title: sgZ8-Input

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina Novaseq6000 sequencer.
Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality clean reads were generated.
Clean reads were aligned to reference genome using bowtie2 software (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v2.2.7.1).
Differentially enriched regions were identified by diffReps software (v1.55.4).The enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: hg38
Supplementary files format and content: bigWig, Browser Extensible Data(except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated for ChIP-seq.
Chromatin Immunoprecipitation was performed with GenSeq® Chromatin Immunoprecipitation (ChIP) Kit (GenSeq Inc.) according to the manufacturer’s instructions. The yield of ChIPed DNA was determined via Quant IT fluorescence assay (ThermoFisher), and sequencing libraries were generated with GenSeq® Rapid DNA Library Prep Kit (GenSeq Inc.) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina NovaSeq sequencer.


title: RNA-seq_MRC5_SVI_6h_exp1_2023

status: Public on Feb 24 2025

type: SRA

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

library_source: transcriptomic

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control (QC) steps were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.74+galaxy0).
Processed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the HISAT2 alignment tool (Galaxy Version 2.2.1+galaxy1) under “single-end”, “stranded” and “reverse” options.
RNA integrity was measured by the Transcript Integrity Number tool (Galaxy Version 5.0.1+galaxy2). The enrichment of RNA-sequencing reads within gene bodies was examined using Gene Body Coverage (ΒΑΜ) tool.
Calculation of sequencing reads that are mapped into genes was performed with the htseq-count tool (Galaxy Version 0.9.1+galaxy1), in “union” mode, with “stranded”, “reverse”, and “minimum alignment quality 1” and “–nonunique All" options.
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal

molecule: polyA RNA

organism: Homo sapiens

source_name: MRC-5 (ATCC, CCL-171)

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. MRC-5 cells (ATCC, CCL-171™) and NIH/3T3 cells (ATCC, CRL-1658™) were grown in DMEM medium (Sigma-Aldrich). All culture media were supplemented with 1% Pen-Strep (Biowest) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Biowest). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted from cells using the Monarch Total RNA Miniprep Kit (T2010S, NEB) that includes treatment with DNase I for 15 minutes at 37°C to remove any DNA remnants.
RNA quality was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies). RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) for Illumina following the manufacturer's instructions. Samples were subjected to beads-purification (NEBNext Sample Purification Beads, E7767L), and the quality of the isolated libraries was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies).

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3, or 6 (MRC-5 cells) or 7 hrs (NIH/3T3 cells), prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

tag: cell line

value: MRC-5 (ATCC, CCL-171)

tag: cell type

value: Lung Fibroblasts

tag: treatment

value: Sendai Virus Cantell strain, Charles River lab

tag: time

value: 6 hrs


title: B Cells, Control replicate 1

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

country: USA

institute: National Institutes Of Health

data_processing:
Differentially expressed genes and corresponding adjusted p-values were determined using DEseq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw transcript level counts for each sample

molecule: total RNA

source_name: Blood

growth_protocol: PBMC was isolated by Ficoll-Paque density gradient centrifugation using the Lymphocyte Separation Medium (Corning, VA, USA).

extract_protocol:
Total RNA was isolated from human B cells using RNeasy plus mini kit (Qiagen)
mRNA was isolated by oligo-dT beads, and a library was prepared using the standard Illumina library protocol (kit: RS-122-2101 TruSeq Stranded mRNA LT Sample prep kit)

treatment_protocol: B cells were isolated from single cell suspension of PBMC using Human B-cell isolation kit (Miltenyi Biotec, Cat# 130-091-151) and were stimulated with 2µM human CpG and 5ug/mL anti-CD40 for 72h.

tag: tissue

value: Blood

value: B cells

value: Control


title: ACHN-Ctrl-repeat1

city: Shanghai

first: Jianxiu

last: Yu

address: No. 280, Chongqing South Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
For RNA-seq data, paired-end reads were harvested from illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
3’ adaptor-trimming and low quality reads were removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes.
Assembly: hg19
Supplementary files format and content: Excel file includes lncRNA expression profiling
Supplementary files format and content: Excel file includes mRNA expression profiling

source_name: ACHN

extract_protocol:
RNA was extracted from total cell lysates.
Total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.

value: ACHN

tag: genotype


title: B Cells, Control replicate 2


title: sgZ8-K27m3,ChIP

library_source: genomic

molecule: genomic DNA


title: Ctrl-K27m3,ChIP


title: ACHN-Ctrl-repeat2


title: Ctrl-EZH2,ChIP


title: ACHN-sgzccHc8-repeat1


title: Ctrl-Input


title: RNA-seq_MRC5_SVI_0h_exp2_2023

value: 0 hrs (naive)


title: MED1-ChIP-seq_HL_SVI_6h_ROSE_analysis_for_identification_of_SEs_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
ROSE algorithm was employed to identify Typical enhancers and Super-enhancers (SEs) in naïve and infected HeLa and Namalwa cells. The ROSE code was implemented through Python 2.7.18, R (4.1 version), and SAMtools (1.10 version).
The Super-enhancers and Typical enhancers analyses were conducted on BAM files derived from paired-end and single-end analyses of ChIP-seq NGS data.
H3K27ac- and MED1-ChIP-seq bound chromatin loci in both uninfected (0h) and 6h upon virus infection in HeLa and Namalwa cells were used and a 12.5 kb stitching distance was applied in order to create constituent enhancers from H3K27ac or MED1 peaks in close proximity, excluding peaks overlapping known promoters (±2 kb around TSS), unless within a constituent enhancer upon stitching.
Stitched regions are ranked based on their background (input) subtracted ChIP-signal (RPM) and Super-enhancers are separated from typical enhancers according to the computed inflection point (cutoff) in ChIP-signal intensity.
Assembly: hg19
Supplementary files format and content: BED files of total peaks

source_name: HeLa cells

extract_protocol: none provided

value: HeLa cells

value: Epithelial cells


title: MED1-ChIP-seq_HL_SVI_0h_ROSE_analysis_for_identification_of_SEs_2023


title: H3K27ac-ChIP-seq_NM_SVI_6h_ROSE_analysis_for_identification_of_SEs_2023

source_name: Namalwa cells

value: Namalwa cells

value: B-lymphocytes


title: H3K27ac-ChIP-seq_HL_SVI_6h_ROSE_analysis_for_identification_of_SEs_2023


title: H3K27ac-ChIP-seq_NM_SVI_0h_ROSE_analysis_for_identification_of_SEs_2023


title: H3K27ac-ChIP-seq_HL_SVI_0h_ROSE_analysis_for_identification_of_SEs_2023


title: sgZ8-EZH2,ChIP


title: DNaseI-seq_HL_SVI_0h_exp2_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0).
Trimmed sequencing reads were mapped to the reference human (hg19) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package. Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05. Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0).
Assembly: hg19
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich), Namalwa cells (ATCC, CRL-1432™) in RPMI 1640 medium (Sigma-Aldrich).  All culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
DNaseI-seq assays were conducted based on a published protocol (John et al. 2013) with modifications. Intact nuclei were isolated from 15-20*10^6 cells, by sequential incubation in extraction buffers. In detail, upon completion of the time course of infection, the culture medium was removed and cells were collected and washed twice with ice-cold 1x-PBS. Cell pellets were diluted in 200μl 1xBuffer A [15mM Tris pH 8.0, 15mM NaCl, 60mM KCl, 1mM EDTA, 0.5 mM spermidine] by gentle pipetting using cut tips, followed by the addition of an equal volume of 1xBuffer A enriched in NP-40, and incubation for 4 minutes on ice. For HL 1% final (v/v) NP-40 and for NM 0.05% final (v/v) NP-40 were utilized. Cells were centrifuged at 2,000 rpm for 1 min, at 4 °C followed by aspiration, and dilution in 100μl of 1xDNaseI incubation buffer (04716728001, Roche) by gentle finger flick. Nuclei were digested by the addition of 80 units of DNase I (04716728001, Roche) for 3 minutes at room temperature, followed by quenching of the reaction by the addition of an equal volume of 2x Stop-Buffer (50 mM Tris-Cl pH 8.0, 100mM NaCl, 0.1% SDS, 100mM EDTA), gentle finger flick, incubation for 10 minutes at room temperature, addition of 20 units of RNaseI and 30 minutes incubation at room temperature. Next, the digested chromatin filaments were subjected to Proteinase K treatment (100 μg enzyme, 0.50% SDS, 400 μl total digestion reaction) (Proteinase K, recombinant, PCR Grade, 3115836001, Sigma-Aldrich) overnight at 55°C, followed by phenol chloroform extraction and ethanol-based precipitation of the isolated DNA, agarose gel (2%) electrophoresis and extraction of the digested DNA fragments, ranging from 100-300 bp, by standard procedures.
Multiplexed-DNA-libraries were prepared according to a published protocol (Ford et al. 2014).

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3 or 6 hrs, prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

value: 0 hrs


title: Input-ChIP-seq_HL_SVI_0h_exp2_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0). Trimmed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters (Langmead and Salzberg, 2012). The input data were utilized as controls.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package (Li et al., 2009). Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05 (Feng et al., 2012).
Peaks detected in chrY and unplaced contigs (chrUn, chrM) and in ENCODE hg19 and mm9 blacklisted regions were excluded from the downstream analyses (Amemiya HM, et al., Sci Rep. 2019). Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0) (Quinlan and Hall, 2010).
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich), Namalwa cells (ATCC, CRL-1432™) in RPMI 1640 medium (Sigma-Aldrich), and NIH/3T3 cells (ATCC, CRL-1658™) in DMEM medium (Sigma-Aldrich).  All culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
ChIP-seq assays on human and mouse cells were carried out based on published protocols (Agelopoulos et al 2014; Agelopoulos et al 2012; Agelopoulos and Thanos 2006) with modifications. Cells were fixed in 1% formaldehyde (F8775, Sigma-Aldrich), for 30 minutes at room temperature, followed by quenching of the reaction by 0.125M Glycine. Cell pellets were diluted in 15 ml Buffer I [10 mM Tris-Cl pH 8.0, 10 mM EDTA, 0.25% Triton X-100] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in 15 ml Buffer II [10 mM Tris-Cl pH 8.0, 200 mM NaCl, 1 mM EDTA] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in sonication Buffer [10 mM Tris-Cl pH 8.0, 1 mM EDTA] and chromatin filaments were sheared to a range of 200-2,000 bp using a Covaris S220 Sonicator , followed by two sequential steps of 2,000 rpm and 12,000 rpm centrifugation, for 8 minutes at 4 °C, to avoid trapping of chromatin by the cell debris.
Multiplexed-DNA-libraries were prepared according to a published protocol (Ford et al., 2014) with modifications. The NEBNext Multiplex Oligos for illumina (Index Primers Set 1 and 2) (E7335S and E7500S, illumina) were used to produce compatible ends to the DNA fragments.

