title: P1_PA4_P2633_N704.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S518-NX-xt

tag: cell type

value: Smart-seq2; full-length RNA-seq


title: Hu5 [snRNA-seq]

status: Public on Nov 16 2021

type: SRA

city: Seattle

first: David

last: Beier

state: WA

address: 1900 9th Avenue

department: CDBRM

country: USA

institute: Seattle Children's Research Institute

library_source: transcriptomic

data_processing:
Cell Ranger (for snRNA-seq experiments) or Cell Ranger ATAC (for snATAC-seq experiments) was used to demultiplex input files and generate feature-barcode matrices, which were then further analyzed via Seurat (RNA) or ArchR (ATAC). Specific details including software versions and parameters are described in Thomas, et al bioRxiv 2021.07.31.454254.
Genome_build: hg38
Supplementary_files_format_and_content: .tsv; fragment/feature/barcode matrices for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Adult human retina

growth_protocol: Human induced pluripotent stem cells (hiPSCs) and Retinal Organoids were generated according to Olemacher et al., (2015) doi:10.1002/9780470151808.sc01h08s32 ; Gantner et al., (2020) doi:10.1056/NEJMoa1815111

extract_protocol:
Nuclear isolation from flash frozen tissue described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254
10X Genomics scATAC-Seq and scRNA-Seq protocols. Detail described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254
single-nucleus (sn)ATAC-Seq and snRNA-Seq

treatment_protocol: Enhancer knockout iPSCs generated as described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254

tag: donor apparent sex

value: Male

tag: donor age

value: 54 years

tag: donor apparent race

value: unknown

tag: postmortem interval

tag: molecule subtype

value: single nucleus RNA

tag: library type

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: 25-shEGR2 #38_9 PALM  #3

type: RNA

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

description: Neural fraction cells from strom derived from shEGR2_38.9 orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

label: biotin

organism: Mus musculus

source_name: shEGR2_38.9 / SCC25 oral carcinoma cell line / PA-rich diet

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Cells were grown in an orthotopic xenograft model in NOD-SCIDγ mice (NSG)

extract_protocol: RNA was isolated using magnetic beads. Library preparation and amplification were performed as described by Gonzalez et al., 2010.

tag: sample id

tag: scan batch

tag: diet

value: PA-rich diet

tag: sh

tag: cell line

value: SCC25 oral carcinoma cell line


title: 25-shEGR2 #38_9 PALM  #2


title: 25-shEGR2 #38_9 PALM  #1


title: NckL_male_15wk_pathogenicCD4_rep5

city: Dallas

first: Eva Marie

last: Moresco

state: TX

address: 5323 Harry Hines Boulevard

department: Center for the Genetics of Host Defense

institute: University of Texas Southwestern Medical Center

description: Gene expression in male NOD/NckL mouse spleen CD4+CD25- T cells recovered at 15 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).

hyb_protocol: Sample hydridization (Agilent whole mouse genome oligo microarrays) was performed by Miltenyi Biotech (Cologne, Germany).

scan_protocol: Microarray probe fluorescence signals produced by the Agilent Feature Extraction (AFE) image analysis software were converted to expression values using Bioconductor Agi4x44PreProcess package with a custom annotation package. All the steps were performed by Miltenyi Biotech (Cologne, Germany).

source_name: Pathogenic Cd4

label_protocol: Preparation of RNA, amplification of RNA, sample labeling, sample hydridization (Agilent whole mouse genome oligo microarrays) scanning and data acquisition were performed by Miltenyi Biotech (Cologne, Germany).

growth_protocol: Not applicable

extract_protocol: Cell and islet pellets and tissues were lysed using SuperAmpTMlysis buffer (Miltenyi Biotech, Waldbronn, Germany) and stored at -80°C until all samples were collected. RNA quality and purity were assessed on the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Islets of Langerhans: NOD/NckH and NOD/NckL male mice pancreata were perfused with a solution of collagenase P (0.6 mg/mL; Roche), dissected free from surrounding tissues and then digested at 37°C for 13 minutes. After extensive washes, islets were purified by hand-picking. NOD/NckH and NOD/NckL male mice spleen CD4+CD25- T cells recovered at 6 and 15 weeks of age. This population was depleted of regulatory T cells (CD4+CD25+FoxP3+) as previously described (You S, Belghith M, Cobbold S, Alyanakian MA, Gouarin C, Barriot S, et al. Autoimmune diabetes onset results from qualitative rather than quantitative age-dependent changes in pathogenic T-cells. Diabetes 2005; 54:1415-1422)

tag: strain

value: NOD/NckL

tag: age

value: 15 weeks

tag: Sex


title: 18wk/d132 [snRNA-seq]

source_name: Developing human retina

value: 132 days


title: 16wk/d113 [snRNA-seq]

value: Female

value: 113 days


title: NckL_male_15wk_pathogenicCD4_rep4

data_processing: Microarray probe fluorescence signals produced by the Agilent Feature Extraction (AFE) image analysis software were converted to expression values using Bioconductor Agi4x44PreProcess package with a custom annotation package. All the steps were performed by Miltenyi Biotech (Cologne, Germany).


title: P1_PA4_P2633_N704.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S517-NX-xt

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Human:  GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

growth_protocol: SCC-25 (ATCCR CRL-168TM) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

extract_protocol:
Live SCC-25 sorted cells were lysed using lysis buffer (0.2% Triton-100, 1U/ul RNase inhibitor). Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Libraries were prepared according to the Nextera XT (Illumina) instructions.

treatment_protocol: Cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for sorting of live SCC-25 cells into 96 well sorting plates.

value: oral squamous cell carcinoma (OSCC) cell line

tag: shRNA

value: control pLKO.1

tag: protocol


title: P1_PA4_P2633_N704.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S516-NX-xt

tag: cell type


title: 25-shEGR2 #38_9 CT  #2

description: Neural fraction cells from strom derived from shEGR2_38.9 orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: shEGR2_38.9 / SCC25 oral carcinoma cell line / control diet

value: control diet


title: 11wk/d78 [snRNA-seq]

tag: donor apparent sex

value: 78 days


title: 10wk/d74 [snRNA-seq]

tag: donor age

value: 74 days


title: P1_PA4_P2633_N704.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S513-NX-xt

value: Smart-seq2; full-length RNA-seq


title: P1_PA4_P2633_N704.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S515-NX-xt


title: 25-shEGR2 #38_9 CT  #3


title: 25-shEGR2 #38_9 CT  #1


title: NckL_male_15wk_pathogenicCD4_rep2

value: Male


title: NckL_male_15wk_pathogenicCD4_rep3


title: 7wk/d53 [snRNA-seq]

value: 53 days

tag: donor apparent race

value: unknown


title: P1_UN4_P2633_N703.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S521-NX-xt


title: Hu7 [snATAC-seq]

library_source: genomic

molecule: genomic DNA

value: 50 years

value: black

tag: postmortem interval

value: single nucleus ATAC

value: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1


title: 25-shEGR2 #40_9 PALM #2

description: Neural fraction cells from strom derived from shEGR2_40.9 orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: shEGR2_40.9 / SCC25 oral carcinoma cell line / PA-rich diet

value: PA-rich diet

value: SCC25 oral carcinoma cell line


title: 25-shEGR2 #40_9 PALM #3


title: NckL_male_6wk_pathogenicCD4_rep2

description: Gene expression in male NOD/NckL mouse spleen CD4+CD25- T cells recovered at 6 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).

value: NOD/NckL

value: 6 weeks


title: 25-shEGR2 #40_9 PALM #1


title: NckL_male_6wk_pathogenicCD4_rep5


title: NckL_male_6wk_pathogenicCD4_rep4


title: P1_UN4_P2633_N703.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S520-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line


title: NckL_male_6wk_pathogenicCD4_rep3


title: NckL_male_15wk_pathogenicCD4_rep1

value: 15 weeks


title: 8wk/d59 [snRNA-seq]

value: 59 days

tag: molecule subtype

value: single nucleus RNA

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: 25-shEGR2 #40_9 CT #3

description: Neural fraction cells from strom derived from shEGR2_40.9 orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: shEGR2_40.9 / SCC25 oral carcinoma cell line / control diet

value: control diet


title: 25-shEGR2 #40_9 CT #1


title: 25-shEGR2 #40_9 CT #2


title: P1_UN4_P2633_N703.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S518-NX-xt

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: P1_UN4_P2633_N703.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S522-NX-xt


title: P1_UN4_P2633_N703.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S517-NX-xt


title: 18wk/d132 [snATAC-seq]

value: Male

value: 132 days

value: unknown

tag: library type


title: P1_UN4_P2633_N703.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S516-NX-xt


title: 25-PLKO PALM #3

description: Neural fraction cells from strom derived from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: PLKO / SCC25 oral carcinoma cell line / PA-rich diet

tag: sample id

value: PLKO


title: 11wk/d78 [snATAC-seq]

value: 78 days

value: single nucleus ATAC

value: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1


title: 16wk/d113 [snATAC-seq]

value: Female

value: 113 days


title: Hu5 [snATAC-seq]

value: 54 years


title: P1_UN4_P2633_N703.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S515-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line


title: NckH_Islets_3wk_rep5

description: Gene expression in islets from 3-week-old NOD/NckH male mice

source_name: Islets

value: NOD/NckH

value: 3 weeks


title: NckH_Islets_3wk_rep3


title: NckH_Islets_3wk_rep2


title: 25-PLKO PALM #2

tag: scan batch

value: PA-rich diet

value: SCC25 oral carcinoma cell line


title: NckH_Islets_3wk_rep4


title: NckL_male_6wk_pathogenicCD4_rep1

value: NOD/NckL

value: 6 weeks


title: P1_UN4_P2633_N703.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N703-S513-NX-xt

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: P1_UN4_P2633_N702.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S522-NX-xt


title: 25-PLKO PALM #1

tag: diet


title: 8wk/d59 [snATAC-seq]

value: Male

value: 59 days

value: unknown


title: P1_UN4_P2633_N702.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S521-NX-xt


title: 25-PLKO CT #3

description: Neural fraction cells from strom derived from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: PLKO / SCC25 oral carcinoma cell line / control diet

value: control diet

tag: sh

value: PLKO


title: 7wk/d53 [snATAC-seq]

value: Female

value: 53 days

value: single nucleus ATAC

value: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1


title: P1_UN4_P2633_N702.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S518-NX-xt

tag: cell line

value: oral squamous cell carcinoma (OSCC) cell line


title: 25-PLKO CT #2


title: NckH_Islets_3wk_rep1

tag: strain

value: NOD/NckH

value: 3 weeks


title: NckL_Islets_3wk_rep5

description: Gene expression in islets from 3-week-old NOD/NckL male mice

tag: age


title: P1_UN4_P2633_N702.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S517-NX-xt


title: NckL_Islets_3wk_rep4

tag: Sex


title: 15-shCD36  PALM_Neu nb.1

description: Neural fraction cells from strom derived from shCD36 orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: shCD36 / VDH15 oral carcinoma cell line / PA-rich diet

tag: hybridization batch

tag: biological replicate

tag: technical replicate

value: PA-rich diet

value: VDH15 oral carcinoma cell line


title: 15-shCD36 PALM_Neu nb.3


title: 25-PLKO CT #1

value: SCC25 oral carcinoma cell line


title: ANP32E_CUTnTag_MCF7

city: Rochester

first: Garrett

last: Ruff

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Library strategy: CUT&Tag
aligned to Hg38 genome witih bowtie2 (v2.2.5) and samtools (v1.9) used to generate bam file
duplicates removed from bam file with Picard MarkDuplicates (v2.5.0)
bigWig generated with Deeptools bamCoverage (v3.5.1) with RPKM normalization, binsize 10
Genome_build: Hg38
Supplementary_files_format_and_content: bigWig file of CUT&Tag reads

source_name: MCF7 cells

extract_protocol: isolated nuclei were used in CUT&Tag assay following methods described in Kaya-Okur et al. (2019) paper, "CUT&Tag for efficient epigenomic profiling of small samples and single cells

treatment_protocol: untreated

tag: cut&tag antibody

value: ANP32E (Thermo PA5-42860)

tag: treatment

value: untreated


title: NckL_Islets_3wk_rep3

value: NOD/NckL

value: Male


title: NckL_Islets_3wk_rep2


title: 15-shCD36  PALM_Neu nb.2


title: P1_UN4_P2633_N702.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S516-NX-xt

tag: cell type

tag: shRNA

value: control pLKO.1

tag: protocol

value: Smart-seq2; full-length RNA-seq


title: P1_UN4_P2633_N702.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S515-NX-xt


title: P1_UN4_P2633_N702.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S513-NX-xt


title: P1_UN4_P2633_N701.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S521-NX-xt


title: P1_UN4_P2633_N701.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S522-NX-xt


title: 15-shCD36  CT_Neu nb.3

description: Neural fraction cells from strom derived from shCD36 orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: shCD36 / VDH15 oral carcinoma cell line / control diet

value: control diet


title: NckL_Islets_3wk_rep1


title: A375 shCtrl rep2

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
Raw fastq files were trimmed by trim-galore to remove adapters and low-quality bases
Trimed reads were aligned to hg38 by Hisat2
Read counts were summaried by StringTie2

source_name: A375 cell

growth_protocol: DMEM medium containing with 10% FBS, 1% L-glutamine (200 mM) and 1% penicillin/streptomycin.

