseq_27013


title: RNAseq_92395


title: RNAseq_32262


title: RNAseq_21648


title: RNAseq_00601


title: RNAseq_85326


title: RNAseq_06539


title: RNAseq_31083


title: RNAseq_40422


title: RNAseq_44803


title: RNAseq_26282


title: RNAseq_67064


title: RNAseq_33741


title: RNAseq_24268


title: RNAseq_06288


title: RNAseq_95037


title: RNAseq_15280


title: RNAseq_53179


title: RNAseq_10115


title: RNAseq_10614


title: RNAseq_23642


title: RNAseq_86993


title: RNAseq_59753


title: RNAseq_12870


title: RNAseq_21769


title: RNAseq_10231


title: RNAseq_40075


title: RNAseq_99334


title: RNAseq_47538


title: RNAseq_14547


title: RNAseq_90099


title: RNAseq_11840


title: RNAseq_65943


title: RNAseq_15325


title: RNAseq_01080


title: RNAseq_00813


title: 293FT RNaseR

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
RNA-seq fragments were mapped by HISAT2 (version 2.0.5; parameters: hisat2 --no-softclip --scoremin L, -16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --dta -k 1 --max-seeds 20) against the GRCh38/hg38 human reference genome with known gene annotations (gencode.v31.annotation.gtf). HISAT2-unmapped fragments were then re-aligned to the same GRCh38/hg38 reference genome using TopHat-Fusion (2.0.12; parameters: tophat2 -fusion-search --keep-fasta-order --bowtie1 --nocoverage-search) to identify high-confidence BSJ sites by CIRCexplorer2 (2.3.6) (Zhang et al., 2016a) with additional parameters: mapped fragments ≥ 3, containing GU/AG splice site motif with 3-nt offset, length between two splice sites ≤ 30,000 nt. Predominantly back-spliced exons spanning high-confidence BSJs were identified by requiring HISAT2-mapped fragments ≤ 3 from canonical splicing of these (back-)spliced exons in 293FT poly(A)+ RNA-seq.
Bam to Bedgraph using genomeCoverageBed  Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg38 for 293FT RNA-seq
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: 293FT RNaseR RNA-seq

growth_protocol: 293FT cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Polyadenylated and non-polyadenylated RNA separation, and RNaseR treatment were carried out as previously described(Yang et al., 2011; Zhang et al., 2013). Briefly, total RNAs were incubated with oligo(dT) magnetic beads to isolate either poly(A)+ RNAs, which were bound to beads, or non-poly(A)+ RNAs, which were present in the flowthrough after incubation. Oligo(dT) magnetic bead selection was performed three times individually to ensure pure poly(A)+ or non-poly(A)+ RNA populations. The non-poly(A)+ RNA population was further processed with the RiboMinus kit (Human/Mouse Module, Invitrogen, Carlsbad, CA, USA) to deplete most of the abundant ribosomal RNAs to obtain poly(A)-/rRNA- RNAs (poly(A)- RNAs for simplicity). An aliquot of poly(A)- RNAs was incubated with 40 U of RNase R (Epicenter) for 3 hr at 37°C and then were subjected to purification with Trizol to obtain RNaseR-treated RNAs.
All three groups of poly(A)+, poly(A)- and RNaseR-treated RNAs were individually subject to RNA-seq library preparation by using Illumina TruSeq RNA Sample Prep Kit V2 and to then deep sequencing with Illumina HiSeq 2000 at Shanghai Institute of Nutrition and Health, CAS for Computational Biology Omics Core, Shanghai, China.

tag: cell line

value: RNaseR treatment

value: scramble


title: RNAseq_94131

tag: current smoker


title: 293FT polyAplus

source_name: 293FT p(A)+ RNA-seq

value: Polyadenylated RNA separation


title: RNAseq_36629

tag: pack years


title: RNAseq_46537

tag: race (1=white, 2=black)


title: 293FT polyAminus

source_name: 293FT p(A)- RNA-seq

value: non-polyadenylated RNA separation


title: RNAseq_26761

tag: gender (1=male, 2=female)


