title: a2_3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v20.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome (MC38 cell line) or GRCh38_hg38 (cell lines MEL-HO, SK-MEL, D41-MEL, NCI-H1650, NCI-H226, A549) . Expression value unit is TPM.
Assembly: GRCm38 or GRCh38 dependent on cell line
Supplementary files format and content: tab-delimited text files include TPM, RPKM and total gene reads values for each sample

source_name: Colon

growth_protocol: MC38, SK-MEL-37 and A549 were cultured in DMEM supplemented with 10% FCS, 2 mM glutamine, 1 mM sodium-pyruvate, 100 units/ml penicillin and 100 mg/ml streptomycin. MEL-HO, D41-MEL, NCI-H226 and NCI-H1650 were cultured in RPMI with 10% FCS, 2 mM glutamine, 1 mM sodium-pyruvate, 100 units/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer.
Barcoded mRNA seq libraries were prepared from 150 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual (with a final amplification of 12 cycles) . Concentration was determined using Invitrogen’s Qubit HS assay and fragment size was analyzed on Agilent’s 2100 Bioanalyzer on a HS DNA chip.

treatment_protocol: After culturing the different tumor cells for 20 h in their appropriate media containing either 0.2 mM methionine or 0.1 mM AHA, cells were harvested and washed twice with PBS before lysis by RLT plus buffer (Qiagen)

value: Colon

tag: cell line

value: Colon carcinoma

value: AHA


title: RNA-Seq WT_120h_rep1

status: Public on Jul 05 2023

type: SRA

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

library_source: transcriptomic

data_processing:
Quality control of FASTQ reads was performed using FastQC version v.0.11.3. Reads were aligned to the mm10 genome using STAR version 2.5.0a. Gene counts were quantified using STAR (--quantMode GeneCounts). Normalized counts were calculated out using DESeq2 version 1.14.1 and were log2 transformed.
Assembly: mm10
Supplementary files format and content: log2(DESeq2 Normalized Counts) for each gene and each experiment are provided as a tab-delimited file.
Supplementary files format and content: Raw Counts for each gene and each experiment are provided as a tab-delimited file.

molecule: total RNA

organism: Mus musculus

source_name: Macrophages

growth_protocol: Freshly isolated B cells were infected with C/EBPα-ER-hCD4 retrovirus and hCD4 positive cells were plated at 500 cells/cm2 in gelatinized 12-well plates onto wild type inactivated MEF feeders in 20%-FBS (10270-106, GIBCO) RPMI medium (12633012, GIBCO) with 10 ng/mL IL-7(217-17, Preprotech)

extract_protocol:
B cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from B cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
For RNA-sequencing (RNA-seq), libraries were prepared with a TruSeq Stranded mRNA Library Preparation Kit (Illumina) followed by single-end sequencing (50 bp) on a HiSeq2500 instrument (Illumina), obtaining at least 40 million reads per sample.

treatment_protocol: B cell infection with C/EBPα-ER-hCD4 retrovirus as described in (Di Stefano et al., 2014).

tag: cell type

value: Macrophages

tag: treatment

value: Transdifferentiation

tag: time


title: Cow 4 Day 1 Morning

city: Zurich

first: Maria

middle: Desemparats

last: Saenz-de-Juano

address: Universitatstrasse 2

country: Switzerland

institute: ETH Zurich

data_processing:
Remove Adapter: Tool “Clip” from Galaxy
Remove short reads (<25 nucleotides): Tool “Clip” from Galaxy
Remove Low Quality reads: Tool "FASTQ Quality Trimmer" from galaxy
Remove PCR duplicates: Tool “Collapse” from galaxy
Filtering: "Count Per Million (CPM) Filter" from Galaxy
Assembly: miRBase database v22.1
Supplementary files format and content: Normalization of read count using TMM and GLM robust (estimateGLMRobustDisp) included in edgeR

organism: Bos taurus

source_name: skimmed milk

extract_protocol:
miRNeasy MicroKit  (QIAGEN) following manufacturer's instructions
NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific)  following manufacturer's instructions

tag: subject

value: Cow 4

tag: timepoint

value: Morning

tag: scc (cells/ml_of_milk)

tag: tissue

value: skimmed milk


title: eIF4E1c RIP biol rep 2

city: Vienna

first: Laura

last: Lorenzo-Orts

address: Institute of Molecular Pathology (IMP), Campus Vienna Biocenter 1

country: Austria

institute: IMP

data_processing:
RNA-seq reads were trimmed using trim-galore v0.5.0, and reads mapping to abundant sequences (Dr mitochondrial chromosome, SILVA Dr ribosomal RNA, phiX174 genome) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter -s 0 for unstranded analysis (subread v1.6.2).
Differential gene expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1.
Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files with per gene read counts

organism: Danio rerio

source_name: Embryo lysate RIP

extract_protocol:
RNA Clean & Concentrator kit (Zymo Research) of RIP and input samples
SMARTerStrandedRNA library (Ribo-Zero) for input samples; SMARTer ultra low RNA kit for RIP samples
RNA-Seq (RIP) and ssRNA-seq (Ribo-Ziro)

value: Embryo lysate RIP

value: 8-cell stage

tag: genotype


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-H11

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files
Assembly: hg38-donor-snp-substituted
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Supplementary files format and content: tab-delimited files (HIC files) describing the chromatin contacts. Columns are: 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, Conor Fitzpatrick, Carolyn O’Connor,Jesse R. Dixon, Joseph R. Ecker. 2019. “Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.” Nat Methods. 16(10): 999–1006.

tag: brain region

value: SEP

tag: gender

value: M


title: ATAC-Seq R35A_18h_rep2

data_processing:
Read quality was assessed with FastQC version v.0.11.3. Adaptors were removed using Cutadapt (version 0.4.2_dev) TrimGalore! In paired end mode (--340 paired –nextera). Reads were aligned to the mm10 genome using bowtie2 (v 2.2.4) in paired end mode with standard parameters. Output SAM files were converted to BAM files using samtools (v 0.1.19). BAM files were sorted and indexed using the samtools commands sort and index, respectively. Low quality reads and reads associated with a not primary or supplementary alignment SAM flag were filtered out using the samtools command “samtools view -F 2304 -b -q 10”. PCR duplicates were removed with Picard MarkDuplicates (version 2.3.0) with the following options: “REMOVE_DUPLICATES=true ASSUME_SORTED=true VERBOSITY=WARNING”. Filtered BAM files were indexed with samtools index and were used as input in the bamCoverage command of deeptools (v3.0.1) in order to generate bigwig files. bamCoverage was used with the options – binSize 1 –normalizeUsing RPGC –effectiveGenomeSize 2150570000 –extendReads –outFileFormat bigwig.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: B-cells

extract_protocol:
ATAC-seq was performed as previously published (Buenrostro et al., 2015). Briefly, cells were harvested at the mentioned timepoints, feeder-depleted and lysed at 50.000 cells per condition. Immediately, transposition was performed using Nextera Tn5 Transposase (15027865, Illumina) at 37ºC for 30 minutes. Chromatin was then purified using Qiagen MinElute PCR Purification Kit (28004, Qiagen).
DNA was then amplified using NEBNext High Fidelity PCR Master Mix (M0541S, New England Biolabs Inc.) and barcoded primers (see table MMX). qPCR was performed to determine the optimal number of cycles for each condition to stop amplification prior to saturation. Quality was analyzed by gel electrophoresis and in a fragment Bioanalyzer (Agilent 2100 Bioanalyzer DNA 7500 assay).

value: B-cells


title: eIF4E1b RIP biol rep 1


title: pan_TCR_PD1

city: Boston

first: Jenna

middle: Lynn

last: Collier

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard University

description: Sorted TCR-beta+CD11a+ T cells from the pancreases from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis MULTI pipeline (v3.0.2)
Data normalization, dimension reduction, and differential expression analysis were performed using R version 4.0.3 and the Seurat R package (version 4.0.2)
Tissues were integrated across anchors (Stuart T, Butler A, et al. Cell. 2019;177:1888-1902)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files. Integrated .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR data, matching status, and other data in the @meta.data field.

molecule: polyA RNA

source_name: pancreas

growth_protocol: Peripheral blood was isolated using retroorbital collection prior to euthanasia, and the pancreatic lymph nodes and pancreas were collected from the same mice after euthanasia. Leukocytes were enriched from peripheral blood using histopaque gradients. Pancreas-infiltrating lymphocytes were enriched from pancreas samples by performing digestion with collagenase I and DNAse I followed by discontinous percoll gradient. TCR-beta+CD11a+ T cells were sorted using a BD Aria sorter prior to performing 10X library generation.

extract_protocol:
Sorted TCR-beta+CD11A+ T cells from peripheral blood, pancreas, and pancreatic lymph nodes were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
Protocol number CG000330 RevE from 10X Genomics (User Guide, Chromium Next GEM Single Cell V(D)J Reagent Kits v2 with Feature Barcoding technology for Cell Surface Protein) was used.
10X Chromium Single Cell V(D)J kits (5' v2 gene expression with paired T cell receptor sequencing and Feature Barcode detection)

treatment_protocol: Spontaneously diabetic mice received no treatment. Anti-PD-1 and isotype control treated mice received two doses of 0.2mg of antibody by intraperitoneal injection on days -4 and -2 before sacrifice. Three individual mice from each group were stained with hashtag antibodies before pooling for sequencing.

value: pancreas

value: TCR-beta+CD11A+ T cells

value: NOD/ShiLtJ

value: IP injection of 0.2mg anti-mouse PD-1 (clone:29F.1A12) on days -4, -2 before analysis

tag: age

value: 16 weeks

tag: Sex

value: Female

tag: disease

value: Diabetes


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-F24


title: Cow 4 Day 4 Evening

value: Evening


title: a2_2

country: Germany

value: Colon

value: Colon carcinoma

value: AHA


title: RNA-Seq WT_3h_rep1

value: Transdifferentiation


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-H24


title: Cow 4 Day 4 Morning

value: Cow 4

value: Morning

value: skimmed milk


title: ATAC-Seq R35A_18h_rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-H23

value: SEP

value: M


title: pan_FB_PD1

description:
Sorted TCR-beta+CD11a+ T cells from the pancreases from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
pan_PD1_barcodes.tsv.gz
pan_PD1_features.tsv.gz
pan_PD1_matrix.mtx.gz

value: pancreas


title: pan_FB_Spt

description:
Sorted TCR-beta+CD11a+ T cells from the pancreases from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
pan_Spt_barcodes.tsv.gz
pan_Spt_features.tsv.gz
pan_Spt_matrix.mtx.gz

value: TCR-beta+CD11A+ T cells

value: 18 weeks


title: Cow 4 Day 3 Morning


title: pan_FB_IgG

description:
Sorted TCR-beta+CD11a+ T cells from the pancreases from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
pan_IgG_barcodes.tsv.gz
pan_IgG_features.tsv.gz
pan_IgG_matrix.mtx.gz

value: NOD/ShiLtJ

value: IP injection of 0.2mg IgG2a isotype control (clone:2A3) on days -4, -2 before analysis


title: Cow 3 Day 4 Morning

value: Cow 3


title: Cow 4 Day 2 Evening


title: a1_1

value: Meth


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-G24


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-F12


title: 28day, SCI, Boldine #5 (RRBS)

city: Birmingham

first: Luke

middle: Allen

last: Potter

state: Alabama

address: 901 19th St S

department: Pathology

institute: UAB

data_processing:
Sequence reads were quality control tested using FastQC, then trimmed for adaptor sequence/low-quality sequence using Trim Galore and CutAdapt
Sequence read were then aligned against the mm10 reference genome using Bismark, which also generated the methylation coverage files
Assembly: mm10
Supplementary files format and content: CpG reports are text files that contain Bismark methylation coverage information.