extract_protocol:
The cells were collected and and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor cell line A375

tag: morphology

value: epithelial

tag: genotype

value: wild type


title: A375 shCCDC50 rep2

value: CCDC50 knock-down


title: Mutu RAD21 ChIP

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

description: Immunoprecipitated DNA by RAD21, olpaprib treated

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605) using bowtie2.
Peak calling was performed using MACS2 with the broadPeaks option and input DNA used as a reference set.
Integrative Genomics Viewer was used for data visualization.
Genome_build: EBV
Supplementary_files_format_and_content: The result peaks are in broadPeak files, which are in the BED6+3 format. The columns are chromosome, start of peak, end of peak, name of peak, integer score for display, fold-change at peak summit, -log10pvalue at peak summit and -log10qvalue at peak summit.

organism: human gammaherpesvirus 4

source_name: LCL

growth_protocol: LCL and MUTU cells were cultured in RPMI medium with 15% fetal bovine serum. Cells were treated with or without 2.5 uM olaparib for 72 hours

extract_protocol:
The de-crosslinked DNA was purified with Zymo Spin I columns and eluted twice with 25 μL of 10 mM Tris-HCl (pH. 7.5)
12 ng of Immunoprecipitated DNA was ligated to adapter primers using the TruSeq ChIP Library Preparation Kit (Illumina)

treatment_protocol: Chromatin immunoprecipitation with next generation sequencing (ChIP-seq) was performed as described: 2.5×107 cells were crosslinked with 1% formaldehyde for 10 min and chromatin was sonicated with a Qsonica sonicator. 1/10 of the sonicated chromatin was collected and used as input material while the rest of the chromatin was immunoprecipitated using 5 µg of RAD21 antibody. DNA fragments of ∼150–300 bp were visualized by agarose gel purification. Immunoprecipitated DNA was ligated to adapter primers using the TruSeq ChIP Library Preparation Kit (Illumina) and then sequenced using the Illumina HiSeq 2500 platform according to the manufacturer’s recommendations (Illumina) at the Fox Chase Cancer Center Sequencing Facility. For both untreated and olaparib-treated cells, ~15 ng of RAD21 immunoprecipitated or input DNA were recovered from each biological replicate, while ~15 ng of RAD21 immunoprecipitated DNA were recovered after pooling two biological replicates.

value: B-cells

tag: antibody

tag: agent

value: olpaprib


title: A375 shCtrl rep1


title: P1_UN4_P2633_N701.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S520-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line


title: A375 shCCDC50 rep1


title: Mutu RAD21 ChIP olaparib treated

description: Immunoprecipitated DNA by RAD21


title: 15-PLKO PALM_Neu nb.2

description: Neural fraction cells from strom derived from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: PLKO / VDH15 oral carcinoma cell line / PA-rich diet

tag: sample id

tag: scan batch

tag: diet

value: PA-rich diet

value: PLKO


title: 15-PLKO PALM_Neu nb.3

tag: cell line

value: VDH15 oral carcinoma cell line


title: 15-shCD36  CT_Neu nb.1


title: P1_UN4_P2633_N701.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S518-NX-xt


title: P1_UN4_P2633_N701.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S516-NX-xt


title: Mutu input olaparib treated

description: DNA input olaparib treated

value: DNA input

value: olaparib


title: 15-PLKO PALM_Neu nb.1


title: 15-shCD36 CT_Neu nb.2


title: 15-PLKO CT_Neu nb.3

description: Neural fraction cells from strom derived from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: PLKO / VDH15 oral carcinoma cell line / control diet


title: Mutu input

description: DNA input


title: P1_UN4_P2633_N701.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S515-NX-xt


title: LCL RAD21 ChIP olaparib treated

description: Immunoprecipitated DNA by RAD21


title: P1_UN4_P2633_N701.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S513-NX-xt


title: 15-PLKO CT_Neu nb.2


title: 15-PLKO CT_Neu nb.1


title: 30-shCD36 PALM_Neu nb.2

description: Neural fraction cells from strom derived from shCD36 orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

source_name: shCD36 / SCC25 oral carcinoma cell line / PA-rich diet

value: SCC25 oral carcinoma cell line


title: P1_UN4_P2633_N701.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N701-S517-NX-xt


title: 29-shCD36 PALM_Neu nb.1


title: LCL input

description: DNA input


title: LCL input olaparib treated

description: DNA input olaparib treated


title: 31-shCD36 PALM_Neu nb.3


title: 26-shCD36 CT_Neu nb.2

description: Neural fraction cells from strom derived from shCD36 orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: shCD36 / SCC25 oral carcinoma cell line / control diet


title: 27-shCD36 CT_Neu nb.3


title: LCL RAD21 ChIP


title: R-gly-3, replicate 1

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

country: France

institute: INSA

description:
ribodepleted RNA
Ion004_RGly_3_1

data_processing:
Basecalling with IonTorrent Suite software v5.0.4
reads were aligned with IonTorrent Suite Software v5.0.4 (Tmap from Thermofisher)
reads count with htseq-count (v 0.9.1) (option -f bam –stranded=yes  -t gene -m intersection-nonempty -a 0)
Stastitical analysis was made with R and the package edgeR, the data were log2 transformed and normalized with RLE and Bonferroni  correction for the differential analysis between samples (adjusted pvalue  <1%).
Genome_build: E coli BW25113 (CP009273.1)
Supplementary_files_format_and_content: tab-delimited text files include raw reads count values for each Sample and matrix of normalized data

organism: Escherichia coli

source_name: Culture in fed-batch bioreactor

growth_protocol: Growth in a 2 L-bioreactor in fed-batch mode, M9 medium with glucose, 37 C and pH 6.8

extract_protocol:
Ribodepletion and sequencing (200pb oriented single end) with the Ion 540 kit on the Ion S5 using the Ion 540 chip
Oriented RNA-seq

treatment_protocol: 500 μL of the culture broth was placed in 500 μL of phenol/ethanol (5:95 v/v), then mixed by inverting the tube and kept at -80°C until further use

tag: strain

value: R-gly

tag: time point (h)


title: R-gly-4, replicate 1

description:
ribodepleted RNA
Ion001_RGly_4_1


title: R-gly-4, replicate 3

description:
ribodepleted RNA
Ion009_RGly_4_3


title: R-gly-3, replicate 3

description:
ribodepleted RNA
Ion002_RGly_3_3


title: R-gly-4, replicate 2

description:
ribodepleted RNA
Ion015_RGly_4_2


title: R-gly-3, replicate 2

description:
ribodepleted RNA
Ion003_RGly_3_2


title: R-gly-2, replicate 1

description:
ribodepleted RNA
Ion007_RGly_2_1


title: 23-PLKO PALM_Neu nb.3

description: Neural fraction cells from strom derived from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

tag: hybridization batch

tag: biological replicate


title: R-gly-1, replicate 3

description:
ribodepleted RNA
Ion008_RGly_1_3


title: 18-PLKO CT_Neu nb.2

description: Neural fraction cells from strom derived from PLKO orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

tag: technical replicate


title: 22-PLKO PALM_Neu nb.2


title: 21-PLKO PALM_Neu nb.1


title: R-gly-1, replicate 2

description:
ribodepleted RNA
Ion009_RGly_1_2


title: 25-shCD36 CT_Neu nb.1


title: 17-PLKO CT_Neu nb.1


title: OL-Neu3

description: Neural fraction cells from strom derived from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to OA-rich diet

source_name: PLKO / VDH15 oral carcinoma cell line / OA-rich diet

value: OA-rich diet


title: OL-Neu2


title: OL-Neu4


title: HeLa transfection rep2 sRNA batch 2

city: Solna

first: Wenjing

last: Kang

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
Hela_R2_transfection_CRG_1006.sRNA

data_processing:
Basecalls were performed using bcl2fastq v2.17.1 with the option --barcode-mismatches 0
The small RNA sequencing data were quality control (QC) checked using miRTrace v 1.0.1 qc mode. Human (miRTrace option -s hsa) databases were used as references for HEK-293T and HeLa samples and mouse (-s mmu) databases were used as references for NIH-3T3 and MEF samples. Illumina 3’ adapter sequence TGGAATTCT was provided for 3’ adapter trimming.
For MapToCleave data, The QC qualified reads of each sample were then aligned to the prepared reference sequences, which contained the sequences from the MapToCleave library and the endogenous human (for HEK-293T and HeLa sample) or mouse (for NIH-3T3 and MEF sample) miRNA hairpin sequences that are excluded from the MapToCleave library but are included in miRbase v 21. The alignment was performed using bowtie v 1.1.2 without allowing mismatches (-v 0). The reads that were uniquely mapped to the forward strand of the reference sequences were considered for the hairpin expression measurement.
For validation data, the QC qualified reads were used to quantify expression of the human miRNA hairpins and the modified hairpins (see Supplementary Data 10 of the linked publication) using miRDeep2 v 2.0.0.8 quantifier.pl with allowing 0 mismatches (-g 0) and allowing multi-mapping. The human miRNA hairpin sequences downloaded from miRBase v21 and the modified hairpin sequences were used as the precursor reference (-p). The corresponding human miRNA sequences from miRBase v21 and the manually curated miRNA sequences of the modified hairpins (see Supplementary Data 10 of the linked publication) are used as the mature reference (-m). The hairpin sequence counts are measured by summing up the number of small RNA reads that mapped to an interval 2 nucleotides upstream and 5 nucleotides downstream of the 5p or/and 3p miRNA sequence from the hairpin.
Supplementary_files_format_and_content: tab-delimited text file includes raw counts of MapToCleave sequences for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes raw counts and normalized counts of the modified hairpins and the endogenous human miRNA hairpins for each sample.

organism:
Homo sapiens
synthetic construct

source_name: HeLa transfected cells

extract_protocol:
For MapToCleave samples, total RNA and DNA were isolated using TRIzol reagent (Ambion). For validation samples, total RNA was extracted using a Zymo quick-RNA microprep kit (Zymo Research).
For MapToCleave samples, 1 ug of HEK-293T total RNA was used for standard small RNA library preparation using TruSeq small RNA kit v2 (Illumina). 1 ug of NIH-3T3 total RNA was used for preparation of small RNA libraries. 30 ng of the total RNA extracted from FACS-isolated MEF cells were used for preparation of small RNA libraries. The small RNA cDNA libraries were PCR-amplified in 15 cycles; the 75-bp single-end sequencing was carried out on a NextSeq500 (Illumina). DNA libraries were prepared in two steps: i) the DNA isolated from the HEK-293T and NIH-3T3 transfected cells was pre-amplified using custom primers compatible with Illumina TruSeq adapter sequences, ii) pre-amplified DNA fragments were multiplexed by PCR using Illumina TruSeq universal forward and single-indexed reverse PCR primers. The DNA libraries were resolved on a 6% Novex TBE gel (Invitrogen), and the 280 – 300 bp fraction was isolated. The 150-bp single-end sequencing was carried out using Illumina NextSeq500. For validation samples, RNA libraries were prepared using TruSeq small RNA kit v2 (Illumina).

value: HeLa

tag: treatment

value: MapToCleave library


title: W-gly-2, replicate 3

description:
ribodepleted RNA
Ion011_WGly_2_3

value: W-gly


title: W-gly-2, replicate 2

description:
ribodepleted RNA
Ion012_WGly_2_2


title: HeLa transfection rep1 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
Hela_R1_transfection_CRG_1005.sRNA

tag: cell type


title: W-gly-2, replicate 1

description:
ribodepleted RNA
Ion013_WGly_2_1


title: R-gly-2, replicate 2

description:
ribodepleted RNA
Ion006_RGly_2_2


title: R-gly-1, replicate 1

description:
ribodepleted RNA
Ion010_RGly_1_1


title: P1_UN4_P2633_N702.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N702-S520-NX-xt

tag: shRNA

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: HEK-293T transfection rep2 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R2_transfection_CRG_1002.sRNA

source_name: HEK-293T transfected cells


title: W-gly-1, replicate 2

description:
ribodepleted RNA
Ion015_WGly_1_2


title: W-gly-1, replicate 1

description:
ribodepleted RNA
Ion016_WGly_1_1


title: 19-PLKO CT_Neu nb.3

value: control diet


title: HEK-293T transfection rep1 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R1_transfection_CRG_1001.sRNA


title: 10wk/d74 [snATAC-seq]

source_name: Developing human retina

tag: donor apparent sex

value: Male

tag: donor age

value: 74 days

tag: donor apparent race

value: unknown

tag: postmortem interval

tag: molecule subtype

value: single nucleus ATAC

tag: library type

value: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1


title: W-gly-1, replicate 3

description:
ribodepleted RNA
Ion014_WGly_1_3

tag: genotype


title: PLM-Neu2

description: Neural fraction cells from strom derived from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to PA-rich diet

tag: sample id

tag: scan batch

tag: diet

value: PA-rich diet

value: PLKO

value: VDH15 oral carcinoma cell line


title: PLM-Neu1

tag: cell line


title: PLM-Neu4

tag: hybridization batch


title: CT-Neu4

tag: biological replicate


title: control RNAi day 9 replicate 2

status: Public on Nov 15 2021

first: George

last: Wendt

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

description: Whole adult male parasite

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Schistosoma mansoni genome (v7) using STAR (version 020201).
Pairwise comparisons of differential gene expression were performed with DESeq2 (version 1.12.2).
Genome_build: Schistosoma mansoni v7
Supplementary_files_format_and_content: Smftz-f1_RNAi_RNAseq.csv: Comma-separated values file containing analysis of data generated from three replicates of control RNAi samples and 3 replicates of Smftz-f1 RNAi samples. Statistical significance determined by the Wald test in DESeq2 (version 1.12.2).
Supplementary_files_format_and_content: ALL_Days.xlsx: Excel file containing differential gene expression.