tag: chip antibody


title: H3K27ac-ChIP-seq_NM_SVI_6h_exp3_2023

value: H3K27ac (Abcam #Ab4729)


title: DNaseI-seq_HL_SVI_3h_exp2_2023

value: 3 hrs


title: Input-ChIP-seq_NM_SVI_6h_exp3_2023


title: H3K27ac-ChIP-seq_NM_SVI_0h_exp2_2023


title: Input-ChIP-seq_NM_SVI_3h_exp3_2023


title: H3K27ac-ChIP-seq_HL_SVI_6h_exp2_2023


title: H3K27ac-ChIP-seq_NM_SVI_6h_exp2_2023


title: H3K27ac-ChIP-seq_NM_SVI_3h_exp1_2023


title: Input-ChIP-seq_NM_SVI_3h_exp4_2023


title: Input-ChIP-seq_NM_SVI_6h_exp4_2023


title: Input-ChIP-seq_HL_SVI_6h_exp2_2023


title: H3K27ac-ChIP-seq_NM_SVI_6h_exp1_2023


title: H3K27ac-ChIP-seq_NM_SVI_0h_exp1_2023


title: Input-ChIP-seq_HL_SVI_3h_exp2_2023


title: H3K27ac-ChIP-seq_NM_SVI_3h_exp3_2023


title: H3K27ac-ChIP-seq_NM_SVI_3h_exp2_2023


title: Input-ChIP-seq_NM_SVI_0h_exp4_2023


title: H3K27ac-ChIP-seq_NM_SVI_0h_exp3_2023


title: H3K27ac-ChIP-seq_HL_SVI_3h_exp2_2023


title: DNaseI-seq_HL_SVI_6h_exp2_2023


title: H3K27ac-ChIP-seq_HL_SVI_0h_exp2_2023


title: Input-ChIP-seq_NM_SVI_0h_exp3_2023


title: H3K27ac-ChIP-seq_HL_SVI_6h_exp1_2023


title: H3K4me3-ChIP-seq_NM_SVI_6h_exp2_2023

value: H3K4Me3 (Abcam #Ab8580)


title: RNA_polII-ChIP-seq_NM_SVI_3h_2023

value: RNA polII (Santa Cruz #H224 sc-9001)


title: RNA_polII-ChIP-seq_HL_SVI_6h_2023


title: CBP-ChIP-seq_NM_SVI_3h_2023

value: CBP (Santa Cruz #sc-369)


title: H3K27ac-ChIP-seq_HL_SVI_3h_exp1_2023

value: Sendai Virus Cantell strain, Charles River lab


title: H3K27ac-ChIP-seq_HL_SVI_0h_exp1_2023


title: H3K4me3-ChIP-seq_HL_SVI_0h_exp2_2023


title: H3K4me3-ChIP-seq_HL_SVI_6h_exp2_2023

value: 6 hrs


title: MED1-ChIP-seq_HL_SVI_0h_exp2_2023

value: Med1 (Bethyl #A300-793A)


title: MED1-ChIP-seq_HL_SVI_6h_exp1_2023


title: RNA_polII-ChIP-seq_NM_SVI_0h_2023


title: RNA_polII-ChIP-seq_NM_SVI_6h_2023


title: H3K4me3-ChIP-seq_NM_SVI_3h_exp2_2023


title: MED1-ChIP-seq_HL_SVI_6h_exp2_2023


title: MED1-ChIP-seq_HL_SVI_3h_exp1_2023


title: H3K4me3-ChIP-seq_NM_SVI_0h_exp2_2023


title: H3K4me3-ChIP-seq_HL_SVI_3h_exp2_2023


title: CBP-ChIP-seq_HL_SVI_6h_2023


title: RNA_polII-ChIP-seq_HL_SVI_3h_2023


title: RNA_polII-ChIP-seq_HL_SVI_0h_2023


title: CBP-ChIP-seq_HL_SVI_0h_2023


title: CBP-ChIP-seq_NM_SVI_0h_2023


title: CBP-ChIP-seq_NM_SVI_6h_2023


title: CBP-ChIP-seq_HL_SVI_3h_2023


title: MED1-ChIP-seq_HL_SVI_3h_exp2_2023


title: MED1-ChIP-seq_HL_SVI_0h_exp1_2023


title: p65-ChIP-seq_NM_SVI_6h_2023


title: p65-ChIP-seq_NM_SVI_3h_2023


title: p65-ChIP-seq_NM_SVI_0h_2023


title: p65-ChIP-seq_HL_SVI_6h_2023


title: p65-ChIP-seq_HL_SVI_3h_2023


title: IRF3-ChIP-seq_NM_SVI_6h_2023

value: IRF3 (CST;Cell Signaling Technology,#4302S)


title: p65-ChIP-seq_HL_SVI_0h_2023


title: IRF3-ChIP-seq_NM_SVI_3h_2023


title: IRF3-ChIP-seq_HL_SVI_3h_exp1_2023


title: IRF3-ChIP-seq_HL_SVI_6h_exp2_2023


title: IRF3-ChIP-seq_NM_SVI_0h_2023


title: IRF3-ChIP-seq_HL_SVI_6h_exp1_2023


title: Breast cancer PD36054a

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulfite-converted genomic DNA was hybridised to Illumina EPIC 850K arrays using standard manufacturer protocols

scan_protocol: Standard Illumina scanner and settings

data_processing:
Raw signal values extracted using minfi::preprocessRaw() followed by minfi::getUnmeth and minfi::getMeth. Normalized betas were obtained by minfi::preprocessFunnorm(), betas were then scaled to adjust for difference in Infinium I/II beta distribution using the method of Karlsson et al. 2014 (PMID: 25278450), finally Zhou et al. 2016 (PMID: 27924034) annotations (20180909 data freeze) were used to filter out unreliable probes.
normalized data file includes: Normalized Average Beta

source_name: Breast cancer

label_protocol: Standard Illumina protocol

extract_protocol: Standard DNA extraction protocol according to SCAN-B workflow

value: Breast cancer

tag: subtype

value: TNBC

value: wt

tag: gender

value: female


title: Breast cancer PD36071a


title: Breast cancer PD36067a


title: Breast cancer PD36066a


title: Breast cancer PD36073a


title: Breast cancer PD36069a


title: Breast cancer PD36051a


title: IRF3-ChIP-seq_HL_SVI_0h_exp1_2023

value: HeLa cells

value: Epithelial cells


title: Breast cancer PD36053a


title: Breast cancer PD36064a


title: Breast cancer PD36049a


title: Breast cancer PD36063a


title: Breast cancer PD36055a


title: Breast cancer PD36048a


title: Breast cancer PD36052a


title: Breast cancer PD36044a


title: Breast cancer PD36043a


title: Breast cancer PD36042a


title: IRF3-ChIP-seq_HL_SVI_3h_exp2_2023


title: Breast cancer PD36040a


title: Breast cancer PD36068a


title: Breast cancer PD36041a


title: IRF3-ChIP-seq_HL_SVI_0h_exp2_2023


title: Breast cancer PD36031a


title: Breast cancer PD36056a


title: Breast cancer PD36036a


title: Breast cancer PD36032a


title: Breast cancer PD36024a


title: Breast cancer PD36027a


title: Breast cancer PD36021a


title: Breast cancer PD36022a


title: Breast cancer PD36018a


title: Breast cancer PD36011a


title: Breast cancer PD36005a


title: Breast cancer PD36003a


title: Breast cancer PD36002a


title: Breast cancer PD36015a


title: Breast cancer PD36012a


title: Breast cancer PD36001a


title: Breast cancer PD36019a


title: Breast cancer PD36020a


title: Breast cancer PD36047a


title: Breast cancer PD36000a


title: Breast cancer PD35998a


title: Breast cancer PD35994a


title: Breast cancer PD35997a


title: Breast cancer PD35988a


title: Breast cancer PD35991a


title: Breast cancer PD35993a


title: Breast cancer PD35981a


title: Breast cancer PD35977a


title: Breast cancer PD35968a


title: Breast cancer PD35975a


title: Breast cancer PD35967a


title: Breast cancer PD35978a


title: Breast cancer PD36009a


title: Breast cancer PD36008a


title: Breast cancer PD35966a


title: Breast cancer PD36014a


title: Breast cancer PD35956a


title: Breast cancer PD35960a


title: Breast cancer PD35965a


title: Breast cancer PD35944a


title: Breast cancer PD35948a


title: Breast cancer PD35963a


title: Breast cancer PD35959a


title: Breast cancer PD35950a


title: Breast cancer PD35958a


title: Breast cancer PD35940a


title: Breast cancer PD35943a


title: Breast cancer PD35964a


title: Breast cancer PD35951a


title: Breast cancer PD35936a


title: Breast cancer PD35934a


title: Breast cancer PD35931a


title: Breast cancer PD35928a


title: Breast cancer PD35930a


title: Breast cancer PD35927a


title: Breast cancer PD35961a


title: Breast cancer PD31181a


title: Breast cancer PD31179a


title: Breast cancer PD31174a


title: Breast cancer PD31172a


title: Breast cancer PD31173a


title: Breast cancer PD31167a


title: Breast cancer PD31165a


title: Breast cancer PD31163a


title: Breast cancer PD31170a


title: Breast cancer PD31160a


title: Breast cancer PD31159a


title: Breast cancer PD31155a


title: Breast cancer PD31153a


title: Breast cancer PD31164a


title: Breast cancer PD35937a


title: Breast cancer PD31166a


title: Breast cancer PD31156a


title: Breast cancer PD31148a


title: Breast cancer PD31161a


title: Breast cancer PD31152a


title: Breast cancer PD31157a


title: Breast cancer PD31150a


title: Breast cancer PD31151a


title: Breast cancer PD31146a


title: Breast cancer PD31142a


title: Breast cancer PD31145a


title: Breast cancer PD31137a


title: Breast cancer PD31139a


title: Breast cancer PD31177a


title: Breast cancer PD31134a


title: Breast cancer PD31133a


title: Breast cancer PD31128a


title: Breast cancer PD31126a


title: Breast cancer PD31124a


title: Breast cancer PD31122a


title: Breast cancer PD31123a


title: Breast cancer PD31120a


title: Breast cancer PD31117a


title: Breast cancer PD31113a


title: Breast cancer PD31109a


title: Breast cancer PD31108a


title: Breast cancer PD31098a


title: Breast cancer PD31121a


title: Breast cancer PD31090a


title: Breast cancer PD31111a


title: Breast cancer PD31082a


title: Breast cancer PD31104a


title: Breast cancer PD31088a


title: Breast cancer PD31089a


title: Breast cancer PD31086a


title: Breast cancer PD31081a


title: Breast cancer PD31074a


title: Breast cancer PD31116a


title: Breast cancer PD31066a


title: Breast cancer PD31097a


title: Breast cancer PD31072a


title: Breast cancer PD31063a


title: Breast cancer PD31080a


title: Breast cancer PD31065a


title: Breast cancer PD31078a


title: Breast cancer PD31075a


title: Breast cancer PD31053a


title: Breast cancer PD31048a


title: Breast cancer PD31037a


title: Breast cancer PD31042a


title: Breast cancer PD31030a


title: Breast cancer PD31056a


title: Breast cancer PD31032a


title: Breast cancer PD31046a


title: Breast cancer PD31028a


title: Breast cancer PD31031a


title: Breast cancer PD31033a


title: Breast cancer PD31058a


title: Breast cancer PD31041a


title: S15

type: RNA

city: Daejeon

first: In Soo

last: Kim

address: Mun-hwa ro 266

country: South Korea

institute: Chungnam National University

description: standard protocol

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data were normalized and log2 transformed using nSolver 4.0 (Nanostring Technologies). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString indexing

source_name: PBMCs

label_protocol: NanoString indexing

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter짰 platform (Nanostring Technologies) using 100 ng of RNA per skin sample.

tag: disease state

value: NTM-PD


title: Breast cancer PD31045a


title: Breast cancer PD31057a


title: S21

description: standard protocol


title: S22

description: standard protocol


title: S23

description: standard protocol


title: S24

description: standard protocol


title: S14

description: standard protocol


title: S18

description: standard protocol


title: M12

description: standard protocol


title: Breast cancer PD31040a


title: S16

description: standard protocol


title: S20

description: standard protocol


title: S19

description: standard protocol


title: M13

description: standard protocol


title: Breast cancer PD31047a


title: S17

description: standard protocol


title: M11

description: standard protocol


title: M10

description: standard protocol


title: HC06

description: standard protocol

value: healthy


title: M09

description: standard protocol


title: M07

description: standard protocol


title: HC05

description: standard protocol


title: HC04

description: standard protocol


title: M08

description: standard protocol


title: RpoS stationary phase 2 (ChIP-exo)

city: Ulsan

first: Donghyuk

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

data_processing:
Files for a single read were concatenated.
ChIP-exo reads were aligned to the the reference files (NC_009648 for the chromosome, NC_009649 for plasmid pKPN3, NC_009650 for plasmid pKPN4, NC_009651 for plasmid pKPN5, NC_009652 for plasmid pKPN6, and NC_009653 for plasmid pKPN7) using bowtie with default options
Used DEep-learning Optimized ChIP-exo peak calling Suite (DEOCSU), a novel machine learning-based ChIP-exo peak-calling suite pipeline (https://github.com/SBML-Kimlab/DEOCSU) to identify and define binding peak candidates.
Concatenated gff files for each sample
Assembly: NC_009648, NC_009649, NC_009650, NC_009651, NC_009652, NC_009653
Supplementary files format and content: Tab-delimited text files (gff) with 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Klebsiella pneumoniae

growth_protocol: Klebsiella pneumoniae MGH 78578 wild type was grown aerobically at 37 °C in M9 minimal media supplemented with 0.2% glucose.

