title: RB14_REP1 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 11

source_name: retinoblastoma sample RB14 replicat 1


title: Monocytes primed with live L. plantarum Live3_6d

status: Public on Jul 06 2021

type: SRA

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
Monocytes primed with live L. plantarum
Group_2

library_source: transcriptomic

data_processing:
FASTQ files were aligned to Genome data base using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/],and read counts obtained for each gene
Differential Expression was estimated using DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281] and edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]
Genome_build: human (hg38)
Supplementary_files_format_and_content: A plain text file (*.tsv) was generated for the whole project, consisting in a matrix with two sort of columns: 1st column contains gene IDs (ENTREZ_GENE_ID), and then, from the 2nd to the 10th columns, the numbers of raw counts obtained by STAR per gene and per sample are depicted

molecule: total RNA

organism: Homo sapiens

source_name: Monocytes

growth_protocol: Monocytes were obtained from buffy coats from healthy human donors

extract_protocol:
RNA was extracted using NucleoSpin RNA extraction kit from Macherey-Nagel
Sequencing libraries were prepared following the protocol NuGEN Universal Plus mRNA-Seq kit (PART NO. 0508, 9133, 9134) (Tecan Genomics, Inc.; NuGEN) following the manufacturer’s instructions.
mRNA stranded library sequencing

treatment_protocol: Monocytes were stimulated with culture medium alone or in the presence of either live or heat-killed L. plantarum for 24 h. Stimuli were washed away and cells were rested for 6 days. After that, all monocytes were re-stimulated with live L. plantarum for 24 h.

tag: cell type

value: Monocytes

tag: treatment

value: Live L. plantarum-Live L. plantarum


title: Monocytes primed with heat-killed L. plantarum HK1_6d

description:
Monocytes primed with heat-killed L. plantarum
Group_3

value: Heat-killed L. plantarum-Live L. plantarum


title: D3stG: moDC stimulated with B. pertussis strain G

city: Bilthoven

first: Alberto

last: Miranda-Bedate

state: Utrecht

address: Antonie van Leeuwenhoeklaan 9

department: Department of Immune Mechanisms (IMM)

country: Netherlands

institute: RIVM

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq2 Conversion Software v2.20
RNAseq reads were aligned to the Homo sapiens reference genome (GRCh38) and most recent transcript annotations using STAR (2.6.1a)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_counts_moDC_all_samples.txt: Tab-delimited text file includes raw gene counts of all moDC samples

source_name: peripheral blood mononuclear cells

growth_protocol: CD14 positive monocytes were isolated from  peripherial blood of healthy humans and cultured for 6d with 500U/ml GM-CSF and 800U/ml IL-4 to generate monocyte-derived dendritic cells

extract_protocol:
The column-based miRNeasy RNA isolation kit (Qiagen) was used. RNA was isolated according to the manufacturer’s instructions with minor modifications (extra column-washing step with 80% ethanol before extracting the RNA with RNase-free water)
To determine RNA quality and integrity we used Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with an RNA integrity number above 8 were used.
The TruSeq Stranded mRNA Library Prep Kit from Illumina was used to construct libraries

treatment_protocol: human monocyte-derived dendritic cells were stimulated with live B. pertussis at MOI 10 for 3 hours

value: moDC

tag: donor

tag: stimulated with b . pertussis

value: Yes

tag: b. pertussis strain

value: G

tag: b. pertussis year of isolation

tag: pertactin genotype

value: Positive

tag: batch of sequencing

tag: sample name in supplementary file


title: RB715 (SNP_CytoScan)

type: genomic

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description: SNP array data from retinoblastoma samples

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
SNP arrays were analyzed using the Genome Alteration Print method71 (Popova et al., 2009), which takes into account both the log ratio and B allele frequency signals to determine normal cell contamination, tumor ploidy and the absolute copy-number of each segment.
CN : Copy Number, BA : B allete Frequency

label: biotin

molecule: genomic DNA

source_name: retinoblastoma sample RB715

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Immediately following enucleation, a needle was inserted through the anterior chamber of the eye to extract a tumor sample by aspiration. The tumor specimen was placed in RPMI medium on ice, cells were re-suspended, counted and separated into two tubes (for DNA and RNA preparation). The tubes were then centrifuged to remove all media and snap frozen for later extraction.

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A.  DNA was then extracted using a standard phenol-chloroform protocol

tag: geo dataset serie

value: SAMPLE 109

tag: tissue

value: retinoblastoma


title: D3stH: moDC stimulated with B. pertussis strain H

value: H


title: D6stG: moDC stimulated with B. pertussis strain G


title: RB714 (SNP_CytoScan)

source_name: retinoblastoma sample RB714

value: SAMPLE 108


title: uninfected A549 cells rep1 (miRNA)

city: Harbin

first: Zhiyuan

last: Qu

address: Haping road 678

department: State Key Laboratory of Veterinary Biotechnology

country: China

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.Bowtie2(2.2.8) was used for mapping reads to ribosome RNA database.The remaining reads were further used in assembly and analysis of mRNAs and circRNAs.
The rRNA removed reads of each sample were then mapped to reference genome by Tophat2(2.1.1). The alignment parameters were as follows: 1) maximum read mismatch is 2. 2) Diables the coverage based search for junctions. 3) The distance between mate-pair reads is 50 bp. 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80 bp. The mapped reads were used for mRNA analysis and the unmapped reads were used for circRNA analysis
The reconstruction of mRNA was carried out with software Cufflinks(2.2.1), and then we used Cuffmerge to merge mRNA from different replicas of a group into comprehensive set of mRNA, and then merge the mRNA for further downstream differential expression analysis
20mers from both ends of the unmapped reads that aligned to GRCh38.p12 in the reversed orientation (head-to-tail) were extracted and then were subjected to find_circ to identify circRNAs
All of the clean tags of miRNA were then searched against miRBase database (release 21) to identify known miRNAs.
The mRNA expression level was normalized by using FPKM (Fragments per kilobase of transcript per million mapped reads) and the circRNAs expression level was normalized by RPM (Reads per million mapped reads). The miRNA expression level was calculated and normalized to TPM (transcripts per million).
The edge R package was used for differentially expression of mRNAs and circRNAs and miRNAs.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each mRNA Sample.
tab-delimited text files include RPM values for each circRNA Sample.
tab-delimited text files include TPM values for each miRNA Sample.

source_name: A549 cells

growth_protocol: A549 cells were grown in nutrient mixture F-12 Ham Kaighn’s modified medium or Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum  at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA was harvested using Trizol reagent.
After removing the rRNAs, half of the total enriched RNA was used for circRNA and mRNA library construction, and the other half was size-selected by polyacrylamide gel electrophoresis to enrich for 18–30 nt RNAs for small RNA library construction. To construct circRNA and mRNA libraries, fragmented RNAs were reverse-transcribed into cDNA by using random primers, and the cDNA fragments were purified with a QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to illumina sequencing adapters. Then, Uracil-N-Glycosylase was used to digest the second-strand cDNA. The digested products were amplified by PCR.To construct the small RNA library, the 3’ and 5’ illumina sequencing adaptors were ligated to the RNAs, and the ligation products were reverse-transcribed, amplified.

treatment_protocol: A549 cells were mock-infected or infected with H9N2 virus for 12 h

tag: cell line

tag: infection

value: untreated


title: Monocytes primed with live L. plantarum Live2_6d


title: RB716 (SNP_CytoScan)

source_name: retinoblastoma sample RB716

value: SAMPLE 110


title: RB11 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 10

hyb_protocol: Standard Illumina Protocol

scan_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing:
R Software, MinFi R package
Average Beta

label: Cy5 and Cy3

source_name: retinoblastoma sample RB11

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A. DNA was then extracted using a standard phenol-chloroform protocol.

tag: batch

tag: geo dataset serie sample id

value: SAMPLE 9


title: RBsjd7 (SNP_CytoScan)

source_name: retinoblastoma sample RBsjd7

value: SAMPLE 113


title: RB10 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 9

source_name: retinoblastoma sample RB10

value: SAMPLE 8


title: D2stG: moDC stimulated with B. pertussis strain G


title: RB9 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 8

source_name: retinoblastoma sample RB9

value: SAMPLE 7


title: RB708 (SNP_CytoScan)

source_name: retinoblastoma sample RB708

value: SAMPLE 107


title: RB707 (SNP_CytoScan)

source_name: retinoblastoma sample RB707

value: SAMPLE 106


title: Monocyes unprimed Uns3_6d

description:
Monocyes unprimed
Group_1

value: Monocytes

value: Medium-Live L. plantarum


title: D1stG: moDC stimulated with B. pertussis strain G

value: moDC

value: Yes


title: Monocytes primed with live L. plantarum Live1_6d

value: Live L. plantarum-Live L. plantarum


title: C3: moDC stimulated with B. pertussis strain H

value: Positive


title: RB704 (SNP_CytoScan)

source_name: retinoblastoma sample RB704

value: SAMPLE 105

value: retinoblastoma


title: Monocyes unprimed Uns2_6d

description:
Monocyes unprimed
Group_1


title: RB6 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 6

source_name: retinoblastoma sample RB6

value: SAMPLE 5


title: H2: moDC stimulated with B. pertussis strain F

value: F


title: RB7 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 7

source_name: retinoblastoma sample RB7

value: SAMPLE 6


title: Monocyes unprimed Uns1_6d

description:
Monocyes unprimed
Group_1


title: RB702 (SNP_CytoScan)

source_name: retinoblastoma sample RB702

value: SAMPLE 104


title: B3: moDC stimulated with B. pertussis strain G

value: G


title: RB671 (SNP_CytoScan)

source_name: retinoblastoma sample RB671

value: SAMPLE 103


title: E1: moDC stimulated with B. pertussis strain F


title: D6stF: moDC stimulated with B. pertussis strain F


title: SU_DIPG13_Methylation

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg19 (human) whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM
Reads mapped to hg38 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: DIPG cells

growth_protocol: Patient-derived DIPG cells were maintained in serum-free media supplemented with B27, EGF, FGF, PDGF-AA, PDGF-BB, and Heparin