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: adult male parasites

extract_protocol:
Parasites were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Library Prep (Cat# 20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Puerto Rico

tag: Sex

tag: tissue

value: Whole body

tag: age

value: 6 weeks + 9 days culture

tag: RNAi

value: Control


title: Smftz-f1 RNAi day 9 replicate 1

description: Whole adult male parasite


title: control RNAi day 9 replicate 3

description: Whole adult male parasite


title: PLM-Neu3

tag: technical replicate


title: CT-Neu3


title: Smftz-f1 RNAi day 9 replicate 3

description: Whole adult male parasite


title: Smftz-f1 RNAi day 9 replicate 2

description: Whole adult male parasite


title: CT-Neu2


title: Smftz-f1 RNAi day 5 replicate 1

description: Whole adult male parasite

value: 6 weeks + 5 days culture


title: Smftz-f1 RNAi day 5 replicate 2

description: Whole adult male parasite


title: Smftz-f1 RNAi day 5 replicate 3

description: Whole adult male parasite


title: CT-Neu1


title: control RNAi day 5 replicate 2

description: Whole adult male parasite


title: 98_H209_M/M-51

city: Charlottesville

first: Kwon

last: Park

state: VA

address: 1340 Jefferson Park Ave., Pinn Hall 7039

department: Microbiology, Immunology, & Cancer Biology

institute: University of Virginia School of Medicine

data_processing:
First, the sequencing quality was evaluated by FastQC v0.11.8. Second, the adaptor sequences were trimmed by Trimmomatic v0.39. Third, the trimmed raw data was mapped to the human reference genome (hh19) by BBMap v38.61. Fourth, the number of fragments that overlaps each gene was assessed by STAR v2.5. Fifth, the TPM (transcripts per million) data was generated by RSEM v1.3.1.
Genome_build: hg19
Supplementary_files_format_and_content: TPM of genes or isoforms

source_name: Small-cell lung cancer cells; infected with lentiviral transgene expressing M/M-51 upon doxycyline treatment

growth_protocol: Cells were maintained in RPMI1640 plus 10% bovine growth serum and 1% Pen-Strep and at 5% CO2 and 37 Celcius degree

extract_protocol:
RNeasy kit (Qiagen) was used to extract total RNAs from cells.
Oligo dT-purified mRNA from 500ng of total RNA was used to generate the sequencing libraries using the NEBNext Ultra RNA library preparation kit (New England Biolabs)

treatment_protocol: The cells that express peptides designated as M/M-WT and M/M-51 were treated with doxycycline (1ug/mL) for 48 hours before harvest for RNA extraction

tag: cell type

value: SCLC line

tag: transfected with

value: lentiviral transgene expressing M/M-51


title: 76_H209_M/M-51


title: 96_H209_M/M-WT

source_name: Small-cell lung cancer cells; infected with lentiviral transgene expressing M/M-WT upon doxycyline treatment

value: lentiviral transgene expressing M/M-WT


title: 95_H209_M/M-WT


title: 94_H524_M/M-51


title: control RNAi day 5 replicate 1

description: Whole adult male parasite


title: 74_H524_M/M-51


title: 92_H524_M/M-WT


title: 93_H524_M/M-51


title: 91_H524_M/M-WT


title: 97_H209_M/M-51


title: bovine Line 6 p17

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description:
Cow_EDSC_raw_counts.txt
bovine Line 6 p17

data_processing:
Trim-Galore!
STAR
FeatureCounts
Supplementary_files_format_and_content: raw counts text file

organism: Bos taurus

growth_protocol: EDSCs were cultured in AFX medium on Laminin/Fibronectin coated dish.

extract_protocol:
Cells were lysed in Trizol and total RNAs are prepared by PureLink RNA Mini Kit
Libraries were prepared by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: EDSCs

tag: passage


title: bovine Line 13 p17

description:
Cow_EDSC_raw_counts.txt
bovine Line 13 p17


title: bovine Line 16 p17

description:
Cow_EDSC_raw_counts.txt
bovine Line 16 p17


title: bovine Line 13 p16

description:
Cow_EDSC_raw_counts.txt
bovine Line 13 p16


title: bovine Line 6 p14

description:
Cow_EDSC_raw_counts.txt
bovine Line 6 p14


title: bovine Line 16 p16

description:
Cow_EDSC_raw_counts.txt
bovine Line 16 p16


title: control RNAi day 5 replicate 3

description: Whole adult male parasite

value: Male


title: bovine Line 13 p19

description:
Cow_EDSC_raw_counts.txt
bovine Line 13 p19


title: 73_H524_M/M-WT


title: ATCC 17978 OXA-23 overexp rep 1

city: Decatur

first: Philip

middle: N

last: Rather

state: Georgia

address: 1670 Clairmont Rd, Room 5A-183

department: Microbiology & Immunology

institute: Emory University

data_processing:
Basecalling performed by Genewiz
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ATCC17978-mmf whole genome using bowtie v2.4.2
Differential gene expression was quantified using DESeq2 v2.11.40.6
Genome_build: ATCC17978-mmf (CP012004.1)
Supplementary_files_format_and_content: normalized abundance measurements
Supplementary_files_format_and_content: raw gene counts

organism: Acinetobacter baumannii

source_name: Bacterial cells

growth_protocol: Glycerol stock used to inoculated 2 ml fresh LB media in 5 ml culture tube.  Grown shaking at 37 degrees Celcius to optical density of 0.8.

extract_protocol:
Bacterial cells were pelleted and flash frozen on dry ice. Pellets were shipped to Genewiz for RNA extraction, Illumina Ribo-Zero rRNA removal, Illumina library construction, and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Final concentration of 2 mM IPTG added to culture at OD600 of 0.05

tag: treatment

value: Treated with 2 mM IPTG for 2 hours


title: ATCC 17978 WT rep 3

tag: genotype

value: wildtype

value: Untreated


title: ATCC 17978 OXA-23 overexp rep 2


title: ATCC 17978 WT rep 2


title: ATCC 17978 WT rep 1


title: bovine Line 16 p15

description:
Cow_EDSC_raw_counts.txt
bovine Line 16 p15


title: ATCC 17978 OXA-23 overexp rep 3


title: bovine Line 6 p16

description:
Cow_EDSC_raw_counts.txt
bovine Line 6 p16


title: GR iKO_PBS Replicate 4

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Colon from PBS injected ADX GR iKO mice

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Mouse Genome Microarray 4x44K following the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent, version 12.0.0.7) using default parameters (protocol GE1_1200_Jun14 and Grid: 014868_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. The log2-transformed Processed Signal intensities were imported to Partek Genomics Suite (version 6.6) for quantile normalization and subsequent analysis.

source_name: ADX GR iKO control, colon

label_protocol: Sample labeling was performed based on the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: Mice were maintained on normal chow diet

extract_protocol: TRIzol reagent, followed by RNA clean up using the Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: 6-8 week old Flox and GR iKO male mice were ADX for 2 weeks, then injected with 1 mg/Kg DEX. Colon tissues were harvested 6 hours after the injection.

tag: gender

value: male

value: 8-10 weeks

value: colon

value: chow diet


title: GR iKO_DEX Replicate 2

description: Colon from DEX injected ADX GR iKO mice

source_name: ADX GR iKO DEX, colon


title: GR iKO_PBS Replicate 2

description: Colon from PBS injected ADX GR iKO mice


title: NT0203T

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

data_processing:
Clean raw reads were mapped to the reference human genome (hg19) by using STAR with default parameters.
The alignment BAM files were splitted into forward and reverse strands based on SAM flags.
The BAM files were then visualized in IGV.
Quantified gene expression or other output files were not generated.
Genome_build: hg19

source_name: Clinical sample

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Directional mRNA library preparation (rRNA removal)
strand-specific RNA-Seq

value: Hepatocellular cancer

tag: pair

value: Pair 5, HCC


title: NT0410T

value: Pair 6, HCC


title: NT10T

value: Pair 2, HCC


title: NT11N

value: Liver normal adjacent tissue

value: Pair 3, normal adjacent


title: NT10N

value: Pair 2, normal adjacent


title: NT0410N

value: Pair 6, normal adjacent


title: NT0203N

value: Pair 5, normal adjacent


title: NT08N

value: Pair 1, normal adjacent


title: GR iKO_DEX Replicate 3

description: Colon from DEX injected ADX GR iKO mice

tag: diet


title: GR iKO_DEX Replicate 4

description: Colon from DEX injected ADX GR iKO mice


title: GR iKO_PBS Replicate 3

description: Colon from PBS injected ADX GR iKO mice


title: hiPSC_Mut_RNA-Seq_Rep3

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Alignment (CUT&RUN, MapR): Bowtie2
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization. Normalized MapR bigwigs were generated by subtracting MapR-GST-MNase tracks from MapR tracks using deepTools bigwigCompare.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C. Human induced pluripotent stem cell lines were grown on Geltrex (ThermoFisher A1413302) coated plates in Essential 8 media (Gibco A1517001).

extract_protocol:
CUT&RUN for CTCF, ADNP, and HA was performed on cells as previously described (Skene and Henikoff, eLife 2017).
R-loop containing DNA was collected using MapR protocol as previously described (Yan et al., Cell Reports 2019).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

tag: protocol

value: RNA-Seq


title: GR iKO_DEX Replicate 1

description: Colon from DEX injected ADX GR iKO mice


title: Flox_PBS Replicate 3

description: Colon from PBS injected ADX Flox mice

source_name: ADX Flox PBS, colon


title: Flox_DEX Replicate 4

description: Colon from DEX injected ADX Flox mice

source_name: ADX Flox DEX, colon


title: Flox_PBS Replicate 4

description: Colon from PBS injected ADX Flox mice


title: Flox_PBS Replicate 2

description: Colon from PBS injected ADX Flox mice


title: Flox_DEX Replicate 1

description: Colon from DEX injected ADX Flox mice


title: Flox_PBS Replicate 1

description: Colon from PBS injected ADX Flox mice


title: Flox_DEX Replicate 2

description: Colon from DEX injected ADX Flox mice


title: NT08T

value: Pair 1, HCC


title: control RNAi day 9 replicate 1

description: Whole adult male parasite

value: Puerto Rico

value: Male

value: Whole body

value: 6 weeks + 9 days culture

value: Control


title: NT0011T

value: Hepatocellular cancer

value: Pair 4, HCC


title: NT11T

value: Pair 3, HCC


title: NT0011N

value: Pair 4, normal adjacent


title: hiPSC_WT_RNA-Seq_Rep3

value: Wildtype


title: hiPSC_Mut_MapR_GST-MNase_Rep2

data_processing:
Alignment (CUT&RUN, MapR)
Bowtie2
Alignment (RNA-Seq)
STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization. Normalized MapR bigwigs were generated by subtracting MapR-GST-MNase tracks from MapR tracks using deepTools bigwigCompare.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

value: MapR

tag: fusion protein

value: GST-MNase


title: hiPSC_Mut_MapR_Rep2

value: GST-RHΔ-Mnase


title: hiPSC_Mut_RNA-Seq_Rep1


title: hiPSC_Mut_MapR_GST-MNase_Rep1


title: hiPSC_Mut_RNA-Seq_Rep2


title: hiPSC_Mut_MapR_Rep1


title: hiPSC_Mut_CTCF_Rep1

value: CUT&RUN

tag: antibody

value: CTCF


title: hiPSC_WT_MapR_GST-MNase_Rep2


title: hiPSC_Mut_CTCF_Rep2


title: hiPSC_WT_RNA-Seq_Rep2

value: RNA-Seq


title: hiPSC_WT_MapR_Rep2


title: hiPSC_WT_MapR_GST-MNase_Rep1


title: hiPSC_WT_MapR_Rep1


title: R-gly-2, replicate 3

description:
ribodepleted RNA
Ion005_RGly_2_3

tag: strain

value: R-gly

tag: time point (h)


