title: DCM3-H3K4me3_PLACseq

city: Cleveland

first: Chia-Feng

last: Liu

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Library strategy: PLAC-seq
We applied the Model-based analysis of PLAC-seq (MAPS)  pipeline to analyze PLAC-seq data.
MAPS used bwa-mem to map the raw reads to the reference genome hg19, and then filtered reads with low mapping quality. Next, MAPS used samtools to remove PCR duplicates. The remaining reads are binned into 10Kb bins. Read pairs that are close to each other (<= 1Kb) are considered as short-range reads, and used to measure ChIP enrichment level. Read pairs with genomic distance between 20Kb and 1Mb are considered as long-range reads, and used to measure long-range chromatin interactions. We further partition bin pairs into the AND, XOR and NOR sets, based on the presence of ChIP-seq peak in both, one, or none of the anchor bins, respectively. We only used the AND and XOR sets to detect statistically significant long-range chromatin interactions. We fitted positive Poisson regression model to adjust for systematic bias factors including genomic distance, effective fragment size, GC content, mappability and ChIP enrichment level. For each bin pair, we computed a p-value based on the positive Poisson distribution, and then converted p-values into false discovery rates (FDR). Bin pairs with FDR <1% are considered as statistically significant long-range chromatin interactions.
Genome_build: hg19
Supplementary_files_format_and_content: hic

source_name: Left ventricle tissues

extract_protocol:
120 mg of the left ventricle (LV) tissues were used for each PLAC-seq experiment. Lysates were clarifeid from sonicated nuclei and histone-DNA complexs were isoalted with antibodies
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: protocol

value: Dilated cardiomyopathy

value: male


title: PBMCs, YUPIXEL, BCR scVDJ-seq

status: Public on Jan 13 2022

type: SRA

city: Stanford

first: Aaron

middle: M

last: Newman

state: California

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

country: USA

institute: Stanford University

description: Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v3.1.0

library_source: transcriptomic

data_processing:
Raw scV(D)J-seq reads were mapped with Cell Ranger v3.1.0 or v5.0.1 to reference “refdata-cellranger-vdj-GRCh38-altsensembl-4.0.0”.
The resulting clonotype assemblies were downloaded from Loupe V(D)J browser v3.0.0 (10x Genomics, Pleasanton, CA).
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values (CSV) files per patient, with separate files for TCR and BCR scVDJ-seq, including cell barcodes, TCR or immunoglobulin chain types, CDR3 amino acid sequences, CDR3 nucleotide sequences, and V, D, J and C genes.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Single-cell suspensions from PBMC samples were obtained and prepared to a concentration of 700-1,200 viable cells/μl using a hemacytometer (Thermo Fisher Scientific, Waltham, MA) or Coulter Counter (Beckman Coulter Life Sciences, Indianapolis, IN) for cell counting, per the manufacturers’ instructions.
Chromium Single Cell 5’ Library Construction Kit (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol.
Single-cell suspensions underwent library preparation for scRNA-seq with paired single-cell V(D)J sequencing (scVDJ-seq) for T cell receptor (TCR) and B cell receptor (BCR) clonotypes using the 5’ transcriptome kit (10x Genomics, Pleasanton, CA) per the manufacturer’s instructions. Complementary DNA libraries were sequenced on a NovaSeq instrument (Illumina, San Diego, CA) with 2 x  92 bp paired-end reads targeting a mean of 20k reads per cell.