extract_protocol: DNA Methylation: Genomic DNA from DIPG cells were extracted using QIAamp DNA Mini Kit (Qiagen). DNA bisulfite conversion was conducted using EZ DNA Methylation-Lightning Kits (Zymo Research)

value: patient-derived DIPG cells


title: RB4_REP1 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 4

source_name: retinoblastoma sample RB4 replicat 1

value: SAMPLE 4


title: RB4_REP2 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 5

source_name: retinoblastoma sample RB4 replicat 2


title: SU_DIPG4_Methylation


title: RB3 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 3

source_name: retinoblastoma sample RB3

value: SAMPLE 3


title: D3stF: moDC stimulated with B. pertussis strain F

source_name: peripheral blood mononuclear cells


title: RB663 (SNP_CytoScan)

source_name: retinoblastoma sample RB663

value: SAMPLE 102


title: CC_DIPG2_Methylation


title: RB659 (SNP_CytoScan)

source_name: retinoblastoma sample RB659

value: SAMPLE 101


title: RB2 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 2

source_name: retinoblastoma sample RB2

value: SAMPLE 2


title: D2stF: moDC stimulated with B. pertussis strain F

value: moDC

value: Yes


title: D1stF: moDC stimulated with B. pertussis strain F

value: Positive


title: SU_DIPG13_Olig2KO_RNAseq

extract_protocol:
RNA-seq: Total RNA from DIPG cells and NSC cells were extracted using Trizol (Life Technologies) protocol followed by purification using an RNeasy Micro Kit (Qiagen).
RNA-seq: RNA-seq libraries from DIPG cells and NSC cells were prepared using Illumina RNA-Seq Preparation Kit.

tag: sample type


title: RB634 (SNP_CytoScan)

source_name: retinoblastoma sample RB634

value: SAMPLE 98


title: RB647 (SNP_CytoScan)

source_name: retinoblastoma sample RB647

value: SAMPLE 100

value: retinoblastoma


title: P rep3

city: Shanghai

first: yang

last: xu

state: Shanghai

address: 180 Fenglin road shanghai

institute: Zhongshan Hospital, Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2-2.1.0
Reads Counts were calculated using htseq-count , Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples
Supplementary_files_format_and_content: tab-delimited text files include counts values for all Samples

organism: Mus musculus

source_name: HCC murine

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: treated by anti-PD-1 antibody


title: G2: moDC stimulated with B. pertussis strain D

value: D

value: Negative


title: RB632 (SNP_CytoScan)

source_name: retinoblastoma sample RB632

value: SAMPLE 97


title: RB630 (SNP_CytoScan)

source_name: retinoblastoma sample RB630

value: SAMPLE 96


title: NSC_RNAseq_2

source_name: human NSC

value: Human Neural Stem Cells


title: P rep2


title: D3stD: moDC stimulated with B. pertussis strain D


title: P rep1


title: D6stD: moDC stimulated with B. pertussis strain D


title: NSC_RNAseq_1


title: RB603 (SNP_CytoScan)

source_name: retinoblastoma sample RB603

value: SAMPLE 93


title: D2stD: moDC stimulated with B. pertussis strain D


title: SU_DIPG13_RNAseq

value: patient-derived DIPG cells


title: D1stD: moDC stimulated with B. pertussis strain D


title: RB617 (SNP_CytoScan)

source_name: retinoblastoma sample RB617

value: SAMPLE 94


title: L rep3

value: mIFNalpha combined with anti-PD-1 antibody


title: SU_DIPG4_RNAseq_2


title: CC_DIPG1_Methylation


title: L rep1


title: RB598 (SNP_CytoScan)

source_name: retinoblastoma sample RB598

value: SAMPLE 92


title: RB593 (SNP_CytoScan)

source_name: retinoblastoma sample RB593

value: SAMPLE 91


title: RB1 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 1

source_name: retinoblastoma sample RB1

value: SAMPLE 1


title: D1: moDC stimulated with B. pertussis strain D

value: moDC

value: Yes


title: SU_DIPG4_Olig2KO_RNAseq

description: DIPG-IV-KO

source_name: DIPG cells


title: CC_DIPG2_RNAseq_2


title: RB590 (SNP_CytoScan)

source_name: retinoblastoma sample RB590

value: SAMPLE 90

value: retinoblastoma


title: G rep3

value: Liver

value: treated by mIFNalpha


title: D6stB: moDC stimulated with B. pertussis strain B

source_name: peripheral blood mononuclear cells

value: B

value: Negative


title: G rep2


title: CC_DIPG2_RNAseq_1


title: D3stB: moDC stimulated with B. pertussis strain B


title: G rep1


title: CC_DIPG1_RNAseq_2


title: RB307 (SNP_CytoScan)

source_name: retinoblastoma sample RB307

value: SAMPLE 89


title: F2: moDC stimulated with B. pertussis strain B


title: RB63 (SNP_CytoScan)

source_name: retinoblastoma sample RB63

value: SAMPLE 53


title: D2stB: moDC stimulated with B. pertussis strain B


title: RB62 (SNP_CytoScan)

source_name: retinoblastoma sample RB62

value: SAMPLE 52


title: CC_DIPG1_RNAseq_1

value: patient-derived DIPG cells


title: D1stB: moDC stimulated with B. pertussis strain B


title: RB61 (SNP_CytoScan)

source_name: retinoblastoma sample RB61

value: SAMPLE 51


title: CC_DIPG_2_H3K27AC

data_processing:
ATAC-seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to hg19 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
ChIP-seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to hg19 whole genome by Bowtie2 with default options
Genome_build: hg19
Supplementary_files_format_and_content: bw

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500.

tag: chip antibody


title: SU_DIPG4_RNAseq_1

tag: cell type


title: C rep2

tag: treatment

value: untreated


title: C rep3


title: C rep1


title: C1: moDC stimulated with B. pertussis strain B

tag: donor


title: CC_DIPG_1_H3K27AC


title: E2: moDC stimulated with B. pertussis strain A

tag: stimulated with b . pertussis

value: A


title: D6stA: moDC stimulated with B. pertussis strain A

tag: b. pertussis strain


title: CC_DIPG_2_ATAC

extract_protocol:
ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 50,000 cultured DIPG cells in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.
Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500.


title: CC_DIPG_1_ATAC


title: wild-type_E14.5_ATACseq_replicate2

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

description: CD15+ NPCs isolated by FACS

data_processing:
Basecalling and demultiplexing: CASAVA 1.9
Initial quality control: FastQC 0.11.8
Read mapping: bowtie 2.3.5.1
SAM to BAM conversion, sorting and indexing: samtools 1.9
Remove mitochondrial reads using samtools and bash commands
Generating bigwigs (RSPD normalization): deeptools bamCoverage v.3.3.0
Called peaks using MACS2:  macs2 callpeak -t <BAM> -f BAMPE --broad --broad-cutoff 0.05 -n <sample_name> -g mm --keep-dup 1 --outdir <outdir>
Genome_build: GRCm38 Ensembl
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: broadPeak: chrom; chromStart; chromEnd; score; strand; signalValue; pValue; qValue

source_name: Mouse embryonic brain

growth_protocol: Mouse primary cells from wild-type, L3mbtl3 het and KO were used

extract_protocol: ATACseq libraries were prepared using Nextera DNA library preparation Kit (Cat. No. FC-121-1030) by the protocal published in Buenrostro et al., 2015

tag: age

value: embryonic day 14

tag: strain

tag: genotype

value: wild-type


title: wild-type_E14.5_ATACseq_replicate3

description: CD15+ NPCs isolated by FACS


title: D3stA: moDC stimulated with B. pertussis strain A

value: moDC

tag: b. pertussis year of isolation

tag: pertactin genotype

tag: batch of sequencing

tag: sample name in supplementary file


title: L3mbtl3 KO_E14.5_ATACseq_replicate4

description: CD15+ NPCs isolated by FACS

value: L3mbtl3 -/-


title: wild-type_E14.5_ATACseq_replicate1

description: CD15+ NPCs isolated by FACS


title: sema5c_Pol_NR3

city: Santiago

first: Esteban

middle: Gonzalo

last: Contreras Sepúlveda

address: Independencia 1027

country: Chile

institute: Universidad de Chile

data_processing:
damidseq_pipeline. From Marshall and Brand. Bioinformatics 2015
Genome_build: dmel_r6
Supplementary_files_format_and_content: damidseq_pipeline. From Marshall and Brand. Bioinformatics 2015

organism: Drosophila melanogaster

source_name: larval brain

extract_protocol:
Targeted DamID protocol from Marshall OJ, et al. Nat Protoc 2016.
Targeted DamID protocol from Marshall OJ, et al. Nat Protoc 2016.
DamID-seq

value: R71C08-GAL4 x tub-GAL80ts, UAS-LT3-NDam-RpII215

tag: nutrient condition

value: NR


title: sema5c_Dam_NR3

value: R71C08-GAL4 x tub-GAL80ts, UAS-LT3-NDam


title: Naïve_CD8_CD44Lo_3

city: Philadelphia

first: Luis

last: Sigal

state: Pennsylvania

address: 233 S 10th St, BLSB709

department: Microbiology and Immunology

institute: Thomas Jefferson University

description: Naïve CD8

data_processing:
Raw image data file from high-throughput sequencing (Illumina) is transformed to Sequenced Reads by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ format files, which contain reads sequence and corresponding base quality.  FASTQ format described by four lines: Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).  Line 2 is the raw sequence letters.  Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.  Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.
The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. As we can see in Fig 1.3, which will affect the further analysis results. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.  RNA-seq Adapter information:  NEBNext® UltraTM RNA Library Prep Kit  RNA 5' Adapter(5'Adaptor)  5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT  RNA 3' Adapter(3'Adaptor,The underlined 6bp bases is Index)  5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
STAR software is used to map reads to reference genome
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package.
KEGG analysis was performed using KEGG database.  Heatmap cluster analysis, PCA, and volcano plots were generated using python packages matplotlib, seaborn, and pandas
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files.  Two files contain total count or relative count (fpkm) of all genes for every sample.  Differentially expressed gene (DEG) files compare two populations of T cells as indicated in file name and lists any genes that are significantly different between the two groups of samples.  Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis files highlight enriched pathways between two groups listed in file name.