title: RNAseq_91759

tag: fev1 % predicted


title: RNAseq_18968

tag: neutrophil percent


title: RNAseq_63208

tag: lymphocyte percent


title: RNAseq_60016

tag: monocyte percent


title: RNAseq_02363

tag: eosinophil percent


title: RNAseq_34003

tag: batch


title: RNAseq_64695


title: RNAseq_86614


title: RNAseq_34073


title: RNAseq_52834


title: RNAseq_46451


title: RNAseq_57821


title: RNAseq_04270


title: RNAseq_46143


title: RNAseq_84445


title: RNAseq_44519


title: RNAseq_99528


title: RNAseq_89886


title: RNAseq_93397


title: RNAseq_40616


title: RNAseq_18575


title: RNAseq_59843


title: RNAseq_48921


title: RNAseq_88658


title: RNAseq_04670


title: RNAseq_15235


title: RNAseq_99270


title: RNAseq_68095


title: RNAseq_55459


title: RNAseq_00980


title: RNAseq_86586


title: RNAseq_13563


title: RNAseq_76914


title: RNAseq_16351


title: RNAseq_54852


title: RNAseq_83627


title: RNAseq_71384


title: RNAseq_66031


title: RNAseq_36890


title: RNAseq_98847


title: RNAseq_31949


title: RNAseq_55421


title: RNAseq_74116


title: RNAseq_24420


title: RNAseq_39918


title: RNAseq_64339


title: RNAseq_95653


title: RNAseq_82494


title: RNAseq_38536


title: RNAseq_26824


title: RNAseq_96082


title: RNAseq_43154


title: RNAseq_50585


title: RNAseq_40409


title: RNAseq_34968


title: RNAseq_68689


title: RNAseq_93860


title: RNAseq_33476


title: RNAseq_83369


title: RNAseq_58581


title: RNAseq_75118


title: RNAseq_49348


title: RNAseq_78751


title: RNAseq_99485


title: RNAseq_56565


title: RNAseq_13323


title: RNAseq_73518


title: RNAseq_42289


title: RNAseq_55893


title: RNAseq_88345


title: RNAseq_84006


title: RNAseq_51390


title: RNAseq_13268


title: RNAseq_65869


title: RNAseq_04386


title: RNAseq_35541


title: RNAseq_11005


title: RNAseq_77522


title: RNAseq_05992


title: RNAseq_77668


title: RNAseq_32241


title: RNAseq_76390


title: RNAseq_95699


title: RNAseq_69535


title: RNAseq_48941


title: RNAseq_93556


title: RNAseq_24120


title: RNAseq_76363


title: RNAseq_09147


title: RNAseq_63617


title: RNAseq_97195


title: RNAseq_30254


title: RNAseq_76074


title: RNAseq_38101


title: RNAseq_79674


title: RNAseq_74668


title: RNAseq_94955


title: RNAseq_46688


title: RNAseq_93265


title: RNAseq_31698


title: RNAseq_60652


title: RNAseq_75445


title: RNAseq_24983


title: RNAseq_68672


title: RNAseq_65449


title: RNAseq_58399


title: RNAseq_21702


title: RNAseq_51150


title: RNAseq_31063


title: RNAseq_53996


title: RNAseq_54758


title: RNAseq_28484


title: RNAseq_63155


title: RNAseq_51577


title: RNAseq_53600


title: RNAseq_17572


title: RNAseq_31132


title: RNAseq_60980


title: RNAseq_15087


title: RNAseq_14195


title: RNAseq_62102


title: RNAseq_55133


title: RNAseq_56029


title: RNAseq_97847


title: RNAseq_53760


title: RNAseq_64694


title: RNAseq_56283


title: RNAseq_17758


title: RNAseq_29325


title: RNAseq_39725


title: RNAseq_04452


title: RNAseq_61910


title: RNAseq_47748


title: RNAseq_16059


title: RNAseq_26358


title: RNAseq_64392


title: RNAseq_70495


title: RNAseq_06496


title: RNAseq_41598


title: RNAseq_89002


title: RNAseq_35622


title: RNAseq_41396


title: RNAseq_80155


title: RNAseq_45120


title: RNAseq_21320


title: RNAseq_52318


title: RNAseq_75217


title: RNAseq_80613


title: RNAseq_55637


title: RNAseq_67430


title: RNAseq_76422


title: RNAseq_83184


title: RNAseq_16233


title: RNAseq_03700


title: RNAseq_56800


title: RNAseq_87302


title: RNAseq_01374


title: RNAseq_60537


title: RNAseq_65467


title: RNAseq_44174


title: RNAseq_79376


title: RNAseq_98503


title: RNAseq_22429


title: RNAseq_67325


title: RNAseq_64665


title: RNAseq_43699


title: RNAseq_56844


title: RNAseq_12549


title: RNAseq_14325


title: RNAseq_18641


title: RNAseq_81873


title: RNAseq_48830


title: RNAseq_33924


title: RNAseq_74240


title: RNAseq_53918


title: RNAseq_32438


title: RNAseq_27080


title: RNAseq_74115


title: RNAseq_19900


title: RNAseq_34666


title: RNAseq_26759


title: RNAseq_28081


title: RNAseq_29638


title: RNAseq_56736


title: RNAseq_46413


title: RNAseq_71459


title: RNAseq_07353


title: RNAseq_86541


title: RNAseq_30827


title: RNAseq_77984


title: RNAseq_40906


title: RNAseq_48056


title: RNAseq_73875


title: RNAseq_73235


title: RNAseq_85456


title: RNAseq_99974


title: RNAseq_12124


title: RNAseq_66901


title: RNAseq_42302


title: RNAseq_58245


title: RNAseq_31313


title: RNAseq_88622


title: RNAseq_74677


title: RNAseq_85612


title: RNAseq_20988


title: RNAseq_23521


title: RNAseq_80110


title: RNAseq_47782


title: RNAseq_72562


title: RNAseq_63102


title: RNAseq_28238


title: RNAseq_21295


title: RNAseq_42126


title: RNAseq_56671


title: RNAseq_25338


title: RNAseq_10967


title: RNAseq_75538


title: RNAseq_75874


title: RNAseq_09241


title: RNAseq_02972


title: RNAseq_61393


title: RNAseq_97855


title: RNAseq_88354


title: RNAseq_97141


title: RNAseq_67898


title: RNAseq_20390


title: RNAseq_34981