source_name: gastrocnemius

extract_protocol:
Mice were euthanized at 7 or 28 d post-surgery. The gastrocnemius was carefully excised, wet-weighed, then flash frozen in liquid nitrogen-cooled isopentane.
~10 mg of the left gastrocnemius was cut to contain equal amounts of both medial and lateral heads  and DNA was isolated after an overnight incubation in proteinase K at 60˚C using the Qiagen Blood and Tissue kit following the manufacturer’s guidelines. DNA was sent to Novogene, LLC for bisulfite conversion, library preparation and reduced representation bisulfite sequencing (RRBS).

value: gastrocnemius

value: 28 days

tag: stress

value: SCI

value: Boldine


title: ATAC-Seq R35A_6h_rep2

value: B-cells

value: Transdifferentiation


title: Cow 4 Day 2 Morning

value: Cow 4

value: Morning


title: ATAC-Seq R35A_120h_rep2

value: Macrophages


title: ATAC-Seq R35A_6h_rep1


title: Cow 4 Day 1 Evening

value: Evening

value: skimmed milk


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-G23

value: SEP

value: M


title: a2_1

value: Colon

value: Colon carcinoma

value: AHA


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-G12


title: ATAC-Seq R35A_120h_rep1


title: ATAC-Seq R35A_3h_rep2


title: a1_3

value: Meth


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-E24


title: ATAC-Seq R35A_3h_rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-E11


title: Cow 3 Day 4 Evening

value: Cow 3


title: a1_2


title: Cow 3 Day 1 Morning


title: ATAC-Seq R35A_1h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-F23


title: Cow 3 Day 2 Evening


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-F11


title: 28day, SCI, Boldine #4 (RRBS)

value: gastrocnemius

value: 28 days


title: 28day, SCI, Vehicle, #6 (RRBS)

value: SCI

value: Vehicle


title: ATAC-Seq R35A_1h_rep1

value: B-cells

value: Transdifferentiation


title: ATAC-Seq R35A_0h_rep2


title: Cow 3 Day 1 Evening


title: 28day, SCI, Vehicle, #5 (RRBS)


title: Cow 3 Day 2 Morning

value: Morning


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-D11


title: Cow 2 Day 3 Morning

value: Cow 2


title: 28day, SCI, Vehicle, #4 (RRBS)


title: 28day, SCI, Boldine #2 (RRBS)

value: Boldine


title: Cow 2 Day 4 Evening

value: Evening

value: skimmed milk


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-D24

value: SEP

value: M


title: 28day, SCI, Boldine #1 (RRBS)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-C23


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-D23


title: Cow 2 Day 4 Morning


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-C12


title: 28day, SCI, Vehicle, #3 (RRBS)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-D12


title: Cow 2 Day 3 Evening


title: ATAC-Seq WT_120h_rep2

value: Macrophages


title: ATAC-Seq R35A_0h_rep1


title: ATAC-Seq WT_18h_rep1


title: 28day, SCI, Boldine #3 (RRBS)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-C24


title: 28day, SCI, Boldine #6 (RRBS)


title: ATAC-Seq WT_120h_rep1


title: Cow 2 Day 2 Morning


title: ATAC-Seq WT_18h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-B23


title: Cow 1 Day 4 Morning

value: Cow 1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-C11


title: 28day, Sham, Vehicle, #3 (RRBS)

value: Sham


title: 28day, SCI, Vehicle, #2 (RRBS)


title: 28day, SCI, Vehicle, #1 (RRBS)


title: Cow 2 Day 1 Morning


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-B24


title: ATAC-Seq WT_6h_rep2


title: Cow 1 Day 4 Evening


title: Cow 2 Day 2 Evening


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-A24


title: ATAC-Seq WT_6h_rep1


title: 28day, Sham, Vehicle, #4 (RRBS)


title: 7day, SCI, Boldine, #6 (RRBS)

value: 7 days


title: ATAC-Seq WT_3h_rep2


title: ATAC-Seq WT_1h_rep1


title: Cow 1 Day 1 Evening


title: Cow 2 Day 1 Evening


title: Cow 1 Day 3 Evening


title: 28day, Sham, Vehicle, #2 (RRBS)

value: gastrocnemius


title: ATAC-Seq WT_3h_rep1


title: 7day, SCI, Boldine, #5 (RRBS)


title: Cow 1 Day 1 Morning


title: 28day, Sham, Vehicle, #1 (RRBS)

value: 28 days


title: ATAC-Seq WT_1h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-A23


title: Cow 1 Day 3 Morning


title: ATAC-Seq WT_0h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-B11


title: 7day, SCI, Boldine, #4 (RRBS)

value: SCI


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-P9


title: GR24+IAA 2

city: Baoding

first: li

middle: jing

last: rui

address: lekainan Street

country: China

institute: HeBei Agricultural University

data_processing:
Illumina HiSeq 4000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: DHL92 4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Cucumis melo

source_name: hypocotyls of melon seedlings, submerged ,2day

growth_protocol: Melon seeds of ‘Xizhoumi No. 25’ were placed in culture dishes  with wet filter paper and then cultured in an incubator at 28°C

extract_protocol:
After treatment, the cut hypocotyls of 12 plants in each  treatment were placed in liquid nitrogen for RNA-Seq, and 30  plants from each treatment group were cultured in half-strength  Murashige and Skoog medium for AR formation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
control treatment (Control): the hypocotyls of melon  seedlings were submerged in water.
SL treatment (GR24): the hypocotyls of melon seedlings  were submerged in 0.1 mg/L of GR24.
SL and IAA treatment (GR24+IAA): the hypocotyls of melon seedlings were submerged in 0.1 mg/L of GR24 and 250 mg/L of IAA.

value: hypocotyls of melon seedlings

tag: cultivar

value: Xizhoumi No. 25

value: Day 2


title: GR24+IAA 3


title: GR24+IAA 1


title: 7day, SCI, Boldine, #3 (RRBS)


title: 7day, SCI, Boldine, #2 (RRBS)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-P22


title: 7day, SCI, Boldine, #1 (RRBS)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-A12


title: GR24 3


title: GR24 1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-O9


title: GR24 2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-O22


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-P10


title: 7day, SCI, Vehicle, #6 (RRBS)

value: Vehicle


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-O21


title: control 3

value: control

value: Day 0


title: control 2


title: 7day, SCI, Vehicle, #4 (RRBS)


title: 7day, SCI, Vehicle, #3 (RRBS)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-P21


title: ATAC-Seq WT_0h_rep1

value: B-cells

value: Transdifferentiation


title: control 1


title: BBS Mut_MCF7_Hypoxia_1

type: RNA

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

description: Transcriptome data after culturing PKM2 knockout MCF7 cells in 1% O2 (Biological Rep 1)

hyb_protocol: Hybridization was done on Affymetrix GeneChipTM Human Transcriptome Array 2.0 (HTA 2.0) chips at 45 ⁰C for 16 hrs.

scan_protocol: Chips were scanned using Affymetrix Scanner 7G

data_processing:
Transcriptome Analysis Console 4.0 was used to analyze files generated after scanning
HTA-2_0.r1.pgf
HTA-2_0.na33.1.hg19

label: Biotin

source_name: PKM2 knockout of MCF7

label_protocol: 100 ng of total RNA was used to prepare biotinylated cDNA using GeneChipTM WT Plus Reagent Kit (Applied Biosystems) as per the instructions given by the manufacturer.

growth_protocol: MCF7 and its PKM2 knockout cells were cultured in media recommended by American Type Cell Culture in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol: Samples were lysed using TRIzol reagent (Invitrogen), and total RNA was isolated using the PureLink RNA Mini Kit (Invitrogen)

treatment_protocol: For analyzing global transcriptional alterations, cell were either cultured at 21% O2 (normoxia) or at 1% O2 (hypoxia) for 24hours.

tag: genotype/variation

value: PKM2 knockout

value: Breast cancer (luminal)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-N21

value: SEP

value: M


title: 7day, SCI, Vehicle, #5 (RRBS)


title: BBS Mut_MCF7_Normoxia_1

description: Transcriptome data after culturing PKM2 knockout MCF7 cells in 21% O2 (Biological Rep 1)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-M21


title: BBS Mut_MCF7_Hypoxia_2

description: Transcriptome data after culturing PKM2 knockout MCF7 cells in 1% O2 (Biological Rep 2)


title: BBS Mut_MCF7_Normoxia_2

description: Transcriptome data after culturing PKM2 knockout MCF7 cells in 21% O2 (Biological Rep 2)


title: aMHC-Cre;Arid1a f/f cKO rep2

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts in matrix table

source_name: P7 Ventricles

extract_protocol:
standard Trizol totalRNA extraction
Truseq stranded mRNA (Illumina)

value: aMHC-Cre;Arid1a f/f cKO

value: Ventricles


title: aMHC-Cre;Arid1a f/f cKO rep3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-A11


title: 7day, SCI, Vehicle, #2 (RRBS)

value: gastrocnemius

value: 7 days


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-M10


title: WT BBS_MCF7_Hypoxia_1

description: Transcriptome data after culturing MCF7 cells in 1% O2 (Biological Rep 1)

source_name: Breast cancer cell line MCF7

value: WT


title: WT BBS_MCF7_Hypoxia_2

description: Transcriptome data after culturing MCF7 cells in 1% O2 (Biological Rep 2)


title: 7day, SCI, Vehicle, #1 (RRBS)

value: SCI


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-L9


title: aMHC-Cre;Arid1a f/f cKO rep4


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-M22


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-L21


title: 7day, Sham, Vehicle, #4 (RRBS)

value: Sham


title: 7day, Sham, Vehicle, #3 (RRBS)


title: Arid1a f/f control rep3

value: Arid1a f/f control


title: 7day, Sham, Vehicle, #2 (RRBS)

value: Vehicle


title: WT BBS_MCF7_Normoxia_1

description: Transcriptome data after culturing MFC7 cells in 21% O2 (Biological Rep 1)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-O10


title: WT BBS_MCF7_Normoxia_2

description: Transcriptome data after culturing MCF7 cells in 21% O2 (Biological Rep 2)


title: Arid1a f/f control rep2


title: Arid1a f/f control rep1


title: Arid1a f/f control rep5


title: 7day, Sham, Vehicle, #1 (RRBS)


title: aMHC-Cre;Arid1a f/f cKO rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-K22


title: H3K27Ac Arid1a cKO rep2

data_processing:
mapping to reference genome with BWA 0.7.17-r1188
peak caliing with Homer v4.11 findPeaks -style histone
differential peak occupancy analysis with Diffbind 2.12.0 with option -minOverlap 2 and DESeq2_1.24.0
generate bedGraph files with Homer v4.11 makeUCSCfile normalized to 1e7 reads
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files

extract_protocol:
Formaldehyde crosslinked nuclei were sonicated and histone-DNA complexes were isolated using anti-H3K27Ac (Active Motif, cat# 39133).
NEXTFLEX® Rapid DNA-Seq Library Prep Kit for Illumina® Platforms

tag: chip antibody

value: anti-H3K27Ac (Active Motif, cat# 39133)


title: Arid1a f/f control rep4


title: 28day, SCI, Boldine #1 (RNA-seq)

data_processing:
Sequence reads were quality control tested using FastQC, then trimmed for adaptor sequence/low-quality sequence using Trim Galore and CutAdapt
Spliced Transcripts Alignment to a Reference (STAR) was used to align the trimmed reads to the mm10 genome and generate gene counts
Assembly: mm10
Supplementary files format and content: The rawCounts spreadsheet contains the raw counts, as given by STAR for each sample and each Ensembl ID.