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin cross-linked to transcription factors was isolated with an antibody.
Libraries were prepared for sequencing according to standard Illumina rotocols.

tag: strain

value: wild type

tag: cultured in

value: M9 minimal media

tag: growth phase

value: early stationary phase

value: anti-E. coli RpoS (1RS1, Neoclone)

tag: chip antibody_vendor

value: BioLegend

tag: chip antibody_cat


title: RpoS stationary phase 3 (ChIP-exo)


title: RpoS stationary phase 1 (ChIP-exo)


title: RpoD stationary phase 3 (ChIP-exo)

value: anti-E. coli RpoD (2G10, Neoclone)


title: HC02

description: standard protocol


title: HC03

description: standard protocol


title: RpoS exponential growth 2 (ChIP-exo)

value: mid exponential growth


title: RpoD exponential growth 2 (ChIP-exo)


title: HC01

description: standard protocol


title: RpoD exponential growth 1 (ChIP-exo)


title: RpoS exponential growth 1 (ChIP-exo)


title: RpoD stationary phase 1 (ChIP-exo)


title: RpoD stationary phase 2 (ChIP-exo)


title: DNA-methylation array data_207716530065_R02C01

city: Berlin

first: Philipp

last: Euskirchen

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k or 935k Beadchip, respectively, using standard Illumina protocol.

scan_protocol: Arrays were scanned on the iscan instument acording to standarad protocol.

data_processing:
IDAT files were preprocessed using R/minfi.
*processed value definition: Average beta value

label: Cy3, Cy5

source_name: tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions.

value: tumor

tag: tumor type

value: Meningioma

tag: beadchip name


title: DNA-methylation array data_203867050020_R02C01

value: Subependymoma

tag: age

tag: Sex

value: Female


title: DNA-methylation array data_207513910087_R01C01


title: DNA-methylation array data_205689110069_R01C01

value: Spinal ependymoma

value: Male


title: DNA-methylation array data_205832310023_R07C01


title: DNA-methylation array data_203028210063_R08C01


title: DNA-methylation array data_206486300176_R04C01


title: DNA-methylation array data_205041750149_R01C01


title: DNA-methylation array data_206486300125_R02C01


title: DNA-methylation array data_207166150139_R07C01


title: DNA-methylation array data_207166150139_R02C01


title: DNA-methylation array data_202790040014_R06C01


title: DNA-methylation array data_204860510029_R02C01


title: M24_000860

description:
Library name: M24_000860
low-pass WGS

data_processing:
Processing of WGBS data from 22 human diffuse glioma samples was erformed using the One Touch Pipeline (OTP) which uses bwa v0.6.1 for alignment and methylCtools v1.0.0 for methylation calling. Plus- and minus-strand methylated allele frequencies at CpG sites were merged using custom scripts. For nanopore sequencing data, raw sequencing data were basecalled using ONT's proprietary software (guppy or dorado) and aligned to hg19 using minimap2. Methylated allele frequencies were extracted using modkit.
Assembly: hg19
Supplementary files format and content: bedMethyl
The BED files adhere to the ENCODE bedMethyl standard outlined in 'Whole-Genome Bisulfite Sequencing Data Standards and Processing Pipeline – ENCODE' (encodeproject.org)
https://www.encodeproject.org/data-standards/wgbs/

extract_protocol:
Genomic DNA was extracted from tumor tissue using commercial extraction kits as part of neuropathological routine workup.
WGBS libraries were prepared using a NEBNext Methyl-seq Kit (NEB), and were then sequenced on an Illumina NovaSeq 6000 platform at the BIH Core Unit Genomics over two S4 flow cells in a paired-end setting of 2 x 150 bp. Nanopore libraries were prepared using Rapid Barcoding Kit (ONT) and sequenced on R9 or R10.4.1 flow cells on MinION/GridION or P2 Solo devices.


title: M24_000721

description:
Library name: M24_000721_BC13
low-pass WGS


title: M24_000595

description:
Library name: M24_000595_BC11
low-pass WGS


title: DNA-methylation array data_206439840040_R06C01


title: DNA-methylation array data_205814880056_R07C01

value: Solitary fibrous tumour


title: DNA-methylation array data_207521860168_R03C01


title: M24_000576

description:
Library name: M24_000576_BC10
low-pass WGS


title: M24_000571

description:
Library name: M24_000571_BC9
low-pass WGS

value: Atypical meningioma


title: M24_000475

description:
Library name: M24_000475_BC8
low-pass WGS


title: DNA-methylation array data_203821710014_R03C01


title: DNA-methylation array data_204088040016_R08C01

value: Schwannoma


title: DNA-methylation array data_203867050048_R04C01


title: M24_000756

description:
Library name: M24_000756_BC15
low-pass WGS


title: DNA-methylation array data_206238130124_R01C01


title: M24_000439

description:
Library name: M24_000439_BC7
low-pass WGS


title: M24_000674

description:
Library name: M24_000674_BC12
low-pass WGS


title: DNA-methylation array data_206152230098_R02C01


title: DNA-methylation array data_203866300081_R04C01


title: M24_000438

description:
Library name: M24_000438_BC6
low-pass WGS


title: M24_000302

description:
Library name: M24_000302_BC3
low-pass WGS


title: DNA-methylation array data_205828600101_R08C01


title: DNA-methylation array data_206178930022_R08C01


title: DNA-methylation array data_205096370110_R01C01


title: DNA-methylation array data_205915530047_R08C01


title: DNA-methylation array data_206600570019_R07C01


title: DNA-methylation array data_205041760083_R07C01


title: DNA-methylation array data_206600570024_R04C01

value: Choroid plexus papilloma


title: M24_000301

description:
Library name: M24_000301_BC2
low-pass WGS


title: DNA-methylation array data_203821710038_R02C01


title: M24_000180

description:
Library name: M24_000180_BC18
low-pass WGS


title: DNA-methylation array data_206486300107_R01C01

value: Sparsely granulated somatotroph pituitary adenoma


title: M24_000011

description:
Library name: M24_000011
low-pass WGS


title: DNA-methylation array data_203810690011_R01C01


title: DNA-methylation array data_205832310017_R03C01

value: Somatotroph pituitary adenoma


title: M24_001414

description:
Library name: M24_001414_BC21
low-pass WGS

value: Pilocytic astrocytoma


title: M24_000280

description:
Library name: M24_000280_BC1
low-pass WGS


title: DNA-methylation array data_205096370115_R02C01

value: Choroid plexus carcinoma


title: M24_000210

description:
Library name: M24_000210_BC19
low-pass WGS


title: M24_000211

description:
Library name: M24_000211_BC20
low-pass WGS


title: DNA-methylation array data_206486300051_R03C01


title: DNA-methylation array data_205832320128_R03C01

value: Densely granulated somatotroph pituitary adenoma


title: DNA-methylation array data_203821710034_R06C01

value: Corticotroph pituitary adenoma


title: DNA-methylation array data_205735150124_R01C01

value: Atypical choroid plexus papilloma


title: M24_001028

description:
Library name: M24_001028_BC22
low-pass WGS

value: tumor

value: Pineal parenchymal tumor of intermediate differentiation


title: M24_001291

description:
Library name: M24_001291_BC23
low-pass WGS

value: Diffuse midline glioma, H3 K27-altered


title: M24_000163

description:
Library name: M24_000163_BC16
low-pass WGS


title: DNA-methylation array data_206443740153_R08C01

value: Pineoblastoma


title: DNA-methylation array data_203808720144_R01C01

value: Pineal parenchymal tumour of intermediate differentiation

value: Female


title: M22_3104_v14_150

description:
Library name: M22_3104_v14_150_v1_1
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: UKE-N2024-1643

description:
Library name: UKE-N2024-1643
low-pass WGS

value: Medulloblastoma, non-WNT/non-SHH


title: M24_001203

description:
Library name: M24_001203_BC24
low-pass WGS

value: Astrocytoma (CNS WHO grade 2), IDH-mutant


title: DNA-methylation array data_203020780015_R02C01

value: Cauda equina neuroendocrine tumour

value: Male


title: UKE-N2024-1390

description:
Library name: UKE-N2024-1390
low-pass WGS

value: Medulloblastoma, WNT-activated


title: DNA-methylation array data_205046550112_R07C01

value: Papillary tumour of the pineal region


title: UKE-N2024-8

description:
Library name: UKE-N2024-8
low-pass WGS

value: Medulloblastoma, SHH-activated


title: DNA-methylation array data_206100100005_R04C01


title: DNA-methylation array data_203072530029_R01C01


title: N1437_24

description:
Library name: N1437_24_barcode12_cnn
low-pass WGS


title: DNA-methylation array data_205016910053_R03C01


title: UKE-N2024-410

description:
Library name: UKE-N2024-410
low-pass WGS


title: M23_002778

description:
Library name: M23_002778_BC20
low-pass WGS

value: Posterior fossa group B (PFB) ependymoma


title: N1502_24

description:
Library name: N1502_24_barcode10_cnn
low-pass WGS

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: N1996_24

description:
Library name: N1996_24_barcode27_cnn
low-pass WGS

value: Pituicytoma


title: DNA-methylation array data_202995850006_R07C01

value: tumor


title: DNA-methylation array data_204229190073_R06C01


title: DNA-methylation array data_202995850006_R02C01


title: N1451_24

description:
Library name: N1451_24_barcode09_cnn
low-pass WGS


title: N1794-24

description:
Library name: N1794-24-barcode22_cnn
low-pass WGS


title: N1436_24

description:
Library name: N1436_24_barcode11_cnn
low-pass WGS


title: N1472_24

description:
Library name: N1472_24_barcode13_cnn
low-pass WGS

value: Spinal ependymoma


title: DNA-methylation array data_206100100029_R02C01

value: Meningioma


title: DNA-methylation array data_202995850009_R03C01


title: DNA-methylation array data_205689110071_R02C01


title: DNA-methylation array data_205041760028_R06C01

value: Choroid plexus papilloma


title: DNA-methylation array data_204503540034_R01C01


title: N1394_24

description:
Library name: N1394_24_barcode07_cnn
low-pass WGS


title: DNA-methylation array data_204229190126_R02C01


title: N1327_24

description:
Library name: N1327_24_barcode04_cnn
low-pass WGS


title: DNA-methylation array data_207513910082_R01C01


title: N1243_24

description:
Library name: N1243_24_barcode02_cnn
low-pass WGS

value: Diffuse midline glioma, H3 K27-altered


title: DNA-methylation array data_206600570021_R02C01

value: Female


title: DNA-methylation array data_207335100095_R05C01


title: N1219_24

description:
Library name: N1219_24_barcode01_cnn
low-pass WGS

value: Pleomorphic xanthoastrocytoma


title: DNA-methylation array data_206486300107_R03C01


title: MET-FR-06715316-T01A-D01A-W02

description:
Library name: MET-FR-06715316-T01A-D01A-W02
low-pass WGS

value: Bladder carcinoma


title: MET-FR-06715344-T01A-D01A-W01

description:
Library name: MET-FR-06715344-T01A-D01A-W01
low-pass WGS

value: Squamous cell carcinoma


title: DNA-methylation array data_206999330180_R04C01


title: MET-FR-06715195-T01A-D01A-W02

description:
Library name: MET-FR-06715195-T01A-D01A-W02
low-pass WGS

value: NSCLC Adenocarcinoma


title: MET-FR-06713759-T01A-D01A-W02

description:
Library name: MET-FR-06713759-T01A-D01A-W02
low-pass WGS


title: MET-FR-06715194-T01A-D01A-W01

description:
Library name: MET-FR-06715194-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_205814880056_R02C01