title: RNAseq_11383


title: RNAseq_11587


title: RNAseq_57400


title: RNAseq_01043


title: RNAseq_53355


title: RNAseq_74707


title: RNAseq_64127


title: RNAseq_46504


title: RNAseq_06891


title: RNAseq_80830


title: RNAseq_17976


title: RNAseq_21445


title: RNAseq_22301


title: RNAseq_37366


title: RNAseq_17157


title: RNAseq_44946


title: RNAseq_41426


title: RNAseq_04355


title: RNAseq_47587


title: RNAseq_25769


title: RNAseq_34710


title: RNAseq_81522


title: RNAseq_62582


title: RNAseq_91630


title: RNAseq_89190


title: RNAseq_18652


title: RNAseq_05685


title: RNAseq_01285


title: RNAseq_13656


title: RNAseq_48452


title: RNAseq_77776


title: RNAseq_68098


title: RNAseq_93314


title: RNAseq_67550


title: RNAseq_52675


title: RNAseq_50634


title: RNAseq_68677


title: RNAseq_55669


title: RNAseq_42726


title: RNAseq_23389


title: RNAseq_94153


title: RNAseq_70085


title: RNAseq_01245


title: RNAseq_97888


title: RNAseq_12068


title: RNAseq_36760


title: RNAseq_78849


title: RNAseq_91034


title: RNAseq_01786


title: RNAseq_39067


title: RNAseq_46281


title: RNAseq_99130


title: RNAseq_76495


title: RNAseq_91924


title: RNAseq_24633


title: RNAseq_57368


title: RNAseq_07730


title: RNAseq_50744


title: RNAseq_52094


title: RNAseq_42185


title: RNAseq_71865


title: RNAseq_54450


title: RNAseq_53509


title: RNAseq_60091


title: RNAseq_37743


title: RNAseq_84816


title: RNAseq_85002


title: RNAseq_90066


title: RNAseq_84755


title: RNAseq_43554


title: RNAseq_69268


title: RNAseq_96694


title: RNAseq_01733


title: RNAseq_22513


title: RNAseq_13976


title: RNAseq_07784


title: RNAseq_86596


title: RNAseq_52406


title: RNAseq_13674


title: RNAseq_79918


title: RNAseq_19158


title: RNAseq_06466


title: RNAseq_23198


title: RNAseq_36860


title: RNAseq_88493


title: RNAseq_92488


title: RNAseq_76718


title: RNAseq_43562


title: RNAseq_10229


title: RNAseq_60783


title: RNAseq_29254


title: RNAseq_08141


title: RNAseq_51164


title: RNAseq_70985


title: RNAseq_62400


title: RNAseq_13456


title: RNAseq_46920


title: RNAseq_80784


title: RNAseq_97138


title: RNAseq_16506


title: RNAseq_74383


title: RNAseq_24798


title: RNAseq_71151


title: RNAseq_42829


title: RNAseq_83210


title: RNAseq_25400


title: RNAseq_48141


title: RNAseq_74742


title: RNAseq_90623


title: RNAseq_88837


title: RNAseq_28309


title: RNAseq_50121


title: RNAseq_58887


title: RNAseq_11795


title: RNAseq_68607


title: RNAseq_74542


title: RNAseq_74391


title: RNAseq_83643


title: RNAseq_23412


title: RNAseq_33631


title: RNAseq_58087


title: RNAseq_04920


title: RNAseq_14391


title: RNAseq_15933


title: RNAseq_15644


title: RNAseq_43787


title: RNAseq_28482


title: RNAseq_91139


title: RNAseq_47200


title: RNAseq_34913


title: RNAseq_98692


title: RNAseq_99006


title: RNAseq_34310


title: RNAseq_20840


title: RNAseq_47621


title: RNAseq_44634


title: RNAseq_92883


title: RNAseq_77053


title: RNAseq_27252


title: RNAseq_60880


title: RNAseq_03519


title: RNAseq_45917


title: RNAseq_01685


title: RNAseq_49664


title: RNAseq_87960


title: RNAseq_67221


title: RNAseq_96840


title: RNAseq_02843


title: RNAseq_35364


title: RNAseq_83344


title: RNAseq_01019


title: RNAseq_68118


title: RNAseq_79422


title: RNAseq_73229


title: RNAseq_11342


title: RNAseq_96788


title: RNAseq_13772


title: RNAseq_78266


title: RNAseq_59091


title: RNAseq_32654


title: RNAseq_48314


title: RNAseq_43849


title: RNAseq_79795


title: RNAseq_99950


title: RNAseq_76111


title: RNAseq_74174


title: RNAseq_99560


title: RNAseq_74776


title: RNAseq_54899


title: RNAseq_31638


title: RNAseq_85124


title: RNAseq_18639


title: RNAseq_15433


title: RNAseq_06683


title: RNAseq_92100


title: RNAseq_29933


title: RNAseq_65305


title: RNAseq_98360


title: RNAseq_71578


title: RNAseq_96199


title: RNAseq_61846


title: RNAseq_29123


title: RNAseq_19829


title: RNAseq_79439


title: RNAseq_70473


title: RNAseq_23576


title: RNAseq_18429


title: RNAseq_11321


title: RNAseq_38853


title: RNAseq_09475


title: RNAseq_74926


title: RNAseq_20086


title: RNAseq_57527


title: RNAseq_29672


title: RNAseq_57285


title: RNAseq_09916


title: RNAseq_72220


title: RNAseq_74269


title: RNAseq_20367


title: RNAseq_74206


title: RNAseq_69579


title: RNAseq_18692


title: RNAseq_61442


title: RNAseq_50954


title: RNAseq_10709


title: RNAseq_41108


title: RNAseq_43035


title: RNAseq_55341


title: RNAseq_00278


title: RNAseq_58253


title: RNAseq_07278


title: RNAseq_86851


title: RNAseq_06770


title: RNAseq_38402


title: RNAseq_18599


title: RNAseq_30392


title: RNAseq_43488


title: RNAseq_78109


title: RNAseq_71349


title: RNAseq_29188


title: RNAseq_25909


title: RNAseq_72962


title: RNAseq_15401


title: RNAseq_92318


title: RNAseq_28949


title: RNAseq_01616


title: RNAseq_37123


title: RNAseq_31965


title: RNAseq_44829


title: RNAseq_41176


title: RNAseq_07126


title: RNAseq_91824


title: RNAseq_82526


title: RNAseq_31179