extract_protocol:
Mice were euthanized at 7 or 28 d post-surgery. The gastrocnemius was carefully excised, wet-weighed, then flash frozen in liquid nitrogen-cooled isopentane.
RNA was isolated from ~20 mg of the gastrocnemius cut to contain equal amounts of both medial and lateral heads  of the gastrocnemius using the miRNeasy kit (Qiagen) according to manufacturer’s recommendations, with minor deviations. Samples were then shipped to Novogene, LLC for library preparation and mRNA sequencing with 1 μg of RNA per sample being used as input material for all RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (New England BioLabs) following manufacturer’s recommendations.

value: 28 days

value: Boldine


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-L22


title: 28day, SCI, Boldine #4 (RNA-seq)


title: 28day, SCI, Boldine #5 (RNA-seq)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-J9


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-L10


title: 28day, SCI, Boldine #3 (RNA-seq)


title: 28day, SCI, Boldine #2 (RNA-seq)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-K9


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-J22


title: 28day, SCI, Vehicle, #4 (RNA-seq)


title: Input Arid1a cKO rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-J10


title: 28day, SCI, Vehicle, #6 (RNA-seq)


title: H3K27Ac Arid1a cKO rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-K21


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-K10


title: Input Control rep1

value: Arid1a f/f Control


title: 28day, SCI, Vehicle, #1 (RNA-seq)


title: 28day, SCI, Vehicle, #5 (RNA-seq)


title: H3K27Ac Control rep1


title: Input Arid1a cKO rep1


title: 28day, SCI, Vehicle, #2 (RNA-seq)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-J21


title: T738, Tumor Sample 29

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
150 bp reads, Illumina raw reads were trimmed to remove adaptor and low-quality sequences (phred score <20) using Trimmomatic.
Trimmed sequence reads were mapped to CanFam3.1 genome using STAR aligner with default settings.
Read count extraction was done using HTSeq-Count tool and normalized using DESeq2.
Assembly: CanFam3.1
Supplementary files format and content: comma-separated csv file include raw count values for each tumor samples
Supplementary files format and content: comma-separated csv file include DESeq2 normalized counts for each tumor samples

organism: Canis lupus familiaris

source_name: Subcutaneous

extract_protocol:
TRIzol (Invitrogen), was used to extract total RNA from 29 primary tumors. The RNA samples were cleaned using RNeasy cleanup (Qiagen), respectively. RNA was quantified on a NanoDrop Microvolume  Spectrophotometer and quality was assessed by Bioanalyzer (Agilent).
The total RNA extracted from 29 samples were processed using Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (product number: 0520-A01), following manufacturer's protocol, and the resulting cDNA library was sequenced on Illumina NovaSeq6000 to generate

value: Subcutaneous

tag: breed

value: Pointer

value: Soft tissue sarcoma

value: Male


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-I9

value: SEP

value: M


title: 28day, SCI, Boldine #6 (RNA-seq)

value: gastrocnemius

tag: treatment


title: Input Control rep2

value: Ventricles


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-I22


title: 28day, Sham, Vehicle, #4 (RNA-seq)

tag: time


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-I21


title: 28day, SCI, Vehicle, #3 (RNA-seq)


title: 28day, Sham, Vehicle, #3 (RNA-seq)


title: H3K27Ac Control rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-I10


title: T697, Tumor Sample 28

value: Labrador Retriever

value: Female


title: T485, Tumor Sample 27

source_name: Oral cavity

value: Oral cavity

value: Mix


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-H9


title: 28day, Sham, Vehicle, #1 (RNA-seq)

value: Sham

value: Vehicle


title: T479, Tumor Sample 26

value: German Shepherd


title: 28day, Sham, Vehicle, #2 (RNA-seq)

value: 28 days


title: 7day, SCI, Boldine, #6 (RNA-seq)

value: 7 days

value: SCI

value: Boldine


title: T416, Tumor Sample 25

value: Subcutaneous

value: Alaskan Malamute

value: Soft tissue sarcoma


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-H21

value: SEP

value: M


title: T344, Tumor Sample 24

value: Basset Hound


title: 7day, SCI, Boldine, #4 (RNA-seq)

value: gastrocnemius


title: T336, Tumor Sample 23

value: Female


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-G9


title: T311, Tumor Sample 21

value: Male


title: 7day, SCI, Boldine, #3 (RNA-seq)


title: 7day, SCI, Boldine, #2 (RNA-seq)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-G10


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-G22


title: 7day, SCI, Boldine, #1 (RNA-seq)


title: T282, Tumor Sample 20

value: Oral cavity

value: Border Collie


title: 7day, SCI, Vehicle, #6 (RNA-seq)

value: Vehicle


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-F9


title: 7day, SCI, Vehicle, #5 (RNA-seq)


title: T232, Tumor Sample 19

value: Poodle


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-F22


title: T230, Tumor Sample 18

value: Mix


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-H22


title: 7day, SCI, Vehicle, #4 (RNA-seq)

value: 7 days


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-F21


title: T218, Tumor Sample 17


title: 7day, SCI, Boldine, #5 (RNA-seq)

value: SCI


title: 428_DC12W + Lixi

city: Frankfurt

first: Paulus

last: Wohlfart

state: Hessen

address: Industriepark Höchst, K703

department: MSAT M&I

institute: Sanofi Aventis Deutschland GmbH

description: 8489R2_428_IndexD705-D506_ATTCAGAA+TAATCTTA_L004_R1_001.FN

data_processing:
Array Studio Version 10.1.3.3. (Omicsoft Qiagen)
RNA sequencing raw data were analyzed using a standardized RNA Seq analysis workflow. This work- flow included alignment to a reference rat gene model, quantification, and normalization.
Normalized expressions were assessed on differentially expressed genes using the DESeq2 module (EMBL, Love et al., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, 2014;15(12):550)
Further pathway and in silico analyses were performed using the online software tool GNCPro (SABiosciences) and Astrocyte RNAseq Database.
Assembly: Rat.B5.0 Ensembl.R78
Supplementary files format and content: raw counts for each gene (by ensembl ID) and sample
Supplementary files format and content: normalized FKPM expression counts for each gene (by ensembl ID) and sample

organism: Rattus norvegicus

source_name: Retina

growth_protocol: 8-weeks-old male Wistar rats (Harlan Winkelmann, Borchen, Germany). Animals were held in a 12-hours light-dark cycle with food and water ad libitum.  Hemoglobin A1c (HbA1c) was determined using an A1cNow+ System from pts Diagnostics (EuroMedix Health am Dom GmbH, Köln, Germany).

extract_protocol:
After a total duration of hyperglycemia of 12 weeks, rats were killed, and the eyes were obtained and stored at -80°C until further use. Total retinal RNA was isolated using Trizol reagent according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA). Six retinae total RNA samples from each group were randomly selected for RNA-sequencing to obtain an unbiased view of retinal transcriptome.
mRNA-focused library preparation with total RNA and using an Ilumina sampe prep kit. Thereafter, single-end sequencing with 50bp reads. Per sample 40x10E6 to 50x10E6 reads were obtained.

treatment_protocol:
Hyperglycemia was induced by intravenous injection of streptozotocin (STZ) (35 mg/kg body weight; Roche Diagnostics GmbH, Mannheim, Germany). Rats with a blood glucose level above 14 mmol/L (250 mg/dL) one week after STZ injection were considered diabetic (DC).  Age-matched male Wistar rats served as controls (NC). The study was approved by the regional ethics committee (Regierungspräsidium Karlsruhe, Germany; protocol code “Aktenzeichen: 35-9185.81/G-15/15”; date of approval 16.07.2015). All experiments were conducted in accordance with the Association for Research in Vision and Ophthalmology statement for the Use of Animals in Ophthalmic and Vision Research.
Lixisenatide (Sanofi, Frankfurt) was administered 5 days a week to diabetic rats subcutaneously at a concentration of 150 µg/kg body weight from week 1 to week 12 (DC+Lixi) after STZ treatment.

value: Retina

tag: strain

value: Wistar

tag: cell type

value: whole retina / neurovascular unit

value: lixisenatide s.c.


title: 7day, SCI, Vehicle, #3 (RNA-seq)


title: 419_DC12W + Lixi

description: 8489R2_419_IndexD705-D505_ATTCAGAA+AGGCGAAG_L004_R1_001.FN


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-F10

value: SEP


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-H10

value: M


title: T320, Tumor Sample 22

value: Subcutaneous

value: Soft tissue sarcoma


title: 403_DC12W + Lixi

description: 8489R2_403_IndexD704-D507_GAGATTCC+CAGGACGT_L004_R1_001.FN


title: 7day, SCI, Vehicle, #2 (RNA-seq)

value: gastrocnemius


title: T1989, Tumor Sample 15

value: Labrador Retriever

value: Female


title: 401_DC12W + Lixi

description: 8489R2_401_IndexD704-D506_GAGATTCC+TAATCTTA_L004_R1_001.FN


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-E22


title: 7day, SCI, Vehicle, #1 (RNA-seq)


title: T1923, Tumor Sample 14

value: Siberian Husky

value: Male


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-E21


title: 7day, Sham, Vehicle, #4 (RNA-seq)

value: Sham

value: Vehicle


title: 388_DC12W + Lixi

description: 8489R2_388_IndexD704-D505_GAGATTCC+AGGCGAAG_L004_R1_001.FN


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-E10


title: 430_DC12W

description: 8489R2_430_IndexD703-D508_CGCTCATT+GTACTGAC_L004_R1_001.FN

value: placebo


title: 7day, Sham, Vehicle, #3 (RNA-seq)

value: 7 days


title: T1891, Tumor Sample 12


title: 7day, Sham, Vehicle, #2 (RNA-seq)


title: T1860, Tumor Sample 11

value: Cock-a-poo


title: T1921, Tumor Sample 13

value: Golden Retriever


title: 418_DC12W + Lixi

description: 8489R2_418_IndexD704-D508_GAGATTCC+GTACTGAC_L004_R1_001.FN

value: Retina

value: Wistar

value: whole retina / neurovascular unit


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-D9

value: SEP

value: M


title: T2063, Tumor Sample 16

value: Subcutaneous

value: Mix

value: Soft tissue sarcoma


title: 407_DC12W

description: 8489R2_407_IndexD703-D506_CGCTCATT+TAATCTTA_L004_R1_001.FN


title: 7day, Sham, Vehicle, #1 (RNA-seq)

value: gastrocnemius


title: T1834, Tumor Sample 10

value: Oral cavity


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-E9


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-D22


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-D21


title: 396_DC12W

description: 8489R2_396_IndexD703-D505_CGCTCATT+AGGCGAAG_L004_R1_001.FN


title: T167, Tumor Sample 9

value: Male


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-D10


title: 390_DC12W

description: 8489R2_390_IndexD702-D508_TCCGGAGA+GTACTGAC_L004_R1_001.FN


title: SNAP4_nodule_rep2

city: Guangzhou

first: Xin

last: Wang

address: waihuanxi road

institute: Guangzhou University

data_processing:
Paired-end raw reads were trimmed by trim_galore v0.6.6 for adaptors and low quality with default parameters.
high-quality reads were then aligned to the reference genome using Bowtie2 v2.3.4.3 with very-sensitive model.
Properly paired and uniquely mapped reads were then filtered by mapping quality (MAPQ > 30) using samtools
Read coverage was calculated using bamCoverage function in deeptools v3.5.1
Peak calling was performed by MACS2 v2.2.7.1 with parameters of -q 0.05 and -g 1.0e9.
Assembly: soybean Wm82 v4 reference genome
Supplementary files format and content: narrowPeak

organism: Glycine max

source_name: soybean root nodule

extract_protocol:
Root tissues with nodules were fixed with 1% formaldehyde in PBS for 15 min under vacuum. After nuclei extraction, the chromatin was sonicated to 300-500 bp by using Covaris M220.
Chip-seq libraries were performed by a Tn5-mediated method. 1 g sample was used to extract nucleus, which were sonicated and IP with beads complement with Flag antibody (Sigma F1804). The beads were then washed with wash buffer and treated by Tn5. The libraries were amplified with N50x and N70x index primers.