value: Male


title: MET-FR-06715017-T01A-D01A-W01

description:
Library name: MET-FR-06715017-T01A-D01A-W01
low-pass WGS

value: Breast carcinoma


title: DNA-methylation array data_205689140053_R01C01


title: N1278_24

description:
Library name: N1278_24_barcode03_cnn
low-pass WGS

value: Glioblastoma, IDH-wildtype


title: DNA-methylation array data_205799780079_R01C01


title: DNA-methylation array data_206486310052_R01C01


title: DNA-methylation array data_207335100077_R06C01


title: MET-FR-06714996-T01A-D01A-W01

description:
Library name: MET-FR-06714996-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_206486300128_R04C01


title: MET-FR-06714972-T01A-D01A-W01

description:
Library name: MET-FR-06714972-T01A-D01A-W01
low-pass WGS


title: MET-FR-06714968-T01A-D01A-W02

description:
Library name: MET-FR-06714968-T01A-D01A-W02
low-pass WGS

value: SCLC


title: MET-FR-06713699-T01A-D01A-W01

description:
Library name: MET-FR-06713699-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_207335100077_R05C01


title: DNA-methylation array data_207521860161_R02C01


title: DNA-methylation array data_207513910035_R01C01


title: MET-FR-06713715-T01A-D01A-W02

description:
Library name: MET-FR-06713715-T01A-D01A-W02
low-pass WGS


title: DNA-methylation array data_207331540088_R03C01


title: MET-FR-06713688-T01A-D01A-W02

description:
Library name: MET-FR-06713688-T01A-D01A-W02
low-pass WGS

value: Clear cell renal cell carcinoma


title: DNA-methylation array data_206503150048_R05C01


title: MET-FR-06713680-T01A-D01A-W01

description:
Library name: MET-FR-06713680-T01A-D01A-W01
low-pass WGS


title: MET-FR-06713664-T01A-D01A-W02

description:
Library name: MET-FR-06713664-T01A-D01A-W02
low-pass WGS


title: DNA-methylation array data_207309920062_R02C01


title: DNA-methylation array data_206100100005_R05C01


title: MET-FR-06713565-T01A-D01A-W01

description:
Library name: MET-FR-06713565-T01A-D01A-W01
low-pass WGS

value: Medulloblastoma Group 3


title: MET-FR-06713532-T01A-D01A-W02

description:
Library name: MET-FR-06713532-T01A-D01A-W02
low-pass WGS

value: Melanoma


title: DNA-methylation array data_206486300069_R08C01

value: tumor


title: MET-FR-06713469-T01A-D01A-W02

description:
Library name: MET-FR-06713469-T01A-D01A-W02
low-pass WGS


title: MET-FR-06713455-T01A-D01A-W02

description:
Library name: MET-FR-06713455-T01A-D01A-W02
low-pass WGS


title: DNA-methylation array data_206687210001_R04C01


title: DNA-methylation array data_207385100072_R04C01


title: MET-FR-06712825-T01A-D01A-W01

description:
Library name: MET-FR-06712825-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_207577170112_R07C01


title: MET-FR-06712626-T01A-D01A-W01

description:
Library name: MET-FR-06712626-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_207577170005_R05C01


title: DNA-methylation array data_206443740177_R06C01


title: DNA-methylation array data_207385100072_R06C01


title: DNA-methylation array data_205915530069_R08C01


title: DNA-methylation array data_207166150007_R03C01


title: MET-FR-06713446-T01A-D01A-W02

description:
Library name: MET-FR-06713446-T01A-D01A-W02
low-pass WGS

value: Adenocarcinoma gastrointestinal tract


title: MET-FR-06712538-T01A-D01A-W01

description:
Library name: MET-FR-06712538-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_206486300068_R05C01

value: Meningioma


title: MET-FR-06712766-T01A-D01A-W01

description:
Library name: MET-FR-06712766-T01A-D01A-W01
low-pass WGS


title: MET-FR-06712602-T01A-D01A-W01

description:
Library name: MET-FR-06712602-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_206486300166_R08C01


title: MET-FR-06712471-T01A-D01A-W01

description:
Library name: MET-FR-06712471-T01A-D01A-W01
low-pass WGS

value: Glioblastoma


title: DNA-methylation array data_206486300166_R06C01


title: MET-FR-06712492-T01A-D01A-W01

description:
Library name: MET-FR-06712492-T01A-D01A-W01
low-pass WGS


title: MET-FR-06712245-T01A-D01A-W01

description:
Library name: MET-FR-06712245-T01A-D01A-W01
low-pass WGS


title: DNA-methylation array data_204808700110_R08C01


title: DNA-methylation array data_206503150043_R08C01


title: DNA-methylation array data_205617080146_R06C01


title: DNA-methylation array data_204234660050_R01C01


title: DNA-methylation array data_203810690095_R02C01


title: DNA-methylation array data_204776820085_R02C01

value: Atypical meningioma


title: DNA-methylation array data_205589750027_R07C01

value: Female


title: DNA-methylation array data_204860510029_R03C01


title: DNA-methylation array data_206503150068_R06C01


title: MET-FR-06712450-T01A-D01A-W01

description:
Library name: MET-FR-06712450-T01A-D01A-W01
low-pass WGS

value: Embryonal Rhabdomyosarcoma


title: DNA-methylation array data_206999330185_R05C01


title: Atg14het_cTreg2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

organism: Mus musculus

source_name: Atg14 heterozygous cTreg from mixed bone barrow chimera

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Mixed bone marrow chimeras were generated by mixing CD45.2+ bone marrow from Foxp3CreAtg14+/fl or Foxp3CreAtg14fl/fl mice at a 1:1 ratio with CD45.1+ WT spike bone marrow, followed by adoptive transfer into sublethally irradiated Rag1–/– mice. Bone marrow was allowed to reconstitute for 6–8 weeks before experiments.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen

tag: cell type


title: Atg14het_eTreg2

source_name: Atg14 heterozygous eTreg from mixed bone barrow chimera


title: Atg14het_eTreg3

value: Atg14 heterozygous eTreg from mixed bone barrow chimera


title: DNA-methylation array data_203810690133_R04C01


title: DNA-methylation array data_205771810142_R02C01


title: Atg14KO_eTreg3

source_name: Atg14KO eTreg from mixed bone barrow chimera


title: DNA-methylation array data_203866300058_R06C01


title: Atg14het_eTreg1


title: Atg14KO_cTreg3

source_name: Atg14KO cTreg from mixed bone barrow chimera


title: Atg14KO_eTreg2

value: Atg14KO eTreg from mixed bone barrow chimera


title: Atg14KO_cTreg2

value: Atg14KO cTreg from mixed bone barrow chimera


title: DNA-methylation array data_205828600005_R02C01


title: Atg14het_cTreg1

value: Atg14 heterozygous cTreg from mixed bone barrow chimera


title: Atg14het_cTreg3


title: Atg14het_eTreg4


title: Atg14het_cTreg4


title: DNA-methylation array data_204930630091_R04C01


title: Atg14KO_eTreg1


title: DNA-methylation array data_205771820056_R04C01

value: Male


title: DNA-methylation array data_203866300058_R08C01


title: DNA-methylation array data_206119350037_R04C01

value: Anaplastic meningioma


title: DNA-methylation array data_204964480101_R01C01


title: DNA-methylation array data_205828600004_R06C01


title: DNA-methylation array data_206503150006_R03C01


title: DNA-methylation array data_207015200114_R06C01


title: Atg14KO_cTreg1


title: DNA-methylation array data_204229190148_R01C01


title: Kat6a KO Kat6b Tg, rep 4

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Library name: F_498_1

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 2.10.5
Fragment (read pair) counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and NCBI's RefSeq annotation.
Assembly: mm39
Supplementary files format and content: tab-delimited text files (tsv). Columns represent Entrez Gene Id, Gene Symbol, total gene length (total base count of all exons) and the number of fragments mapping to that gene.

source_name: Whole embryo

extract_protocol:
Total RNA from whole E9.5 embryos was extracted using an RNA extraction kit (Qiagen RNeasy mini kit; Qiagen, 74104), according to the manufacturer’s instructions and including the optional DNaseI digestion step. RNA quality and quantity were assessed on an automated analyser (Tapestation 4200; Agilent, G2991BA)
500 ng RNA were used to generate libraries using a library construction kit (TruSeq RNA prep kit v2; Illumina, RS-122-2002), according to the manufacturer’s instructions.

value: Whole embryo

tag: litter

tag: embryo numbner

tag: kat6a genotype

value: KO

tag: kat6b genotype

value: Tg


title: DNA-methylation array data_206152230098_R04C01

tag: tissue

value: Melanoma


title: DNA-methylation array data_204229190126_R08C01

value: tumor


title: wt3

source_name: Wildtype Treg from mixed bone barrow chimera

growth_protocol: Mixed bone marrow chimeras were generated by mixing CD45.2+ bone marrow from Foxp3CrePik3c3+/+ or Foxp3CrePik3c3fl/fl mice at a 1:1 ratio with CD45.1+ WT spike bone marrow, followed by adoptive transfer into sublethally irradiated Rag1–/– mice. Bone marrow was allowed to reconstitute for 6–8 weeks before experiments.

treatment_protocol: Not applicable


title: DNA-methylation array data_202787550069_R08C01

value: Medulloblastoma, WNT-activated


title: Kat6a KO Kat6b Tg, rep 3

description: Library name: M_483_10


title: Vps34KO2

source_name: Vps34 KO Treg from mixed bone barrow chimera


title: Vps34KO1

value: Vps34 KO Treg from mixed bone barrow chimera


title: Kat6a KO Kat6b Tg, rep 1

description: Library name: M_483_1


title: Kat6a KO Kat6b Tg, rep 2

description: Library name: F_483_3


title: Vps34KO5


title: DNA-methylation array data_205049770014_R01C01


title: Vps34KO4


title: DNA-methylation array data_204316970005_R03C01


title: wt1

value: Wildtype Treg from mixed bone barrow chimera


title: Vps34KO3


title: DNA-methylation array data_206503150048_R01C01

value: Medulloblastoma, SHH-activated and TP53-wildtype


title: DNA-methylation array data_204667540074_R04C01

value: Female


title: Kat6a WT Kat6b Tg, rep 3

description: Library name: M_2597_7

value: WT


title: Kat6a WT Kat6b Tg, rep 2

description: Library name: F_2597_3


title: DNA-methylation array data_205041760132_R08C01


title: wt4


title: Kat6a WT Kat6b Tg, rep 4

description: Library name: F_2598_5


title: wt2


title: Kat6a WT Kat6b Tg, rep 1

description: Library name: M_2597_2


title: DNA-methylation array data_203010900150_R06C01


title: Kat6a KO Kat6b WT, rep 4

description: Library name: M_803_7


title: DNA-methylation array data_204339300057_R07C01

value: Medulloblastoma, SHH-activated


title: DNA-methylation array data_205915530047_R05C01


title: DNA-methylation array data_204425710094_R05C01


title: Kat6a KO Kat6b WT, rep 2

description: Library name: F_801_11


title: DNA-methylation array data_203020900048_R05C01


title: Kat6a KO Kat6b WT, rep 3

description: Library name: M_803_6


title: DNA-methylation array data_201465940044_R03C01


title: Kat6a KO Kat6b WT, rep 1

description: Library name: F_801_10


title: DNA-methylation array data_205814880087_R05C01

value: Medulloblastoma, non-WNT/non-SHH


title: Kat6a WT Kat6b WT, rep 4

description: Library name: F_2598_2


title: DNA-methylation array data_205291540189_R02C01


title: DNA-methylation array data_203013220074_R07C01


title: DNA-methylation array data_206419180176_R06C01


title: Kat6a WT Kat6b WT, rep 2

description: Library name: M_803_9


title: Kat6a WT Kat6b WT, rep 1

description: Library name: M_801_2


title: Kat6a cfdcfd Kat6b Tg, H3K23ac, rep 4

description: Library name: cfdcfd_Tg_4

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned simultaneously to a combinded mouse and drosophila genome by Rsubread version 2.18.0
Reads were included if there were uniquely mapped, non-chimeric, and not identified as a PCR duplicate
Fragment (read pair) counts were summarized by mouse Entrez Gene ID and drosophila chromosome using the Rsubread's featureCounts function and NCBI's RefSeq annotation to the mouse genome.
Assembly: mm39
Supplementary files format and content: All files are tab-delimited text files (tsv).  Columns represent Entrez Gene Id, Gene Symbol, and the number of fragments mapping to that gene region.
Supplementary files format and content: _TSS files are counts for transcriptional start site (TSS) region - 1kbp upstream to TSS
Supplementary files format and content: _TES files are counts for transcriptional end site TES) region - TES to 1kbp downstream of TES
Supplementary files format and content: _GB files are counts for gene body (GB) region - TSS to TES
Library strategy: CUT&Tag