tag: patient

value: YUPIXEL

tag: tissue

value: Blood

tag: diagnosis

value: Melanoma

tag: Sex

value: Male

tag: age

tag: immunotherapy type

value: Combination

tag: highest irae grade

tag: cohort

value: Single-cell discovery

tag: sequencing batch

value: A


title: G-H_P5

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

country: Germany

institute: University Hospital, LMU Munich

description: CITE-seq

data_processing:
Cell Ranger software (10x Genomics, v.6.1) was used to demultiplex samples, process raw data, align reads to the GRCh38 human reference genome and summarize unique molecular identifier (UMI) counts. Filtered gene-barcode and CSP-barcode matrices that contained only barcodes with UMI counts that passed the threshold for cell detection were used for further analysis
We processed the filtered UMI count matrices using the R package Seurat (version 4.0.3).
As a QC steps we filtered out cells that expressed fewer than 500 genes and/or >15% mitochondrial reads, and genes expressed in less than 3 cells were removed from the count matrix. After QC, only raw gene counts in high-quality singlets were submitted to: log-normalization; identification of high variable genes by using the vst method; scaling; and regression against the number of UMIs and mitochondrial RNA content per cell.
Integration was performed to remove bath effects and the integrated assay was used for principal component analysis and unsupervised clustering. After marker identification for each CD4+ T cell cluster, only cells where a TCR clonotype was detected, were used for upstream analysis of TCR repertoire. Single-cell TCR annotation was performed using the 10x cellranger vdj pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with filtered feature-barcode counts for every gene and every cell
Supplementary_files_format_and_content: Matrix table with filtered feature-barcode counts for every TotalSeq-C antibody and every cell
Supplementary_files_format_and_content: Seurat meta.data file

molecule: polyA RNA

source_name: PBMCs

tag: cell type sorted

tag: disease state

value: non-MS

tag: treatment

tag: disease course

value: healthy

value: f

tag: gex _ file-name-prefix

tag: csp _ file-name-prefix

tag: tr _ file-name-prefix


title: DCM2-H3K4me3_PLACseq

state: OH

library_source: genomic

molecule: genomic DNA

tag: protocol


title: PBMCs, YUKEND, BCR scVDJ-seq

tag: patient

value: YUKEND

value: Female


title: NF2-H3K4me3_PLACseq

value: Non-failing


title: A108411

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

institute: UC Davis

data_processing:
library strategy: WGS
Raw read files were mapped to human reference genome hg38 using Burrows-Wheeler Aligner (BWA) with the default setting. SAMtools was utilized to sort the bam files and Picard was used to merge bam files from the same sample identify duplicate reads. Single nucleotide polymorphisms (SNPs), small insertion, and deletions (InDels) were called using GATK and annotated variant using ANNOVAR. Copy number variations (CNVs), longer than 50 bp, were identified using control-FREEC and CREST. Structural variants (SVs) detection and genotyping, larger than 50 bp were performed using DELLY with the default settings.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for SV, INDEL, CNV and variant call format VCF files for SNP at each sample

source_name: TD_Cord Blood

extract_protocol:
DNA was extracted from whole umbilical cord blood with the Gentra Puregene Blood kit (Qiagen, Hilden, Germany) and quantified with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Waltham, MA, USA).
Sequencing libraries were generated using NEBNest DNA library prep kit (NEB, Ipswich, MA, USA) with 150 bp paired-end reads in HiSeq X Ten (San Diego, CA, USA) by Novogene (Sacramento, CA, USA) with at least 30x coverage per sample.

tag: genotype

value: TD

tag: tissue

value: Cord Blood


title: PBMCs, YUHERN, BCR scVDJ-seq

value: YUHERN

tag: diagnosis

tag: Sex


title: A108187

source_name: ASD_Cord Blood

value: ASD


title: NF1-H3K4me3_PLACseq

value: male


title: AZD1

city: Columbus

first: Kalpana

last: Ghoshal

address: 420 W 12th Ave

institute: The Ohio State University

data_processing:
NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L)
NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490)
NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6442S/L)
Library input amount: 200ng total RNA (quantified using Qubit Fluorometer) and total RNA achieved a RIN of >7
Libraries were sequenced with Illumina NovaSeq 6000 flow cell using paired-end 150-bp format to at least 17 million passed-filter clusters/sample (equivalent to 34 million reads)
Genome_build: hg38

source_name: hepatocellular carcinoma

growth_protocol: HCCLM3 cells were maintained in DMEM supplemented with L-glutamine (2 mM), 10% FBS, sodium pyruvate (1 mM) and penicillin/ streptomycin/amphotericin (Thermo Fisher Scientific, Pittsburg, PA) at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCCLM3 cells were treated with AZD (10 uM) or DMSO for 24 hours