value: root nodule

value: SNAP4 mutant

value: Flag antibody (Sigma F1804)


title: T1585, Tumor Sample 8

value: Beagle

value: Female


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-C9


title: SNAP3_nodule_rep2

value: SNAP3 mutant


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-C22


title: 439_NC12W

description: 8489R2_439_IndexD702-D506_TCCGGAGA+TAATCTTA_L004_R1_001.FN

value: Retina

value: placebo


title: SNAP3_nodule_rep1


title: 386_DC12W

description: 8489R2_386_IndexD702-D507_TCCGGAGA+CAGGACGT_L004_R1_001.FN

value: Wistar

value: whole retina / neurovascular unit


title: SNAP4_nodule_rep1


title: T1490, Tumor Sample 7

value: Golden Retriever


title: T148, Tumor Sample 6

value: Subcutaneous


title: 438_NC12W

description: 8489R2_438_IndexD702-D505_TCCGGAGA+AGGCGAAG_L004_R1_001.FN


title: SNAP2_nodule_rep2

value: SNAP2 mutant


title: T1462, Tumor Sample 5

value: Labrador Retriever

value: Soft tissue sarcoma


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-C21

value: SEP

value: M


title: 437_NC12W

description: 8489R2_437_IndexD701-D508_ATTACTCG+GTACTGAC_L004_R1_001.FN


title: 425_DC12W

description: 8489R2_425_IndexD703-D507_CGCTCATT+CAGGACGT_L004_R1_001.FN


title: SNAP2_nodule_rep1

value: root nodule


title: T1407, Tumor Sample 4

value: Oral cavity

value: Mix

value: Male


title: T1292, Tumor Sample 3

value: Beagle


title: SNAP1_nodule_rep2

value: SNAP1 mutant

value: Flag antibody (Sigma F1804)


title: 432_NC12W

description: 8489R2_432_IndexD701-D506_ATTACTCG+TAATCTTA_L004_R1_001.FN

value: Retina

value: placebo


title: 433_NC12W

description: 8489R2_433_IndexD701-D507_ATTACTCG+CAGGACGT_L004_R1_001.FN

value: Wistar

value: whole retina / neurovascular unit


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-B22


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-B9


title: SNAP1_nodule_rep1


title: T1238, Tumor Sample 2

value: Subcutaneous


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-B21


title: 431_NC12W

description: 8489R2_431_IndexD701-D505_ATTACTCG+AGGCGAAG_L004_R1_001.FN


title: T1124, Tumor Sample 1

value: Greyhound


title: Npas4 CUT&Tag (fear conditioning + saline)

city: Pohang-si

first: Dahun

last: Um

address: 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673

department: Life science

country: South Korea

institute: Pohang University of Science and Technology(POSTECH)

data_processing:
Library strategy: CUT&Tag
low quality and adapter sequences were trimmed using ‘Trim Galore’ with ‘-q 30 –paired’ options.
Trimmed reads were aligned for mm10 reference FASTA using ‘Bowtie2’ with ‘-local --very-sensitive-local --no-mixed --no-discordant'  options.
Aligned reads were sorted using ‘sambamba’.
bigWig file was generated using “makeUCSCfile” in HOMER package. Reads were normalized with 1e7(default).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Brain

growth_protocol: Mice were housed under 12-hour light and dark cyle with ad libitum for water and food

extract_protocol:
Tissue was homogenized in NE buffer
CUTANATM High fidelity 2X PCR maswer mix

treatment_protocol: Discriminative fear conditioning composed of two cues, first (10 kHz, 75 db, 30 sec) paired with electric shock (0.4 mA, 0.5 sec) and the second (2 kHz, 75 db, 30 sec) with out shock. 8 CS-US pairings.

value: brain (amygdala)

value: fear conditioning + saline

tag: antibody

value: Rabbit Anti-Npas4 (Activity signaling)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-5-O21-C10

value: SEP

value: M


title: control_50_me [206375080192_R05C01]

status: Public on Jul 04 2023

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description: Methylation titration controls

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.17
matrix processed value definition: Normalized average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Human cell line DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from cell lines following Laird et al. 1991 (PMID: 1870982)

tag: cell line

value: control


title: control_5_me [206375080192_R02C01]

description: Methylation titration controls


title: control_100_me [206375080192_R07C01]

description: Methylation titration controls


title: HCT116_V1_Rep2_Lab2 [206648970096_R01C01]

description: Evaluating cross-lab reproducibility


title: control_25_me [206375080192_R04C01]

description: Methylation titration controls


title: control_75_me [206375080192_R06C01]

description: Methylation titration controls


title: HCT116_V1_Rep1_Lab2 [206648970013_R03C01]

description: Evaluating cross-lab reproducibility


title: control_0_me [206375080192_R01C01]

description: Methylation titration controls


title: control_10_me [206375080192_R03C01]

description: Methylation titration controls


title: GM12878_low_input_50ng   [206375080148_R05C01]

description: Testing EPICv2 on low input DNA


title: GM12878_low_input_100ng   [206375080148_R04C01]

description: Testing EPICv2 on low input DNA


title: GM12878_low_input_1ng   [206375080148_R08C01]

description: Testing EPICv2 on low input DNA


title: GM12878_rep2 [206375080148_R03C01]

description: Cell line methylation profiles


title: LNCaP  [206375080148_R02C01]

description: Cell line methylation profiles

value: LNCaP


title: Wing Rep3

city: Cambridge

first: Soumen

last: Khan

address: Babraham Hall

department: Epigenetics

country: United Kingdom

institute: Babraham Institute

data_processing:
Reads were aligned to the Drosophila genome (version dm6) using hisat2 with deafult settings
Aligned reads were converted to BAM format using Bamtools. Duplicate and unaligned reads were filtered (bamtools view -F 0x200 -F 0x4 )
Raw counts were calculated using the Htseq software
Differentially expressed genes list identified using the edgeR software
Assembly: dm6
Supplementary files format and content: Differentially expressed genes list

organism: Drosophila melanogaster

source_name: Wing imaginal discs

extract_protocol:
Wing and haltere imaginal discs were isolated and snap frozen in Trizol. RNA was isolated using Trizol method and then further purified using Qiagen Rneasy mini kit. RNA quality and quantity was checked on Bioanalyzer (Agilent Bioystems).
100ng of Total RNA was taken for mRNA isolation, fragmentation and priming. The fragmented and primed mRNA was further subjected to first strand synthesis in the presence of Actinomycin D (Gibco, life technologies, CA, USA) followed by second strand synthesis. The double stranded cDNA was purified using HighPrep PCR magnetic beads (Magbio Genomics Inc, USA). The purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® UltraTM Directional RNA Library Prep Kit protocol.

value: Canton S

tag: tissue

value: Wing imaginal discs

tag: larval stage

value: Third instar wandering (L3)

tag: genotype

value: Wild Type


title: K562  [206375080148_R01C01]

description: Cell line methylation profiles


title: GM12878_rep1 [206375080192_R08C01]

description: Cell line methylation profiles


title: Wing Rep2


title: Haltere Rep3

source_name: Haltere imaginal discs

value: Haltere imaginal discs


title: GM12878_low_input_5ng   [206375080148_R07C01]

description: Testing EPICv2 on low input DNA


title: Haltere Rep2


title: Wing Input Rep3

data_processing:
Trimming adapter sequences using Trimmomatic (version 0.36)
Trimmed reads were aligned to the Drosophila genome (version BDGP6.28) using bwa-mem with deafult settings
Aligned reads were converted to BAM format using Bamtools (version). Duplicate and unaligned reads were filtered (bamtools view -F 0x200 -F 0x4 )
Peak calling was performed using MACS2 using parameters (maxdup=1, FDR=0.05)
Consensus peaks were identified using a R program (https://ro-che.info/articles/2018-07-11-chip-seq-consensus)
Assembly: BDGP6.28
Supplementary files format and content: Peak text files and consensus peaks file

extract_protocol:
Wing and haltere imaginal discs were crosslinked using 1.5% para-formaldehyde solution. Sonication was perfomed using the Covaris S2 sonicator. Chromatin Immunoprecipitation was perfomed using polyclonal Ubx antibodies raised against the N-terminal region.
Equal amounts of DNA (~2 ng) was used as an input fo each sample and libraries prepared using standard protocol using NEB Ultra II DNA library prep kits (NEB #E7645). Number of cycles for amplification of adapter ligated libraries were estimated by the qPCR before final amplification to avoid any bias arising due to PCR amplification and indexing (NEB #E7350).


title: Haltere Rep1


title: Wing Input Rep1


title: Wing ChIP Rep3


title: Wing ChIP Rep2


title: GM12878_low_input_10ng   [206375080148_R06C01]

description: Testing EPICv2 on low input DNA


title: Wing Rep1


title: Wing ChIP Rep1


title: Haltere Input Rep2


title: Haltere Input Rep3


title: Wing Input Rep2


title: Haltere Input Rep1


title: Haltere ChIP Rep3


title: Haltere ChIP Rep2


title: Haltere ChIP Rep1


title: Tau_3

city: Hangzhou

first: Xue

middle: Xiu

last: Min

address: cangqian

institute: Hangzhou normal university

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: 200 uM Tau for 24 h


title: Tau_2


title: Tau_1


title: CTL_3

value: Without special treatment


title: CTL_2


title: CTL_1


title: P7_1 DSM

city: Parma

first: Ilaria

last: Minato

address: Parco Area delle Scienze 23/a

country: Italy

institute: Università di Parma

data_processing:
Read quality analysis was performed with the FastQC.
Adapters’ sequences were trimmed with BBduk from the suite BBtools (http://jgi.doe.gov/data-and-tools/bb-tools/).
RNA-seq reads were aligned on the rabbit genome (Oryctolagus cuniculus, OryCun2.0) with STAR (Dobin et al., 2013).
Gene counts were obtained with HTSeq-count (Anders et al., 2015), using the latest Ensembl available annotation on rabbit. A custom script, accessible at https://github.com/danilotat/UTR_add_extend_GTF, was employed to account for reads mapping to unannotated 3’ UTRs of protein coding genes.
Assembly: OryCun2.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Oryctolagus cuniculus

source_name: Lung

growth_protocol: Fetal animals were extracted by C-section, and the lungs were immediately harvested at the 20th, 23rd, 25th, 27th, 28th, and 29th days of gestation. Term rabbits were naturally delivered at term on the 31st day of gestation. After birth, pups were maintained with their mothers at room air in individual cages up the lung samples collection. Instead, preterm pups were delivered through C-section on the 28th day of gestation, maintained in custom-made incubators and were fed twice daily via a milk replacer

extract_protocol:
After collection, lungs were immediately placed in RNA Later (Sigma Aldrich, USA) and stored at -20°C. Samples were homogenized in QIAzol® Lysis Reagent. Total RNA was extracted with the miRNeasy Mini Kit protocol (QIAGEN, Germany), using an automated method (QIAcube: QIAGEN, Germany), adapted to include DNase I treatment.
Libraries for massive parallel RNA sequencing (RNA-seq) were prepared with the QuantSeq FWD (Lexogen) kit and sequenced with the use of an Illumina NextSeq500 platform, which generated at least 20 million reads/sample (75 bp Single End).