source_name: spleen T cell

extract_protocol:
RNA was extracted using RNA Clean and Concentrator-5' kit from Zymo Research eluting in 25 microliter of elution buffer following manufacturer instructions.  Samples were treated in column with Dnase I.  Up to 1 million sorted cells were used for each sample in RNA extraction.
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer.  Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

tag: lineage

tag: infection state

value: Naïve

tag: population

value: CD44 lo


title: Naïve_CD8_CD44Hi_3

description: Memory-like CD8

value: CD44 hi


title: L3mbtl3 KO_E14.5_ATACseq_replicate3

description: CD15+ NPCs isolated by FACS


title: D2stA: moDC stimulated with B. pertussis strain A

value: Yes

value: Negative


title: Naïve_CD4_CD44Hi_3

description: Memory-like CD4


title: L3mbtl3 KO_E14.5_ATACseq_replicate2

description: CD15+ NPCs isolated by FACS


title: Naïve_CD4_CD44Lo_3

description: Naïve CD4


title: L3mbtl3 KO_E14.5_ATACseq_replicate1

description: CD15+ NPCs isolated by FACS


title: Naïve_CD8_CD44Hi_1

description: Memory-like CD8


title: sema5c_Pol_NR2


title: L rep2

source_name: HCC murine

tag: tissue

value: Liver

value: mIFNalpha combined with anti-PD-1 antibody

tag: cell line


title: Naïve_CD8_CD44Hi_2

description: Memory-like CD8


title: B1: moDC stimulated with B. pertussis strain A

tag: cell type


title: sema5c_Pol_NR1


title: sema5c_Dam_NR2


title: Treatment 3 [S234_09B_CHG009177-hunyang1-D_L004]

first: Xiaoyun

last: Zhang

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description: NGPF2 treatment group repeat 3

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: cortical primary neuronal cultures_NGPF2

growth_protocol: Cortical cultures were prepared from postnatal day 1 (P1) pups as described previously. Briefly, pups were sacrificed cortical regions were dissected in ice-cold 0.1 M PBS. Tissues were trypsinized (0.25%) at 37oC for 15 minutes, dissociated by trituration, and plated onto poly-D-lysine (50 µg/ml) coated glass coverslips (60,000 cells/ml). The cultures were maintained by replacing half of the medium with fresh medium every 4 days. The maintenance medium contained Neurobasal A, 0.5 mM GlutaMax and B27.

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) were used to isolate mRNA, then fragmented into short fragments. cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. After agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates.

treatment_protocol: Mouse cortical primary neuronal cultures (DIV12-13) were treated with NGPF2 (1.5 ng/ml)  or vehicle (PBS) for 2 hours and then fixed for RNA sequencing

value: cortical primary neuronal cultures

tag: treatment

value: NGPF2 (1.5 ng/ml)


title: Naïve_CD8_CD44Lo_1

description: Naïve CD8


title: Naïve_CD8_CD44Lo_2

description: Naïve CD8


title: Treatment 2 [S234_09B_CHG009177-hunyang1-C_L004]

description: NGPF2 treatment group repeat 2


title: sema5c_Dam_NR1


title: Treatment 1 [Treatment]

description: NGPF2 treatment group repeat 1


title: Naïve_CD4_CD44Lo_2

description: Naïve CD4


title: Naïve_CD4_CD44Hi_2

description: Memory-like CD4


title: sema5c_Pol_Fed3

value: Fed


title: sema5c_Dam_Fed3


title: sema5c_Pol_Fed2


title: Naïve_CD4_CD44Hi_1

description: Memory-like CD4


title: Control 2 [S234_09B_CHG009177-hunyang1-A_L004]

description: control group repeat 2

source_name: cortical primary neuronal cultures_control

value: vehicle (PBS)


title: Control 3 [S234_09B_CHG009177-hunyang1-B_L004]

description: control group repeat 3


title: D1stA: moDC stimulated with B. pertussis strain A

tag: donor

tag: stimulated with b . pertussis

value: A


title: Human_Control_adult4

type: RNA

city: Seoul

first: Soo-Jong

last: Hong

state: Seoul

address: Department of Medicine, 88, OLYMPIC-RO 43-GIL, SONGPA-GU

country: South Korea

institute: University of Ulsan Collage of Medicine

description: Gene expression data from lung FFPE

hyb_protocol: 5.5 μg of labeled DNA target was hybridized to the GeneChip® Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45°C for 16hour for human samples, and hybridized to the GeneChip® Rat Gene 2.0 ST Array (Affymetrix) at 45°C for 16hour for rat samples.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: Adjacent normal tissues of lung tumors

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: For rat experimenmt, twelve-week-old nulliparous female and male Sprague-Dawley rats were purchased from Orient Bio (Seoul, Korea).

extract_protocol: mRNAs were extracted from FFPE of human lung tissues and frozen rat lung tissues with a miRNeasy FFPE kit (Qiagen, Hilden, Germany) and TRIzol reagent (Invitrogen, Carlsbad, CA, USA), respectively, according to the manufacturer’s protocol.

treatment_protocol: All patients were confirmed to have HDLI based on both pathological and radiological findings. In the case of rat experiment, PHMG phosphate was exposed to whole-body target PHMG phosphate concentrations of 0 (Control) or 3.20 mg/m3 for 6 hours per day, 7 days per week, from day 6 to day 20.

value: Lung

tag: age


title: Control 1 [Ctrl]

description: control group repeat 1


title: sema5c_Pol_Fed1


title: Human_Control_adult3

description: Gene expression data from lung FFPE


title: sema5c_Dam_Fed1


title: ECTV_CD4_Gzmb_3

description: Cytotoxic CD4

source_name: liver T cell

value: ECTV

value: CD44 hi Gzmb


title: ECTV_CD8_Gzmb_3

description: Cytotoxic CD8


title: mdr65_Pol_NR3

value: R54C07-GAL4 x tub-GAL80ts, UAS-LT3-NDam-RpII215

value: NR


title: Human_Control_adult1

description: Gene expression data from lung FFPE


title: Human_Control_child4

description: Gene expression data from lung FFPE


title: ECTV_CD4_CD44Lo_3

description: Antigen-inexerienced CD4


title: mdr65_Dam_NR3

value: R54C07-GAL4 x tub-GAL80ts, UAS-LT3-NDam


title: mdr65_Pol_NR2


title: sema5c_Dam_Fed2

value: R71C08-GAL4 x tub-GAL80ts, UAS-LT3-NDam


title: mdr65_Dam_NR2


title: Human_Control_child3

description: Gene expression data from lung FFPE


title: 28_PD_Fasting_9_M5FB

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using GeneSpring Gx v12.0

source_name: Pre-diabetic fasting sample

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

growth_protocol: This study was conducted with freshly isolated PBMCs

extract_protocol: Peripheral blood mono-nuclear cells (PBMCs) were isolated by density gradient centrifugation by layering blood over Histopaque. Post isolation, the PBMC pellet was washed with 1X PBS, subjected to RBC lysis followed by another wash. The final cell pellet was resuspended in TRI reagent for cell lysis. RNA was isolated as per the kit manufacturer’s protocol (RNeasy mini kit was used for RNA isolation, Qiagen). Briefly, phase separation was done by adding chloroform to the TRI suspension and ethanol was used to precipitate RNA from the aqueous phase. The pellet was then loaded on the columns and washed with RW1 and RPE buffers provided by the manufacturer and finally the total RNA was eluted from the column in 30µl nuclease free water. RNA quantity was measured using Qubit4.0 fluorometer from Invitrogen. RNA quality was estimated using electrophoresis-based RNA Screentape kit in the TapeStation system from Agilent technologies and only those samples with RNA integrity number (RIN) greater than 8.0 were used for array hybridization.

treatment_protocol: PBMCs were isolated from fasting and 2-hour post oral glucose load conditions from study participants. No ex-vivo treatment was given to these cells

tag: ethnicity

value: Asian-Indian

tag: gender

value: Male

tag: glucose metabolism status

value: Pre-diabetic

value: Peripheral blood mononuclear cells


title: Naïve_CD4_CD44Lo_1

description: Naïve CD4

value: Naïve

value: CD44 lo


title: mdr65_Pol_NR1

tag: genotype


title: ECTV_CD4_Gzmb_2

description: Cytotoxic CD4


title: Human_Control_child2

description: Gene expression data from lung FFPE


title: Human_Control_child5

description: Gene expression data from lung FFPE


title: Human_Control_child1

description: Gene expression data from lung FFPE


title: Human_Control_adult2

description: Gene expression data from lung FFPE


title: ECTV_CD8_Gzmb_2

description: Cytotoxic CD8


title: Human_HDLI_case_adult4

description: Gene expression data from lung FFPE

source_name: Lung of patient exposed to humidifier disinfectant


title: 27_PD_Fasting_8_M4FB


title: 26_PD_Fasting_7_M18FA


title: 25_PD_Fasting_6_M15FA


title: ECTV_CD4_CD44Lo_2

description: Antigen-inexerienced CD4


title: 23_PD_Fasting_4_M10FA


title: mdr65_Pol_Fed5


title: Human_HDLI_case_adult3

description: Gene expression data from lung FFPE


title: Human_HDLI_case_adult2

description: Gene expression data from lung FFPE


title: ECTV_CD8_Gzmb_1

description: Cytotoxic CD8


title: 22_PD_Fasting_3_M8FB


title: ECTV_CD4_CD44Hi_2

description: Antigen-experienced CD4

value: CD44 hi


title: 24_PD_Fasting_5_M12FA


title: ECTV_CD4_Gzmb_1

description: Cytotoxic CD4


title: mdr65_Dam_Fed5

value: Fed


title: mdr65_Dam_NR1


title: Human_Control_adult5

description: Gene expression data from lung FFPE


title: mdr65_Dam_Fed4


title: ECTV_CD4_CD44Hi_1

description: Antigen-experienced CD4


title: Ssbp1_sRNA_KO_brep3 [S6]