title: hiPSC_WT_CTCF_Rep1


title: hiPSC_WT_ADNP

value: ADNP


title: hiPSC_WT_RNA-Seq_Rep1


title: hiPSC_WT_CTCF_Rep2


title: 66_2020_9_E15_iXEN

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Single-cell data were demultiplexed using bcl2fastq2 v2.20.
raw reads were pseudoaligned using Kallisto with default settings (v0.44.0)78. Based on the pseudo alignment estimated by Kallisto
reads mapped to each transcript against the mouse transcriptome GRCm38, Gencode vM16 primary assembly
Normalization using Seurat
Genome_build: transcriptome GRCm38, Gencode vM16
Supplementary_files_format_and_content: tab separated txt files; containing raw seurat input matrices

source_name: mESC

extract_protocol:
Rosette-to-Lumen stage embryoids and 2D mono-culturestem cells were harvested by washing with PBS and incubation in StemPro Accutase Cell Dissociation Reagent to create a single-cell solution
Cells lysed in Guanidine Hydrochloride (50 mM), dNTPs (17.4mM), 2.2µM SMART dT30VN primer lysis buffer
Nextera XT DNA Library Preparation Kit (Illumina)
NextSeq500 system SR 75bp with 2*8bp index reads

treatment_protocol: Cell lines with doxycycline-inducible transgenes were incubated with 2 µg/ml doxycycline

value: iXEN


title: 66_2020_9_E19_iXEN


title: 66_2020_9_E16_iXEN


title: 66_2020_9_E23_iXEN


title: 66_2020_9_E24_iXEN


title: 66_2020_9_E22_iXEN


title: 66_2020_9_E21_iXEN


title: 66_2020_9_E17_iXEN


title: 66_2020_9_E1_iXEN


title: 66_2020_9_E13_iXEN


title: 66_2020_9_E12_iXEN


title: 66_2020_9_E20_iXEN


title: 66_2020_9_E14_iXEN


title: 66_2020_9_E10_iXEN


title: 66_2020_9_D8_iXEN


title: 66_2020_9_D7_iXEN


title: 66_2020_9_E18_iXEN


title: 66_2020_9_E2_iXEN


title: 66_2020_9_D4_iXEN


title: 66_2020_9_D3_iXEN


title: 66_2020_9_D5_iXEN


title: 66_2020_9_D23_iXEN


title: 66_2020_9_D24_iXEN


title: 66_2020_9_D22_iXEN


title: 66_2020_9_D21_iXEN


title: OL-Neu1

data_processing: RMA normalization method as implemented in affy Bioconductor R package