title: RNAseq_53757


title: RNAseq_98104


title: RNAseq_00571


title: RNAseq_16052


title: RNAseq_62317


title: RNAseq_70527


title: RNAseq_28648


title: RNAseq_89744


title: RNAseq_04473


title: RNAseq_81305


title: RNAseq_71390


title: RNAseq_82432


title: RNAseq_33984


title: RNAseq_79372


title: RNAseq_22659


title: RNAseq_46642


title: RNAseq_12670


title: RNAseq_97231


title: RNAseq_25754


title: RNAseq_85919


title: RNAseq_77288


title: RNAseq_38793


title: RNAseq_66504


title: RNAseq_09507


title: RNAseq_51501


title: RNAseq_47760


title: RNAseq_07441


title: RNAseq_50713


title: RNAseq_22919


title: RNAseq_07638


title: RNAseq_58453


title: RNAseq_04003


title: RNAseq_52649


title: RNAseq_78042


title: RNAseq_81466


title: RNAseq_28786


title: RNAseq_45656


title: RNAseq_72511


title: RNAseq_87437


title: RNAseq_08928


title: RNAseq_02525


title: RNAseq_72390


title: RNAseq_11503


title: RNAseq_16162


title: RNAseq_18016


title: RNAseq_54291


title: RNAseq_78629


title: RNAseq_33697


title: RNAseq_38576


title: RNAseq_17370


title: RNAseq_68201


title: RNAseq_39474


title: RNAseq_00298


title: RNAseq_67267


title: RNAseq_01597


title: RNAseq_62573


title: RNAseq_05392


title: RNAseq_22286


title: RNAseq_03186


title: RNAseq_52975


title: RNAseq_21995


title: RNAseq_94879


title: RNAseq_26555


title: RNAseq_78173


title: RNAseq_69073


title: RNAseq_49178


title: RNAseq_17675


title: RNAseq_78486


title: RNAseq_39526


title: RNAseq_03333


title: RNAseq_87612


title: RNAseq_94690


title: RNAseq_44318


title: RNAseq_87424


title: H-WT input

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Use Unique mapped reads for subsequent information analysis
Use the cutadapt program to remove the joint sequence in the original offline data
Use Trimmomatic program to remove low-quality sequences to get clean data; Use the Fastqc program to count the amount of clean data, the ratio of q20 to q30; Use bowtie2 program to compare clean data to the reference genome;
Calculate the capture efficiency of sequencing experiments, the coverage of the ChIP area and the average sequencing depth
Peak-calling on the genome using MACS1.4; Make peak notes;
Use MEME for motif detection of binding peaks; The difference and annotation of peak between samples
Supplementary_files_format_and_content: tab-delimited text files include peak annotation and related analysis for each sampl2

source_name: Multiple myeloma cells

extract_protocol:
Combination of Acetyl-H3 antibody with protein A+G magnetic beads (Magna ChIP™ 16-663). Add cell lysate, protease inhibitor, ice-water bath ultrasound; take 20ul as Input sample and store at 4℃; add the sample to protein A+G magnetic beads bound with antibody and mix overnight; wash magnetic column to elute bound protein The fragments on the A+G magnetic beads are added to ProteinaseK together with the Input sample, and de-crosslinked at 65°C overnight; DNA is extracted with phenol chloroform and digested with RNase. Repair DNA fragment ends, add A bases to the 3'end, and connect sequencing adapters; PCR amplification and fragment size selection of DNA products (generally 100-300bp, including the adapter sequence).
Illumina HiSeq/NextSeq platform for sequencing

treatment_protocol: Prepare at least 107 cells, add 37% formaldehyde to the culture medium (final concentration of formaldehyde is 1%), shake on a shaker for 10 minutes; add glycine solution to a final concentration of 0.125 mol/L, pipette to mix; wash cells with PBS, as much as possible Discard the supernatant, and freeze the cell pellet at -80°C.

value: Homo Multiple myeloma cells

tag: genotype/variation

value: wildtype

tag: antibody


title: H-OE input

value: overexpression


title: H-WT


title: H-OE


title: control4

first: Guoxin

last: Ren

address: 639 Zhi-zao-ju Road, Shanghai, China

institute: Shanghai ninth hospital

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: adjacent normal tissue

extract_protocol:
RNA extraction protocol
library construction protocol

tag: tissue

value: adjacent normal tissue


title: control2


title: RNAseq_90943


title: Sorted Cell Population CD105+ Reactive Anemia 17

city: Linz

first: Johannes

last: Pröll

state: Upper Austria

address: Krankenhausstraße 7a

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University

description: Gene expression data from Reactive Anemia Subjects

hyb_protocol: Samples were hybridized with GeneChip HG-U133  Plus Arrays (Affymetrix) and scanned at site.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: We determined the Gene Cell intensity scaling using GeneChip Operating Software. Partek genomics suite was used to normalize and to apply RMA.

label: Biotin

source_name: Human Bone Marrow

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: not applicable

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

treatment_protocol: Cell sorting was performed using the Aria III sorter equipped with FACSDiva software Version 6.1.3 to obtain pure 95% subsets by sorting with specific marker combinations.