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed of adapter sequences with BBDuk (ktrim=r, kink=4, k=18) and trimmed paired ends merged with BBMerge (useoverlap=t pfilter=1 mininsert=18 mininsert0=18 trimonoverlapping=t) of the BBMap suite v38.79.
Merged reads were aligned to the mouse genome with bowtie2 v2.4.1.
Mitochondrial coverage profiles were generated with samtools v1.10 and bedtools v2.26.0 genomecov, normalised to total reads mapped to the mitochondrial genome.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bedgraph files of normalised mitochondrial genome coverage, per strand

growth_protocol: SSBP1+/loxp were mated with mice expressing cre-recombinase under ckmm (the muscle creatinine kinase) promoter. All mice maintaining an inbred C57BL/6N nuclear background were housed in a 12-hour light/dark cycle at 21°C and fed ad libitum on a standard mouse food (ssniff RM-H Low-Phytoestrogen).

extract_protocol:
RNA was isolated from total hearts from three Ssbp1+/+ and Ssbp1-/- mice, using a bead-beating RNA extraction strategy based on the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Sequencing libraries were prepared according to the Illumina TruSeq Small RNA protocol.

tag: strain background

value: inbred C57BL/6N nuclear background

value: Heart


title: ECTV_CD4_CD44Hi_3

description: Antigen-experienced CD4


title: mdr65_Pol_Fed3


title: ECTV_CD4_CD44Lo_1

description: Antigen-inexerienced CD4


title: Ssbp1_sRNA_WT_brep3 [S5]


title: ΔrecA after treatment 1 [D1]

city: shenzhen

first: guan

last: yunpeng

address: 1088 Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong Province

department: BME

institute: Southern University of Science and Technology

data_processing:
Bcl2fastq (v2.17.1.14) software used for basecalling, after Preliminary quality analysis, obtaining Pass Filter Data.
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1）
Mapping:Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Bowtie2 (v2.2.6) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2 (v2.2.6).
Expression analysis:In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Genome_build: NC_000913
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample, FPKM (Fragments Per Kilo bases per Million reads) (Mortazavi, 2008）

organism: Escherichia coli

source_name: ΔrecA_8h culture with antibiotics

growth_protocol: Luria-Bertani (LB) was used as broth or in agar plates. E. coli cells were grown on LB agar (1.5% w/v) plates at 37ºC

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit(Qiagen)/other kits, 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generationsequencing library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: For the single exposure to antibiotic experiment, an overnight culture (0.6 ml; 1 x 109 CFU/ml cells) was diluted 1:50 into 30 ml LB medium supplemented with antibiotics (50 μg/ml ampicillin, 1 mg/ml penicillin G, or 200 μg/ml carbenicillin) and incubated at 37ºC with shaking at 250 rpm for 8 hours. After treatment, the remain pellet was collected, repeated and abundant batch of samples are mixed for RNA-seq.

tag: strain

value: str. K-12 substr. MG1655

value: 8h culture with antibiotics

value: {delta}recA


title: Human_HDLI_case_child4

description: Gene expression data from lung FFPE

value: Lung


title: Human_HDLI_case_child2

description: Gene expression data from lung FFPE


title: 21_PD_Fasting_2_211


title: Ssbp1_sRNA_KO_brep2 [S4]


title: Human_HDLI_case_child5

description: Gene expression data from lung FFPE


title: Human_HDLI_case_child1

description: Gene expression data from lung FFPE


title: mdr65_Dam_Fed3

tag: nutrient condition


title: mdr65_Pol_Fed2

value: R54C07-GAL4 x tub-GAL80ts, UAS-LT3-NDam-RpII215


title: 17_PD_2_hour_5_M122A

source_name: Pre-diabetic 2-hour post oral glucose load sample


title: 18_PD_2_hour_6_M152A


title: ΔrecA after treatment 2 [D2]


title: Human_HDLI_case_child3

description: Gene expression data from lung FFPE


title: wild type after treatment 2 [C2]

source_name: wild type_8h culture with antibiotics

value: wild type


title: Ssbp1_sRNA_KO_brep2 [S3]


title: 14_PD_2_hour_2_212


title: mdr65_Pol_Fed4


title: wild type after treatment 1 [C1]


title: mdr65_Pol_Fed1


title: Ssbp1_sRNA_WT_brep2 [S2]


title: ΔrecA 2 [B2]

source_name: ΔrecA_8h culture without pressure

value: 8h culture without pressure


title: Ssbp1_sRNA_WT_brep1 [S1]


title: Human_HDLI_case_adult1

description: Gene expression data from lung FFPE


title: wor_Pol_NR2

value: worniu-GAL4 x tub-GAL80ts, UAS-LT3-NDam-RpII215

value: NR


title: 20_PD_Fasting_1_201

value: Asian-Indian

value: Male

value: Pre-diabetic


title: 13_PD_2_hour_1_202

value: Peripheral blood mononuclear cells


title: ΔrecA 1 [B1]


title: 15_PD_2_hour_3_M82B


title: 12_NGT_Fasting_6_241

source_name: Normal glucose tolerance fasting sample

value: Normal


title: mdr65_Dam_Fed1

value: R54C07-GAL4 x tub-GAL80ts, UAS-LT3-NDam

value: Fed


title: 19_PD_2_hour_7_M182A


title: Ssbp1_TruSeq_WT_brep3_trep2 [585H_2]

data_processing:
Where applicable, technical replicates were pooled.
Sequenced reads were aligned to the mouse genome (GRCm38.p6 primary assembly, masked for nuclear mitochondrial sequences) using STAR v2.7.3a and the GENCODE vM24 gene annotation with a customised mitochondrial annotation.
Gene expression quantification was performed with Salmon v1.1.0 (-l ISR --seqBias) in alignment-based mode on the transcriptome alignment produced by STAR using a transcriptome sequence file generated with gffread v0.11.7.
Differential expression analysis was performed with DESeq2 1.26.0 using counts summarised by tximport 1.14.0 and effect size estimation performed using apeglm v1.8.1.
Full fragment length mitochondrial coverage profiles were generated with samtools v1.10 and bedtools v2.26.0, and normalised to total reads mapped to mitochondria.
Genome_build: GRCm38.p6

extract_protocol:
RNA was isolated from total hearts from three Ssbp1+/+ and Ssbp1-/- mice, using a bead-beating RNA extraction strategy based on the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Sequencing libraries were prepared according to the Illumina Tru-Seq protocol.

value: inbred C57BL/6N nuclear background

value: Heart


title: wor_Dam_NR2

value: worniu-GAL4 x tub-GAL80ts, UAS-LT3-NDam


title: wor_Pol_NR1


title: mdr65_Dam_Fed2


title: Ssbp1_TruSeq_KO_brep3_trep1 [586H_1]


title: 10_NGT_Fasting_4_151


title: 11_NGT_Fasting_5_231


title: wor_Dam_NR1


title: 9_NGT_Fasting_3_141


title: wor_Pol_Fed2


title: RNase SAR-seq rep2

city: Worcester

first: Kevin

last: Creamer

state: MA

address: 55 Lake Ave N

institute: UMMS

data_processing:
Library strategy: SAR-seq
RNA-seq reads were mapped to hg19 using TopHat2 using Ensembl (build 82) gene annotations. DNA sequencing reads were mapped to hg19 using Bowtie2 with –no-mixed –nodiscordant –very-sensitive parameters
Transcript abundance was calculated using RSEM.
Coverage maps were generated using DeepTools bamCoverage and -bs –maxFragmentLength 120 –normalizeTo1x –ignoreFoorNormalization chrX chrM parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RSEM count matrix, TPM calculations, and Deseq2 calculations

source_name: normal human fetal lung fibroblasts

growth_protocol: MEM + 15% FBS

extract_protocol:
Scaffold attached DNA was isolated from 108 TIG-1 fibroblasts harvested with trypsin and thoroughly washed with ice cold PBS. Buffers at all steps contained protease inhibitors (Roche) and RNase inhibitor where appropriate (RNasin, Promega). First, nuclei were isolated by thoroughly resuspending in 1 ml Isotonic Lysis Buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 3 mM MgCl2, 10% glycerol, 0.5% NP-40, 0.5 mM PMSF) and incubating for 5 min. Nuclei were pelleted by centrifugation at 4°C for 3 min at 800 g. The cytosolic supernatant was removed and permeabilized nuclei were washed once in Isotonic Lysis Buffer lacking NP-40. Nuclei were then incubated for 5 minutes at 37°C in 0.5 ml Isotonic Lysis Buffer lacking NP-40 with the addition of RNase inhibitor or RNase A (Thermo Fisher, 0.1 mg/ml) before pelleting as before. The insoluble material was then extracted with 0.5 ml Ammonium Sulfate Extraction Buffer (10 mM Tris-HCl pH 7.5, 250 mM ammonium sulfate, 300 mM sucrose, 3 mM MgCl2, 0.5% Triton X-100, 0.5 mM PMSF) for 5 minutes on ice with vortexing to disrupt the insoluble pellet. The high salt extracted insoluble material was then pelleted at 4°C for 10 min at 5,000 g. The insoluble pellet was then washed with 0.5 ml DNase Digestion Buffer (40 mM Tris-HCl pH 7.9, 10 mM NaCl, 6 mM MgCl2, 1mM CaCl2, 300 mM sucrose, 0.05% NP-40, 0.5mM PMSF). Insoluble material was again suspended in 0.5 ml DNase Digestion Buffer before addition of 5 µl DNase I (Roche). Nuclei were incubated 30 minutes at 37°C before the addition of an equal volume 4 M High Salt Stop Buffer (10 mM Tis-HCl pH 7.5, 300 mM sucrose, 4M NaCl, 20 mM EDTA). The highly digested, insoluble chromatin was pelleted by centrifugation at 4°C for 10 min at 10,000 g. Time of digestion was titrated to yield majority subnucleosomal DNA fragments. The insoluble pellet was washed once more in in Isotonic Lysis Buffer lacking NP-40 and again harvested by centrifugation. RNA was removed from fragmented, insoluble genomic DNA by the addition of RNase A  (ThermoFisher, 0.1 mg/ml) in TE buffer and incubation for 30 minutes at 37°C. Remaining protein was then digested by the addition of SDS to 0.5 % and Proteinase K to 1 mg/ml and incubating for 90 minutes at 37°C. Samples were the subjected to phenol:chloroform:isoamyl alcohol extraction and ethanol precipitated.
Libraries were prepared from isolated DNA using the Hyper Prep Kit from Kapa Biosystems using NEB TruSeq adapters and indexed primers for amplification.