treatment_protocol: Preterm animals were maintained in custom-made incubators at 21% of Oxygen for 7 days and fed twice daily via an orogastric tube with a milk replacer

value: New Zealand White

value: Total Right Lung Homogenate

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 7 days

tag: gestational age

value: 35th day

tag: rna-sequencing run

value: run 3


title: HCT116_20_Lab2 [206909630028_R05C01]

description: Evaluating cross-lab reproducibility


title: HCT116_V2_Rep2_Lab2 [206909630030_R01C01]

description: Evaluating cross-lab reproducibility


title: T35_11 DSJ

value: Delivered on 31st day of gestation (term birth) and manteined for 4 days


title: HCT116_50_Lab2 [206909630028_R04C01]

description: Evaluating cross-lab reproducibility


title: T35_6 DSI


title: F28_7 DSH

value: Delivered on 28th day of gestation

value: 28th day


title: AMC-HN-8 cells, control, replicate-2

city: shanghai

first: Xiaohui

last: Yuan

state: shanghai

address: 83 fenyang road

institute: Eye & ENT Hospital of Fudan University

scan_protocol: Bisulfite-converted DNA was analysed on an Illumina Infinium MethylationEPIC(850K) BeadChip (Illumina)

data_processing: Idat files were imported and then preprocessed with ChAMP[1] (version 2.12.4) package in R to get raw data. Next, the raw data was normalized with BMIQ method.

label: cy3 and cy5

source_name: LSCC cell

label_protocol: DNA was bisulfite treated using the Zymo Research EZ DNA methylaiton-Glod Kits (Zymo Research, Irvine, CA, USA).

extract_protocol: total DNA was extracted from AMC-HN-8 cells using QIAamp DNA Mini Kit

value: laryngeal cancer

value: control


title: F28_2 DSF


title: pSLIK_IDH1_R132H_48hours

city: Magdeburg

first: Ulf

last: Kahlert

address: Leipziger Str 44

institute: Otto-vo-Guericke University

data_processing: Standard Illumina Protocol

label: Cy3 and Cy5

source_name: human brain

growth_protocol: Genomic DNA was extracted and purified from cell culture samples using Qiagen DNeasy Kit according to standard instructions

extract_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC chip according to standard protocol

treatment_protocol: Standard Illumina Protocol

tag: gender

value: male

value: human foreskin

tag: disease state

value: glioblastoma


title: pSin_P53+pSLIK_EV_48hours


title: HCT116_100_Lab2 [206909630028_R03C01]

description: Evaluating cross-lab reproducibility


title: pSin_P53+pSLIK_IDH1_R132H_24hours


title: iPS11 p53R175H 2D ind.

description: 2D neural induction neurosphere culture overexpressing  P53R175H

value: Glioblastoma


title: F25_13 DSD

value: Delivered on 25th day of gestation

value: 25th day


title: T42_50 DSB

value: Delivered on 31st day of gestation (term birth) and manteined for 11 days

value: 42nd day


title: HCT116_250_Lab2 [206909630028_R02C01]

description: Evaluating cross-lab reproducibility


title: pSLIK_EV_48hours

description: Empty Vector


title: T42_33 DSA

value: New Zealand White

value: Total Right Lung Homogenate


title: pSLIK_IDH1_48hours


title: AMC-HN-8 cells, control, replicate-1


title: pSin_P53+pSLIK_EV_24hours


title: HCT116_V2_Rep1_Lab2 [206909630028_R01C01]

description: Evaluating cross-lab reproducibility


title: rtel1-1, ATAC-seq

city: Clermont-Ferrand

first: Olivier

last: Mathieu

state: Auvergne

address: 28 Place Henri Dunant

department: UMR 6293 - iGReD

country: France

institute: CNRS

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with default parameters.
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.2b (Dobin et al 2013) retaining multi-mapped reads mapping up to 10 positions. Subsequent read counting was performed with featureCounts version 2.0.0 (Liao, Smyth, and Shi 2014) on the TAIR10 TE and PCG annotations. Normalization and differential analyses were done using DESeq2 version 1.26.0 (Love, Huber, and Anders 2014) with default parameters. Only loci with Benjamini-Hochberg adjusted p-values < 0.05 and with a log2-fold change ≥ 0.585 or ≤ − 0.585 were considered differentially expressed.
BS-seq datasets : data analysis was done using the Methylpy analysis pipeline v1.4.6 (Schultz et al. 2015). Reads were filtered to remove PCR duplicates using Picard v2.23.3 and mapped to TAIR10 using Bowtie2 v2.4.1 (Langmead and Salzberg 2012). Only cytosines with a minimum coverage of 6 reads were retained.
ATAC-seq datasets : Reads were mapped to the Arabidopsis TAIR10 reference genome using STAR version 2.7.2b (--outFilterMultimapNmax 1 --outFilterMatchNmin 10 --alignIntronMax 10000, all other parameters default).Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite v2.23.3.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq: bigWig format files with methylation levels for CG, CHG and CHH methylation. Only positions with 6+ coverage were used to generate the bigWig files. RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins. ATAC-seq: bigWig format files with normailzed read densities (Reads Per Genomic Content) calculated in 1 bp bins.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol:
Sixteen-day-old seedlings (100 mg) were ground and nuclei were isolated with 4 °C buffer (0.25 M sucrose, 10 mM Tris-HCl, 10 mM MgCl2, 1% Triton, 5 mM β-mercaptoethanol) containing proteinase inhibitor cocktail (Roche) and filtered with a 63 μm filter.
Nuclei were resuspended in 1× TD buffer (Illumina FC-121-1030) and 2.5 μL of Tn5 transposes (Illumina FC-121-1030) were added. The transposition reaction was performed at 37 °C for 30 min, and DNA was purified using a Qiagen MinElute Kit.

treatment_protocol: no treatment

tag: developmental stage

value: 16-day-old seedlings

value: seedling


title: AMC-HN-8 cells, F. nucleatum-treated, replicate-3

value: F. nucleatum-treated


title: T42_14 DRZ

value: run 3


title: T37_47 DRU

value: Delivered on 31st day of gestation (term birth) and manteined for 6 days

value: 37th day


title: iPS11 P53R175H EGFRvIII 2D ind.

description: 2D neural induction neurosphere culture overexpressing  P53R175H EGFRvIII


title: iPS11 Blank 2D ind.

description: 2D neural induction neurosphere culture

value: Control


title: rtel1-3, ATAC-seq


title: T37_46 DRT


title: control_75_me [206909630042_R06C01]

description: Methylation titration controls

value: control


title: pSLIK_EV_24hours

description: Empty Vector

value: male

value: human foreskin


title: iPS11 cMyc 2D ind.

description: 2D neural induction neurosphere culture  overexpressing  cMYC

value: Medulloblastoma


title: pSin_P53+pSLIK_IDH1_48hours

value: glioblastoma


title: iPS11 pSin EGFRvIII

description: IPS11- EGFRv,III overexpressing cell culture

value: Glioblastoma


title: WT, ATAC-seq


title: pSLIK_IDH1_24hours


title: T37_27 DRS


title: control_50_me [206909630042_R05C01]

description: Methylation titration controls


title: T37_12 DRR


title: T31_18 DRQ

value: Delivered on 31st day of gestation (term birth)

value: 31st day


title: AMC-HN-8 cells, F. nucleatum-treated, replicate-2

value: laryngeal cancer


title: AMC-HN-8 cells, control, replicate-3+B37


title: iPS11 pSin p53R175H/EGFRvIII

description: IPS11- p53R175H/EGFRvIII overexpressing cell culture


title: iPS11 pSin p53R175H

description: IPS11- cMYC overexpressing cell culture


title: pSLIK_IDH1_R132H_24hours


title: CFs, Input

city: Wuhan

first: Zhen-Guo

last: Ma

state: Hubei

address: No.238 Jiefang Road

institute: Renmin Hospital fo Wuhan University

description: ChIP-Seq was performed with IgG.

data_processing:
ChIP-seq with input DNA and ChIP DNA was performed by Seqhealth (Wuhan, China)
Raw reads were processed to include only high-quality reads using Trimmomatic
Clean data were compared to a human genome (hg19) using STAR software (version 2.5.3a)
To identify a significant binding site of IRX2, peak calling was performed with MACS2, with the input used as the control. Peaks with P values <0.01 were kept for further analyses
Peak annotation was performed with BEDTools (Version v2.25.0). Motif analysis was performed with Homer (version 4.10)
Assembly: hg19
Supplementary files format and content: peaks file (except for Input sample)

source_name: Human cardiac fibroblast

growth_protocol: Human CFs were maintained in DMEM/F12 containing 10% FBS for 48 h

extract_protocol:
After that, the cells were cross-linked with 1% formaldehyde for 10 min. Then, glycine (0.125 mol/l) was added to terminate the cross-linking reaction. The cross-linked cells were harvested with lysis buffer containing a complete protease inhibitor mixture, and the nuclei were collected by centrifugation at 2000 g for 5 min. After that, the nuclei were further treated with nuclear lysis buffer and sonicated (15 times, 30 s on/off)
Sequencing libraries were prepared by using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (#ND607, Vazyme)

value: Human cardiac fibroblast


title: T31_4 DRO

value: New Zealand White

value: Total Right Lung Homogenate


title: pSin_P53+pSLIK_IDH1_24hours


title: CFs, IRX2, #PCRP-1C1

description: ChIP-Seq was performed with an anti-IRX2 antibody (#PCRP-IRX2-1C1).

value: IRX2 (DSHB, #PCRP-1C1)


title: control_5_me [206909630042_R02C01]

description: Methylation titration controls


title: control_25_me [206909630042_R04C01]

description: Methylation titration controls


title: AMC-HN-8 cells, F. nucleatum-treated, replicate-1

value: F. nucleatum-treated


title: F23_40 DRM

value: Delivered on 23rd day of gestation

value: 23rd day

value: run 3


title: CFs, IRX2, #PCRP-1B7

description: ChIP-Seq was performed with an anti-IRX2 antibody (#PCRP-IRX2-1B7).

value: IRX2 (DSHB, #PCRP-1B7)


title: F23_23 DRN


title: control_100_me [206909630042_R07C01]

description: Methylation titration controls

value: control


title: control_10_me [206909630042_R03C01]

description: Methylation titration controls


title: T31_11 DRP


title: RNA-72 hours-3

city: Nanjing

first: Feng

last: Jiang

state: Jiangsu

address: Baiziting 42

institute: Jiangsu Institute of Cancer Research

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCC was used to identify the circRNA and to estimate the circRNA expression.
Differentially expressed genes were identified using the edgeR program.
Assembly: hg38
Supplementary files format and content: EXCEL files include normalized abundance measurements for each Sample

growth_protocol: H1975  cells were cultured in DMEM with 10% FBS (Corning). Before the experiment, cells were tested for mycoplasma, cross-contamination between species and authenticity. Cell lines in the experiments were used within 20 passages.