tag: sample id

tag: hybridization batch

tag: scan batch

tag: biological replicate

value: OA-rich diet

value: PLKO

tag: cell line

value: VDH15 oral carcinoma cell line


title: 66_2020_9_D9_iXEN

tag: cell type


title: 66_2020_9_D20_iXEN


title: 66_2020_9_D2_iXEN


title: 66_2020_9_D6_iXEN


title: 66_2020_9_D17_iXEN


title: 66_2020_9_D19_iXEN


title: 66_2020_9_C6_iXEN


title: 66_2020_9_D11_iXEN


title: 66_2020_9_C8_iXEN


title: 66_2020_9_C23_iXEN


title: 66_2020_9_D12_iXEN


title: 66_2020_9_D10_iXEN


title: 66_2020_9_C7_iXEN


title: 66_2020_9_D16_iXEN


title: 66_2020_9_D18_iXEN


title: 66_2020_9_C5_iXEN


title: 66_2020_9_C9_iXEN


title: 66_2020_9_C4_iXEN


title: 66_2020_9_D15_iXEN


title: 66_2020_9_C21_iXEN


title: 66_2020_9_D14_iXEN


title: 66_2020_9_D13_iXEN


title: 66_2020_9_C24_iXEN


title: 66_2020_9_C22_iXEN


title: 66_2020_9_C20_iXEN


title: 66_2020_9_C2_iXEN


title: 66_2020_9_C19_iXEN


title: 66_2020_9_C18_iXEN


title: 66_2020_9_C16_iXEN


title: 66_2020_9_C3_iXEN


title: 66_2020_9_C13_iXEN


title: 66_2020_9_C14_iXEN


title: 66_2020_9_C15_iXEN


title: 66_2020_9_C12_iXEN


title: 66_2020_9_C10_iXEN


title: 66_2020_9_C1_iXEN


title: 66_2020_9_B3_iXEN


title: 66_2020_9_B6_iXEN


title: 66_2020_9_B5_iXEN


title: 66_2020_9_B8_iXEN


title: 66_2020_9_B2_iXEN


title: 66_2020_9_D1_iXEN


title: 66_2020_9_B23_iXEN


title: 66_2020_9_B19_iXEN


title: 66_2020_9_B7_iXEN


title: 66_2020_9_B4_iXEN


title: 66_2020_9_B17_iXEN


title: 66_2020_9_B20_iXEN


title: 66_2020_9_B24_iXEN


title: 66_2020_9_B21_iXEN


title: 66_2020_9_B22_iXEN


title: 66_2020_9_B15_iXEN


title: 66_2020_9_B16_iXEN


title: 66_2020_9_B14_iXEN


title: 66_2020_9_B13_iXEN


title: 66_2020_9_B11_iXEN


title: 66_2020_9_B10_iXEN


title: 66_2020_9_B9_iXEN


title: 66_2020_9_C11_iXEN


title: 66_2020_9_B12_iXEN


title: 66_2020_9_A9_iXEN


title: 66_2020_9_A7_iXEN


title: 66_2020_9_A6_iXEN


title: 66_2020_9_A4_iXEN


title: 66_2020_9_A24_iXEN


title: 66_2020_9_A3_iXEN


title: 66_2020_9_A5_iXEN


title: 66_2020_9_B1_iXEN


title: 66_2020_9_A8_iXEN


title: 66_2020_9_E11_iXEN


title: 66_2020_9_A17_iXEN


title: 66_2020_9_A20_iXEN


title: 66_2020_9_A14_iXEN


title: 66_2020_9_A19_iXEN


title: 66_2020_9_A2_iXEN


title: 66_2020_9_A15_iXEN


title: 66_2020_9_A18_iXEN


title: 66_2020_9_A16_iXEN


title: 66_2020_9_A21_iXEN


title: 66_2020_9_A10_iXEN


title: 65_2020_8_P14_iTSCs

value: iTSCs


title: 65_2020_8_P6_iTSCs


title: 65_2020_8_P12_iTSCs


title: 65_2020_8_P18_iTSCs


title: 66_2020_9_A11_iXEN


title: 65_2020_8_P16_iTSCs


title: 65_2020_8_P2_iTSCs


title: 65_2020_8_P4_iTSCs


title: 65_2020_8_P24_iTSCs


title: 66_2020_9_A1_iXEN


title: 65_2020_8_P22_iTSCs


title: 65_2020_8_P8_iTSCs


title: 65_2020_8_P20_iTSCs


title: 66_2020_9_A12_iXEN


title: 65_2020_8_P10_iTSCs


title: 66_2020_9_A22_iXEN


title: 65_2020_8_O6_iTSCs


title: 65_2020_8_O8_iTSCs


title: 65_2020_8_O20_iTSCs


title: 65_2020_8_O4_iTSCs


title: 65_2020_8_O22_iTSCs


title: 65_2020_8_O24_iTSCs


title: 65_2020_8_O2_iTSCs


title: 65_2020_8_O18_iTSCs


title: 65_2020_8_O16_iTSCs


title: 65_2020_8_O12_iTSCs


title: 65_2020_8_O10_iTSCs


title: 65_2020_8_N6_iTSCs


title: 65_2020_8_N23_iTSCs


title: 65_2020_8_N4_iTSCs


title: 65_2020_8_N20_iTSCs


title: 65_2020_8_N19_iTSCs


title: 65_2020_8_N2_iTSCs


title: 65_2020_8_N21_iTSCs


title: 65_2020_8_N22_iTSCs


title: 65_2020_8_N7_iTSCs


title: 65_2020_8_N9_iTSCs


title: 65_2020_8_N8_iTSCs


title: 65_2020_8_N24_iTSCs


title: 65_2020_8_N18_iTSCs


title: 65_2020_8_N17_iTSCs


title: 65_2020_8_N16_iTSCs


title: 65_2020_8_O14_iTSCs


title: 65_2020_8_N12_iTSCs


title: 65_2020_8_N13_iTSCs


title: 65_2020_8_N14_iTSCs


title: 65_2020_8_N15_iTSCs


title: 65_2020_8_N3_iTSCs


title: 65_2020_8_N10_iTSCs


title: 65_2020_8_N1_iTSCs


title: 65_2020_8_M8_iTSCs


title: 65_2020_8_M7_iTSCs


title: 66_2020_9_A23_iXEN


title: 65_2020_8_M4_iTSCs


title: 65_2020_8_M3_iTSCs


title: 65_2020_8_M22_iTSCs


title: 65_2020_8_M19_iTSCs


title: 65_2020_8_M20_iTSCs


title: 65_2020_8_M2_iTSCs


title: 65_2020_8_M21_iTSCs


title: 65_2020_8_M23_iTSCs


title: 65_2020_8_M6_iTSCs


title: 65_2020_8_M5_iTSCs


title: 65_2020_8_M18_iTSCs


title: 65_2020_8_M24_iTSCs


title: 65_2020_8_M14_iTSCs


title: 65_2020_8_M15_iTSCs


title: 65_2020_8_M13_iTSCs


title: 65_2020_8_L21_iTSCs


title: 65_2020_8_M10_iTSCs


title: 65_2020_8_M11_iTSCs


title: 65_2020_8_M1_iTSCs


title: 65_2020_8_K24_iTSCs


title: 66_2020_9_C17_iXEN


title: 66_2020_9_B18_iXEN


title: 65_2020_8_L18_iTSCs


title: 65_2020_8_L24_iTSCs


title: 66_2020_9_A13_iXEN


title: 65_2020_8_K20_iTSCs


title: 65_2020_8_M17_iTSCs


title: 65_2020_8_M12_iTSCs


title: 65_2020_8_M16_iTSCs


title: 65_2020_8_J4_iTSCs


title: 65_2020_8_J20_iTSCs


title: 65_2020_8_J7_iTSCs


title: 65_2020_8_J2_iTSCs


title: 65_2020_8_J22_iTSCs


title: 65_2020_8_J19_iTSCs


title: 65_2020_8_J14_iTSCs


title: 65_2020_8_J18_iTSCs


title: 65_2020_8_I9_iTSCs


title: 65_2020_8_J24_iTSCs


title: 65_2020_8_J8_iTSCs


title: 65_2020_8_J6_iTSCs


title: 65_2020_8_I8_iTSCs


title: 65_2020_8_I14_iTSCs


title: 65_2020_8_I16_iTSCs


title: 65_2020_8_H9_iTSCs


title: 65_2020_8_I12_iTSCs


title: 65_2020_8_I2_iTSCs


title: 65_2020_8_I24_iTSCs


title: 65_2020_8_I20_iTSCs


title: 65_2020_8_J12_iTSCs


title: 65_2020_8_I18_iTSCs


title: 65_2020_8_I4_iTSCs


title: 65_2020_8_I23_iTSCs


title: 65_2020_8_I6_iTSCs


title: 65_2020_8_I10_iTSCs


title: 65_2020_8_H7_iTSCs


title: 65_2020_8_H5_iTSCs


title: 65_2020_8_H6_iTSCs


title: 65_2020_8_H21_iTSCs


title: 65_2020_8_H3_iTSCs


title: 65_2020_8_H4_iTSCs


title: 65_2020_8_J10_iTSCs


title: 65_2020_8_H20_iTSCs


title: 65_2020_8_H2_iTSCs


title: 65_2020_8_I22_iTSCs


title: 65_2020_8_H19_iTSCs


title: 65_2020_8_H23_iTSCs


title: 65_2020_8_H24_iTSCs


title: 65_2020_8_H13_iTSCs


title: 65_2020_8_H14_iTSCs


title: 65_2020_8_H22_iTSCs


title: 65_2020_8_G6_iTSCs


title: 65_2020_8_H17_iTSCs


title: 65_2020_8_G24_iTSCs


title: 65_2020_8_H12_iTSCs


title: 65_2020_8_H10_iTSCs


title: 65_2020_8_G5_iTSCs


title: 65_2020_8_H15_iTSCs


title: 65_2020_8_G19_iTSCs


title: 65_2020_8_G23_iTSCs


title: 65_2020_8_G21_iTSCs


title: 65_2020_8_G8_iTSCs


title: 65_2020_8_G15_iTSCs


title: 65_2020_8_G3_iTSCs


title: 65_2020_8_G18_iTSCs


title: 65_2020_8_G17_iTSCs


title: 65_2020_8_G7_iTSCs


title: 65_2020_8_G14_iTSCs


title: 65_2020_8_G22_iTSCs


title: 65_2020_8_F9_iTSCs


title: 65_2020_8_F8_iTSCs


title: 65_2020_8_G11_iTSCs


title: 65_2020_8_J16_iTSCs


title: 65_2020_8_H1_iTSCs


title: 65_2020_8_G2_iTSCs


title: 65_2020_8_F7_iTSCs


title: 65_2020_8_F5_iTSCs


title: 65_2020_8_F21_iTSCs


title: 65_2020_8_F20_iTSCs


title: 65_2020_8_F3_iTSCs


title: 65_2020_8_F14_iTSCs


title: 65_2020_8_F6_iTSCs


title: 65_2020_8_F22_iTSCs


title: 65_2020_8_F11_iTSCs


title: 65_2020_8_F2_iTSCs


title: 65_2020_8_F17_iTSCs


title: 65_2020_8_F19_iTSCs


title: 65_2020_8_G20_iTSCs


title: 65_2020_8_F16_iTSCs


title: 65_2020_8_F23_iTSCs


title: 65_2020_8_F24_iTSCs


title: 65_2020_8_E8_iTSCs


title: 65_2020_8_E4_iTSCs


title: 65_2020_8_F15_iTSCs


title: 65_2020_8_E3_iTSCs


title: 65_2020_8_F18_iTSCs


title: 65_2020_8_F13_iTSCs


title: 65_2020_8_F12_iTSCs


title: 65_2020_8_F10_iTSCs


title: 65_2020_8_E19_iTSCs


title: 65_2020_8_F4_iTSCs


title: 65_2020_8_E18_iTSCs


title: 65_2020_8_E9_iTSCs


title: 65_2020_8_E23_iTSCs


title: 65_2020_8_E24_iTSCs


title: 65_2020_8_E7_iTSCs


title: 65_2020_8_E5_iTSCs


title: 65_2020_8_E6_iTSCs


title: 65_2020_8_E21_iTSCs


title: 65_2020_8_E13_iTSCs


title: 65_2020_8_F1_iTSCs


title: 65_2020_8_E1_iTSCs


title: 65_2020_8_E20_iTSCs


title: 65_2020_8_E2_iTSCs


title: 65_2020_8_D7_iTSCs


title: 65_2020_8_E17_iTSCs


title: 65_2020_8_E16_iTSCs


title: 65_2020_8_E10_iTSCs


title: 65_2020_8_E15_iTSCs


title: 65_2020_8_E14_iTSCs


title: 65_2020_8_E12_iTSCs


title: 65_2020_8_D9_iTSCs


title: 65_2020_8_D20_iTSCs


title: 65_2020_8_D4_iTSCs


title: 65_2020_8_E22_iTSCs


title: 65_2020_8_D6_iTSCs


title: 65_2020_8_D17_iTSCs


title: 65_2020_8_D2_iTSCs


title: 65_2020_8_D18_iTSCs


title: 65_2020_8_D3_iTSCs


title: 65_2020_8_D21_iTSCs


title: 65_2020_8_D24_iTSCs


title: 65_2020_8_D19_iTSCs


title: 65_2020_8_E11_iTSCs


title: 65_2020_8_D13_iTSCs


title: 65_2020_8_D16_iTSCs


title: 65_2020_8_D12_iTSCs


title: 65_2020_8_D5_iTSCs


title: 65_2020_8_D23_iTSCs


title: 65_2020_8_D10_iTSCs


title: 65_2020_8_D1_iTSCs


title: 65_2020_8_D11_iTSCs


title: 65_2020_8_D15_iTSCs


title: 65_2020_8_C8_iTSCs


title: 65_2020_8_C9_iTSCs


title: 65_2020_8_C6_iTSCs


title: 65_2020_8_C5_iTSCs


title: 65_2020_8_D14_iTSCs


title: 65_2020_8_D22_iTSCs


title: 65_2020_8_C4_iTSCs


title: 65_2020_8_D8_iTSCs


title: 65_2020_8_C3_iTSCs


title: 65_2020_8_C24_iTSCs


title: 65_2020_8_C23_iTSCs


title: 65_2020_8_C21_iTSCs


title: 65_2020_8_C22_iTSCs


title: 65_2020_8_C20_iTSCs


title: 65_2020_8_C18_iTSCs


title: 65_2020_8_C19_iTSCs


title: 65_2020_8_C17_iTSCs


title: 65_2020_8_C14_iTSCs


title: 65_2020_8_C13_iTSCs


title: 65_2020_8_C7_iTSCs


title: 65_2020_8_C15_iTSCs


title: 65_2020_8_C16_iTSCs


title: 65_2020_8_C11_iTSCs


title: 65_2020_8_C12_iTSCs


title: 65_2020_8_C10_iTSCs


title: 65_2020_8_B9_iTSCs


title: 65_2020_8_B6_iTSCs


title: 65_2020_8_B8_iTSCs


title: 65_2020_8_B5_iTSCs


title: 65_2020_8_B7_iTSCs


title: 65_2020_8_B4_iTSCs


title: 65_2020_8_B3_iTSCs


title: 65_2020_8_B23_iTSCs


title: 65_2020_8_B24_iTSCs


title: 65_2020_8_B22_iTSCs


title: 65_2020_8_B20_iTSCs


title: 65_2020_8_B21_iTSCs


title: 65_2020_8_C2_iTSCs


title: 65_2020_8_B2_iTSCs


title: 65_2020_8_B18_iTSCs


title: 65_2020_8_B17_iTSCs


title: 65_2020_8_B19_iTSCs


title: 65_2020_8_B16_iTSCs


title: 65_2020_8_B13_iTSCs


title: 65_2020_8_B14_iTSCs


title: 65_2020_8_C1_iTSCs


title: 65_2020_8_B12_iTSCs


title: 65_2020_8_B15_iTSCs


title: 65_2020_8_B10_iTSCs


title: 65_2020_8_A8_iTSCs


title: 65_2020_8_A9_iTSCs


title: 65_2020_8_A7_iTSCs


title: 65_2020_8_A6_iTSCs


title: 65_2020_8_A4_iTSCs


title: 65_2020_8_A24_iTSCs


title: 65_2020_8_A22_iTSCs


title: 65_2020_8_A23_iTSCs


title: 65_2020_8_A21_iTSCs