tag: cell type

value: CD105-positive erythroid cells


title: Sorted Cell Population CD105+ Reactive Anemia 18


title: control1


title: Sorted Cell Population CD105+ Reactive Anemia 15


title: Sorted Cell Population CD105+ Reactive Anemia 19


title: Sorted Cell Population CD105+ Reactive Anemia 14


title: treat4

source_name: HNSCC tissue

value: HNSCC tissue


title: treat3


title: Sorted Cell Population CD105+ Reactive Anemia 20


title: Sorted Cell Population CD105+ Reactive Anemia 12


title: treat2


title: Sorted Cell Population CD105+ Reactive Anemia 16


title: Sorted Cell Population CD105+ MDS 23

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 22

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 24

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 21

description: Gene expression data from MDS Subjects


title: RNAseq_43139


title: treat1


title: Sorted Cell Population CD105+ MDS 20

description: Gene expression data from MDS Subjects


title: S25

city: Los Angeles

first: Alice

last: Mouton

state: CA

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

description: processed data file: *count_6hours.txt

data_processing:
The alignment of the samples was performed using STAR 2.5.3 (Dobin et al., 2013)
We filtered reads for low counts and remaining were normalized using TMM (trimmed mean of M-values) in the edgeR package (Robinson and Oshlack, 2010) in R
Reads were then processed by voomwithqualityweight in Limma to convert into log2 counts per million (logCPM) with associated precision weights (Law et. al 2014; Ritchie et al 2015), followed by contrast comparisons.
Genome_build: GRCh38.90
Supplementary_files_format_and_content: Tab-delimited text file

source_name: TH17 clones_Low_α-CD3/α-CD28 for 6hrs

extract_protocol:
Total RNA was isolated at two time points (6 and 12h) after treatment using RLT buffer supplemented with 1% β-mecaptoethanol (QIAGEN). RNA extraction was performed on a total of forty samples according to manufacturer’s instructions using RNAeasy Micro Kit (QIAGEN), including the on-column DNase treatment step.
Illumina TruSeq mRNALibrary Prep , polyA capture

treatment_protocol: Fifteen AMTH17 and five n-AMTH17 clones (control) generated from six healthy donors were stimulated with α-CD3/α-CD28 (BD) in T cell media

tag: cell type source

value: Peripheral blood mononuclear cells

value: C. acnes-specific antimicrobial TH17 clones (AMTH17)

tag: genotype

tag: antimicrobial activity against c. acnes

value: Low

tag: treatment

value: stimulated with α-CD3/α-CD28 (BD) for 6hrs

tag: lane


title: S24

description: processed data file: *count_6hours.txt

source_name: TH17 clones_High_α-CD3/α-CD28 for 6hrs

value: High


title: Sorted Cell Population CD105+ MDS 18

description: Gene expression data from MDS Subjects


title: control3


title: Sorted Cell Population CD105+ MDS 19

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ Reactive Anemia 13


title: S23

description: processed data file: *count_6hours.txt

source_name: TH17 clones_Medium_α-CD3/α-CD28 for 6hrs

value: Medium


title: S22

description: processed data file: *count_6hours.txt


title: S21

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 16

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 15

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ Reactive Anemia 11


title: Sorted Cell Population CD105+ MDS 14

description: Gene expression data from MDS Subjects


title: S19

description: processed data file: *count_6hours.txt

source_name: TH17 clones_control_α-CD3/α-CD28 for 6hrs

value: n-AMTH17 (control)


title: Sorted Cell Population CD105+ MDS 12

description: Gene expression data from MDS Subjects


title: S20

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 13

description: Gene expression data from MDS Subjects


title: S18

description: processed data file: *count_6hours.txt


title: S16

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 11

description: Gene expression data from MDS Subjects


title: S12

description: processed data file: *count_6hours.txt


title: S13

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 7

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 9

description: Gene expression data from MDS Subjects


title: S9

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 8

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 17

description: Gene expression data from MDS Subjects


title: S5

description: processed data file: *count_6hours.txt


title: S7

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 6

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 4

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 5

description: Gene expression data from MDS Subjects


title: RE0005-TT-Y-1

first: Sachin

last: Mulmi Shrestha

address: Dingjiaqiao Street-87

department: Gastroenterology

institute: Southeast University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The RNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: hg19

source_name: Esophageal squamous cell carcinoma

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment;2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: patient diagnosis

value: Esophageal squamous cell carcinoma

value: Moderately Differentiated Squamous cell carcinoma (Ulcerative  type), Stage II