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were derived from E14.5 foetuses and grown in Dulbecco’s modified Eagle medium (Gibco, 11995) supplemented with 100 U/ml penicillin/streptomycin (Gibco, 15140122) and 10% foetal calf serum. Cells were cultured in at 37oC, 5% CO2 and 3% O2. Cell counts were determined at each passage using a CountessTM cell counter (ThermoFisher).

extract_protocol:
Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing was performed on 50,000 mouse embryonic fibroblasts (MEFs) combined with 50,000 Drosophila melanogaster S2 cells, as described in Kaya-Okur et al., 2019, with minor modifications as described in. All buffers were prepared fresh with complete EDTA-free protease inhibitors (Roche, 11873580001) and 0.5 mM sodium butyrate (Sigma, B5887). Per sample, 10 µl concanavalin-A beads (Bangs Laboratories, BP531) were washed twice in 10 volumes binding buffer (20 mM HEPES pH 7.5 (Sigma, 83264), 10 mM KCl (Sigma, 60142), 1 mM CaCl2 (Sigma, 21115), and 1 mM MnCl2 (Sigma, M1787) and resuspended in 10 µl binding buffer. Combined MEFs and S2 D. melanogaster cells were washed twice in 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl (Sigma, 71386), 0.5 mM spermidine (Sigma, S0266) and resuspended in 90 µl wash buffer. Concanavalin-A beads and samples were combined and incubated (RT, 10 min), immobilised using a magnetic rack (ThermoFisher, MR02) and beads resuspended in 100 µl ice-cold antibody buffer (wash buffer supplemented with 0.05 % (w/v) digitonin (Merck, 300410), 2 mM EDTA (Invitrogen, 15575020), and 0.1 % (w/v) BSA (Sigma, A8577) containing 1:100 H3K23ac (Millipore, 07-355) primary antibody. Samples were incubated overnight at 4oC. The following morning, beads were resuspended in 100 µl wash buffer supplemented with 0.05% (w/v) digitonin containing 1:100 secondary antibody (Guinea pig anti-rabbit IgG, Antibodies Online, ABIN101961), incubated (RT, 1 hr), washed thrice and resuspended in 100 µl ice-cold dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine and 0.01 % (w/v) digitonin), supplemented with 1 2.5 µl pAG-Tn5 (EpiCypher, 15-1017). Samples were incubated (RT, 1 hr), washed thrice, resuspended in 100 µl tagmentation buffer (wash buffer supplemented with 0.01 mM MgCl2 (Sigma, 63069) and incubated at 37°C for 1 hr. Tagmentation was stopped using 3.34 µl 0.5 M EDTA, 1 µl 10% (w/v) SDS (Sigma, 71736), and 0.83 µl 20 mg/ml thermolabile proteinase K (NEB, P8111S), incubating at 37°C for 1 hr and 800 rpm, followed by heat inactivation at 55°C for 10 min. DNA was extracted using Ampure XP beads (Beckman, A63880), eluting in 25 µl 10 mM Tris-HCl pH=8.0 (Invitrogen, 15568025), 1 mM EDTA, and 25 µg/ml RNAse A (ThermoFisher, EN0531) at 37°C for 10 min.
10 µl sample DNA elutes were used to generate sequencing libraries, which were amplified using PCR for 13 cycles. PCR products were cleaned up using 30 µl Ampure XP beads and eluted in 25 µl 10 mM Tris-HCl pH 8.0. Cleaned libraries were analysed using High Sensitivity D1000 gels (Agilent, 5067- 5584) on an Agilent 2200 tape station.

treatment_protocol: Not applicable.

value: mouse embryonic fibroblasts

value: cfdcfd

tag: replicate

tag: sample type

tag: drosophila count


title: Kat6a WT Kat6b WT, rep 3

description: Library name: F_2597_5


title: DNA-methylation array data_205689130023_R04C01


title: DNA-methylation array data_200992340007_R02C01

value: Male


title: DNA-methylation array data_205735150126_R07C01


title: Kat6a cfdcfd Kat6b Tg, H3K23ac, rep 1

description: Library name: cfdcfd_Tg_1


title: DNA-methylation array data_207521860168_R06C01


title: Kat6a cfdcfd Kat6b Tg, H3K23ac, rep 3

description: Library name: cfdcfd_Tg_3


title: Kat6a WT Kat6b Tg, H3K23ac, rep 4

description: Library name: WT_Tg_4


title: DNA-methylation array data_206439840021_R04C01


title: Kat6a cfdcfd Kat6b Tg, H3K23ac, rep 2

description: Library name: cfdcfd_Tg_2


title: DNA-methylation array data_205814880005_R07C01


title: Kat6a WT Kat6b Tg, H3K23ac, rep 3

description: Library name: WT_Tg_3


title: DNA-methylation array data_205689130023_R01C01


title: Kat6a WT Kat6b Tg, H3K23ac, rep 2

description: Library name: WT_Tg_2


title: Kat6a WT Kat6b Tg, H3K23ac, rep 1

description: Library name: WT_Tg_1


title: Kat6a cfdcfd Kat6b WT, H3K23ac, rep 3

description: Library name: cfdcfd_WT_3


title: DNA-methylation array data_204958110017_R06C01


title: Kat6a WT Kat6b WT, H3K23ac, rep 4

description: Library name: WT_WT_4


title: DNA-methylation array data_208160540160_R07C01

value: Astrocytoma (CNS WHO grade 3), IDH-mutant


title: Kat6a cfdcfd Kat6b WT, H3K23ac, rep 1

description: Library name: cfdcfd_WT_1


title: DNA-methylation array data_207953350102_R04C01


title: Kat6a cfdcfd Kat6b WT, H3K23ac, rep 2

description: Library name: cfdcfd_WT_2


title: DNA-methylation array data_206359150189_R05C01

value: Diffuse large B-cell lymphoma of the CNS


title: DNA-methylation array data_206036370031_R04C01

value: Subependymal giant cell astrocytoma


title: DNA-methylation array data_202995850016_R02C01

value: Pilocytic astrocytoma


title: Kat6a WT Kat6b WT, H3K23ac, rep 3

description: Library name: WT_WT_3


title: DNA-methylation array data_203810690095_R05C01


title: DNA-methylation array data_203810690005_R04C01


title: Kat6a WT Kat6b WT, H3K23ac, rep 2

description: Library name: WT_WT_2


title: Kat6a WT Kat6b Tg, IgG

description: Library name: WT_Tg_IgG

value: Tg

value: IgG


title: DNA-methylation array data_207355710034_R06C01

value: tumor


title: Kat6a WT Kat6b WT, IgG

description: Library name: WT_WT_IgG


title: Leptin-antibiotic, rep 5

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

data_processing:
Raw reads passed the quality controls established in the FastQC software and mapped to the reference genome mm10 by using Hisat2. Gene counts were acquired by applying featureCounts. Expression reads matrix cutoff was set at an average of 10 reads. Read counts were normalized to CPMs (count per million) using the R package, EdgeR (v3.42.0).
Assembly: mm10
Supplementary files format and content: Tab delimited file with filtered counts matrix

source_name: Duodenum

growth_protocol: Male mice C57BL/6 were kept under controlled temperature, in a 12-hour light/dark cycle and allowed to freely access water and standard chow (Teklad maintenance diet 14% protein; Envigo).

extract_protocol:
Duodenal mRNA was isolated using Trizol (Invitrogen) following standard protocols. Quantification and integrity analysis of total RNA were performed by analysing 1 μl of each sample in an Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit; Agilent).
Total RNA strand-specific RNA libraries were generated using 150 ng of total RNA with the Illumina® Stranded RNA Prep Ligation kit with RiboZero Plus following the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq2000 (Illumina, Inc.) in paired-end mode with a read length of 2×50 bp.

treatment_protocol: Leptin (L3772, Sigma) intracerebroventricular (ICV) treatments were performed 3 days after cannula implantation. One hour after the start of the light period, mice were food-deprived for 2 hours before the treatment. At the moment of injection, mice were immobilized, and the cannula was opened to inject leptin (3 µg/mouse) or sterile saline for controls, using a 25 µL syringe (Gastight Syringe, Hamilton). Animals were euthanized 2 h after the ICV injection for sample collection.

value: Duodenum

value: All cells present in duodenum

tag: genotype

tag: treatment

value: Leptin-antibiotic

value: male


title: Kat6a cfdcfd Kat6b WT, H3K23ac, rep 4

description: Library name: cfdcfd_WT_4

value: WT


title: Kat6a cfdcfd Kat6b WT, IgG

description: Library name: cfdcfd_WT_IgG


title: DNA-methylation array data_208197680089_R05C01

value: Astrocytoma (CNS WHO grade 2), IDH-mutant


title: DNA-methylation array data_202995740123_R05C01

value: Medulloblastoma, non-WNT/non-SHH

value: Female


title: Leptin-antibiotic, rep 6


title: Leptin-antibiotic, rep 4


title: DNA-methylation array data_204964480108_R03C01


title: Kat6a WT Kat6b WT, H3K23ac, rep 1

description: Library name: WT_WT_1

value: mouse embryonic fibroblasts


title: DNA-methylation array data_208125020147_R05C01

value: Astrocytoma (CNS WHO grade 4), IDH-mutant

value: Male


title: DNA-methylation array data_206486300125_R08C01


title: Leptin-antibiotic, rep 3


title: Kat6a cfdcfd Kat6b Tg, IgG

description: Library name: cfdcfd_Tg_IgG

value: cfdcfd


title: DNA-methylation array data_208069740055_R01C01

value: Astrocytoma (CNS WHO grade 3), IDH-mutant


title: DNA-methylation array data_203890880054_R07C01

value: Pilocytic astrocytoma


title: Leptin-antibiotic, rep 2


title: DNA-methylation array data_208197680025_R03C01


title: DNA-methylation array data_208197680110_R03C01


title: DNA-methylation array data_208197680089_R03C01


title: DNA-methylation array data_202790040014_R02C01


title: Saline-antibiotic, rep 6

value: Saline-antibiotic


title: DNA-methylation array data_204674430008_R02C01


title: DNA-methylation array data_208182410097_R06C01


title: Saline-antibiotic, rep 4


title: Saline-antibiotic, rep 2


title: Saline-antibiotic, rep 3


title: DNA-methylation array data_203821710008_R03C01


title: DNA-methylation array data_204229180126_R07C01


title: Leptin-water, rep 13

value: Leptin-water


title: Saline-antibiotic, rep 1


title: DNA-methylation array data_208010440120_R04C01

value: tumor

value: Diffuse leptomeningeal glioneuronal tumor


title: DNA-methylation array data_204068280071_R08C01


title: Leptin-water, rep 11

value: Duodenum

value: All cells present in duodenum


title: Saline-antibiotic, rep 5

value: male


title: DNA-methylation array data_208010440031_R03C01


title: DNA-methylation array data_208010440031_R01C01

value: Atypical teratoid/rhabdoid tumour


title: Leptin-water, rep 12

value: WT


title: DNA-methylation array data_208356130015_R08C01

value: Astrocytoma, IDH-mutant


title: Leptin-water, rep 9


title: Leptin-antibiotic, rep 1

value: Leptin-antibiotic


title: DNA-methylation array data_206999330143_R04C01

value: Female


title: Leptin-water, rep 8


title: DNA-methylation array data_208271520042_R04C01


title: DNA-methylation array data_203821710008_R04C01


title: Saline-water, rep 14

value: Saline-water


title: DNA-methylation array data_204234160046_R05C01


title: DNA-methylation array data_208271520049_R06C01

value: Male


title: Saline-water, rep 12


title: Saline-water, rep 13


title: Saline-water, rep 10


title: DNA-methylation array data_208105370047_R05C01

value: Astrocytoma (CNS WHO grade 4), IDH-mutant


title: Saline-water, rep 11


title: DNA-methylation array data_207513910038_R06C01

value: Glioblastoma, IDH-wildtype


title: Saline-water, rep 9


title: DNA-methylation array data_207755820017_R02C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: DNA-methylation array data_207385100013_R03C01