title: 65_2020_8_A3_iTSCs


title: 65_2020_8_A18_iTSCs


title: 65_2020_8_A19_iTSCs


title: 65_2020_8_A2_iTSCs


title: 65_2020_8_A20_iTSCs


title: 65_2020_8_A17_iTSCs


title: 65_2020_8_A16_iTSCs


title: 65_2020_8_A13_iTSCs


title: 65_2020_8_A11_iTSCs


title: 65_2020_8_B1_iTSCs


title: 65_2020_8_A10_iTSCs


title: 65_2020_8_B11_iTSCs


title: 65_2020_8_A12_iTSCs


title: 64_2020_7_P6_2i/LIF_ESC


title: 64_2020_7_P8_2i/LIF_ESC


title: 64_2020_7_P5_2i/LIF_ESC


title: 64_2020_7_P24_2i/LIF_ESC


title: 65_2020_8_A1_iTSCs


title: 64_2020_7_P22_2i/LIF_ESC


title: 64_2020_7_P20_2i/LIF_ESC


title: 64_2020_7_P4_2i/LIF_ESC


title: 65_2020_8_A5_iTSCs


title: 64_2020_7_P16_2i/LIF_ESC


title: 64_2020_7_P23_2i/LIF_ESC


title: 64_2020_7_P2_2i/LIF_ESC


title: 65_2020_8_A15_iTSCs


title: 65_2020_8_A14_iTSCs


title: 64_2020_7_P14_2i/LIF_ESC


title: 64_2020_7_P10_2i/LIF_ESC


title: 64_2020_7_P1_2i/LIF_ESC


title: 64_2020_7_P12_2i/LIF_ESC


title: 64_2020_7_O3_2i/LIF_ESC


title: 64_2020_7_O4_2i/LIF_ESC


title: 64_2020_7_O6_2i/LIF_ESC


title: 64_2020_7_O24_2i/LIF_ESC


title: 64_2020_7_O22_2i/LIF_ESC


title: 64_2020_7_O8_2i/LIF_ESC


title: 64_2020_7_O20_2i/LIF_ESC


title: 64_2020_7_O16_2i/LIF_ESC


title: 64_2020_7_O18_2i/LIF_ESC


title: 64_2020_7_O21_2i/LIF_ESC


title: 64_2020_7_O2_2i/LIF_ESC


title: 64_2020_7_O14_2i/LIF_ESC


title: 64_2020_7_O10_2i/LIF_ESC


title: 64_2020_7_P18_2i/LIF_ESC


title: 64_2020_7_O12_2i/LIF_ESC


title: 64_2020_7_N9_2i/LIF_ESC


title: 64_2020_7_N8_2i/LIF_ESC


title: 64_2020_7_N7_2i/LIF_ESC


title: 64_2020_7_N6_2i/LIF_ESC


title: 64_2020_7_N4_2i/LIF_ESC


title: 64_2020_7_N5_2i/LIF_ESC


title: 64_2020_7_O15_2i/LIF_ESC


title: 64_2020_7_N3_2i/LIF_ESC


title: 64_2020_7_N23_2i/LIF_ESC


title: 64_2020_7_N22_2i/LIF_ESC


title: 64_2020_7_N20_2i/LIF_ESC


title: 64_2020_7_N24_2i/LIF_ESC


title: 64_2020_7_N18_2i/LIF_ESC


title: 64_2020_7_N17_2i/LIF_ESC


title: 64_2020_7_N15_2i/LIF_ESC


title: 64_2020_7_N12_2i/LIF_ESC


title: 64_2020_7_N14_2i/LIF_ESC


title: 64_2020_7_N11_2i/LIF_ESC


title: 64_2020_7_N16_2i/LIF_ESC


title: 64_2020_7_N21_2i/LIF_ESC


title: 64_2020_7_M8_2i/LIF_ESC


title: 64_2020_7_M9_2i/LIF_ESC


title: 64_2020_7_N10_2i/LIF_ESC


title: 64_2020_7_N1_2i/LIF_ESC


title: 64_2020_7_M7_2i/LIF_ESC


title: 64_2020_7_M6_2i/LIF_ESC


title: 64_2020_7_M5_2i/LIF_ESC


title: 64_2020_7_M22_2i/LIF_ESC


title: 64_2020_7_M23_2i/LIF_ESC


title: 64_2020_7_M24_2i/LIF_ESC


title: 64_2020_7_M4_2i/LIF_ESC


title: 64_2020_7_M20_2i/LIF_ESC


title: 64_2020_7_M2_2i/LIF_ESC


title: 64_2020_7_M19_2i/LIF_ESC


title: 64_2020_7_N2_2i/LIF_ESC


title: 64_2020_7_M18_2i/LIF_ESC


title: 64_2020_7_M16_2i/LIF_ESC


title: 64_2020_7_M17_2i/LIF_ESC


title: 64_2020_7_M14_2i/LIF_ESC


title: 64_2020_7_M13_2i/LIF_ESC


title: 64_2020_7_M12_2i/LIF_ESC


title: 64_2020_7_M11_2i/LIF_ESC


title: 64_2020_7_M1_2i/LIF_ESC


title: 64_2020_7_M10_2i/LIF_ESC


title: 64_2020_7_L8_2i/LIF_ESC


title: 64_2020_7_M15_2i/LIF_ESC


title: 64_2020_7_L7_2i/LIF_ESC


title: 64_2020_7_M3_2i/LIF_ESC


title: 64_2020_7_L6_2i/LIF_ESC


title: 64_2020_7_L22_2i/LIF_ESC


title: 64_2020_7_L23_2i/LIF_ESC


title: 64_2020_7_L18_2i/LIF_ESC


title: 64_2020_7_L12_2i/LIF_ESC


title: 64_2020_7_L10_2i/LIF_ESC


title: 64_2020_7_K2_2i/LIF_ESC


title: 64_2020_7_M21_2i/LIF_ESC


title: 64_2020_7_L11_2i/LIF_ESC


title: 64_2020_7_K21_2i/LIF_ESC


title: 64_2020_7_K22_2i/LIF_ESC


title: 64_2020_7_K4_2i/LIF_ESC


title: 64_2020_7_J8_2i/LIF_ESC


title: 64_2020_7_K10_2i/LIF_ESC


title: 64_2020_7_K12_2i/LIF_ESC


title: 64_2020_7_J7_2i/LIF_ESC


title: 64_2020_7_J6_2i/LIF_ESC


title: 64_2020_7_J4_2i/LIF_ESC


title: 64_2020_7_J24_2i/LIF_ESC


title: 64_2020_7_J20_2i/LIF_ESC


title: 64_2020_7_J2_2i/LIF_ESC


title: 64_2020_7_J14_2i/LIF_ESC


title: 64_2020_7_J22_2i/LIF_ESC


title: 64_2020_7_J18_2i/LIF_ESC


title: 64_2020_7_J16_2i/LIF_ESC


title: 64_2020_7_J12_2i/LIF_ESC


title: 64_2020_7_J15_2i/LIF_ESC


title: 64_2020_7_J10_2i/LIF_ESC


title: 64_2020_7_I8_2i/LIF_ESC


title: 64_2020_7_I6_2i/LIF_ESC


title: 64_2020_7_I7_2i/LIF_ESC


title: 64_2020_7_I5_2i/LIF_ESC


title: 64_2020_7_I24_2i/LIF_ESC


title: 64_2020_7_I4_2i/LIF_ESC


title: 64_2020_7_I3_2i/LIF_ESC


title: 64_2020_7_I2_2i/LIF_ESC


title: 64_2020_7_I20_2i/LIF_ESC


title: 64_2020_7_I18_2i/LIF_ESC


title: 64_2020_7_I19_2i/LIF_ESC


title: 64_2020_7_I13_2i/LIF_ESC


title: 64_2020_7_I17_2i/LIF_ESC


title: 64_2020_7_I14_2i/LIF_ESC


title: 64_2020_7_I12_2i/LIF_ESC


title: 64_2020_7_I10_2i/LIF_ESC


title: 64_2020_7_H7_2i/LIF_ESC


title: 64_2020_7_I1_2i/LIF_ESC


title: 64_2020_7_H9_2i/LIF_ESC


title: 64_2020_7_H6_2i/LIF_ESC


title: 64_2020_7_H5_2i/LIF_ESC


title: 64_2020_7_H4_2i/LIF_ESC


title: 64_2020_7_I22_2i/LIF_ESC


title: 64_2020_7_I16_2i/LIF_ESC


title: 64_2020_7_H24_2i/LIF_ESC


title: 64_2020_7_H23_2i/LIF_ESC


title: 64_2020_7_I15_2i/LIF_ESC


title: 64_2020_7_H22_2i/LIF_ESC


title: 64_2020_7_H16_2i/LIF_ESC


title: 64_2020_7_H21_2i/LIF_ESC


title: 64_2020_7_H19_2i/LIF_ESC


title: 64_2020_7_H17_2i/LIF_ESC


title: 64_2020_7_H18_2i/LIF_ESC


title: 64_2020_7_H15_2i/LIF_ESC


title: 64_2020_7_I11_2i/LIF_ESC


title: 64_2020_7_H10_2i/LIF_ESC


title: 64_2020_7_G9_2i/LIF_ESC


title: 64_2020_7_H11_2i/LIF_ESC


title: 64_2020_7_G8_2i/LIF_ESC


title: 64_2020_7_H13_2i/LIF_ESC


title: 64_2020_7_H3_2i/LIF_ESC


title: 64_2020_7_G6_2i/LIF_ESC


title: 64_2020_7_G4_2i/LIF_ESC


title: 64_2020_7_G7_2i/LIF_ESC


title: 64_2020_7_H1_2i/LIF_ESC


title: 64_2020_7_N19_2i/LIF_ESC


title: 64_2020_7_G5_2i/LIF_ESC


title: 64_2020_7_G24_2i/LIF_ESC


title: 64_2020_7_H20_2i/LIF_ESC


title: 64_2020_7_G23_2i/LIF_ESC


title: 64_2020_7_H2_2i/LIF_ESC


title: 64_2020_7_G2_2i/LIF_ESC


title: 64_2020_7_G22_2i/LIF_ESC


title: 64_2020_7_G20_2i/LIF_ESC


title: 64_2020_7_H12_2i/LIF_ESC


title: 64_2020_7_G16_2i/LIF_ESC


title: 64_2020_7_G18_2i/LIF_ESC


title: 64_2020_7_G19_2i/LIF_ESC


title: 64_2020_7_G17_2i/LIF_ESC


title: 64_2020_7_G21_2i/LIF_ESC


title: 64_2020_7_G13_2i/LIF_ESC


title: 64_2020_7_G14_2i/LIF_ESC


title: 64_2020_7_F9_2i/LIF_ESC


title: 64_2020_7_G10_2i/LIF_ESC


title: 64_2020_7_G15_2i/LIF_ESC


title: 64_2020_7_G1_2i/LIF_ESC


title: 64_2020_7_G3_2i/LIF_ESC


title: 64_2020_7_F8_2i/LIF_ESC


title: 64_2020_7_F4_2i/LIF_ESC


title: 64_2020_7_F7_2i/LIF_ESC


title: 64_2020_7_F5_2i/LIF_ESC


title: 64_2020_7_F6_2i/LIF_ESC


title: 64_2020_7_F24_2i/LIF_ESC


title: 64_2020_7_F20_2i/LIF_ESC


title: 64_2020_7_F3_2i/LIF_ESC


title: 64_2020_7_F23_2i/LIF_ESC


title: 64_2020_7_G12_2i/LIF_ESC


title: 64_2020_7_F22_2i/LIF_ESC


title: 64_2020_7_F2_2i/LIF_ESC


title: 64_2020_7_F21_2i/LIF_ESC


title: 64_2020_7_F15_2i/LIF_ESC


title: 64_2020_7_F19_2i/LIF_ESC


title: 64_2020_7_F14_2i/LIF_ESC


title: 64_2020_7_F13_2i/LIF_ESC


title: 64_2020_7_F16_2i/LIF_ESC


title: 64_2020_7_F10_2i/LIF_ESC


title: 64_2020_7_F1_2i/LIF_ESC


title: 64_2020_7_F18_2i/LIF_ESC


title: 64_2020_7_F12_2i/LIF_ESC


title: 64_2020_7_E7_2i/LIF_ESC


title: 64_2020_7_E9_2i/LIF_ESC


title: 64_2020_7_E8_2i/LIF_ESC


title: 64_2020_7_E5_2i/LIF_ESC


title: 64_2020_7_E6_2i/LIF_ESC


title: 64_2020_7_E22_2i/LIF_ESC


title: 64_2020_7_E24_2i/LIF_ESC


title: 64_2020_7_E23_2i/LIF_ESC


title: 64_2020_7_E20_2i/LIF_ESC


title: 64_2020_7_F17_2i/LIF_ESC


title: 64_2020_7_E2_2i/LIF_ESC


title: 64_2020_7_F11_2i/LIF_ESC


title: 64_2020_7_E19_2i/LIF_ESC


title: 64_2020_7_E13_2i/LIF_ESC


title: 64_2020_7_E17_2i/LIF_ESC


title: 64_2020_7_E16_2i/LIF_ESC


title: 64_2020_7_E15_2i/LIF_ESC


title: 64_2020_7_E18_2i/LIF_ESC


title: 64_2020_7_E1_2i/LIF_ESC


title: 64_2020_7_E14_2i/LIF_ESC


title: 64_2020_7_E11_2i/LIF_ESC


title: 64_2020_7_D9_2i/LIF_ESC


title: 64_2020_7_D8_2i/LIF_ESC


title: 64_2020_7_D4_2i/LIF_ESC


title: 64_2020_7_D6_2i/LIF_ESC


title: 64_2020_7_E3_2i/LIF_ESC


title: 64_2020_7_E10_2i/LIF_ESC


title: 64_2020_7_E4_2i/LIF_ESC


title: 64_2020_7_D5_2i/LIF_ESC


title: 64_2020_7_D24_2i/LIF_ESC


title: 64_2020_7_E21_2i/LIF_ESC


title: 64_2020_7_D22_2i/LIF_ESC


title: 64_2020_7_D2_2i/LIF_ESC


title: 64_2020_7_D20_2i/LIF_ESC


title: 64_2020_7_E12_2i/LIF_ESC


title: 64_2020_7_D19_2i/LIF_ESC


title: 64_2020_7_D13_2i/LIF_ESC


title: 64_2020_7_D14_2i/LIF_ESC


title: 64_2020_7_D18_2i/LIF_ESC


title: 64_2020_7_D17_2i/LIF_ESC


title: 64_2020_7_D16_2i/LIF_ESC


title: 64_2020_7_D15_2i/LIF_ESC


title: 64_2020_7_D12_2i/LIF_ESC


title: 64_2020_7_D1_2i/LIF_ESC


title: 64_2020_7_D7_2i/LIF_ESC


title: 64_2020_7_C9_2i/LIF_ESC


title: 64_2020_7_C8_2i/LIF_ESC


title: 64_2020_7_D11_2i/LIF_ESC


title: 64_2020_7_C7_2i/LIF_ESC


title: 64_2020_7_C5_2i/LIF_ESC


title: 64_2020_7_D10_2i/LIF_ESC


title: 64_2020_7_C6_2i/LIF_ESC


title: 64_2020_7_C3_2i/LIF_ESC


title: 64_2020_7_D21_2i/LIF_ESC


title: 64_2020_7_D23_2i/LIF_ESC


title: 64_2020_7_C23_2i/LIF_ESC


title: 64_2020_7_C21_2i/LIF_ESC


title: 64_2020_7_C22_2i/LIF_ESC


title: 64_2020_7_C24_2i/LIF_ESC


title: 64_2020_7_D3_2i/LIF_ESC


title: 64_2020_7_C20_2i/LIF_ESC


title: 64_2020_7_C4_2i/LIF_ESC


title: 64_2020_7_C2_2i/LIF_ESC


title: 64_2020_7_C19_2i/LIF_ESC


title: 64_2020_7_C18_2i/LIF_ESC


title: 64_2020_7_C17_2i/LIF_ESC


title: 64_2020_7_C15_2i/LIF_ESC


title: 64_2020_7_C16_2i/LIF_ESC


title: 64_2020_7_B8_2i/LIF_ESC


title: 64_2020_7_B9_2i/LIF_ESC


title: 64_2020_7_C10_2i/LIF_ESC


title: 64_2020_7_C13_2i/LIF_ESC


title: 64_2020_7_C1_2i/LIF_ESC


title: 64_2020_7_C12_2i/LIF_ESC


title: 64_2020_7_C11_2i/LIF_ESC


title: 64_2020_7_B7_2i/LIF_ESC


title: 64_2020_7_B5_2i/LIF_ESC


title: 64_2020_7_B6_2i/LIF_ESC


title: 64_2020_7_B22_2i/LIF_ESC


title: 64_2020_7_B23_2i/LIF_ESC


title: 64_2020_7_B24_2i/LIF_ESC


title: 64_2020_7_B4_2i/LIF_ESC


title: 64_2020_7_B21_2i/LIF_ESC


title: 64_2020_7_B19_2i/LIF_ESC


title: 64_2020_7_B2_2i/LIF_ESC


title: 64_2020_7_B20_2i/LIF_ESC


title: 64_2020_7_B17_2i/LIF_ESC


title: 64_2020_7_B16_2i/LIF_ESC


title: 64_2020_7_B18_2i/LIF_ESC


title: 64_2020_7_C14_2i/LIF_ESC


title: Bmal1 KO 2

city: Seoul

first: Yina

last: Fang

address: 64, Goryeodae-ro 17ga-gil, Seongbuk-gu

country: South Korea

institute: Korea University Anam Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Kidney