title: S3

description: processed data file: *count_6hours.txt


title: S2

description: processed data file: *count_6hours.txt


title: Sorted Cell Population CD105+ MDS 1

description: Gene expression data from MDS Subjects


title: RE0002-TT-Y-1

value: Moderately Differentiated Squamous cell carcinoma, Stage 0


title: S14

description: processed data file: *count_6hours.txt


title: S50

description: processed data file: *count_12hours.txt

source_name: TH17 clones_Low_α-CD3/α-CD28 for 12hrs

value: stimulated with α-CD3/α-CD28 (BD) for 12hrs


title: RE0005-TN-Y-1

value: Normal tissue


title: Sorted Cell Population CD105+ MDS 2

description: Gene expression data from MDS Subjects


title: Sorted Cell Population CD105+ MDS 10

description: Gene expression data from MDS Subjects


title: RE0002-TN-Y-1


title: RE00014-TT-Y-1

value: Squamous cell carcinoma (Fungating  type), Stage III


title: S10

description: processed data file: *count_6hours.txt


title: RE0002-TP-Y-1

value: Cancer adjacent tissue


title: S48

description: processed data file: *count_12hours.txt


title: S49

description: processed data file: *count_12hours.txt

source_name: TH17 clones_Medium_α-CD3/α-CD28 for 12hrs


title: S46

description: processed data file: *count_12hours.txt


title: S45

description: processed data file: *count_12hours.txt


title: RE00014-TP-Y-1


title: S43

description: processed data file: *count_12hours.txt


title: RE00014-TN-Y-1


title: S47

description: processed data file: *count_12hours.txt


title: RE00013-TT-Y-1

value: Medullary  Squamous cell carcinoma, Stage II


title: RE00013-TP-Y-1


title: S41

description: processed data file: *count_12hours.txt


title: RE00013-TN-Y-1


title: S44

description: processed data file: *count_12hours.txt

source_name: TH17 clones_control_α-CD3/α-CD28 for 12hrs


title: RE0005-TP-Y-1


title: S38

description: processed data file: *count_12hours.txt


title: Sorted Cell Population CD105+ MDS 3

description: Gene expression data from MDS Subjects

value: CD105-positive erythroid cells


title: TR4383

city: Gdańsk

first: Anna

last: Supernat

address: Dębinki 1

department: Division of Translational Oncology

institute: Medical University of Gdansk

data_processing:
Trimmomatic was used for adapter trimming using TruSeq3-SE.fa  reference file. Reads were alligned to Hg19 reference genome using STAR. Picard tools were used for adding a read group.
SAMtools were used for .sam-to-.bam file conversion and data sorting per read name and chromosome.
A custom filterBamCigar.pl script [PMID: 30894694] was used for intron-spanning read selection, and finally HTSeq for read summarization.
Gencode GRCh37.p13 was used for annotation
Data normalization was performed using DESeq-2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2-normalized expression

source_name: Tumor educated platelets from blood

extract_protocol:
Blood collected in Gdańsk was processed within 48 hours upon collection, strictly according to thromboSeq protocol [PMID: 30894694]. Briefly, tubes were centrifuged to obtain platelet rich plasma (20 minutes, 120g), pelleted (20 minutes 360g) and carefully resuspended in RNAlater (Thermo Scientific). After overnight incubation at 4°C, platelets were stored at -80°C. Blood collected in Gdańsk was shipped to Cancer Center Amsterdam, VU University Medical Center for further processing. RNA was extracted with mirVana miRNA isolation kit (Ambion, Thermo Scientific). For RNA quality verification the RNA 6000 Picochip (Bioanalyzer 2100, Agilent) was used. Subsequently, SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech) was used for cDNA amplification. Next, cDNA was subjected to nucleic acid shearing by sonication (Covaris Inc) and then labeled with single index barcodes for Illumina sequencing using the Truseq Nano DNA Sample Prep Kit (Illumina). Labeled platelet cDNA library was measured with the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High quality samples were pooled and submitted for 100 bp Single-Read sequencing on the Illumina HiSeq 2500 and HiSeq 4000 platform.
100 bp single-end reads. Standard Illumina protocol

value: platelets

tag: group

value: EC

tag: Sex

value: F

tag: age

tag: Stage

tag: disease state

value: mucinous endometrial carcinoma


title: TR4382

value: endometrioid adenocarcinoma partial mucinous


title: S35

description: processed data file: *count_12hours.txt

value: Peripheral blood mononuclear cells

value: C. acnes-specific antimicrobial TH17 clones (AMTH17)


title: S30

description: processed data file: *count_12hours.txt

source_name: TH17 clones_High_α-CD3/α-CD28 for 12hrs

value: High


title: TR4350

value: endometrioid adenocarcinoma


title: TR4354

value: mixed clear cell and serous adenocarcinoma


title: S32

description: processed data file: *count_12hours.txt

value: Low


title: S28

description: processed data file: *count_12hours.txt

value: stimulated with α-CD3/α-CD28 (BD) for 12hrs


title: TR4349

value: mucinous adenocarcinoma


title: S27

description: processed data file: *count_12hours.txt


title: S29

description: processed data file: *count_12hours.txt


title: TR4347


title: TR4348


title: S26

description: processed data file: *count_12hours.txt


title: TR4331


title: TR4330


title: TR4333


title: TR4334

value: serous adenocarcinoma


title: hsf-1 RNAi rIIS Heat Shock Rep 1

city: New Delhi

first: Neeraj

last: Kumar

state: Delhi

address: Ansari Nagar

country: India

institute: All India Institute of Medical Sciences, New Delhi

data_processing:
Imaging, base calling and quality scoring were done as per standard manufacturer’s guidelines (Illumina Inc.).
The demultiplexing and conversion of BCL file format reads to FASTQ file format was done with the Illumina-supported CASAVA v1.8.2 software package.
Read counts were then aligned to the reference genome (WBcel 235) and their normalized abundance were calculated as Reads Per Kilobase Million (RPKM) using QIAGEN CLC Genomics Workbench v12.0.3.
Genes fold change was calculated among samples based on negative binomial Generalized Linear Model (GLM) which corrects for differences in library size between samples and the effects of cofounding factors.
Genes with absolute fold change of at least 1.5 and standard-p value below 0.05 were considered as differentially expressed.
Genome_build: WBcel 235
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were grown on nematode growth medium (NGM) supplemented with 100 µg/ml ampicillin and 2mM IPTG.