value: Pilocytic astrocytoma


title: DNA-methylation array data_207755820049_R03C01

value: Papillary tumor of the pineal region


title: Leptin-water, rep 7

value: Leptin-water


title: Leptin-water, rep 10


title: Leptin-water, rep 6


title: DNA-methylation array data_207521860161_R03C01

value: tumor


title: Leptin-water, rep 5

value: Duodenum


title: DNA-methylation array data_207755820093_R03C01

value: Melanoma


title: Leptin-water, rep 4

value: All cells present in duodenum

value: male


title: Leptin-water, rep 3

value: WT


title: DNA-methylation array data_205862290139_R04C01


title: Leptin-water, rep 2


title: DNA-methylation array data_207755820108_R07C01

value: Diffuse hemispheric glioma, H3 G34-mutant


title: DNA-methylation array data_206639830027_R05C01

value: Rosette-forming glioneuronal tumour


title: Saline-water, rep 8


title: DNA-methylation array data_207755820108_R06C01


title: Leptin-water, rep 1


title: Saline-water, rep 7


title: DNA-methylation array data_205915530047_R06C01


title: Saline-water, rep 6


title: DNA-methylation array data_207755820057_R02C01

value: Myxopapillary ependymoma


title: DNA-methylation array data_207755820057_R01C01

value: Melanocytoma


title: Saline-water, rep 5

value: Saline-water


title: DNA-methylation array data_207309920037_R05C01

value: Male


title: Saline-water, rep 2


title: DNA-methylation array data_203010900136_R07C01


title: Saline-water, rep 3


title: DNA-methylation array data_201876940151_R03C01

value: Female


title: Saline-water, rep 4


title: Saline-water, rep 1


title: Ccr2 Qua

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

library_source: transcriptomic single cell

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v6.1.2 with default settings
Reads aligned to mm10 reference genome using Cell Ranger v6.1.2 with --expect-cells=10000
Assembly: mm10
Supplementary files format and content: Tab separated and matrix files

source_name: Skeletal muscle-Quadriceps

extract_protocol:
Cell concentration and viability of mouse samples were measured using a hemocytomter and ranged from 910,000 - 1,280,000 cells/mL with ~80% viability. Cell samples were input into 10x Genomics Single Cell 3′ v3.1D workflow and processed according to the manufacturer’s instructions for a targeted recovery of 10,000 cells (10X Genomics, USA). The resulting gene expression libraries were sequenced on an Illumina NextSeq 2000 instrument with 850pM input and 2% PhiX control library spike-in (Illumina, USA).
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

value: Skeletal muscle-Quadriceps

value: mononuclear cells


title: DNA-methylation array data_201465930056_R08C01

value: Ganglioglioma


title: DNA-methylation array data_207755820096_R04C01

value: Astrocytoma (CNS WHO grade 2), IDH-mutant


title: 5cv Dia

source_name: Skeletal muscle-Diaphragm

value: Skeletal muscle-Diaphragm


title: DNA-methylation array data_207755820096_R05C01

value: tumor

value: Glioblastoma, IDH-wildtype


title: Ccr2 Dia


title: DNA-methylation array data_202010290102_R05C01


title: 5cv Qua


title: DNA-methylation array data_207755820096_R03C01

value: Pleomorphic xanthoastrocytoma


title: DNA-methylation array data_207755820135_R04C01


title: DNA-methylation array data_207385100006_R08C01


title: DNA-methylation array data_206486310040_R03C01


title: DNA-methylation array data_208271520044_R03C01

value: Meningioma


title: DNA-methylation array data_207755820094_R01C01


title: DNA-methylation array data_206702500010_R04C01

value: Dysembryoblastic neuroepithelial tumour


title: DNA-methylation array data_201465970036_R05C01


title: DNA-methylation array data_207755830005_R08C01

value: Astrocytoma, IDH-mutant


title: DNA-methylation array data_207755830118_R04C01


title: whole-intestine_d28_rep-3

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

description: Gene expression data from Gallus Gallus liver 9 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Probeset-level intensity acquisition was performed by using Expression Console 1.1 (Affymetrix, Santa Clara, CA).

organism: Gallus gallus

source_name: whole-intestine 28 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: gender

value: female


title: DNA-methylation array data_207755830124_R03C01

value: Diffuse midline glioma, H3 K27-mutant


title: whole-intestine_d28_rep-4


title: DNA-methylation array data_207755830118_R07C01

value: Densely granulated somatotroph pituitary adenoma


title: DNA-methylation array data_204425700133_R04C01


title: DNA-methylation array data_205828600180_R06C01


title: whole-intestine_d21_rep-4

description: Gene expression data from Gallus Gallus liver 7 days

source_name: whole-intestine 21 days


title: whole-intestine_d28_rep-2

value: male


title: DNA-methylation array data_204958100139_R02C01

value: Male


title: whole-intestine_d28_rep-1


title: DNA-methylation array data_207755830124_R05C01

value: Female


title: DNA-methylation array data_207755830005_R07C01

value: Pilocytic astrocytoma


title: tibiotarsus-growth-plate_d28_rep-4

description: Gene expression data from Gallus Gallus liver 1 days

source_name: tibiotarsus-growth-plate 28 days


title: whole-intestine_d21_rep-1

description: Gene expression data from Gallus Gallus liver 3 days


title: tibiotarsus-growth-plate_d7_rep-4

source_name: tibiotarsus-growth-plate 7 days


title: DNA-methylation array data_206486310040_R08C01


title: DNA-methylation array data_204958100025_R07C01

value: Infant-type hemispheric glioma


title: DNA-methylation array data_207755830124_R08C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: tibiotarsus-growth-plate_d28_rep-1