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: tissue

value: Kidney

value: Bmal1 -/-


title: Bmal1 KO 5


title: Bmal1 KO 3


title: 64_2020_7_B3_2i/LIF_ESC


title: WT4

value: wildtype


title: Bmal1 KO 4


title: WT3


title: Bmal1 KO 1


title: WT1


title: 66_2020_9_I14_iXEN


title: 66_2020_9_H8_iXEN


title: 66_2020_9_H9_iXEN


title: 66_2020_9_I10_iXEN


title: 66_2020_9_I12_iXEN


title: 66_2020_9_H6_iXEN


title: 66_2020_9_H3_iXEN


title: 66_2020_9_H5_iXEN


title: pEXP56sMMrMICROtINHIBiSAMPLE02d20210408v3-0

city: Boston

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

institute: Boston Children's Hospital

data_processing:
Bcl2fastq & Demultiplex by sample: 'mkfastq' Cell Ranger 5.0.0
Alignment/Counts: 'count' Cell Ranger 5.0.0
Aggregate: 'Aggr' Cell Ranger 5.0.0 (normalize = none)
Analysis: Seurat
Genome_build: 10X Default 5.0.0 (GRCm38 (mm10); Annotation: Filtered Ensembl v98)
Supplementary_files_format_and_content: 10X Cell Ranger Count Output (.tsv & .mtx)