extract_protocol:
Worms grown on empty vector or transcription factors RNAi plates. RNA was harvested using Trizol reagent. The cDNA libraries were constructed with TruSeq RNA Library Prep Kit v2 (Illumina Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stains were kept on empty vector and transcription specific RNAi clones

tag: strain

tag: temerature

value: 20 ˚C+33 ˚C for 2 hrs


title: skn-1 RNAi rIIS Rep 2

value: 20 ˚C


title: daf-16 RNAi rIIS Rep 2


title: TR4323


title: TR4322


title: S39

description: processed data file: *count_12hours.txt

value: n-AMTH17 (control)


title: daf-16 RNAi rIIS Rep 1


title: skn-1 RNAi rIIS Rep 1


title: TR4328

value: platelets


title: empty vector rIIS Heat Shock Rep 1


title: TR4319

value: EC


title: empty vector rIIS Rep 2


title: empty vector rIIS Rep 1


title: empty vector Control Heat Shock Rep 2


title: TR4282

value: F


title: empty vector Control Rep 2


title: S37

description: processed data file: *count_12hours.txt


title: TR4218


title: TR4278


title: TR4217


title: empty vector Control Heat Shock Rep 1


title: TR4216

value: relapse


title: hsf-1 RNAi rIIS Heat Shock Rep 2


title: TR4212


title: TR4194


title: TR4150


title: TR4095


title: TR4104


title: TR4321


title: TR4055


title: TR4381

value: endometrioid adenocarcinoma partial mucinous with planoepith. diff.


title: TR4052


title: HH12

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

institute: SciGenom Labs Pvt. Ltd.

data_processing:
Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings
Expression estimation was performed using Cufflinks program
Genome_build: Galgal4 - Ensembl Release 75 database
Supplementary_files_format_and_content: The gene expression contains the gene expression estimation from cufflinks program and differential expression p and q score from cuffdiff program

organism: Gallus gallus

source_name: Area vasculosa

growth_protocol: The embryos were allowed to develop through HH10, HH11,HH12 and HH13 stages in CO2 incubator. Area vasculosa was collected surgically from each stage of embryo and processed for RNA extraction

extract_protocol:
Total RNA was isolated using Trizol reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA samples, free of DNA and protein contamination was resuspended in in nuclease free water. 1ug of RNA sample for each stage was given for Next Generation Sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Area vasculosa

tag: developmental stage


title: HH13


title: HH11


title: TR4051


title: TR4047


title: TR4042


title: TR4020


title: SW620/shMACC1 REP 1

city: Berlin

first: Dennis

last: Kobelt

address: Robert-Rössle-Str. 10

institute: ECRC/Charite Berlin

description: gene expression analysis of SW620 cells with MACC1 knock down

hyb_protocol: Affymetrix: GeneChip WT PLUS Reagent Kit; GeneChip Expression Wash, Stain and Scan Rev.4 (2015)

scan_protocol: Affymetrix: GeneChip Expression Wash, Stain and Scan Rev.4 (2015)

data_processing:
Expression Console, Transcriptome analysis console
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: Streptavidin-Phycoerythrin

source_name: SW620 MACC1 knock down

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit

growth_protocol: DMEM, 10% FBS, humidified incubator 37°C 5% CO2

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: stable gene transfer of shRNA

tag: cell line

value: human cell line

tag: genotype/variation

value: shRNA targeting MACC1

tag: passage

value: Passage 1


title: SW620/shcontrol REP 1

description: gene expression analysis of SW620 control cells

source_name: SW620 shcontrol

tag: cell type

value: control shRNA


title: SW620/shcontrol REP 3

value: Passage 3


title: SW620/shMACC1 REP 2

value: Passage 2


title: HH10

tag: tissue


title: TR4027


title: SW620/shcontrol REP 2


title: TR4025

value: mucinous adenocarcinoma


title: GFI1KO_G2ECs_2_control

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

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

description: GATA2+_ECs derived in GFI1-KO

data_processing:
Library strategy: CUT&TAG
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of flag enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

source_name: Endothelial cells

extract_protocol:
CUT&Tag DNA library was prepared using Hyperactive pG-Tn5 Transposase kit (Vazyme), following the manufacturer’s instructions. and cell sample were sonicated, and then CUT&Taged with flag antibodies(F1804) targeting GFI1 protein.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: hESCs derived Endothelial cells

tag: genotype

tag: flag-tagged protein

tag: chip antibody

value: anti-FLAG


title: Igg

description: GATA2+_ECs derived in WT

value: WT


title: TR4021


title: TR4013

value: serous adenocarcinoma


title: SW620/shMACC1 REP 3


title: TR4016

value: platelets


title: App[NL-G-F/NL-G-F] mouse, Biological replicate 3

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

description: gene expression of 6-month-old female App[NL-G-F/NL-G-F] mouse hippocampus

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into the Transcriptome Analysis Console (TAC) Software 4.0 and CHP files were generated.

source_name: Hippocampus of 6-month-old App[NL-G-F/NL-G-F] mouse

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 6 months of age.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturers’ instructions.

treatment_protocol: Each mouse was anesthetized, transcardially perfused with saline, and hippocamppus was isolated quickly, preserved at –80°C until RNA preparation.

tag: gender

value: Female

value: App[NL-G-F/NL-G-F]

value: hippocampus


title: TR4014

tag: group

value: EC

value: F

value: endometrioid adenocarcinoma


title: 231-502

first: hui

middle: jing

last: Peng

state: China

address: Jiangsu Province Hospital

institute: Department of Breast Surgery, The First Hospital Affiliated Hospital with Nanjing Medical University

data_processing:
Sequencing data control:The original sequence of each sample will be counted Q30:Q=-10log10(P)
Comparison of sequencing data:The original data were preprocessed (cutadapt was used and 5 'and 3' junction sequences were removed and too short fragments ≤16bp were filtered out). Hisat2 was used to compared to the reference genome.
The software StringTie was used to estimate transcriptional abundance.
Solexa pipeline version 1.8 software used for basecalling.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: EXCEL with differential genes and transcript