description: Gene expression data from Gallus Gallus liver 0 days


title: tibiotarsus-growth-plate_d7_rep-3


title: tibiotarsus-growth-plate_d14_rep-4

source_name: tibiotarsus-growth-plate 14 days


title: DNA-methylation array data_205107400096_R03C01

source_name: tumor


title: tibiotarsus-growth-plate_d7_rep-2


title: tibiotarsus-growth-plate_d14_rep-3


title: tibiotarsus-growth-plate_d7_rep-1


title: DNA-methylation array data_208196060022_R06C01


title: DNA-methylation array data_205107400094_R04C01


title: tibiotarsus-growth-plate_d28_rep-2


title: whole-intestine_d21_rep-2


title: tibiotarsus-growth-plate_d14_rep-1

description: Gene expression data from Gallus Gallus leg-muscle 7 days


title: spleen_d7_rep-4

source_name: spleen 7 days


title: DNA-methylation array data_208196060065_R02C01


title: DNA-methylation array data_206100100029_R08C01


title: spleen_d7_rep-2

description: Gene expression data from Gallus Gallus leg-muscle 14 days


title: spleen_d7_rep-3


title: spleen_d7_rep-1


title: DNA-methylation array data_208196060065_R03C01


title: spleen_d1_rep-4

source_name: spleen 1 days


title: DNA-methylation array data_203010900136_R04C01


title: DNA-methylation array data_205832320116_R02C01


title: DNA-methylation array data_208196060022_R02C01


title: spleen_d1_rep-2

description: Gene expression data from Gallus Gallus jejunum 4 weeks


title: DNA-methylation array data_208196060065_R08C01


title: DNA-methylation array data_206467010139_R01C01


title: DNA-methylation array data_203017150041_R02C01


title: spleen_d1_rep-1


title: DNA-methylation array data_208126070071_R08C01

value: Astrocytoma (CNS WHO grade 2), IDH-mutant


title: spleen_d1_rep-3


title: DNA-methylation array data_208197680048_R03C01

value: Schwannoma


title: spleen_d14_rep-3

source_name: spleen 14 days


title: DNA-methylation array data_204234160030_R06C01

value: tumor


title: DNA-methylation array data_205049770014_R04C01


title: retina_d7_rep-4

description: Gene expression data from Gallus Gallus jejunum 21 days

source_name: retina 7 days


title: DNA-methylation array data_208197680048_R04C01


title: spleen_d14_rep-4


title: spleen_d14_rep-2


title: retina_d7_rep-1

description: Gene expression data from Gallus Gallus jejunum 14 days


title: spleen_d14_rep-1


title: retina_d1_rep-4

source_name: retina 1 days


title: DNA-methylation array data_208197680048_R05C01

value: Central neurocytoma


title: retina_d7_rep-3


title: DNA-methylation array data_205046550112_R05C01


title: DNA-methylation array data_208197680048_R01C01


title: DNA-methylation array data_208197680079_R01C01

value: Glioblastoma, IDH-wildtype


title: retina_d1_rep-3


title: retina_d7_rep-2


title: DNA-methylation array data_205460720147_R07C01


title: tibiotarsus-growth-plate_d28_rep-3


title: DNA-methylation array data_208197680079_R06C01


title: DNA-methylation array data_201869690187_R08C01


title: DNA-methylation array data_208197680048_R07C01


title: DNA-methylation array data_202787550049_R03C01


title: DNA-methylation array data_204425700133_R07C01


title: DNA-methylation array data_208285670152_R01C01


title: pineal-gland_d28_rep-4

description: Gene expression data from Gallus Gallus intestine 7 days

source_name: pineal-gland 28 days


title: retina_d1_rep-1


title: pineal-gland_d28_rep-2

description: Gene expression data from Gallus Gallus intestine 3 days


title: retina_d1_rep-2


title: pineal-gland_d1_rep-4

source_name: pineal-gland 1 days


title: DNA-methylation array data_203810690135_R04C01


title: pineal-gland_d28_rep-3


title: pineal-gland_d28_rep-1


title: DNA-methylation array data_203153910042_R04C01


title: DNA-methylation array data_208285670157_R02C01

value: Meningioma


title: DNA-methylation array data_208285670157_R03C01

value: Pleomorphic xanthoastrocytoma


title: pineal-gland_d1_rep-2

description: Gene expression data from Gallus Gallus intestine 1 days


title: pineal-gland_d1_rep-3


title: pineal-gland_d1_rep-1


title: DNA-methylation array data_207355710094_R02C01

value: Astrocytoma, IDH-mutant


title: pectoralis-muscle_d28_rep2-4

source_name: pectoralis-muscle 28 days

value: female


title: DNA-methylation array data_206486300176_R06C01


title: DNA-methylation array data_208197680102_R02C01


title: DNA-methylation array data_206639830027_R04C01


title: DNA-methylation array data_205828600005_R08C01


title: pectoralis-muscle_d21_rep2-4

description: Gene expression data from Gallus Gallus intestine 14 days

source_name: pectoralis-muscle 21 days


title: pectoralis-muscle_d21_rep2-2

description: Gene expression data from Gallus Gallus intestine 0 days


title: DNA-methylation array data_208197680102_R07C01


title: DNA-methylation array data_206036790116_R07C01


title: pectoralis-muscle_d28_rep2-3


title: pectoralis-muscle_d21_rep2-3


title: DNA-methylation array data_205915530037_R08C01


title: DNA-methylation array data_208335150014_R03C01


title: DNA-methylation array data_208285670157_R04C01

value: Diffuse leptomeningeal glioneuronal tumor


title: DNA-methylation array data_205862290132_R05C01


title: DNA-methylation array data_208197680102_R06C01


title: pectoralis-muscle_d21_rep2-1


title: tibiotarsus-growth-plate_d14_rep-2


title: DNA-methylation array data_208285670157_R08C01


title: DNA-methylation array data_206152230086_R02C01


title: DNA-methylation array data_208335150014_R05C01


title: DNA-methylation array data_208197680102_R08C01


title: pectoralis-muscle_d1_rep-2

description: Gene expression data from Gallus Gallus illium 4 weeks

source_name: pectoralis-muscle 1 days


title: pectoralis-muscle_d1_rep-4


title: DNA-methylation array data_205828600180_R01C01


title: lung_d42_rep-4

description: Gene expression data from Gallus Gallus duodenum 7 days

source_name: lung 42 days


title: pectoralis-muscle_d1_rep-3


title: pectoralis-muscle_d14_rep-4

source_name: pectoralis-muscle 14 days


title: pectoralis-muscle_d28_rep2-1


title: pectoralis-muscle_d1_rep-1


title: pectoralis-muscle_d14_rep-1


title: DNA-methylation array data_208335150014_R07C01


title: pectoralis-muscle_d14_rep-3


title: DNA-methylation array data_205873600125_R07C01


title: DNA-methylation array data_208197680102_R04C01

value: Spinal ependymoma


title: DNA-methylation array data_206419180175_R08C01


title: pectoralis-muscle_d28_rep2-2

value: male


title: pectoralis-muscle_d14_rep-2


title: DNA-methylation array data_208356110075_R02C01


title: lung_d35_rep-4

description: Gene expression data from Gallus Gallus duodenum 35 days

source_name: lung 35 days


title: lung_d42_rep-1


title: DNA-methylation array data_208356110075_R06C01

value: Male


title: DNA-methylation array data_208356110075_R07C01

value: Pituitary adenoma gonadotropin producing


title: DNA-methylation array data_207521860161_R08C01

value: Female


title: lung_d42_rep-3


title: DNA-methylation array data_205689140009_R01C01


title: lung_d42_rep-2


title: lung_d1_rep-3

description: Gene expression data from Gallus Gallus duodenum 28 days

source_name: lung 1 days


title: lung_d1_rep-4


title: lung_d35_rep-2


title: DNA-methylation array data_208356110093_R01C01


title: lung_d35_rep-3


title: lung_d1_rep-2

description: Gene expression data from Gallus Gallus duodenum 21 days


title: DNA-methylation array data_208356110075_R05C01


title: DNA-methylation array data_207521860168_R01C01


title: DNA-methylation array data_208369620071_R01C01


title: DNA-methylation array data_204808700038_R05C01


title: lung_d1_rep-1


title: DNA-methylation array data_208369620072_R04C01

value: Posterior fossa subependymoma


title: jejunum_d7_rep-2

description: Gene expression data from Gallus Gallus duodenum 14 days

source_name: jejunum 7 days


title: jejunum_d42_rep-3

source_name: jejunum 42 days


title: jejunum_d7_rep-1


title: DNA-methylation array data_205689140053_R03C01

source_name: tumor


title: jejunum_d7_rep-3


title: jejunum_d42_rep-2

description: Gene expression data from Gallus Gallus duodenum 0 days


title: jejunum_d35_rep-4

source_name: jejunum 35 days


title: jejunum_d7_rep-4


title: DNA-methylation array data_205041760051_R08C01


title: DNA-methylation array data_202060330063_R04C01


title: DNA-methylation array data_208369620073_R01C01


title: DNA-methylation array data_204674430013_R05C01


title: DNA-methylation array data_208369620071_R02C01


title: DNA-methylation array data_203866300034_R03C01


title: DNA-methylation array data_208369620096_R02C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: DNA-methylation array data_208369620072_R07C01