treatment_protocol: Where applicable, cells were treated with DRB for 4 hours at 50 μg/ml

value: normal human fetal lung fibroblasts

value: RNase


title: wild type 2 [A2]

source_name: wild type_8h culture without pressure

value: str. K-12 substr. MG1655


title: wor_Dam_Fed2


title: control SAR-seq rep1

value: control


title: wild type 1 [A1]

value: 8h culture without pressure

value: wild type


title: wor_Pol_Fed1

value: worniu-GAL4 x tub-GAL80ts, UAS-LT3-NDam-RpII215


title: control SAR-seq rep2


title: Ssbp1_TruSeq_KO_brep2_trep1 [494H]


title: 7_NGT_Fasting_1_111

value: Asian-Indian


title: 8_NGT_Fasting_2_131

value: Male


title: Ssbp1_TruSeq_WT_brep1_trep1 [492H]


title: wor_Dam_Fed1


title: Ssbp1_TruSeq_WT_brep3_trep1 [585H_1]


title: Ssbp1_TruSeq_KO_brep1_trep1 [493H]


title: RNase SAR-seq rep1


title: CDNIDRB RNA-seq rep2

data_processing:
RNA-seq reads were mapped to hg19 using TopHat2 using Ensembl (build 82) gene annotations. DNA sequencing reads were mapped to hg19 using Bowtie2 with –no-mixed –nodiscordant –very-sensitive parameters
Transcript abundance was calculated using RSEM.
Coverage maps were generated using DeepTools bamCoverage and -bs –maxFragmentLength 120 –normalizeTo1x –ignoreFoorNormalization chrX chrM parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RSEM count matrix, TPM calculations, and Deseq2 calculations

extract_protocol:
Biochemical fractionation was performed on 108 TIG-1 fibroblasts harvested with trypsin and thoroughly washed with ice cold PBS. Buffers at all steps contained protease inhibitors (Roche) and RNase inhibitor where appropriate (RNasin, Promega). First, nuclei were isolated by thoroughly resuspension in 1 ml Isotonic Lysis Buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 3 mM MgCl2, 10% glycerol, 0.5% NP-40, 0.5 mM PMSF) and incubating for 15 min on ice with gentle vortexing every 5 minutes. Nuclei were pelleted by centrifugation at 4°C for 3 min at 1000 g. The cytosolic supernatant was removed and permeabilized nuclei were washed twice in Isotonic Lysis Buffer lacking NP-40 with 5 min incubations on ice and gentle vortexing between and recovered by centrifugation as above. Loosely bound nucleoplasmic proteins and RNAs were then solubilized by suspension in 1 ml ice cold modified urea/NP-40 Buffer (1 M urea, 1% NP-40, 0.5 mM PMSF) (Bhatt et al., 2012). Nuclei were incubated for 15 minutes with vigorous vortexing every 5 minutes. The insoluble nuclear material was then pelleted by centrifugation at 4°C for 10 min at 10,000 g. The supernatant was collected as the nuclear soluble (NS) fraction. The insoluble material was resuspended in urea/NP-40 buffer and washed after another incubation of 15 minutes on ice with additional vortexing. The insoluble material was then extracted with 0.5 ml Ammonium Sulfate Extraction Buffer (10 mM Tris-HCl pH 7.5, 250 mM ammonium sulfate, 300 mM sucrose, 3 mM MgCl2, 0.5% Triton X-100, 0.5 mM PMSF) for 10 minutes on ice with vigorous vortexing to disrupt the insoluble pellet. Extracted insoluble material was then pelleted at 4°C for 10 min at 10,000 g. The supernatant was collected and the insoluble pellet was again washed as above in Ammonium Sulfate Extraction Buffer. The insoluble pellet was then washed wih 0.5 ml DNase Digestion Buffer (40 mM Trsi-HCl pH 7.9, 10 mM NaCl, 6 mM MgCl2, 1 mM CaCl2, 0.05% NP-40, 0.5 mM PMSF). Insoluble material was again suspended in 0.5 ml DNase Digestion Buffer before addition of 10 µl DNase I (Roche). DNA was digested for 60 minutes at 37°C. Samples were extensively vortexed before an additional 10 µl DNase I (Turbo DNase, Ambion) was added and samples were again incubated for 30 minutes at 37°C. The insoluble nuclear material was then pelleted by centrifugation at 4°C for 10 min at 10,000 g. Supernatants from this step and the ammonium sulfate extraction were combined as the chromatin-dependent fractions. Insoluble material was subjected to an additional high salt wash by being thoroughly resuspended in 0.5ml High Salt Wash Buffer (10 mM Tris-HCl pH 7.5, 10% glycerol, 2 M NaCl, 3 mM MgCl2, 0.05% NP-40, 0.5 mM PMSF). Samples were vortexed and incubated 5 min on ice. The final insoluble scaffold material was then pelleted by centrifugation at 4°C for 10 min at 10,000 g. RNA was recovered by the addition of Trizol (Invitrogen) and EDTA (10 mM final), following ethanol precipitation where necessary. Samples were heated to 65°C for 15 minutes with intermittent vortexing before RNA isolation according to manufacturer recommendations. Trizol isolated RNA was further cleaned up using RNAEasy columns (Qiagen).
Libraries were prepared using a stand specific kit RNA-seq kit with ribosome depletion (KAPA Biosystems) and NEBNext Adapters and Multiplex Oligos for Illumina sequencing.

value: DRB


title: ALSC-RNAseq_3

city: Hohhut

first: Mengyi

last: Wei

state: Inner Mongolia

address: Zhao Jun Road No.24

department: Life Science department

institute: Inner Mongolia University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary_files_format_and_content: Matrix table with clean gene counts for every gene and every sample

molecule: polyA RNA

source_name: mouse embryonic stem cell established in combination of Activin A and LIF

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

value: embryonic stem cell

tag: background

value: female ICR mouse mated with GOF/GFP male mouse

value: epiblasts from E6.5 gastrulae


title: CDNIDRB RNA-seq rep1


title: 6_NGT_2_hour_6_242

source_name: Normal glucose tolerance 2-hour post oral glucose load sample

value: Normal

value: Peripheral blood mononuclear cells


title: 5_NGT_2_hour_5_232


title: Ssbp1_TruSeq_WT_brep2_trep1 [584H]

value: inbred C57BL/6N nuclear background

value: Heart


title: fem3-1_seedling_Bisulfite-Seq

city: Jiangsu Nanjig

first: Kezhi

last: Zheng

address: weigang NO.1

department: College of agriculture

institute: Nanjing Agricultural University

data_processing:
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to MSU7.0 using bismark with default parameters
Genome_build: MSU 7.0

organism: Oryza sativa

growth_protocol: Rice plants grown in soil in Jiangsu province

extract_protocol:
genomic DNA was extrated using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.

tag: cultivar

value: Japponica

value: seedling


title: ALSC-RNAseq_2


title: CDNI RNA-seq rep2

value: normal human fetal lung fibroblasts


title: pol iv-1_seedling_Bisulfite-Seq

description: pol iv-1_seedling_Bs-seq

source_name: pol iv-1


title: ALSC-RNAseq_1


title: CDNI RNA-seq rep1

value: control


title: 3_NGT_2_hour_3_142


title: 4_NGT_2_hour_4_152


title: 2_NGT_2_hour_2_132


title: GAS_seedling_Bisulfite-Seq

source_name: GAS


title: AK2 CRISPR promyelocytes replicate 3 [AK2_PM_3]

city: Stanford

first: Wenqing

last: Wang

state: CA

address: 2500 BMI, 1291 Welch Rd

department: Department of Pediatrics

institute: Stanford University School of Medicine

data_processing:
Reads mapping, transcript quantification and TPM calculation were performed using Kallisto v0.46.0
Genome_build: hg38
Supplementary_files_format_and_content: tsv files include transcript abundance of each sample.
Supplementary_files_format_and_content: Matrix table include TPM for all genes and all samples.

source_name: Promyelocytes in vitro derived from AK2 CRISPR-knockout HSPCs

growth_protocol: AAVS1 or AK2 CRISPR-knockout human CD34+ HSPCs were cultured in Myelocult media (StemCell) supplemented with IL-3, SCF and G-CSF to differentiate towards the granulocyte lineage. Cells were FACS sorted to enrich different maturation stages.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Micro kit.
Takara SMARTseq v4

treatment_protocol: We performed CRISPR knock-out of AAVS1 (safe harbor) or AK2 gene in human CD34+ HSPCs

value: AK2 CRISPR

value: Promyelocyte

tag: replicate


title: 1_NGT_2_hour_1_112

tag: tissue


title: AK2 CRISPR neutrophils replicate 3 [AK2_NP_3]

source_name: Neutrophils in vitro derived from AK2 CRISPR-knockout HSPCs

value: Neutrophil


title: NS RNA-seq rep2

tag: cell line


title: CDNS RNA-seq rep2

tag: cell type


title: KPCY cells transduced with shPthlh oligo #2 (replicate 2)

first: Jason

middle: R

last: Pitarresi

address: 364 Plantation Street

institute: University of Massachusetts Chan Medical School

description: shPthlh.vs.Ctrl.salmon.GeneTPM.combined.txt

data_processing:
Raw counts of gene transcripts were obtained using an alignment-independent tool Salmon
The raw count matrix was subsequently imported into R-studio (R version 3.5) and used as input file for DESeq2 analysis
Salmon was used to normalize and quantitate gene expression in transcripts-per-million (tpm) through quasi-alignment
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are DESeq2 output files

source_name: pancreatic tumor cells

growth_protocol: Cells were maintained in complete DMEM

extract_protocol:
Qiagen Rneasy
Libraries were constructed by Novogene according to standard manufacturer recommendations

treatment_protocol: Cells were transduced with the indicated shRNA

tag: condition

value: in vivo sorted tumor cells

value: mouse pancreatic tumor cells

tag: transduced

value: shPthlh oligo #2


title: AK2 CRISPR promyelocytes replicate 2 [AK2_PM_2]

tag: treatment


title: TP309_seedling_Bisulfite-Seq


title: KPCY cells transduced with shPthlh oligo #2 (replicate 1)


title: HepDE19 with HBV production Internal control

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

data_processing:
Library strategy: 4C-seq
Trim the recognition sequence of the first cutter with cutadapt (v 1.12)
Align to human genome (GRCh38) with bwa mem (0.7.12-r1039).A maximus of 10% error rate was allowed and no mismatches were allowed at the 5’ restriction enzyme recognition site. Reads with a single unique hit and mapping quality above 20 were kept.
Reads count at each fragend was calculated and binarized to 0 or 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: zipped plain TXT (1st column: chromosome; 2nd column: Restriction enzyme recognition site; 3rd colum: binarized count)

growth_protocol: The HepG2-NTCP cell, C3A-NTCP cell, and HepG2-NTCP-HBx/tet cell were cultured in DMEM supplemented with 10% FBS before HBV infection, and cultured in PMM medium after infection for 7 days. HepDE19 cell were cultured in DMEM/F-12 supplemented with 10% tet-free FBS with or without Dox in the medium. Perfused PHH cell were cultured in PMM medium before analysis.