extract_protocol:
H1975cells were treated with Osi (1000 nM) after which apoptotic cells were washed away with ice-cold PBS, and the total RNA of the remaining cells together with the cells before treatment was extracted using TRIzol reagent.
The Total RNA was incubated for 30 min at 37 °C with 10 units RNase R (Geneseed) .Then，RNA-seq library was prepared with approximately 2μg of total RNA usingRNA-seq (H/M/R) Library Prep Kit for Illumina® (Geneseed).

treatment_protocol: H1975 cells were treated with  Osi for 0 hours or 72 hours followed by circRNA-sequencing

value: Lung

value: NSCLC

value: WT

value: Osimertinib (1000nM) for 72 hours


title: F23_22 DRL


title: F20_36 DRJ

value: Delivered on 20th day of gestation

value: 20th day


title: F23_6 DRK


title: F20_35 DRI


title: control_0_me [206909630042_R01C01]

description: Methylation titration controls


title: RNA-72 hours-2


title: iPS11 pSin cMyc

description: IPS11- Gli1 overexpressing cell culture

value: male

value: human foreskin

value: Medulloblastoma


title: F20_17 DRH

value: New Zealand White

value: Total Right Lung Homogenate


title: RNA-72 hours-1


title: pSin_P53+pSLIK_IDH1_R132H_48hours

value: glioblastoma


title: K562_5000_cells_rep2 [206909630008_R05C01]

description: Testing EPICv2 on low input DNA


title: RNA-0 hours-3

value: Osimertinib (1000nM) for 0 hours


title: K562_500_cells_rep2 [206909630008_R06C01]

description: Testing EPICv2 on low input DNA


title: RNA-0 hours-1


title: RNA-0 hours-2


title: K562_5000_cells_rep1 [206909630008_R03C01]

description: Testing EPICv2 on low input DNA


title: ips11 pSin Gli1

description: normal IPS11 cell culture


title: K562_500_cells_rep1 [206909630008_R04C01]

description: Testing EPICv2 on low input DNA


title: GM12878_5ng   [206909630040_R07C01]

description: Testing EPICv2 on low input DNA


title: Y79 cells, THZ1 50nM 12h, 3

city: Chengdu

first: Hanyue

last: Xu

state: Sichuan

address: Guoxuexiang street

institute: West China Hospital, Sichuan University

data_processing:
The reads were aligned to GRCh38 (Genome Reference Consortium Human Build 38 Organism).
The expression levels were evaluated using Cufflinks software (Trapnell, Williams et al. 2010) as FPKM (fragments per kilobase of exon per million fragments mapped).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

growth_protocol: The Y-79 and WERI-Rb-1 cell lines were cultured in Roswell Park Memorial Institute medium containing 10% fetal bovine serum and 1% penicillin/streptomycin. Incubation of all cell lines was carried out at 37 °C in a humidified 5% CO2 environment.

extract_protocol:
Y79 and WERI-Rb-1 cells were cultured in six-well plates and treated with dimethyl sulfoxide (0.1%) or THZ1 (50 nM) for 12 hours.
The sequencing libraries were created according to the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500) manufacturer's guidance.

value: Retinoblastoma

value: 50 nM THZ1, 12h


title: Y79 cells, THZ1 50nM 12h, 2


title: F28_9 DHI

value: Delivered on 28th day of gestation

value: 28th day

value: run 2


title: F28_2 DHH


title: T35_11 DHK

value: Delivered on 31st day of gestation (term birth) and manteined for 4 days

value: 35th day


title: T35_6 DHJ


title: F20_1 DRG

value: run 3


title: Control untreated OCI-AML3 30h rep3

city: La Habana

first: Dania

last: Vázquez-Blomquist

department: System Biology

country: Cuba

institute: Center for Genetic Engineering and Biotechnology

description: replicate 3

hyb_protocol: 3.5µg DNA target was hybridized on GeneChip® Clariom S Human (Affymetrix) and incubated at 45ºC in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: Diagnostic plots such as density plot, box plot or profiles of control probes evaluated the relative quality of intensity profiles and identify samples which should be flagged for removal. O-30minC-1_DPA095D02D02_01 array was removed as Outlier. The Robust Multi-array Average (RMA) by Irizarry et al. was applied. This preprocessing method performs background adjutment using the rma convolution model, followed by quantile normalization and log2 transformation. Probes belonging to the same gene are then averaged using a robust model that estimates probe-specific effects using all arrays. Technical replicate arrays were averaged by within the groups defined by variable(s) SampleID. Using the Bioconductor package Limma, a linear model is fit to each gene separately. Moderated t-tests are performed on various coefficients (a.k.a. contrasts or differences) of interest and FDR estimation is carried out using the Benjamini-Hochberg method.

label: biotin

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).

growth_protocol: Human AML cell lines HL-60 and OCI-AML3 were originally obtained from the American Type Culture Collection (ATCC, VA, USA) and the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany), respectively. Both cell lines were cultured in RPMI 1640 medium (Invitrogen, CA, USA) supplemented with 10% (v/v) fetal bovine serum (FBS, Invitrogen, CA, USA) and 50 μg/mL gentamicin (Sigma, MO, USA) under standard cell culture conditions at 37 ºC and 5% CO2.

extract_protocol: After incubations (30min and 3h), cells were pickup in buffer RLT with 1% of β-mercaptoethanol and total RNA purification proceeded following the instructions of RNeasy Plus mini kit (Qiagen, USA). Quality control of total RNA was carried out by spectrophotometric readings of optic density (OD) at 260 and 280nm in Nanodrop 1000 (ThermoFisher, USA) to determine the concentration (> 80ng/µL) and OD260/280 ratio (1.8-2.2). Additionally, RIN (7-10) was calculated by capillary electrophoresis in a Bioanalyzer (Agilent, Waldbronn, Germany).

treatment_protocol: An experiment with three replicates per condition of both cell lines was designed. The eight groups included untreated cells at 30min and 3h and treatment with 40microMolar of CIGB-300 peptide for 30min and 3h.

tag: agent

tag: time point

value: acute myeloid leukemia-derived cell line OCI-AML3


title: OCI-AML3+ CIGB-300 3h rep3

description: replicate 3


title: GM12878_50ng   [206909630040_R05C01]

description: Testing EPICv2 on low input DNA


title: Control untreated OCI-AML3 30h rep2

description: replicate 2


title: GM12878_1ng   [206909630040_R08C01]

description: Testing EPICv2 on low input DNA


title: P7_4 DHG

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 7 days


title: OCI-AML3+ CIGB-300 3h rep2

description: replicate 2


title: Control untreated OCI-AML3 30h rep1

description: replicate 1


title: OCI-AML3+ CIGB-300 3h rep1

description: replicate 1


title: P7_3 DHF


title: Y79 cells, THZ1 50nM 12h, 1

value: WT


title: Y79 cells, DMSO 12h, 3


title: Control untreated OCI-AML3 30min rep3

description: replicate 3


title: GM12878_10ng   [206909630040_R06C01]

description: Testing EPICv2 on low input DNA


title: Y79 cells, DMSO 12h, 2


title: Y79 cells, DMSO 12h, 1


title: P3_3 DHA

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 3 days

value: 31st day


title: GM12878_100ng   [206909630040_R04C01]

description: Testing EPICv2 on low input DNA


title: P3_2 DGZ

value: New Zealand White


title: DNMT1KO [206909630051_R03C01]

description: Analysis of cell lines with DNMTs loss


title: SETD2KO [206909630051_R08C01]

description: Analysis of cell lines with DNMTs loss


title: P3_1 DGY

value: Total Right Lung Homogenate


title: WERI-Rb-1 cells, THZ1 50nM 12h, 3


title: WERI-Rb-1 cells, THZ1 50nM 12h, 2


title: iPS11 pSin Blank_new

description: IPS11- empty vector transformed cell culture

value: male

value: human foreskin

value: Control


title: iPS11 wt

description: normal cell culture


title: 3ABKO [206909630051_R04C01]

description: Analysis of cell lines with DNMTs loss


title: P0_1 DGV

value: Delivered on 28th day of gestation (preterm birth) and kept at 21% O2 for 1 h


title: Control untreated OCI-AML3 30min rep2

description: replicate 2


title: P0_3 DGW


title: WERI-Rb-1 cells, THZ1 50nM 12h, 1

value: Retinoblastoma

value: 50 nM THZ1, 12h


title: P0_4 DGJ

value: 28th day

value: run 2


title: OCI-AML3+ CIGB-300 30min rep1

description: replicate 1


title: DKO1 [206909630051_R06C01]

description: Analysis of cell lines with DNMTs loss


title: WERI-Rb-1 cells, DMSO 12h, 2


title: T35_11 CZS

value: Delivered on 31st day of gestation (term birth) and manteined for 4 days

value: 35th day

value: run 1


title: T35_6 CZR


title: NIH3T3_rep2 [206909630008_R02C01]

description: Cross-species comparative epigenome analysis


title: OCI-AML3+ CIGB-300 30min rep3

description: replicate 3

value: acute myeloid leukemia-derived cell line OCI-AML3


title: OCI-AML3+ CIGB-300 30min rep2

description: replicate 2


title: T35_1 CZQ


title: T31_15 CZP

value: Delivered on 31st day of gestation (term birth)


title: K_346_p300_TNF

city: Bern

first: Kerstin

last: Klein

state: Bern

address: Murtenstrasse 28

department: Department of Rheumatology and Immunology

institute: University Hospital Bern

data_processing:
quality control was conducted using FASTQC
reads were cleaned using Trimmomatic
Reads were mapped to the human reference genome (hg 19) using STAR
Counts per gene were assessed using Feature Counts
Assembly: hg19

source_name: RA synovial tissue (knee)

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit (Qiagen), including Dnase digest.
Librariesfor RNAseq were generated using the Illumina TruSeq Stranded total RNA Sample Preparation Kit.

value: RA synovial tissue (knee)

value: synovial fibroblast

value: TNF


title: Control untreated HL60 3h rep2

description: replicate 2

value: acute myeloid leukemia-derived cell line HL60


title: HL60+ CIGB-300 3h rep3

description: replicate 3


title: Control untreated HL60 3h rep3

description: replicate 3


title: DKO8 [206909630051_R07C01]

description: Analysis of cell lines with DNMTs loss


title: T31_10 CZO

value: New Zealand White

value: Total Right Lung Homogenate

value: 31st day


title: HCT116_rep2 [206909630041_R02C01]

description: Cell line methylation profiles


title: K_346_CTRL_TNF


title: K_346_CBP_TNF


title: HCT116_rep1 [206909630051_R02C01]

description: Cell line methylation profiles


title: T31_1 CZN


title: WERI-Rb-1 cells, DMSO 12h, 3

value: WT


title: Control untreated HL60 3h rep1

description: replicate 1


title: K_346_p300

value: unstimulated


title: 3BKO [206909630051_R05C01]

description: Analysis of cell lines with DNMTs loss


title: WERI-Rb-1 cells, DMSO 12h, 1

value: Retinoblastoma


title: LNCaP_rep2 [206909630051_R01C01]

description: Cell line methylation profiles

value: LNCaP


title: HL60+ CIGB-300 3h rep2

description: replicate 2


title: Control untreated HL60 30min rep2

description: replicate 2


title: F29_11 CZM

value: Delivered on 29th day of gestation

value: 29th day


title: Control untreated HL60 30min rep3

description: replicate 3


title: NIH3T3_rep1 [206909630041_R01C01]


title: HL60+ CIGB-300 3h rep1

description: replicate 1


title: K_346_CBP


title: Control untreated HL60 30min rep1

description: replicate 1


title: LNCaP_rep1 [206909630040_R02C01]

description: Cell line methylation profiles


title: K562_rep2 [206909630008_R01C01]

description: Cell line methylation profiles


title: HL60+ CIGB-300 30min rep3

description: replicate 3


title: K562_rep1 [206909630040_R01C01]

description: Cell line methylation profiles


title: K_330_p300_TNF


title: MIAPaCa2_KRASG12R_RN118RN287_batch_untreated_8d_1

city: Vienna

first: Alexandra

last: Popa

state: Austria

address: Doktor-Boehringer-Gasse 5-11

institute: Boehringer Ingelheim

description: MIAPaCa2 KRASG12R RN118RN287 batch untreated 8d

data_processing:
Base-calling was performed using the Real-Time Analysis (RTA)
Mapping of raw reads was performed with STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences.
Quantification of read counts to transcript annotations was implemented using RSEM(v1.3.0) and featureCounts (v1.5.1).
Normalization of read counts and differential analysis was implemented with the limma and voom R packages.
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text files include normalized count values for all samples.