title: DNA-methylation array data_204229180151_R02C01


title: jejunum_d42_rep-4


title: DNA-methylation array data_208356130014_R01C01


title: DNA-methylation array data_203821710016_R08C01


title: DNA-methylation array data_202995850016_R07C01


title: DNA-methylation array data_208356130014_R03C01


title: lung_d35_rep-1


title: DNA-methylation array data_201532190146_R04C01


title: jejunum_d35_rep-3


title: jejunum_d42_rep-1


title: DNA-methylation array data_208356130014_R04C01


title: jejunum_d35_rep-2

description: Gene expression data from Gallus Gallus cerebral-cortex 7 days


title: jejunum_d1_rep-1

description: Gene expression data from Gallus Gallus cecal-epithelia 14 days

source_name: jejunum 1 days


title: jejunum_d35_rep-1


title: DNA-methylation array data_202995850016_R04C01


title: DNA-methylation array data_208356130014_R02C01


title: DNA-methylation array data_208356130054_R01C01

value: Pilocytic astrocytoma


title: jejunum_d1_rep-3


title: gastrocnemius-muscle_d28_rep-2

description: Gene expression data from Gallus Gallus pectoralis-muscle 7 days

source_name: gastrocnemius-muscle 28 days


title: DNA-methylation array data_205046550112_R01C01


title: jejunum_d1_rep-4


title: DNA-methylation array data_207899840027_R05C01

value: Subependymoma


title: jejunum_d1_rep-2


title: DNA-methylation array data_203810690039_R06C01

value: tumor


title: gastrocnemius-muscle_d28_rep-4


title: whole-intestine_d21_rep-3

description: Gene expression data from Gallus Gallus liver 7 days

source_name: whole-intestine 21 days


title: DNA-methylation array data_208160540161_R01C01


title: gastrocnemius-muscle_d28_rep-3


title: gastrocnemius-muscle_d21_rep-3

source_name: gastrocnemius-muscle 21 days


title: DNA-methylation array data_205041760067_R06C01


title: gastrocnemius-muscle_d28_rep-1


title: DNA-methylation array data_208197680087_R03C01

value: Supratentorial ependymoma, ZFTA fusion positive


title: gastrocnemius-muscle_d1_rep-4

description: Gene expression data from Gallus Gallus pectoralis-muscle 0 days

source_name: gastrocnemius-muscle 1 days


title: gastrocnemius-muscle_d21_rep-4


title: DNA-methylation array data_208004040066_R06C01


title: gastrocnemius-muscle_d21_rep-2


title: gastrocnemius-muscle_d1_rep-2

description: Gene expression data from Gallus Gallus brain 42 weeks


title: DNA-methylation array data_205689110081_R02C01


title: gastrocnemius-muscle_d1_rep-3


title: DNA-methylation array data_208069740057_R02C01

value: Schwannoma


title: DNA-methylation array data_206486300069_R01C01


title: gastrocnemius-muscle_d21_rep-1


title: gastrocnemius-muscle_d1_rep-1


title: DNA-methylation array data_202915420104_R05C01


title: duodenum_d49_rep-4

source_name: duodenum 49 days


title: duodenum_d42_rep-2

description: Gene expression data from Gallus Gallus brain 28 weeks

source_name: duodenum 42 days


title: DNA-methylation array data_205689110061_R03C01


title: duodenum_d49_rep-2

description: Gene expression data from Gallus Gallus brain 35 weeks


title: duodenum_d42_rep-3


title: duodenum_d42_rep-1


title: DNA-methylation array data_203866300119_R03C01


title: duodenum_d1_rep-3

source_name: duodenum 1 days


title: duodenum_d49_rep-3


title: DNA-methylation array data_208061540122_R02C01

value: Pituitary adenoma densely granulated GH/STH producing


title: DNA-methylation array data_207953350017_R07C01


title: DNA-methylation array data_204860510029_R08C01


title: duodenum_d1_rep-4


title: DNA-methylation array data_204930630066_R08C01


title: DNA-methylation array data_208004040066_R05C01


title: DNA-methylation array data_208356130015_R06C01


title: DNA-methylation array data_203867050020_R05C01


title: DNA-methylation array data_207953350017_R02C01


title: DNA-methylation array data_203163300093_R02C01


title: duodenum_d49_rep-1


title: duodenum_d1_rep-1

description: Gene expression data from Gallus Gallus brain 9 days


title: duodenum_d1_rep-2


title: DNA-methylation array data_208160540161_R07C01


title: DNA-methylation array data_203991470086_R07C01


title: DNA-methylation array data_205041760043_R07C01


title: brain_d7_rep2-4

source_name: brain 7 days


title: DNA-methylation array data_208066090054_R07C01


title: DNA-methylation array data_208061540122_R08C01


title: DNA-methylation array data_208066090054_R02C01


title: DNA-methylation array data_203866300017_R07C01


title: brain_d7_rep2-1

description: Gene expression data from Gallus Gallus brain 8 days


title: brain_d7_rep2-3


title: brain_d7_rep2-2


title: DNA-methylation array data_203020780132_R08C01


title: DNA-methylation array data_208197680089_R01C01


title: brain_d49_rep-4

source_name: brain 49 days


title: brain_d49_rep-1

description: Gene expression data from Gallus Gallus brain 7 days


title: duodenum_d42_rep-4


title: brain_d1_rep-1

description: Gene expression data from Gallus Gallus brain 21 days

source_name: brain 1 days


title: DNA-methylation array data_202760950086_R08C01


title: brain_d14_rep-4

source_name: brain 14 days


title: brain_d14_rep-2


title: brain_d49_rep-3


title: brain_d49_rep-2


title: DNA-methylation array data_207899840027_R06C01

value: Meningioma


title: brain_d1_rep-4


title: DNA-methylation array data_202060330099_R06C01

value: Astrocytoma, IDH-mutant


title: brain_d1_rep-3

value: female


title: abdominal-fat_d7_rep-3

description: Gene expression data from Gallus Gallus brain 0 days

source_name: abdominal-fat 7 days


title: brain_d1_rep-2


title: DNA-methylation array data_207899840103_R01C01


title: brain_d14_rep-1


title: abdominal-fat_d7_rep-2


title: brain_d14_rep-3


title: DNA-methylation array data_208160540161_R04C01

value: Atypical meningioma


title: DNA-methylation array data_203017150025_R04C01


title: abdominal-fat_d7_rep-4


title: DNA-methylation array data_208004040066_R07C01


title: abdominal-fat_d7_rep-1


title: DNA-methylation array data_205049770012_R07C01


title: DNA-methylation array data_207899840023_R01C01


title: DNA-methylation array data_202060330088_R06C01


title: DNA-methylation array data_204667550116_R05C01


title: abdominal-fat_d42_rep-4

description: Gene expression data from Gallus Gallus adipose 49 days

source_name: abdominal-fat 42 days


title: DNA-methylation array data_202790040014_R03C01


title: abdominal-fat_d35_rep-4

description: Gene expression data from Gallus Gallus adipose 21 days

source_name: abdominal-fat 35 days


title: abdominal-fat_d42_rep-3


title: abdominal-fat_d42_rep-2


title: DNA-methylation array data_208061540136_R05C01

source_name: tumor


title: DNA-methylation array data_203013220103_R05C01

value: Unknown


title: abdominal-fat_d35_rep-2

value: male


title: DNA-methylation array data_208061540122_R05C01

value: Male


title: abdominal-fat_d35_rep-3


title: abdominal-fat_d42_rep-1


title: abdominal-fat_d35_rep-1


title: DNA-methylation array data_203017150041_R01C01


title: DNA-methylation array data_203084910125_R06C01


title: DNA-methylation array data_208010440031_R05C01


title: abdominal-fat_d28_rep-3

description: Gene expression data from Gallus Gallus adipose 14 days

source_name: abdominal-fat 28 days


title: DNA-methylation array data_208197680089_R06C01


title: DNA-methylation array data_208160540161_R06C01


title: DNA-methylation array data_203249020122_R01C01


title: DNA-methylation array data_208271520042_R05C01


title: abdominal-fat_d28_rep-2


title: DNA-methylation array data_207899840103_R06C01


title: abdominal-fat_d1_rep-3

description: Gene expression data from Gallus Gallus abdominal-fat 10 days

source_name: abdominal-fat 1 days


title: abdominal-fat_d28_rep-1


title: abdominal-fat_d1_rep-4


title: DNA-methylation array data_203249020122_R02C01


title: abdominal-fat_d1_rep-1


title: abdominal-fat_d1_rep-2


title: tibiotarsus-growth-plate_d21_rep-4

description: Gene expression data from Gallus Gallus growth-plate 21 days

source_name: growth-plate 21 days


title: DNA-methylation array data_208160540161_R03C01


title: tibiotarsus-growth-plate_d21_rep-1


title: DNA-methylation array data_201532190165_R08C01


title: DNA-methylation array data_208066090083_R02C01


title: DNA-methylation array data_203084910151_R02C01


title: DNA-methylation array data_204957750066_R03C01


title: DNA-methylation array data_208069740055_R07C01


title: DNA-methylation array data_205107400134_R03C01


title: DNA-methylation array data_206486300166_R03C01


title: DNA-methylation array data_207899840023_R02C01


title: DNA-methylation array data_207953350017_R04C01


title: DNA-methylation array data_206486300125_R06C01


title: DNA-methylation array data_207521860054_R01C01


title: DNA-methylation array data_207953350102_R03C01

value: Glioblastoma, IDH-wildtype


title: DNA-methylation array data_206600570021_R03C01


title: testes_w17_rep-1

description: Gene expression data from Gallus Gallus testes 17 weeks

source_name: testes 17 weeks


title: DNA-methylation array data_208197680089_R02C01

value: Female


title: testes_w17_rep-3


title: tibiotarsus-growth-plate_d1_rep-3

description: Gene expression data from Gallus Gallus growth-plate 1 days

source_name: growth-plate 1 days


title: spleen_d28_rep-4

description: Gene expression data from Gallus Gallus spleen 28 days

source_name: spleen 28 days


title: abdominal-fat_d28_rep-4


title: spleen_d28_rep-3


title: tibiotarsus-growth-plate_d1_rep-2


title: spleen_d28_rep-2


title: DNA-methylation array data_208010440012_R04C01


title: testes_w17_rep-2


title: tibiotarsus-growth-plate_d1_rep-1


title: DNA-methylation array data_206486310004_R03C01


title: tibiotarsus-growth-plate_d21_rep-2


title: spleen_d21_rep-1

description: Gene expression data from Gallus Gallus spleen 21 days

source_name: spleen 21 days


title: DNA-methylation array data_208182410097_R05C01


title: retina_d9_rep-2

description: Gene expression data from Gallus Gallus retina 9 days

source_name: retina 9 days


title: retina_d9_rep-3


title: spleen_d28_rep-1


title: spleen_d21_rep-3


title: retina_d9_rep-4


title: DNA-methylation array data_206486300148_R01C01


title: DNA-methylation array data_206466470176_R04C01


title: retina_d9_rep-1


title: DNA-methylation array data_208061540136_R02C01


title: DNA-methylation array data_208069740057_R05C01


title: DNA-methylation array data_206359150189_R02C01


title: DNA-methylation array data_208069740057_R01C01


title: DNA-methylation array data_207355710054_R03C01


title: DNA-methylation array data_208356130015_R02C01


title: DNA-methylation array data_207521860168_R04C01


title: spleen_d21_rep-2


title: spleen_d21_rep-4


title: DNA-methylation array data_207899840023_R08C01

value: Ganglioglioma


title: DNA-methylation array data_206419180176_R02C01


title: DNA-methylation array data_208061540136_R07C01


title: retina_d35_rep-4

description: Gene expression data from Gallus Gallus retina 35 days

source_name: retina 35 days


title: retina_d35_rep-3


title: DNA-methylation array data_206503150049_R04C01


title: DNA-methylation array data_208234690118_R08C01

value: Diffuse paediatric-type high-grade glioma, H3-wildtype and IDH-wildtype


title: DNA-methylation array data_206486300107_R06C01


title: retina_d35_rep-2


title: retina_d28_rep-2

description: Gene expression data from Gallus Gallus retina 28 days

source_name: retina 28 days


title: retina_d28_rep-3


title: retina_d14_rep-4

description: Gene expression data from Gallus Gallus retina 14 days

source_name: retina 14 days


title: retina_d21_rep-1

description: Gene expression data from Gallus Gallus retina 21 days

source_name: retina 21 days


title: retina_d35_rep-1


title: retina_d21_rep-4


title: retina_d28_rep-1


title: DNA-methylation array data_208160540160_R04C01

value: Diffuse midline glioma, H3 K27-altered


title: DNA-methylation array data_205915530052_R02C01


title: retina_d28_rep-4


title: retina_d21_rep-3


title: DNA-methylation array data_208010440031_R02C01


title: DNA-methylation array data_205862290085_R08C01


title: DNA-methylation array data_207716530064_R01C01

value: Medulloblastoma, SHH-activated


title: DNA-methylation array data_205832320096_R01C01

value: tumor


title: retina_d21_rep-2


title: tibiotarsus-growth-plate_d1_rep-4


title: DNA-methylation array data_207716530065_R04C01


title: retina_d14_rep-3


title: DNA-methylation array data_206067100058_R01C01


title: retina_d14_rep-1


title: retina_d14_rep-2


title: pineal-gland_d7_rep-1

description: Gene expression data from Gallus Gallus pineal-gland 7 days

source_name: pineal-gland 7 days


title: pineal-gland_d7_rep-3


title: pineal-gland_d7_rep-2


title: pineal-gland_d21_rep-3

description: Gene expression data from Gallus Gallus pineal-gland 21 days

source_name: pineal-gland 21 days


title: DNA-methylation array data_207716530065_R01C01

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted


title: pineal-gland_d7_rep-4


title: DNA-methylation array data_206999330185_R02C01


title: DNA-methylation array data_205814880008_R05C01


title: DNA-methylation array data_207716530064_R05C01

value: CIC-rearranged sarcoma


title: pineal-gland_d21_rep-2


title: DNA-methylation array data_207716530064_R07C01

value: Posterior fossa group B (PFB) ependymoma


title: DNA-methylation array data_205828600030_R06C01


title: DNA-methylation array data_206503150048_R02C01


title: pineal-gland_d14_rep-4

description: Gene expression data from Gallus Gallus pineal-gland 14 days

source_name: pineal-gland 14 days


title: pineal-gland_d14_rep-1


title: DNA-methylation array data_207716530064_R03C01


title: pineal-gland_d21_rep-1


title: pineal-gland_d14_rep-3


title: pectoralis-muscle_d21_rep-4

description: Gene expression data from Gallus Gallus pectoralis-muscle 21 days

source_name: pectoralis-muscle 21 days


title: DNA-methylation array data_205617080146_R07C01

source_name: tumor


title: pineal-gland_d21_rep-4


title: DNA-methylation array data_207716530064_R06C01

value: Meningioma


title: DNA-methylation array data_205799780079_R07C01

value: Astrocytoma, IDH-mutant


title: pectoralis-muscle_d21_rep-3

value: female


title: DNA-methylation array data_207716530065_R03C01

value: Supratentorial ependymoma, ZFTA fusion-positive


title: DNA-methylation array data_205799780079_R05C01


title: Mouse pancreatic acinar cell line, DMSO, RNA-seq, rep 2

city: Knoxville

first: Conner

last: Hawkins

address: 309 Ken and Blaire Mossman Bldg.

department: BCMB

institute: University of Tennessee

description:
Library name: No_Ligand_2
NL2

data_processing:
Raw read fastq files were downloaded from the JP Sulzberger Columbia Genome Center and subsequently checked for quality of reads and presence of adaptor sequences through the Fastqc (version v0.12.1) tool. This was followed by the same trimming protocol as mentioned above. These reads were then aligned using HISAT2 (version 2.2.1) as it is better optimized for shorter read alignments and intron sensitivity. The mm10 genome index was downloaded directly from HISAT Download and reads were aligned pair-ended. The resulting sam file output was then converted to bam format via the view function in samtools (version 1.18) prior to being sorted and indexed with the sort and index functions respectively. These sorted files were then subjected to quantification of transcript abundance relating to coding regions through the counting tool HTSeq.
Assembly: mm10
Supplementary files format and content: CSV file of all the raw counts for the samples

growth_protocol: Grown in DMEM, 10% FBS, 1XPen/Strep, 37 Celsius, 5% CO2

extract_protocol:
Isolation and purification of RNA was performed following the Invitrogen TRIzol Reagent protocol for cells grown in a monolayer with 1 ml of TRIzol reagent utilized per sample with corresponding volumes of ensuing reagents
Library construction was done at the JP Sulzberger Columbia Genome Center

treatment_protocol: 24 hour incubtion in stripped DMEM media, 24 hour ligand incubation

tag: cell line

value: Mouse pancreatic acinar cell line

value: DMSO


title: DNA-methylation array data_207716530064_R08C01

tag: tumor type


title: DNA-methylation array data_206144080032_R02C01

value: Male

tag: beadchip name


title: Mouse pancreatic acinar cell line, DMSO, RNA-seq, rep 3

description:
Library name: No_Ligand_3
NL3


title: DNA-methylation array data_206065910157_R02C01

tag: age


title: pectoralis-muscle_d28_rep-6

value: male


title: pectoralis-muscle_d21_rep-1


title: Mouse pancreatic acinar cell line, DMSO, RNA-seq, rep 1

description:
Library name: No_Ligand_1
NL1


title: Mouse pancreatic acinar cell line, AM+CD, RNA-seq, rep 3

description:
Library name: AM+CD_3
C_A3

value: AM+CD


title: pectoralis-muscle_d28_rep-4


title: pineal-gland_d14_rep-2


title: DNA-methylation array data_202995850067_R07C01

tag: Sex


title: pectoralis-muscle_d28_rep-1


title: pectoralis-muscle_d21_rep-2


title: pectoralis-muscle_d28_rep-3


title: DNA-methylation array data_205460720143_R03C01


title: Mouse pancreatic acinar cell line, AM+CD, RNA-seq, rep 2

description:
Library name: AM+CD_2
C_A2

tag: cell type


title: ovary_y2_rep-3

description: Gene expression data from Gallus Gallus ovary 2 weeks

source_name: ovary 2 years


title: pectoralis-muscle_d28_rep-5


title: ovary_y2_rep-1


title: ovary_y2_rep-2


title: ovary_w17_rep-2

description: Gene expression data from Gallus Gallus ovary 17 weeks

source_name: ovary 17 weeks


title: ovarian-cortex_w16_rep-3

description: Gene expression data from Gallus Gallus ovarian-cortex 16 weeks

source_name: ovarian-cortex 16 weeks


title: Mouse pancreatic acinar cell line, AM+CD, RNA-seq, rep 1

description:
Library name: AM+CD_1
C_A1


title: pectoralis-muscle_d28_rep-2


title: DNA-methylation array data_204668820014_R04C01

value: Female


title: DNA-methylation array data_207513910035_R03C01


title: ovarian-cortex_w16_rep-1


title: oocytes_w21_rep-4

description: Gene expression data from Gallus Gallus oocytes 21 weeks

source_name: oocytes 21 weeks


title: DNA-methylation array data_202790040015_R02C01


title: Mouse pancreatic acinar cell line, CD3254, RNA-seq, rep 3

description:
Library name: CD3254_3
CD3


title: oocytes_w21_rep-3


title: Mouse pancreatic acinar cell line, CD3254, RNA-seq, rep 2

description:
Library name: CD3254_2
CD2


title: DNA-methylation array data_204316970009_R05C01


title: ovary_w17_rep-1


title: Mouse pancreatic acinar cell line, CD3254, RNA-seq, rep 1

description:
Library name: CD3254_1
CD1


title: DNA-methylation array data_204237150113_R04C01


title: ovarian-cortex_w16_rep-2


title: DNA-methylation array data_204229180134_R02C01


title: Mouse pancreatic acinar cell line, AM580, RNA-seq, rep 2

description:
Library name: AM580_2
AM2


title: Mouse pancreatic acinar cell line, AM580, RNA-seq, rep 3

description:
Library name: AM580_3
AM3


title: Mouse pancreatic acinar cell line, AM580, RNA-seq, rep 1

description:
Library name: AM580_1
AM1