source_name: brain

extract_protocol: 10X Genomics 3' Version 3 or 3.1 Single Cell Kit

tag: digestion type

value: Cold Dounce

tag: Sex

value: M

tag: inhibitors

value: Yes

tag: 10x version

tag: mouse id

value: Mouse 02

tag: brain region

value: Whole Brain


title: pEXP56sMMrMICROtNONEiSAMPLE01d20210408v3-1

value: No

value: Mouse 01


title: pEXP56sMMrMICROtNONEiSAMPLE01d20210408v3-0


title: 66_2020_9_H4_iXEN


title: WT2

tag: genotype


title: pEXP56sMMrMICROtINHIBiSAMPLE02d20210408v3-1


title: pEXP56sMMrMICROtNONEiSAMPLE03d20210408v3-0

value: Mouse 03


title: pEXP56sMMrMICROtNONEiSAMPLE03d20210408v3-1


title: 66_2020_9_H21_iXEN


title: 66_2020_9_H14_iXEN


title: 66_2020_9_H18_iXEN


title: 66_2020_9_H15_iXEN


title: 66_2020_9_H12_iXEN


title: 66_2020_9_H17_iXEN


title: 66_2020_9_H11_iXEN


title: 66_2020_9_H22_iXEN


title: 66_2020_9_I16_iXEN


title: 66_2020_9_H10_iXEN


title: 66_2020_9_H1_iXEN


title: 66_2020_9_H7_iXEN


title: 66_2020_9_G4_iXEN


title: 66_2020_9_G5_iXEN


title: 66_2020_9_G21_iXEN


title: 66_2020_9_G24_iXEN


title: 66_2020_9_G23_iXEN


title: 66_2020_9_G22_iXEN


title: 66_2020_9_G20_iXEN


title: 66_2020_9_G3_iXEN


title: 66_2020_9_H19_iXEN


title: 66_2020_9_G18_iXEN


title: 66_2020_9_G10_iXEN


title: 66_2020_9_G11_iXEN


title: 66_2020_9_G16_iXEN


title: 64_2020_7_G11_2i/LIF_ESC


title: 66_2020_9_H23_iXEN


title: 66_2020_9_F6_iXEN


title: 66_2020_9_F7_iXEN


title: 66_2020_9_F9_iXEN


title: 66_2020_9_G9_iXEN


title: 66_2020_9_G1_iXEN


title: 66_2020_9_F8_iXEN


title: 66_2020_9_F5_iXEN


title: 66_2020_9_F20_iXEN


title: 66_2020_9_F3_iXEN


title: 66_2020_9_F24_iXEN


title: 66_2020_9_F23_iXEN


title: 66_2020_9_F22_iXEN


title: 66_2020_9_F4_iXEN


title: 66_2020_9_E8_iXEN


title: 66_2020_9_F21_iXEN


title: 66_2020_9_E7_iXEN


title: 66_2020_9_E3_iXEN


title: 64_2020_7_B15_2i/LIF_ESC


title: 66_2020_9_E6_iXEN


title: 66_2020_9_E5_iXEN


title: 66_2020_9_H2_iXEN


title: 66_2020_9_F15_iXEN


title: 66_2020_9_F2_iXEN


title: 66_2020_9_F10_iXEN


title: 64_2020_7_B12_2i/LIF_ESC


title: 66_2020_9_F18_iXEN


title: 66_2020_9_F16_iXEN


title: 66_2020_9_F12_iXEN


title: 66_2020_9_F11_iXEN


title: 64_2020_7_B10_2i/LIF_ESC


title: 66_2020_9_E9_iXEN


title: 66_2020_9_F19_iXEN


title: 66_2020_9_F13_iXEN


title: 66_2020_9_F17_iXEN


title: 66_2020_9_F1_iXEN


title: 64_2020_7_B13_2i/LIF_ESC


title: 66_2020_9_F14_iXEN


title: 64_2020_7_B1_2i/LIF_ESC


title: 64_2020_7_A9_2i/LIF_ESC


title: 64_2020_7_A7_2i/LIF_ESC


title: 64_2020_7_A8_2i/LIF_ESC


title: 64_2020_7_A5_2i/LIF_ESC


title: 66_2020_9_E4_iXEN


title: 64_2020_7_A4_2i/LIF_ESC


title: 64_2020_7_A6_2i/LIF_ESC


title: 64_2020_7_A24_2i/LIF_ESC


title: 64_2020_7_B11_2i/LIF_ESC


title: 64_2020_7_A3_2i/LIF_ESC


title: 64_2020_7_A23_2i/LIF_ESC


title: 64_2020_7_A2_2i/LIF_ESC


title: 64_2020_7_B14_2i/LIF_ESC


title: 64_2020_7_A17_2i/LIF_ESC


title: 64_2020_7_A16_2i/LIF_ESC


title: 64_2020_7_A22_2i/LIF_ESC


title: 64_2020_7_A15_2i/LIF_ESC


title: 64_2020_7_A21_2i/LIF_ESC


title: 64_2020_7_A20_2i/LIF_ESC


title: 64_2020_7_A13_2i/LIF_ESC


title: 64_2020_7_A19_2i/LIF_ESC


title: 64_2020_7_A1_2i/LIF_ESC


title: 64_2020_7_A12_2i/LIF_ESC


title: 64_2020_7_A11_2i/LIF_ESC


title: 5_P8_3D_RtL

value: Rosette-to-Lumen stage embryoid stem cell


title: 64_2020_7_A14_2i/LIF_ESC


title: 5_P7_3D_RtL


title: 64_2020_7_A10_2i/LIF_ESC


title: 5_P9_3D_RtL


title: 5_P6_3D_RtL


title: 5_P24_3D_RtL


title: 5_P4_3D_RtL


title: 5_P3_3D_RtL


title: 5_P22_3D_RtL


title: 5_P23_3D_RtL


title: 64_2020_7_A18_2i/LIF_ESC


title: 5_P20_3D_RtL


title: 5_P21_3D_RtL


title: 5_P19_3D_RtL


title: 5_P2_3D_RtL


title: 5_P5_3D_RtL


title: 5_P16_3D_RtL


title: 5_P14_3D_RtL


title: 5_P18_3D_RtL


title: 5_P1_3D_RtL


title: 5_P10_3D_RtL


title: 5_P15_3D_RtL


title: 5_P12_3D_RtL


title: 5_P11_3D_RtL


title: 5_P13_3D_RtL


title: 5_O8_3D_RtL


title: 5_P17_3D_RtL


title: 5_O9_3D_RtL


title: 5_O5_3D_RtL


title: 5_O24_3D_RtL


title: 5_O3_3D_RtL


title: 5_O4_3D_RtL


title: 5_O7_3D_RtL


title: 5_O23_3D_RtL


title: 5_O21_3D_RtL


title: 5_O22_3D_RtL


title: 5_O18_3D_RtL


title: 5_O20_3D_RtL


title: 5_O2_3D_RtL


title: 5_O17_3D_RtL


title: 5_O19_3D_RtL


title: 5_O16_3D_RtL


title: 5_O13_3D_RtL


title: 5_O15_3D_RtL


title: 5_O11_3D_RtL


title: 5_N9_3D_RtL


title: 5_N8_3D_RtL


title: 5_O1_3D_RtL


title: 5_N5_3D_RtL


title: 5_N24_3D_RtL


title: 5_N7_3D_RtL


title: 5_O10_3D_RtL


title: 5_O6_3D_RtL


title: 5_N2_3D_RtL


title: 5_N4_3D_RtL


title: 5_N19_3D_RtL


title: 5_N21_3D_RtL


title: 5_O14_3D_RtL


title: 5_N20_3D_RtL


title: 5_N16_3D_RtL


title: 5_N22_3D_RtL


title: 5_N23_3D_RtL


title: 5_N12_3D_RtL


title: 5_N14_3D_RtL


title: 5_N11_3D_RtL


title: 5_N13_3D_RtL


title: 5_N15_3D_RtL


title: 5_N10_3D_RtL


title: 5_N6_3D_RtL


title: 5_N1_3D_RtL


title: 5_N3_3D_RtL


title: 5_M5_3D_RtL


title: 5_M7_3D_RtL


title: 5_M4_3D_RtL


title: 5_M6_3D_RtL


title: 5_N17_3D_RtL


title: 5_M3_3D_RtL


title: 5_M22_3D_RtL


title: 5_O12_3D_RtL


title: 5_M2_3D_RtL


title: 5_M18_3D_RtL


title: 5_M17_3D_RtL


title: 5_M23_3D_RtL


title: 5_M20_3D_RtL


title: 5_M21_3D_RtL


title: 5_M16_3D_RtL


title: 5_M14_3D_RtL


title: 5_M15_3D_RtL


title: 5_M12_3D_RtL


title: 5_M13_3D_RtL


title: 5_M10_3D_RtL


title: 5_N18_3D_RtL


title: 5_M1_3D_RtL


title: 5_M11_3D_RtL


title: 5_M9_3D_RtL


title: 5_L9_3D_RtL


title: 5_L8_3D_RtL


title: 5_L6_3D_RtL


title: 5_L7_3D_RtL


title: 5_M24_3D_RtL


title: 5_L5_3D_RtL


title: 5_L4_3D_RtL


title: 5_L24_3D_RtL


title: 5_L23_3D_RtL


title: 5_M19_3D_RtL


title: 5_L21_3D_RtL


title: 5_L20_3D_RtL


title: 5_L2_3D_RtL


title: 5_L18_3D_RtL


title: 5_L17_3D_RtL


title: 5_L22_3D_RtL


title: 5_L16_3D_RtL


title: 5_L14_3D_RtL


title: 5_L19_3D_RtL


title: 5_L13_3D_RtL


title: 5_L10_3D_RtL


title: 5_L1_3D_RtL


title: 5_L11_3D_RtL


title: 5_K9_3D_RtL


title: 5_K6_3D_RtL


title: 5_K5_3D_RtL


title: 5_K4_3D_RtL


title: 5_K3_3D_RtL


title: 5_L3_3D_RtL


title: 5_K23_3D_RtL


title: 5_K22_3D_RtL


title: 5_K20_3D_RtL


title: 5_K24_3D_RtL


title: 5_K21_3D_RtL


title: 5_K19_3D_RtL


title: 5_K2_3D_RtL


title: 5_K17_3D_RtL


title: 5_K15_3D_RtL


title: 5_L12_3D_RtL


title: 5_L15_3D_RtL


title: 5_K14_3D_RtL


title: 5_K1_3D_RtL


title: 5_K13_3D_RtL


title: 5_J9_3D_RtL


title: 5_K11_3D_RtL


title: 5_K8_3D_RtL


title: 5_K7_3D_RtL


title: 5_K10_3D_RtL


title: 5_J8_3D_RtL


title: 5_J7_3D_RtL


title: 5_J4_3D_RtL


title: 5_J5_3D_RtL


title: 5_J6_3D_RtL


title: 5_J3_3D_RtL


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title: 4_D14_3D_RtL


title: 4_D11_3D_RtL


title: 4_C6_3D_RtL


title: 4_C8_3D_RtL


title: 4_D1_3D_RtL


title: 4_D7_3D_RtL


title: 4_D13_3D_RtL


title: 4_C9_3D_RtL


title: 4_C4_3D_RtL


title: 4_C5_3D_RtL


title: 4_C3_3D_RtL


title: 4_C20_3D_RtL


title: 4_C23_3D_RtL


title: 4_C22_3D_RtL


title: 4_C21_3D_RtL


title: 4_C2_3D_RtL


title: 4_C19_3D_RtL


title: 4_C18_3D_RtL


title: 4_D15_3D_RtL


title: 4_C15_3D_RtL


title: 4_C13_3D_RtL


title: 4_C24_3D_RtL


title: 4_C12_3D_RtL


title: 4_C14_3D_RtL


title: 4_C11_3D_RtL


title: 4_B9_3D_RtL


title: 4_B6_3D_RtL


title: 4_B7_3D_RtL


title: 4_B23_3D_RtL


title: 4_B3_3D_RtL


title: 4_B21_3D_RtL


title: 4_B8_3D_RtL


title: 4_C10_3D_RtL


title: 4_B5_3D_RtL


title: 4_B24_3D_RtL


title: 4_C17_3D_RtL


title: 4_B20_3D_RtL


title: 4_C16_3D_RtL


title: 4_B19_3D_RtL


title: 4_B17_3D_RtL


title: 4_B16_3D_RtL


title: 4_B2_3D_RtL


title: 4_B13_3D_RtL


title: 4_B14_3D_RtL


title: 4_B18_3D_RtL


title: 4_B12_3D_RtL


title: 4_B11_3D_RtL


title: 4_B10_3D_RtL


title: 4_B1_3D_RtL


title: 4_A9_3D_RtL


title: 4_A8_3D_RtL


title: 4_C1_3D_RtL


title: 4_B4_3D_RtL


title: 4_B22_3D_RtL


title: 4_A6_3D_RtL


title: 4_A5_3D_RtL


title: 4_A24_3D_RtL


title: 4_A7_3D_RtL


title: 4_A3_3D_RtL


title: 4_A23_3D_RtL


title: 4_A4_3D_RtL


title: 4_A21_3D_RtL


title: 4_A20_3D_RtL


title: 4_A19_3D_RtL


title: 4_A18_3D_RtL


title: 4_B15_3D_RtL


title: 4_A16_3D_RtL


title: 4_A2_3D_RtL


title: 4_A15_3D_RtL


title: 4_A17_3D_RtL


title: 4_A14_3D_RtL


title: 4_A12_3D_RtL


title: 4_A13_3D_RtL


title: 3_P8_3D_RtL


title: 4_A11_3D_RtL


title: 3_P9_3D_RtL


title: 3_P5_3D_RtL


title: 3_P7_3D_RtL


title: 3_P6_3D_RtL


title: 3_P4_3D_RtL


title: 4_A22_3D_RtL


title: 3_P3_3D_RtL


title: 3_P24_3D_RtL


title: 3_P20_3D_RtL


title: 3_P19_3D_RtL


title: 3_P18_3D_RtL


title: 3_P22_3D_RtL


title: 3_P21_3D_RtL


title: 3_P2_3D_RtL


title: 3_P15_3D_RtL


title: 3_P14_3D_RtL


title: 3_P16_3D_RtL


title: 4_A1_3D_RtL


title: 4_A10_3D_RtL


title: 3_P13_3D_RtL


title: 3_O9_3D_RtL


title: 3_P1_3D_RtL


title: 3_P12_3D_RtL


title: 3_P10_3D_RtL


title: 3_O4_3D_RtL


title: 3_O7_3D_RtL


title: 3_O6_3D_RtL


title: 3_O23_3D_RtL


title: 3_P23_3D_RtL


title: 3_O3_3D_RtL


title: 3_O21_3D_RtL


title: 3_O24_3D_RtL


title: 3_O20_3D_RtL


title: 3_O2_3D_RtL


title: 3_O22_3D_RtL


title: 3_P17_3D_RtL


title: 3_O17_3D_RtL


title: 3_O18_3D_RtL


title: 3_O19_3D_RtL


title: 3_O16_3D_RtL


title: 3_O15_3D_RtL


title: 3_O14_3D_RtL


title: 3_O13_3D_RtL


title: 3_O8_3D_RtL


title: 3_O12_3D_RtL


title: 3_O11_3D_RtL


title: 3_O5_3D_RtL


title: 3_O10_3D_RtL


title: 3_N7_3D_RtL


title: 3_O1_3D_RtL


title: 3_N8_3D_RtL


title: 3_N24_3D_RtL


title: 3_N6_3D_RtL


title: 3_N9_3D_RtL


title: 3_N22_3D_RtL


title: 3_N3_3D_RtL


title: 3_N5_3D_RtL


title: 3_N4_3D_RtL


title: 3_N21_3D_RtL


title: 3_N19_3D_RtL


title: 3_N17_3D_RtL


title: 3_N16_3D_RtL


title: 3_N2_3D_RtL


title: 3_N18_3D_RtL


title: 3_N20_3D_RtL


title: 3_N12_3D_RtL


title: 3_N13_3D_RtL


title: 3_N15_3D_RtL


title: 3_N11_3D_RtL


title: 3_N10_3D_RtL


title: 3_N1_3D_RtL


title: 3_M9_3D_RtL


title: 3_M8_3D_RtL


title: 3_M6_3D_RtL


title: 3_M5_3D_RtL


title: 3_M3_3D_RtL


title: 3_M24_3D_RtL


title: 3_M4_3D_RtL


title: 3_N23_3D_RtL


title: 3_M7_3D_RtL


title: 3_M21_3D_RtL


title: 3_M23_3D_RtL


title: 3_M20_3D_RtL


title: 3_M2_3D_RtL


title: 3_M22_3D_RtL


title: 3_M18_3D_RtL


title: 3_M17_3D_RtL


title: 3_N14_3D_RtL


title: 3_M16_3D_RtL


title: 3_M14_3D_RtL


title: 3_M15_3D_RtL


title: 3_M13_3D_RtL


title: 3_M10_3D_RtL


title: 3_M1_3D_RtL


title: 3_M11_3D_RtL


title: 3_L5_3D_RtL


title: 3_L3_3D_RtL


title: 3_L23_3D_RtL


title: 3_L24_3D_RtL


title: 3_L4_3D_RtL


title: 3_L22_3D_RtL


title: 3_L20_3D_RtL


title: 3_L6_3D_RtL


title: 3_L2_3D_RtL


title: 3_L18_3D_RtL


title: 3_L17_3D_RtL


title: 3_L16_3D_RtL


title: 3_L19_3D_RtL


title: 3_M19_3D_RtL


title: 3_L15_3D_RtL


title: 3_L14_3D_RtL


title: 3_M12_3D_RtL


title: 3_L12_3D_RtL


title: 3_L13_3D_RtL


title: 3_L10_3D_RtL


title: 3_L1_3D_RtL


title: 3_L9_3D_RtL


title: 3_L11_3D_RtL


title: 3_L8_3D_RtL


title: 3_K6_3D_RtL


title: 3_L7_3D_RtL


title: 3_K5_3D_RtL


title: 3_L21_3D_RtL


title: 3_K3_3D_RtL


title: 3_K23_3D_RtL


title: 3_K4_3D_RtL


title: 3_K24_3D_RtL


title: 3_K20_3D_RtL


title: 3_K21_3D_RtL


title: 3_K19_3D_RtL


title: 3_K18_3D_RtL


title: 3_K2_3D_RtL


title: 3_K17_3D_RtL


title: 3_K16_3D_RtL


title: 3_K15_3D_RtL


title: 3_K14_3D_RtL


title: 3_K9_3D_RtL


title: 3_K7_3D_RtL


title: 3_K12_3D_RtL


title: 3_J8_3D_RtL


title: 3_K10_3D_RtL


title: 3_J7_3D_RtL


title: 3_J9_3D_RtL


title: 3_K11_3D_RtL


title: 3_J6_3D_RtL


title: 3_J4_3D_RtL


title: 3_K1_3D_RtL


title: 3_J5_3D_RtL


title: 3_K22_3D_RtL


title: 3_J3_3D_RtL


title: 3_J22_3D_RtL


title: 3_J2_3D_RtL


title: 3_J20_3D_RtL


title: 3_J21_3D_RtL


title: 3_J19_3D_RtL


title: 3_J24_3D_RtL


title: 3_J23_3D_RtL


title: 3_K13_3D_RtL


title: 3_J17_3D_RtL


title: 3_J15_3D_RtL


title: 3_J14_3D_RtL


title: Naive Nasal AWCTX_9

city: Toronto

first: Gengming

last: He

address: 27 King's College Circle

department: Biostatistics

country: Canada

institute: University of Toronto

data_processing:
TrimGalore was used to remove Illumina universal adaptors and bases with quality score under 20 from the raw reads data
After trimming, paired-end reads that have length > 40 bases were aligned to the hg19 genome reference using STAR
gene expression raw read was generated by Htseq-count based on UCSC hg19 annotation
transcripts per million reads (TPM) for each sample each gene was generated by RNA-SeQC based on gencode v19 annotation
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts matrix (tab-delimited)
Supplementary_files_format_and_content: TPM matrix (tab-delimited)

source_name: Nasal

extract_protocol:
RNeasy Tissue (ThermoFisher) RNA extraction kit was used per manufacture's instruction
The New England Biolabs NEBNext Ultra II RNA Library Preparation kit was used for library preparation

tag: individual id

value: Nasal

value: Naive

tag: rin


title: Culture Bronchial AWCTX_9

source_name: Bronchial

value: Bronchial

value: Culture


title: Culture Nasal AWCTX_9


title: 3_J12_3D_RtL


title: Culture Nasal AWCTX_8


title: Naive Bronchial AWCTX_9


title: 3_J1_3D_RtL


title: 3_J10_3D_RtL


title: Naive Nasal AWCTX_8


title: 3_J18_3D_RtL


title: 3_J13_3D_RtL


title: Culture Bronchial AWCTX_8


title: Culture Nasal AWCTX_6


title: 3_I9_3D_RtL


title: 3_K8_3D_RtL


title: 3_I8_3D_RtL


title: Culture Bronchial AWCTX_6


title: Naive Nasal AWCTX_6


title: 3_I7_3D_RtL


title: 3_J11_3D_RtL


title: 3_J16_3D_RtL


title: Culture Nasal AWCTX_4


title: Naive Nasal AWCTX_4


title: 3_I6_3D_RtL


title: 3_I5_3D_RtL


title: Culture Bronchial AWCTX_4


title: 3_I4_3D_RtL


title: 3_I24_3D_RtL


title: Culture Nasal AWCTX_3


title: 3_I23_3D_RtL


title: Naive Bronchial AWCTX_4


title: Naive Bronchial AWCTX_3


title: Culture Bronchial AWCTX_3


title: Naive Nasal AWCTX_3


title: 3_I22_3D_RtL


title: 3_I2_3D_RtL


title: 3_I21_3D_RtL


title: Naive Nasal AWCTX_2


title: 3_I19_3D_RtL


title: 3_I18_3D_RtL


title: Culture Nasal AWCTX_20


title: Culture Bronchial AWCTX_2


title: Naive Nasal AWCTX_20


title: 3_I3_3D_RtL


title: Culture Bronchial AWCTX_20


title: Culture Nasal AWCTX_1


title: 3_I15_3D_RtL


title: 3_I14_3D_RtL


title: 3_I16_3D_RtL


title: 3_I17_3D_RtL


title: 3_I12_3D_RtL


title: 3_I13_3D_RtL


title: Culture Bronchial AWCTX_1


title: Naive Nasal AWCTX_1


title: 3_I10_3D_RtL


title: 3_I11_3D_RtL


title: Naive Bronchial AWCTX_1


title: Naive Nasal AWCTX_19


title: Culture Nasal AWCTX_2


title: 3_H8_3D_RtL


title: Culture Bronchial AWCTX_19


title: 3_H7_3D_RtL


title: 3_H9_3D_RtL


title: Naive Bronchial AWCTX_19


title: 3_H6_3D_RtL


title: Culture Nasal AWCTX_18


title: Culture Bronchial AWCTX_18


title: MYC T58I10001

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

institute: Uppsala Universitet

description:
GRCm38_RAW_count_table.csv
t58i_19

data_processing:
The short reads were aligned to the mouse reference genome (build GRCm38.87, obtained from the Ensembl ftp repository with corresponding .gtf annotation file), concatenated with the plasmid vector sequence containing MYC and EGFP as well as the sequences for two other overexpressed human genes BMI1 and BCL2L1 using the splice-aware short read aligner STAR (v2.5.1b), with default options and –sjdbGTFfile pointing to the GRCm38.87 GTF file and --outFilterMultimapNmax set to 1.
Reads per feature (concatenated exons for one gene) were obtained using featurecounts (from the package Subread v1.5.1) with default options and -s set to 0
Normalization and tests for differential expression were conducted using the Bioconductor (v3.3) package EdgeR (v3.22.5) using the glmQLF workflow, features with CPM (counts per million) ≥ 0.95 for at least three samples were included in the analysis.
Genome_build: GRCm38.87
Supplementary_files_format_and_content: Read counts per gene for 49671 genes in GRCm38, plus three overexpressed human genes, MYC, BCL2L1 and BMI1, plus EGFP (comma separated table text file generated using featurecounts from the Subread package)

source_name: Murine B cells from spleen

growth_protocol: Transduced B-cells expressing wild type or mutant cMyc (WtMyc, T58AMyc and T58IMyc) where cultured at 37¡C and 5% CO2 in GluMax-RPMI (Gibco-USA) supplemented with 10%FBS (0.01M of HEPES, 1x sodium pyruvate, 0.05mM 2-Beta mercaptoethanol (Gibco-USA) and 0.1 mg/ml Penicillin-streptomycin (Sigma,USA)) with addition of 2mg/ml Doxycycline.

extract_protocol:
Total RNA was isolated using a kit (QIAGEN,NL)
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: Cells (WtMyc, T58AMyc and T58IMyc) where cultured as described above for 48 hours, except that 7 different concentrations of doxycycline were used (0, 25, 50, 100, 300, 600, 1000 ug/ml).

value: MYC T58I

tag: agent

value: doxycycline

tag: agent concentration

value: B cells from spleen


title: 3_H5_3D_RtL


title: Naive Bronchial AWCTX_18


title: MYC T58I6003

description:
GRCm38_RAW_count_table.csv
t58i_18

value: 600 µg/ml


title: MYC T58I10003

description:
GRCm38_RAW_count_table.csv
t58i_21


title: MYC T58I6001

description:
GRCm38_RAW_count_table.csv
t58i_16


title: MYC T58I6002

description:
GRCm38_RAW_count_table.csv
t58i_17


title: MYC T58I10002

description:
GRCm38_RAW_count_table.csv
t58i_20


title: Culture Nasal AWCTX_17


title: 3_H3_3D_RtL


title: 3_H24_3D_RtL


title: 3_H4_3D_RtL


title: 3_I20_3D_RtL