source_name: MIA PaCa-2 cell line

growth_protocol: PC-9 cells were cultured in McCoy’s 5A medium (Thermo Fisher), supplemented with 10% FBS and 1 x GlutaMAX (Thermo Fisher). MIA PaCa-2 (ATCC: CRL-1420) cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
2x106 Dox-treated and untreated control cells were harvested, washed with PBS, lysed, treated with DNAse I (QIAGEN) and total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Next generation sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.

treatment_protocol: Engineered MIA PaCa-2 and PC-9 cells were cultured in the presence of 1 µg/ml Dox to induce expression of the ARTi shRNA. Samples were taken at the indicated timepoints (d4, d8)

value: MIA PaCa-2

tag: construct

value: untreated

tag: timepoint

value: 8 days

tag: target


title: F29_2 CZK

tag: strain

tag: treatment

value: run 1


title: F29_7 CZL


title: MIAPaCa2_KRASG12R_RN118_untreated_4d_1

description: MIAPaCa2 KRASG12R RN118 untreated 4d

value: 4 days


title: GM12878_rep2 [206909630040_R03C01]

description: Cell line methylation profiles


title: F28_7 CZI

value: Delivered on 28th day of gestation

value: 28th day


title: GM12878_rep1 [206909630042_R08C01]

description: Cell line methylation profiles


title: K_330_CTRL_TNF

value: RA synovial tissue (knee)

tag: cell type

value: synovial fibroblast

value: TNF


title: MIAPaCa2_KRASG12R_RN118_doxycycline_4d_1

description: MIAPaCa2 KRASG12R RN118 doxycycline 4d

tag: cell line

value: doxycycline


title: HL60+ CIGB-300 30min rep2

description: replicate 2

value: acute myeloid leukemia-derived cell line HL60


title: HL60+ CIGB-300 30min rep1

description: replicate 1


title: MIAPaCa2_KRASG12R_RN118RN287_batch_untreated_4d_1

description: MIAPaCa2 KRASG12R RN118RN287 batch untreated 4d


title: K_330_p300

tag: tissue

value: unstimulated


title: F28_2 CZH

value: New Zealand White

value: Total Right Lung Homogenate


title: MIAPaCa2_KRASG12R_RN118RN287_batch_doxycycline_4d_1

description: MIAPaCa2 KRASG12R RN118RN287 batch doxycycline 4d


title: K_330_CBP


title: Dotap-miRNA-2

city: Xiamen

first: James

middle: Yunqing

last: Yang

state: Fujian

address: Xiang'an South Road

department: School of Life Sciences

institute: Xiamen University

data_processing:
Genes expression level is quantified by a software package called RSEM.
Calculate correlation value bewteen each two samples based on normalized expression result and draw correlation heatmap
DEGs screening is aimed to find differential expressed genes between samples and perform further function analysis on them. We use possion distribution method and  NOISeq method to do this analysis.
Perform clustering analysis of differentially expressed genes with cluster and javaTreeview software according to the provided cluster plans for DEGs.
After getting GO annotation for DEGs, WEGO software was used to do GO functional classification.
Supplementary files format and content: Excel files include fpkm for each sample

source_name: spleen

growth_protocol: Splenocytes were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 100 IU/ml penicillin and 100 μg/ml streptomycin with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from six groups of splenocytes using TRIzol Reagent (Invitrogen, Life Technologies).
The six circular single stranded DNA libraries were sequenced by single ended 50 base (SE50) sequencing using the BGIseq500 platform.

treatment_protocol: Splenocytes were transfected with Dotap-only or Dotap-PS-miR-574-5p (Dotap-only-1, -2 and -3 and Dotap-miRNA-1, -2 and -3) at the concentration of 10 μg/ml for 24h

value: spleen

value: splenocytes

value: Primary cell

value: miR-574-6p overexpression


title: F27_7 CZF

value: Delivered on 27th day of gestation

value: 27th day


title: K_346_CTRL


title: Dotap-miRNA-3

value: miR-574-7p overexpression


title: K_330_CTRL


title: F27_11 CZG

value: run 1


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_untreated_4d_1

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 untreated 4d

value: MIA PaCa-2

value: untreated

value: 4 days


title: Dotap-miRNA-1

value: miR-574-5p overexpression


title: F27_1 CZE


title: K_330_CBP_TNF

value: RA synovial tissue (knee)

value: synovial fibroblast

value: TNF


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_doxycycline_4d_1

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 doxycycline 4d

value: doxycycline


title: Dotap-only-3

value: WT


title: F28_9 CZJ

value: New Zealand White

value: Total Right Lung Homogenate

value: Delivered on 28th day of gestation

value: 28th day


title: F25_13 CZC

value: Delivered on 25th day of gestation

value: 25th day


title: F25_18 CZD


title: K_196_CBP_TNF


title: Dotap-only-2

value: spleen

value: splenocytes

value: Primary cell


title: K_196_CTRL_TNF


title: Dotap-only-1


title: F25_3 CZB

value: run 1


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_untreated_8d_1

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 untreated 8d

value: MIA PaCa-2

value: untreated

value: 8 days


title: K_196_p300

value: RA synovial tissue (knee)

value: synovial fibroblast

value: unstimulated


title: K_196_CBP


title: Pyo3

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

data_processing:
featureCounts v 1.5.0-p3 and stringtie v 1.3.3b
Initial quantification was performed using Qubit2.0 Fluorometer, followed by Agilent 2100 BioAnalyzer testing the insert size of the library. When the insert size met expectations, Qrt-pcr accurately quantified effective library concentration (effective library concentration is higher than 2nM) to ensure library quality.
The image data measured by the high-throughput sequencer were converted into sequence data (reads) by CASAVA base recognition.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: FASTA file with transcript sequences is available on the series record.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Uterus

extract_protocol:
 The uterus of dogs for RNA-Seq analysis (the prostatic secretions must be cleaned otherwise RNA quality was poor）. Using the Trizol RNA Reagent (Takara, Dalian, China) to extract total RNA from the tissues and measured the concentration and integrity of the RNA with the ND-1000 Nanodrop, as well as the Agilent 2100 TapeStation (Novogene Bioinformatic Technology, Beijing, China). The quality control parameters used in this study were: A260/A280 ratio ≥1.8, A260/A230 ratio ≥2.0, and RNA integrity number ≥8.0.
The TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) was used to generate cDNA libraries. High-throughput sequencing was run on an Illumina HiSeq 2500 system. Raw RNA-seq data were processed with an in-house computational pipeline.

value: Uterus

value: pyometra

value: Wild type


title: MIAPaCa2_KRASG12R_RN118_doxycycline_8d_1

description: MIAPaCa2 KRASG12R RN118 doxycycline 8d

value: doxycycline


title: MIAPaCa2_KRASG12R_RN118RN287_batch_doxycycline_8d_1

description: MIAPaCa2 KRASG12R RN118RN287 batch doxycycline 8d


title: YUMMER1.7 (YR) tumor (8 days post-tumor initiation, 24 hours post-treatment), scTCR-seq

city: New Haven

first: Miller-Jensen

last: Lab

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma-separated csv files

source_name: skin

extract_protocol:
24 hours post-treatment (if applicable), untreated and TTx-treated tumors for scRNA-seq were minced in RPMI with 2% FBS, then incubated with agitation at 37C, with 1 mg/mL Collagenase IV (C5138, Sigma-Aldrich) and 0.1 mg/mL DNAse I (10104159001, Roche) for 30 minutes. Tumors were then filtered through 70 µM filters into a single-cell suspension. Samples were then FACS-sorted into three populations: CD45+CD3+ (T cells), CD45+CD3- (non-T immune cells), CD45-CD3- (tumor and stroma). The populations were then recombined in a 2:1:1 ratio, and 10,000 cells from each condition (TTx-treated and control) were loaded onto the 10X Chromium System for sequencing. Antibodies used for sorting: CD45 (I3/3.2), CD3 (17A2)
VDJ library construction was performed according to the manufacter’s instructions (single cell 5’ v1 protocol, 10x Genomics).
scTCR-seq

treatment_protocol: For subcutaneous tumors, C57BL6/J mice were injected with 0.5x10^6 YUMMER1.7 cells (BrafV600E/ Pten-/-Cdkn2a -/- UV irradiated melanoma cell line). Mice were treated with 50 µg anti-CD40 (FGK4.5, BioXCell), 200 µg anti-CSF1R (m CSF1R.2 m.G1- D265A, Bristol Myers Squibb) and 200 µg anti-PD-1 (RMP1-14, BioXCell) 7 days post-tumor initation.

value: skin

value: treated with the combination of anti-PD-1, CSF1R blockade, and agonistic CD40 (i.e., TTx) by i.p. injection 24 hours prior to collection for sequencing

tag: time

value: 8 days post-tumor initiation


title: YUMMER1.7 (YR) tumor (8 days post-tumor initiation, untreated), scTCR-seq

description: 10x Genomics


title: K_196_CTRL

tag: genotype


title: F_408_p300_TNF

source_name: RA synovial tissue (finger)

value: RA synovial tissue (finger)

value: TNF


title: K_196_p300_TNF


title: nom3

city: Guangzhou

value: normal


title: MIAPaCa2_KRASG12R_RN118_untreated_4d_2

description: MIAPaCa2 KRASG12R RN118 untreated 4d

value: 4 days


title: F_408_CBP_TNF


title: nom2


title: MIAPaCa2_KRASG12R_RN118_untreated_8d_1

description: MIAPaCa2 KRASG12R RN118 untreated 8d

value: MIA PaCa-2


title: Hnf4-LKO-TM-2181

city: Iowa City

first: David

middle: Thomas

last: Rutkowski

state: IA

address: 51 Newton Rd.