extract_protocol:
The HepDE19 cell genomic DNA was extracted using a Qiagen genomic DNA extraction kit. The 4C-seq and Hi-C sample were extracted following 4C and Hi-C methods. RNA was harvested using Trizol reagent.
For whole genome DNA sequencing and RNA-seq, libraries were prepared according to Illumina's instructions accompanying the Kits. The Hi-C libraries were constructed following the published in situ Hi-C methods (PMID: 25497547). HBV-4C libraries were constructed mainly following the published 4C-seq methods (PMID: 22929766) except necessary adjustment.

treatment_protocol: Different virus or drug treatment were used as described in each experiments.

tag: 4c method

value: random-ligation 4C

tag: hbv infection

value: no infection

tag: dox

value: without Dox (HBV production)


title: CDNS RNA-seq rep1


title: fem3-2_seedling_Bisulfite-Seq


title: WT-rep3

city: JiNan

first: ze

address: GuYunHu

institute: QiLu university of technology

description:
Every gene FPKM value of WT and disruption strain.xlsx
CK3 FPKM

data_processing:
Sequencing of RNA samples was performed on the BGISEQ-500 platform at BGI-Shenzhen, China.
Entire clean reads were mapped to the reference genome with HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and then the gene expression level was evaluated by RSEM (v1.2.12)
Genome_build: GCA_000280675.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Beauveria bassiana ARSEF 2860

source_name: WT

growth_protocol: WT and BbTdp1：culture on SDAY medium

extract_protocol:
Total RNA was extracted from fungal cultures of each mode with TRIzol-A+ reagent.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: Disruption BbTdp1 by homologous recombination

value: WT

tag: sample type

value: fungal culture


title: AK2 CRISPR promyelocytes replicate 1 [AK2_PM_1]


title: NS RNA-seq rep1


title: KPCY cells transduced with shPthlh oligo #1 (replicate 1)

value: shPthlh oligo #1


title: KPCY cells transduced with shPthlh oligo #1 (replicate 2)


title: HepDE19 with HBV production 4C

value: normal 4C


title: WT-rep2

description:
Every gene FPKM value of WT and disruption strain.xlsx
CK2 FPKM

tag: genotype


title: AK2 CRISPR neutrophils replicate 2 [AK2_NP_2]


title: BbTdp1-KO-rep2

description:
Every gene FPKM value of WT and disruption strain.xlsx
TF2 FPKM


title: BbTdp1-KO-rep1

description:
Every gene FPKM value of WT and disruption strain.xlsx
TF1 FPKM


title: AK2 CRISPR neutrophils replicate 1 [AK2_NP_1]


title: KPCY cells transduced with shNT (replicate 1)

value: shNT


title: BbTdp1-KO-rep3

description:
Every gene FPKM value of WT and disruption strain.xlsx
TF3 FPKM


title: AK2 CRISPR myelocytes replicate 2 [AK2_MC_2]

source_name: Myelocytes in vitro derived from AK2 CRISPR-knockout HSPCs

value: Myelocyte


title: AK2 CRISPR myelocytes replicate 3 [AK2_MC_3]


title: WT-rep1

description:
Every gene FPKM value of WT and disruption strain.xlsx
CK1 FPKM


title: AK2 CRISPR myelocytes replicate 1 [AK2_MC_1]


title: miR-96 KO 4

city: Yangpu

first: Changgeng

last: Peng

address: Siping Road 1239

department: School of Medicine

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Hisat2 (http://ccb.jhu.edu/software/hisat2).
Bam files from samples were merged with samtools, and FPKM values were calculated using the Cufflinks program with ENSEMBL annotation of genes and transcripts for each sample.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: spinal dorsal horn

extract_protocol:
Lumbar segment 4-6 spinal drosal horn was dissected and total RNA was extracted using trizol reagent.
Libraries were prepared with NEBNext Ultra RNA Library Prep Kit for Illumina and 1 ug of total RNA of each sample according to the protocol.

value: spinal dorsal horn

tag: age

value: adult

value: miR-96 knock-out


title: HepDE19 No HBV production 4C

value: with Dox (inhibition of HBV production)


title: miR-96 KO 1

tag: strain


title: KPCY cells transduced with shNT (replicate 2)


title: miR-96 KO 3


title: miR-96 KO 2


title: HepG2-NTCP-HBx/tet cell without Dox

source_name: HepG2-NTCP-HBx/tet cell

value: HepG2-NTCP-HBx/tet cell

value: infected with HBV-ΔX

value: without Dox


title: AAVS1 CRISPR promyelocytes replicate 3 [AAVS1_PM_3]

source_name: Promyelocytes in vitro derived from AAVS1 CRISPR-knockout HSPCs

value: AAVS1 CRISPR

value: Promyelocyte


title: HepG2-NTCP-HBx/tet with Dox for 4 days then without Dox for 4 days

value: with Dox induction of HBx expression for 4 days then without Dox for 4 days


title: HepG2-NTCP-HBx/tet with Dox for 8 days

value: with Dox induction of HBx expression for 8 days


title: WT 3

value: Wild type


title: AAVS1 CRISPR promyelocytes replicate 2 [AAVS1_PM_2]


title: WT 2


title: AAVS1 CRISPR neutrophils replicate 3 [AAVS1_NP_3]

source_name: Neutrophils in vitro derived from AAVS1 CRISPR-knockout HSPCs

value: Neutrophil


title: WT 1


title: WT 4


title: AAVS1 CRISPR neutrophils replicate 2 [AAVS1_NP_2]


title: HepG2-NTCP-HBx/tet cell with Dox

value: with Dox induction of HBx expression


title: PHH-HBV

source_name: PHH isolated from HBV-infected liver humanized mouse

value: normal 4C

value: infected with HBV-WT


title: AAVS1 CRISPR promyelocytes replicate 1 [AAVS1_PM_1]


title: C3A-Internal control

source_name: HepG2/C3A-NTCP cell

value: HepG2/C3A-NTCP cell

value: random-ligation 4C


title: fem3-1_seedling_sRNA

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 45 were mapped to MSU7.0 using Bowtie with parameter -v 0.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Genome_build: MSU7.0
Supplementary_files_format_and_content: tdf

growth_protocol: Rice plants grown in soil in jiangsu province

extract_protocol:
RNA was extrated using TRIzol method.
18-45nt small RNA was cut from PAGE gel.

value: Japponica

value: seedling


title: PHH-Internal control

value: PHH isolated from HBV-infected liver humanized mouse


title: AAVS1 CRISPR neutrophils replicate 1 [AAVS1_NP_1]


title: HBV-dX-C3A-4C-rep4


title: pol iv-1_seedling_sRNA

description: pol iv-1_seedling_sRNA-seq


title: HBV-dX-C3A-4C-rep3


title: AAVS1 CRISPR myelocytes replicate 2 [AAVS1_MC_2]

source_name: Myelocytes in vitro derived from AAVS1 CRISPR-knockout HSPCs

value: Myelocyte


title: fem3-2_seedling_sRNA


title: HBV-dX-C3A-4C-rep2

value: infected with HBV-ΔX


title: AAVS1 CRISPR myelocytes replicate 1 [AAVS1_MC_1]


title: PABPN1-GDF9-GO-rep3

city: Hangzhou

first: Xingxing

last: Dai

address: YuHangTang 866

institute: Life Sciences Institute

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

source_name: GO (growing oocytes )

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

value: oocytes


title: PABPN1-GDF9-GO-rep2


title: HBV-dX-C3A-4C-rep1


title: M2

first: Yan

last: Zijun

address: Sohong Road2005

institute: Fudan university

description: scRNAseq

data_processing:
Digital gene expression matrices were generated for each sample using the Cell Ranger (version 3.1.0) pipeline
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering: (i) <2000 UMIs, or (ii) >6000 or <800 genes, or (iii) >15% UMIs derived from the mitochondrial genome
The harmony package (version 1.0) was used to eliminate batch effects from different samples
Genome_build: hg19
Supplementary_files_format_and_content: gene-barcode matrices; genes; barcodes

extract_protocol:
After the perichondrium was stripped on ice immediately, all auricular cartilage  samples were minced into ~1 mm2 pieces and digested for 10 minutes with trypsin at 37°C to remove residual tissue attached to cartilage tissue.
The cell suspension was loaded onto the Chromium single-cell controller (10x Genomics, USA) to generate single-cell gel beads in the emulsion (GEMs) by using Single Cell 3′ Library and Gel Bead Kit V3 (10x Genomics, USA) and Chromium Single Cell A Chip Kit (10x Genomics, USA) (performed by CapitalBio Technology, Beijing)

value: auricular cartilage

tag: type

value: microtia


title: PABPN1-GDF9-GO-rep1


title: HBV-dX-SMC6-4C-rep2

source_name: SMC6 knockout HepG2-NTCP cell

value: SMC6 knockout HepG2-NTCP cell


title: PABPN1-WT-GO-rep3


title: HBV-WT-SMC6-4C-rep2


title: AAVS1 CRISPR myelocytes replicate 3 [AAVS1_MC_3]

value: AAVS1 CRISPR


title: C6

description: scRNAseq

source_name: Normal control6

value: normal control


title: M1

description: scRNAseq


title: PABPN1-WT-GO-rep2


title: C4

description: scRNAseq

source_name: Normal control4


title: HBV-WT-SMC6-4C-rep1


title: HepG2-NTCP_chr19VP

source_name: HepG2-NTCP cell

value: HepG2-NTCP cell

value: no infection


title: PABPN1-WT-GO-rep1


title: RNA-seq human CD8+ T IL7 24h donor3

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: RNA-seq human CD8+ T IL7 24h donor3