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cells were cultivated cultured in high‐-glucose Dulbecco’s Modified Eagle’s Medium (DMEM)  supplemented with 10% (v/v) foetal bovine serum FBS, 100 U/mLl penicillin, and 100 U/mLl streptomycinin a humidified incubator under with 5% CO2 at 37°C °C

extract_protocol:
RNA was extracted as aforementioned from cells following after TRPC5OS was overexpression.sed. Agarose gel electrophoresis was used for assessing the integrity testingof the extracted RNAs,, and quantification and further quality tests were performed using a NanoDrop ND-1000
an NEB Next ®Poly (A) mRNA Magnetic Isolation Module was used for mRNA enrichment by adding it into the total RNA extract. The library of the processed RNA product RNA was established using the KAPA Stranded RNA-Seq Library Prep Kkit

treatment_protocol: Once confluency was reached 50%, cells were transfected with Lentiviral TRPC5OS or NC.

tag: treatment

value: TRPC5OS overexpressed


title: 231

value: negative control


title: GFI1KO_G2ECs_2

description: GATA2+_ECs derived in GFI1KO

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

extract_protocol:
In brief, 5×104 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: GIH-125_r4: Dermis fibroblast cells GIH-125 rep 4

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
salmon (v0.13.1) was used to map the paired-end reads to the human transcriptome (gencode.v28). --validateMappings and -l ISR flags were used.
tximport (v1.14.0) was used to import the salmon quantification files to R (3.6.1)
DESeq2 (v1.26.0) was used to gene expression changes.
Genome_build: hg38
Supplementary_files_format_and_content: tsv (transcript abundance)

source_name: Dermis fibroblast cells

growth_protocol: DMEM high glucose with Sodium pyruvate, FBS, and PenStrep

extract_protocol:
Quick rna microprep kit from Zymo Research #R1051
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (#634413 Takara)

value: Dermis fibroblast cells

tag: tissue collection

value: During life - skin biopsy

tag: tissue storage

value: Fresh


title: Wild-type mouse, Biological replicate 2

description: gene expression of 6-month-old female wild type mouse hippocampus

source_name: Hippocampus of 6-month-old wild type mouse

tag: age

value: wild type


title: Wild-type mouse, Biological replicate 3


title: GIH-125_r1: Dermis fibroblast cells GIH-125 rep 1


title: WM902B_E+B_RES

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

data_processing:
Raw sequencing data (fastq) were aligned to human reference genome version GRCh38 using HISAT2 algorithm and BAM files were generated. Downstream analysis was performed using StrandNGS software (www.strand-ngs.com).
BAM files were imported into the software DESeq1 algorithm was used for normalization.
To identify differentially expressed genes between conditions Moderated T-Test with Benjamini-Hochberg FDR for multiple testing correction was used.
Genome_build: hg38
Supplementary_files_format_and_content: normalized abundance measurements

source_name: melanoma cell line

growth_protocol: The cells were cultured in RPMI-1640 medium (Lonza Group Ltd., Basel, Switzerland) and supplemented with 10 % foetal bovine serum (Gibco, CA, USA), 2 mmol/L glutamine, and antibiotics at 37°C.

extract_protocol:
RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) was used to isolate total RNA from the melanoma cell lines.
cDNA libraries for RNA-Seq analyses were prepared from 1 μg total RNA using Ultra II RNA Sample Prep kit (New England BioLabs Inc., USA) according to the manufacturer’s protocol.

treatment_protocol: Resistant cell lines were generated through long-term high-dose treatment using in-creasing concentrations of ENCO+BINI in every passage. The concentration of the drug combination at the beginning of treatment was 1 nmol/l for each cell line and increased up to 200 nmol/l. To reach the maximum concen-tration of the drug combination, the time window varied between 3 and 5 months. Re-sistant cells were maintained in complete medium supplemented with a 200 nmol/l com-bination of encorafenib + binimetinib.

value: melanoma cell line

tag: tumor stage

value: primary

tag: condition

value: encorafenib and binimetinib resistant cell line


title: WM983B_E+B_RES

value: metastatic


title: WT_G2ECs_2

description: GATA2+_ECs derived in WT

value: hESCs derived Endothelial cells

value: WT


title: MDF104_r3: Dural cells MDF 104 rep 3

source_name: Dural cells

value: Dural cells

value: Postmortem

value: Frozen (no cryoprotectant)


title: App[NL-G-F/NL-G-F] mouse, Biological replicate 1

value: Female

value: App[NL-G-F/NL-G-F]

value: hippocampus


title: GIH-125_r3: Dermis fibroblast cells GIH-125 rep 3


title: WM983A_E+B_RES


title: GIH-125_r2: Dermis fibroblast cells GIH-125 rep 2


title: WM278

value: original WM278 cell line


title: WM1617_E+B_RES


title: Wild-type mouse, Biological replicate 1


title: App[NL-G-F/NL-G-F] mouse, Biological replicate 2


title: WM983B

value: original WM983B cell line


title: MDF104_r4: Dural cells MDF 104 rep 4


title: WM1617

value: original WM1617 cell line


title: MDF104_r2: Dural cells MDF 104 rep 2


title: WT_G2ECs_1

description: GATA2+_ECs derived in WT


title: WM983A

value: original WM983A cell line