department: Anatomy and Cell Biology

institute: University of Iowa Carver College of Medicine

data_processing:
Illumina HiSeq4000 read quality was checked for each sample using FastQC v.0.11.8.
High-quality reads were then imported into Kallisto v.0.45.0 for alignment into the h5 (HDF5) file format.
The h5 (HDF5) files were imported into the RNA-seq pipeline in R studio package v.4.1.2 and TPM counts were calculated.
DESeq2 pipeline in R  studio with various depency files were used for determining the differential gene expression.
Assembly: GrCm38/mm10
Supplementary files format and content: h5 format,  compressed files includes quantification (transcript per million) for each sample

source_name: liver

extract_protocol:
RNA was harvested using an RNeasy mini plus kit (Qiagen). 2ug of total RNA was used for the construction of sequencing libraries.
2ug of total RNA was subjected to library synthesis using Illumina TrueSeq Stranded mRNA kit.

treatment_protocol: Post virus injection mice were housed in a 12hrs day/night cycle with ad-libitum in a barrier facility for a week.  After a week, mice were fasted for 4 hours, injected with ER stressor,tunicamycin (0.5mg/Kg), and housed for 14hrs. The liver was isolated.

value: liver

value: Hnf4a fl/fl  (M)

tag: genotype background

tag: treatment _(virus)

value: Intra Peritoneally- AAV-TGB-iCre (2.5 x 10^11 GC)

tag: treatment (time)

value: 1 week of housing; 12hrs D/N; Ad-libitum

value: Fasted for 4 hrs

tag: treatment _(time)

value: Intra-peritoneally - Tunicamycin , 14hrs

value: Dosage (0.5mg/kg)


title: MIAPaCa2_KRASG12R_RN118_doxycycline_4d_2

description: MIAPaCa2 KRASG12R RN118 doxycycline 4d


title: Hnf4-LKO-TM-2182


title: Hnf4-LKO-TM-2183


title: MIAPaCa2_KRASG12R_RN118RN287_batch_untreated_4d_2

value: untreated


title: F_408_p300

value: synovial fibroblast

value: unstimulated


title: WT-TM-2180

value: Intra Peritoneally - AAV-TGB-eGFP (2.5 x 10^11 GC)


title: MIAPaCa2_KRASG12R_RN118RN287_batch_doxycycline_4d_2

value: doxycycline


title: nom1

value: Uterus

tag: disease state

value: Wild type


title: BCR_Pax5_Leukemia

city: Munich

first: Carolin

last: Prexler

address: Kölner Platz 1, Haus 11

department: School of Medicine and Health, Department of Pediatrics

institute: Technical University of Munich, TUM University Hospital

description: data processed using Cell Ranger version 6.1.1

data_processing:
scRNA- data was aligned with Cell Ranger (version 3 or version 6) to mouse reference (mm10) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR were separately processed using Cell Ranger (version 3 or version 6) by alignment to VDJ-reference (mm10) with default parameters.
Assembly: mm10
Supplementary files format and content: CITE-seq: barcodes.tsv.gz: barcode annotation (raw and filtered); features.tsv.gz: feature annotation (raw and filtered): 10x Cell Ranger feature list; matrix.mtx.gz: count matrix (raw and filtered): 10x Cell Ranger raw UMI count matrix
Supplementary files format and content: VDJ-seq: all_contig_annotations.csv, filtered_contig_annotations.csv
Library strategy: VDJ-seq

source_name: B cell receptor

extract_protocol:
Extract and clean hind legs of the mouse with scalpel and place in mortar. Crush bones with 2 ml FACS buffer (PBS, 2% FCS, 2mM EDTA) and transfer the liquid to a 100 µm filter (blue) on a 15 ml falcon tube with a 22G needle and 3ml syringe. Repeat 2 more times (3 x 2ml in total) and grind remaining liquid through the filter with pipette tip and tap the filter onto the tube to collect remaining drops. Centrifuge 5 min, 400g, 4°C. Discard supernatant and remove remaining liquid by taping the tube onto a tissue. Resuspend the pellet in 500 µl ACK-Lysing buffer; 5 min incubation on ice. Centrifuge 5 min, 400g, 4°C. Resuspend in 1 ml FACS Buffer and transfer to a 30 µm filter (green); repeat with additional 1 ml  (for maximum transfer efficiency hold pipette tip from the first transfer and re-use for the second transfer). Tap and push through the liquid with the pipette tip and fill up to 10 ml. Count cells (1:1 Dilution).
The 5' gene expression and VDJ (BCR) libraries were prepared following manufacturer instructions (10x Genomics). cDNA qualities were assessed using Bioanalyzer. Libraries were index barcoded and sequenced using NovaSeq 6000 S2 runs.
10x Chromium 5' kit for CITE-seq and VDJ-seq

value: bone marrow

value: leukemic population

tag: disease

value: B acute lymphoblastic leukemia

tag: library type

value: BCR

tag: run description

value: run 4:leukemic population from 4 mice (4 Pax5+/- mice) using 4 different hashtags identifying each mouse


title: WT-TM-2179

value: liver

value: Hnf4a fl/fl  (M)


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16__untreated_4d_2

value: MIA PaCa-2

tag: construct

tag: timepoint

value: 4 days


title: Pyo2

value: pyometra


title: Pyo1


title: WT-TM-2178

value: 1 week of housing; 12hrs D/N; Ad-libitum

value: Fasted for 4 hrs

value: Intra-peritoneally - Tunicamycin , 14hrs

value: Dosage (0.5mg/kg)


title: F_408_CTRL

value: RA synovial tissue (finger)

value: synovial fibroblast

value: unstimulated


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_doxycycline_4d_2

value: doxycycline

tag: target


title: WT-TM-2177

value: Intra Peritoneally - AAV-TGB-eGFP (2.5 x 10^11 GC)

tag: treatment


title: MIAPaCa2_KRASG12R_RN118_untreated_8d_2

description: MIAPaCa2 KRASG12R RN118 untreated 8d

value: untreated

value: 8 days


title: F_379_p300_TNF

tag: cell type

value: TNF


title: FBC_Pax5_Leukemia

library_source: other

data_processing:
scRNA- data was aligned with Cell Ranger (version 3 or version 6) to mouse reference (mm10) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR were separately processed using Cell Ranger (version 3 or version 6) by alignment to VDJ-reference (mm10) with default parameters.
Assembly: mm10
Supplementary files format and content: CITE-seq: barcodes.tsv.gz: barcode annotation (raw and filtered); features.tsv.gz: feature annotation (raw and filtered): 10x Cell Ranger feature list; matrix.mtx.gz: count matrix (raw and filtered): 10x Cell Ranger raw UMI count matrix
Supplementary files format and content: VDJ-seq: all_contig_annotations.csv, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Hashtag-derived oligonucleotide (HTO)

value: bone marrow

value: leukemic population

value: B acute lymphoblastic leukemia

value: HTO

tag: hto

value: run 4:leukemic population from 4 mice (4 Pax5+/- mice) using 4 different hashtags identifying each mouse


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_doxycycline_8d_1

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 doxycycline 8d

tag: cell line

value: MIA PaCa-2


title: FBC_Wildtype_BM-subsets

tag: tissue

value: 5 different  B cell populations from WT; preleukemic population (B220+CD19-ckit+CD25+)

value: healthy

value: WT Pro-B:Hashtag 1; WT Pre-BI:Hashtag 2; WT Pre-BII:Hashtag 4; WT immature B:Hashtag 5; WT recirculating B:Hashtag 6; PAX+/- (#5870):Hashtag 7

value: run 3:5 different B cell populations from a pool of 3 WT mice (#324, #325, #327) using 5 different hashtags identifying each  B cell population; preleukemic population from 1 mouse (1 Pax5+/- mouse) using another hashtag identifying this mouse


title: F_379_CBP_TNF

value: RA synovial tissue (finger)

value: synovial fibroblast

tag: genotype


title: MIAPaCa2_KRASG12R_RN118RN287_batch_untreated_8d_2


title: BCR_Wildtype_BM-subsets

value: BCR


title: Hnf4-LKO-NT-2175

value: liver

value: Hnf4a fl/fl  (M)

tag: genotype background

value: Intra Peritoneally- AAV-TGB-iCre (2.5 x 10^11 GC)

value: 1 week of housing; 12hrs D/N; Ad-libitum

value: Fasted for 4 hrs

value: Intra-peritoneally - Vehicle , 14hrs

value: Dosage (0.5mg/kg)


title: MIAPaCa2_KRASG12R_RN118_doxycycline_8d_2

description: MIAPaCa2 KRASG12R RN118 doxycycline 8d

value: doxycycline

value: 8 days


title: F_408_CTRL_TNF

value: TNF


title: F_379_CTRL_TNF


title: mRNA_Wildtype_BM-subsets

data_processing:
scRNA- data was aligned with Cell Ranger (version 3 or version 6) to mouse reference (mm10) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR were separately processed using Cell Ranger (version 3 or version 6) by alignment to VDJ-reference (mm10) with default parameters.
Assembly: mm10
Supplementary files format and content: CITE-seq: barcodes.tsv.gz: barcode annotation (raw and filtered); features.tsv.gz: feature annotation (raw and filtered): 10x Cell Ranger feature list; matrix.mtx.gz: count matrix (raw and filtered): 10x Cell Ranger raw UMI count matrix
Supplementary files format and content: VDJ-seq: all_contig_annotations.csv, filtered_contig_annotations.csv

source_name: polyA RNA

value: bone marrow

value: 5 different  B cell populations from WT; preleukemic population (B220+CD19-ckit+CD25+)

value: mRNA


title: Hnf4-LKO-NT-2176

tag: treatment _(virus)


title: Hnf4-LKO-NT-2174

tag: treatment (time)


title: MIAPaCa2_KRASG12R_RN118RN287_batch_doxycycline_8d_2

value: MIA PaCa-2


title: BCR_Wildtype_Pax5, rep2

description: data processed using Cell Ranger version 3.1.0

value: preleukemic population (pre-BII = B220+IgM/D-CD25+)

value: healthy

value: run 2:preleukemic population from 6 mice (3 WT mice, 3 Pax5+/- mice) using 6 different hashtags identifying each mouse


title: mRNA_Pax5_Leukemia

value: leukemic population

value: B acute lymphoblastic leukemia

value: run 4:leukemic population from 4 mice (4 Pax5+/- mice) using 4 different hashtags identifying each mouse


title: F_379_CBP

value: RA synovial tissue (finger)

value: synovial fibroblast

value: unstimulated


title: WT-NT-2171

value: liver

value: Hnf4a fl/fl  (M)

value: Intra Peritoneally - AAV-TGB-eGFP (2.5 x 10^11 GC)

value: 1 week of housing; 12hrs D/N; Ad-libitum

value: Fasted for 4 hrs

tag: treatment _(time)

value: Intra-peritoneally - Vehicle , 14hrs

value: Dosage (0.5mg/kg)


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_untreated_8d_2

value: MIA PaCa-2

value: untreated

value: 8 days


title: FBC_Wildtype_Pax5, rep2

value: bone marrow

value: preleukemic population (pre-BII = B220+IgM/D-CD25+)

value: healthy

value: HTO

value: run 2:preleukemic population from 6 mice (3 WT mice, 3 Pax5+/- mice) using 6 different hashtags identifying each mouse


title: WT-NT-2170


title: F_379_CTRL

value: RA synovial tissue (finger)

value: synovial fibroblast


title: F_408_CBP

value: unstimulated


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_doxycycline_8d_2

value: doxycycline


title: mRNA_Wildtype_Pax5, rep2

value: mRNA


title: WT-NT-2169

value: liver

value: Hnf4a fl/fl  (M)

value: Intra Peritoneally - AAV-TGB-eGFP (2.5 x 10^11 GC)

value: 1 week of housing; 12hrs D/N; Ad-libitum


title: F_292_p300_TNF

value: TNF