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.1.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. MACS v1.4.2 is used to call peaks using the BED files. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes or differential ATAC-Seq peaks among different conditions.
Genome_build: mm10 and hg19

source_name: PBMC

growth_protocol: CD8+ T lymphocytes or draining lymph nodes were isolated using the EasySep Mouse CD8+ T cell isolation kit (STEMCELL #19853) and cultured in RPMI-1640 medium (ATCC) supplemented with 10% FBS and 50 mM b-mercaptoethanol. For RNA-seq using cells isolated from lymph nodes, CD90.1+ CD8 + cells were sorted and cell libraries were prepared with SMART-Seq Ultra low Input RNA kit (Takara, #634889). For human CD8+ T cells related assays, naïve CD8+ T cells were isolated with EasySep™ Human Naïve CD8+ T Cell Isolation Kit II (STEMCELL, #17968), and activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher Scientific, #111.31D) for two days, and cells were isolated by a magnet per the manufacturer’s protocol.

extract_protocol:
For ChIP-seq, DNA libraries were prepared with the KAPA LTP Library Preparation Kit and barcoded with NEXTflex DNA barcodes. For ATAC-seq, Nuclei were then used for the transposition reaction with the Nextera DNA Library Preparation kit at 37C for 30 min. DNA was purified with the Zymo DNA recovery kit. For RNA-seq, RNA was extracted using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were recovered and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: Purified cells were activated using plate-bound anti-CD3 (2 mg/ml) plus soluble anti-CD28 (1 mg/ml) monoclonal antibodies for two days. After resting overnight in the absence of cytokine, cells were washed and cultured with 1 mg/ml MSA conjugated IL-2, H9 or H9T (unless otherwise specified).

value: Healthy donors

tag: antibody

value: CD8+ T cells


title: C3

city: Shanghai

description: scRNAseq

source_name: Normal control3


title: HepG2-NTCP-Internal control

value: infected with HBV-WT


title: C2

description: scRNAseq

source_name: Normal control2


title: RNA-seq human CD8+ T IL7+IL15 24h donor3


title: RNA-seq human CD8+ T H9T 24h donor3

description: RNA-seq human CD8+ T H9T 24h donor3


title: M3

description: scRNAseq


title: HBV-WT-HepG2-NTCP-4C-rep5

value: normal 4C


title: C1

description: scRNAseq

source_name: Normal control1


title: RNA-seq human CD8+ T IL2 24h donor3

description: RNA-seq human CD8+ T IL2 24h donor3


title: HBV-WT-HepG2-NTCP-4C-rep4


title: C5

description: scRNAseq

source_name: Normal control5


title: 086_ATRA

city: Amsterdam

first: Georges

middle: E.

last: Janssens

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

institute: Amsterdam UMC

data_processing:
Reads were subjected to quality control FastQC, trimmed using Trimmomatic v0.32 and aligned to the C. elegans genome obtained from Ensembl (wbcel235.v91), using HISAT2 v2.1.0
Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads. Statistical analyses were performed using the edgeR v3.26.8 and limma/voom v 3.40.6 R packages
All genes with more than 2 counts in at least 3 of the samples were kept. Count data were transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method and precision weighted using voom.
Genome_build: wbcel235.v91
Supplementary_files_format_and_content: csv file of CMPs (counts per million) for RNAseq data mapped to gene level for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Gravid adult worms were age-synchronized using alkaline hypochlorite treatment, and incubated in M9 buffer overnight. Larval stage 1 worms were seeded to NGM plates and grown to larval stage 4.

extract_protocol:
For isolation of total mRNA, whole worms were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. NovaSeq control software NCS v1.6 was used.

treatment_protocol: ~1000 worms were transferred to plates containing compounds, as well as 5-fluorouracil at larval stage 4 of development. They were treated with atracurium or water control for 24 hours before harvest. At time of harvest, worms were washed in buffer and water, then snap frozen in liquid nitrogen.

value: whole worm

value: day 1 adult

value: 50 μM atracurium


title: HBV-WT-HepG2-NTCP-4C-rep3


title: HBV-dX-SMC6-4C-rep1


title: RNA-seq human CD8+ T IL7 24h donor2

description: RNA-seq human CD8+ T IL7 24h donor2


title: 085_ATRA


title: HBV-WT-HepG2-NTCP-4C-rep2


title: 084_ATRA


title: HBV-WT-HepG2-NTCP-4C-rep1


title: RNA-seq human CD8+ T IL7+IL15 24h donor2


title: RNA-seq human CD8+ T IL2 24h donor2

description: RNA-seq human CD8+ T IL2 24h donor2


title: RNA-seq human CD8+ T IL7 24h donor1

description: RNA-seq human CD8+ T IL7 24h donor1


title: 083_ATRA


title: 082_CTRL

value: water vehicle


title: HBV-dX-HepG2-NTCP-4C-rep5

value: infected with HBV-ΔX


title: HBV-dX-HepG2-NTCP-4C-rep4


title: RNA-seq human CD8+ T IL7+IL15 24h donor1


title: 079_CTRL


title: HBV-dX-HepG2-NTCP-4C-rep2


title: HBV-dX-HepG2-NTCP-4C-rep3


title: HBV-dX-HepG2-NTCP-4C-rep1


title: 080_CTRL


title: RNA-seq human CD8+ T IL2 24h donor1

description: RNA-seq human CD8+ T IL2 24h donor1


title: RNA-seq human CD8+ T H9T 24h donor1

description: RNA-seq human CD8+ T H9T 24h donor1


title: human_normal gastric mucosa _rep6

status: Public on Jul 05 2021

first: yu

middle: zhi

last: long

address: NO.100 Haining Road

department: General Surgery

institute: Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Illumina HiSeqTM 2500 used for basecalling.
Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using the Stringtie software to assemble the reads, the new transcript was spliced. Then the candidate lncRNA transcripts were selected by comparing the gene. annotation information of the reference sequence produced by Cuffcompare software.
Aligning the sequencing reads of each sample with the sequence of mRNA transcript sequences, known lncRNA sequences and lncRNA prediction sequences by bowtie2, and using eXpress to make gene quantitative analysis, the FPKM value and counts value(the number of reads for each gene in each sample) were obtained.
CIRI software was used to scan for PCC signals (paired chiastic clipping signals), and circRNA sequences were predicted based on junction reads and GT-AG cleavage signals.Using the RPM algorithm to quantify the circRNAs, and normalizing the number of junction reads counts and foldchange by DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM or RPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every ncRNA and every sample

source_name: human, normal gastric mucosa, rep7

extract_protocol:
Grind fresh gastric cancer and adjacent tissues at low temperature，and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal gastric mucosa

tag: gender

value: male


title: human_normal gastric mucosa _rep4

source_name: human, normal gastric mucosa, rep5


title: human_normal gastric mucosa _rep5

source_name: human, normal gastric mucosa, rep6

value: female


title: 081_CTRL


title: human_normal gastric mucosa _rep3

source_name: human, normal gastric mucosa, rep4


title: human_normal gastric mucosa _rep2

source_name: human, normal gastric mucosa, rep3


title: human_gastric cancer_rep6

source_name: human，gastric cancer，rep6

value: gastric cancer


title: human_gastric cancer_rep4

source_name: human，gastric cancer，rep4


title: human_gastric cancer_rep5

source_name: human，gastric cancer，rep5


title: human_gastric cancer_rep2

source_name: human，gastric cancer，rep2


title: Cell suspension_HTS15_CD90+CD39-

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: Gene expression of CD90+CD39- fibroblast sorted from cell suspension of HTS15

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 8 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Cell suspension, HTS15, CD90+CD39- fibroblast

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Sorted cells were collected in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA) for RNA isolation. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: Three 10 cm × 10 cm samples of hypertrophic scar and three 5 cm × 5 cm samples of normal skin were cut into small pieces and put into Dispase II (Gibco, 17105041, 0.3% in DMEM) for 30min at 37°C to allow the separation of the epidermis. Scar were then minced and digested with a modified protocol, namely, 2.5 mg/mL Collagenase I (Gibco, 17100017), 1 mg/mL Collagenase II (Gibco, 17101015), 1 mg/mL Collagenase IV (Gibco, 17104019), 0.2 mg/mL Hyaluronidase (Sigma, H3884) and 0.1 mg/mL DNase I (Sigma, D4263) in DMEM + 2% P/S (Gibco, 15070-063) for 4h shaking in a 37°C waterbath. Acquired cell suspension was filtered, lysed with ACK Lysis Buffer, stained with FVS780- APC-CY7 and Human Fc block. Afterwards, cells were stained with anti-human antibodies for 10min at 4°C: Lineage Cocktail-Pacific Blue (BD, 562722, 1:100), CD45- APC-CY7 (BD, 557833, 1:100), E-Cadherin-BV421 (BD, 743712, 1:100), CD31-PE-CY7 (BD, 563651, 1:100), CD49f/ITGA6-PE (BD, 555736, 1:50), CD90-BV510 (BD, 563070, 1:20), and CD39-PE-CF594 (BD, 563678, 1:100). After negative selection (singlets, FVS780-, CD49f-, E-Cadherin-, Lin-, CD45-, and CD31-), CD90+CD39+ and CD90+CD39- Fb from hypertrophic scar tissue and CD90+CD39+ Fb from normal skin were sorted using BD FACS Aria II. Sorted cells were collected in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA) for RNA isolation and subjected to Agilent Human 4x44K Gene Expression Microarrays v2 according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).

value: Hypertrophic scar

tag: subject id

tag: vancouver scar scale

tag: cell markers


title: human_gastric cancer_rep3

source_name: human，gastric cancer，rep3

tag: tissue


title: RNA-seq human CD8+ T H9T 24h donor2

description: RNA-seq human CD8+ T H9T 24h donor2

source_name: PBMC


title: Cell suspension_HTS5_CD90+CD39+

description: Gene expression of CD90+CD39+ fibroblast sorted from cell suspension of HTS5

source_name: Cell suspension, HTS5, CD90+CD39+ fibroblast


title: human_normal gastric mucosa _rep1

source_name: human, normal gastric mucosa, rep2


title: Cell suspension_HTS4_CD90+CD39-

description: Gene expression of CD90+CD39- fibroblast sorted from cell suspension of HTS4

source_name: Cell suspension, HTS4, CD90+CD39- fibroblast


title: human_gastric cancer_rep1

source_name: human，gastric cancer，rep1


title: Cell suspension_HTS15_CD90+CD39+

description: Gene expression of CD90+CD39+ fibroblast sorted from cell suspension of HTS15

source_name: Cell suspension, HTS15, CD90+CD39+ fibroblast


title: HepDE19 No HBV production Internal control

tag: cell line

value: random-ligation 4C

value: with Dox (inhibition of HBV production)


title: Cell suspension_HTS4_CD90+CD39+

description: Gene expression of CD90+CD39+ fibroblast sorted from cell suspension of HTS4

source_name: Cell suspension, HTS4, CD90+CD39+ fibroblast


title: 16_PD_2_hour_4_M102A

first: madavan

address: Kasturi Nagar

institute: Theomics International Private Limited

data_processing: The data were normalised using quantile normalisation using GeneSpring Gx v12.0

source_name: Pre-diabetic 2-hour post oral glucose load sample

extract_protocol: Peripheral blood mono-nuclear cells (PBMCs) were isolated by density gradient centrifugation by layering blood over Histopaque. Post isolation, the PBMC pellet was washed with 1X PBS, subjected to RBC lysis followed by another wash. The final cell pellet was resuspended in TRI reagent for cell lysis. RNA was isolated as per the kit manufacturer’s protocol (RNeasy mini kit was used for RNA isolation, Qiagen). Briefly, phase separation was done by adding chloroform to the TRI suspension and ethanol was used to precipitate RNA from the aqueous phase. The pellet was then loaded on the columns and washed with RW1 and RPE buffers provided by the manufacturer and finally the total RNA was eluted from the column in 30µl nuclease free water. RNA quantity was measured using Qubit4.0 fluorometer from Invitrogen. RNA quality was estimated using electrophoresis-based RNA Screentape kit in the TapeStation system from Agilent technologies and only those samples with RNA integrity number (RIN) greater than 8.0 were used for array hybridization.

tag: ethnicity

value: Asian-Indian

value: Male

tag: glucose metabolism status

value: Pre-diabetic

value: Peripheral blood mononuclear cells


title: 3D_WTPELP_7L_rep3

city: Minneapolis

first: Carol

last: Lange

state: MN

address: 2231 6th ST SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: hg19
Supplementary_files_format_and_content: AI006_ReadCounts.csv includes DESeq2 normalized values.

source_name: MCF-7L cells

growth_protocol: Protocol name: 3D tumorsphere; 5d tumorsphere culture

extract_protocol:
The RNA extraction was done using the Qiagen RNasy kits.
Illumina TruSeq Stranded mRNA Library Prep kit was used to prepare the RNAseq libraries.

treatment_protocol: Cell lines were cultured under tumorsphere conditions for 3 days prior to RNA isolation. Comparisons 1) 3D_LXSN_7L vs. 3D_CytoPELP1; 2) 3D_LXSN_7L vs. 3D_WTPELP1_7L; 3)3D_CytoPELP1_7L vs. 3D_WTPELP1_7L

tag: cell type

value: luminal breast cancer cell line

value: PELP1 CRISPR KO

tag: transfected with

value: PELP1- WT


title: 3D_LXSN_7L_rep3

value: vector control


title: 3D_LXSN_7L_rep2


title: 3D_CytoPELP_7L_rep3

value: PELP1- NLS mutant


title: 3D_LXSN_7L_rep1


title: 3D_WTPELP_7L_rep2


title: 3D_WTPELP_7L_rep1


title: 3D_CytoPELP_7L_rep2


title: 3D_CytoPELP_7L_rep1


title: 84583 [plus_old_H3K4me3]

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

country: Germany

institute: Leipzig University

data_processing:
The sequenced reads underwent a quality trimming using cutadapt to ensure a minimum read length of 40 bases and a Phred quality score above 20.
The high-quality reads were mapped to the mouse reference genome NCBI37/mm9 (GRCh37/hg19) using the software tool segemehl 0.2.0 with parameter settings “-s -t 8”.
Histone modification peaks were identified by applying MACS 1.4.2 with the H3pan data as control and the following parameter settings: “--nomodel -w --space = 30 --bw 300 --pvalue 1e-5 --shiftsize 200".
The histone modification peak lists were summarized for each genotype and treatment. A peak is accepted, if it is detected in both replicates or in one replicate with a high reliability (MACS fold enrichment > 5.0). Finally, a peak is assigned to be within the promoter region of genes ((TSS) ± 1000 bases) and the gene bodies. If the overlap with a promoter or body region is at least 5%, the respective gene-associated histone is considered as modified.
X- and Y-chromosome is excluded from the analysis.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Processed data is stored in comma separated value format and provides modification profiles of mouse genes. The list includes those genes that show a modification in at least one of the lysines K4 or K27 of histone 3 only. If the lysine is modified, the respective value is '1', otherwise '0' (unmodified). In the respective columns (Plus_Young_H3K4me3, Plus_Young_H3K27me3, Plus_Old_H3K4me3, Plus_Old_H3K27me3, Minus_Young_H3K4me3, Minus_Young_H3K27me3, Minus_Old_H3K4me3, Minus_Old_H3K27me3), Plus/Minus identifies the genotype, though Plus is associated with Msh2+/+ and Minus is associated with Msh2-/-. Young/Old refers to short/long term organoid culture of 4 and 20 weeks aged organoids. In addition, beside the gene's name, the following data is provided: ensID: Ensembl transcription ID, chr: chromosome, strand, txStart, txEnd: start and end position.

source_name: Intestinal organoid (jejunum)

growth_protocol: 6 cm of the jejunum was used to generate intestinal organoids of 8 month old Msh2-/- and Msh2+/+ mice

extract_protocol:
Chromatin was prepared from up to 50 mg jejunum using SDS Shearing Buffer and the truChlP Tissue Chromatin Shearing Kit (Covaris, Brighton, UK) according to the manufacturer´s instructions. ChIPs were run on the IP-Star compact system using the Auto iDeal ChIP-seq kit for histones (Diagenode, Seraing, Belgium) according to the manufacturer’s direct method for ChIP preparation. For ChIP-seq validation shredded intestinal tissue was cross-linked in 1% formaldehyde for 8 min at room temperature and homogenized in ZR 2.0 mm BashingBead™ Lysis Tubes (Zymo Research Corp., Tustin, US) with a Precellys24 homogenization device (VWR International GmbH, Darmstadt, Germany). ChIP assays were performed with minor modifications as described [Mannefeld et al. 2009]. DNA from 15 mg tissue was used in each IP with H3K4me3, H3K27me3, and H3pan premium rabbit polyclonal antibodies (Diagenode). A non-targeting IgG rabbit antibody (Cell Signaling, Leiden, Netherlands) was used as a control for non-specific signals. 1 µl of purified chromatin was applied for semi-quantitative real-time PCR using the absolute qPCR SYBR Green Mix (Thermo) performed with the ABI 7500 RealTime PCR System (Applied Biosystems, Forster City, US).
Library preparations were performed according to the TrueSeq LT PCR free or TruSeq Nano DNA Kit instructions (Illumina, San Diego, USA). Sequencing was performed on the Illumina HiSeq 4000 with 76 bp paired-end sequencings.

treatment_protocol: Organoids were split once/week and cultured with or without 1 mM aspirin (Sigma) for a further 18 weeks. After the first and 18th week organoids were stored into liquid nitrogen. These frozen organoids were recultured simultaneously in IntestiCult™ mouse organoid growth medium (Stemcell Technologies GmbH, Cologne, Germany) with or without 1 mM aspirin for further two weeks and analyzed afterwards.

tag: animal id

tag: treatment

value: jejunum

value: 18 weeks

tag: chip antibody


title: 84587 [plus_old_H3pan]

tag: genotype

tag: age


title: 84585 [plus_old_H3K27me3]

tag: strain


title: 78827 [plus_old_H3K27me3]


title: 78825 [plus_old_H3K4me3]


title: 78829 [plus_old_H3pan]


title: 78821 [plus_young_H3K27me3]

value: 1 week


title: 78819 [plus_young_H3K4me3]


title: 78823 [plus_young_H3pan]


title: 84597 [minus_old_H3K27me3]


title: 84581 [plus_young_H3pan]


title: 84595 [minus_old_H3K4me3]


title: Cell suspension_HTS5_CD90+CD39-

description: Gene expression of CD90+CD39- fibroblast sorted from cell suspension of HTS5

source_name: Cell suspension, HTS5, CD90+CD39- fibroblast

value: male


title: 84579 [plus_young_H3K27me3]


title: 78839 [minus_old_H3K27me3]


title: 84599 [minus_old_H3pan]


title: 78837 [minus_old_H3K4me3]


title: 78841 [minus_old_H3pan]


title: 84591 [minus_young_H3K27me3]


title: 84593 [minus_young_H3pan]


title: 84589 [minus_young_H3K4me3]