tag: cell line


title: AZD2


title: PBMCs, YUGRUS, BCR scVDJ-seq

value: YUGRUS

value: Blood

tag: age

tag: immunotherapy type

tag: highest irae grade


title: DMSO2

value: DMSO


title: AW-MS_P5

description: CITE-seq

tag: cell type sorted

value: MS

value: RRMS


title: DCM3-H3K27ac_PLACseq

value: Dilated cardiomyopathy


title: DCM2-H3K27ac_PLACseq


title: PBMCs, YUFURL, BCR scVDJ-seq

value: YUFURL

value: Melanoma

value: Male

value: Combination

tag: cohort

value: Single-cell discovery

tag: sequencing batch

value: A


title: A108133


title: A107912


title: DMSO1

tag: treatment


title: PBMCs, YUFUB, BCR scVDJ-seq

value: YUFUB


title: NF2-H3K27ac_PLACseq

value: Non-failing


title: A107867

value: TD

value: Cord Blood


title: PBMCs, YUENZO, BCR scVDJ-seq

value: YUENZO


title: NF1-H3K27ac_PLACseq

value: male


title: DCM-Input

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then aligned to the human reference genome (hg19) using Bowtie2 (Galaxy version 2.3.4.2)  with the default setting
Model-based analysis of ChIP-seq (MACS, Galaxy version 2.1.2 ) was used for peak calling (nomodel; extension size: 200; FDR [q-value] cutoff: 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: commonPeaks.bed

extract_protocol:
Ninety mg of the left ventricle (LV) tissues were used for each ChIP-seq experiment. Lysates were clarifeid from sonicated nuclei and histone-DNA complexs were isoalted with antibodies
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit


title: A107347

value: ASD


title: HEK293T cell transient overexpressed NHIP 3

data_processing:
Raw fastq files were processed and aligned using STAR. After quality control steps by FASTQC, the count matrixes were generated by featureCounts. Count matrixes were filtered for at least one count in any sample. Size factors estimation and normalization were performed by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: comma-seperated values files include reads counts values for each Sample

source_name: Human Embryonic Kidney cells

growth_protocol: HEK293T cells (ATCC, Manassas, VA, USA, CRL-11268) were grown in DMEM/F12, GlutaMAX medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with MEM non-essential amino acids (Thermo Fisher Scientific, Waltham, MA, USA) and 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) together with Penicillin-streptomycin-glutamine. Low passage HEK293T cells were transfected with plasmids using Lipofectamine 3000 and Opti-MEM (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Transfections were performed with or without piggyBac backbone plasmids for HEK293T cells. Transfection medium was replaced 24 h post-transfection with complete growth media with puromycin at 3 µg/ml for 7 days. All cells were maintained at 37 °C containing 95% O2 and 5% CO2.

extract_protocol:
Total RNA was isolated from HEK293T cells transiently or stably transfected with pb-NHIP-eGFP or negative control pb-NEG-eGFP using AllPrep DNA/RNA/Protein mini kit (Qiagen, Hilden, Germany). Human tissue total RNA samples were obtained commercially, including placenta (Life Technology, Carlsbad, CA, USA), testes (TaKaRa Bio, Kusatsu, Shiga, Japan), and fetal brain (Cell Applications, San Diego, CA, USA). RNA was extracted from frozen placenta samples in the Discovery group samples using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).
RNA from cells and brain was prepared for RNA-seq library using Kapa RNA HyperPrep kits (Roche, Basel, Switzerland) together with the QIAseq FastSelect Human ribodepletion kit (Qiagen, Hilden, Germany). Libraries were assessed for quality and quantify on Agilent Bioanalyzer 2100 and pooled for multiplex sequencing with at least 25 million reads with 150 bp paired-end on Illumina NovaSeq 6000 (San Diego, CA, USA) by DNA Tech Core at University of California, Davis (Davis, CA, USA).

treatment_protocol: A PiggyBac-compatible expression plasmid, pb-NHIP-eGFP was synthesized by VectorBuilder (Chicago, IL, USA) with EF-1α as promoter for NHIP and CMV as promoter for eGFP fused with puromycin resistant gene. A control plasmid was cut using XbaI and AbaI restriction endonucleases based on the pb-NHIP-eGFP, named pb-NEG-eGFP to remove NHIP and maintained the rest of plasmid structure. The backbone piggyBac plasmid was obtained from Sanger Institute Archives and described previous as hyperactive PB transposase (pCMV-hyPBase). Plasmid for NHIP plasmid, pb-NHIP-peptide-eGFP was synthesized by VectorBuilder with EF-1α as promoter for the NHIP peptide, removed the stop codon and fused the end of the NHIP peptide with eGFP, together with CMV as promoter for mCherry fused with puromycin resistant gene. All constructs were sequenced by Sanger sequencing by University of California, Davis, DNA Sequencing Facility (Davis, CA, USA) and analyzed using SnapGene (Genewiz, South Plainfield, NJ, USA) to confirm the expected sequence.

tag: tissue/cell type

value: Human Embryonic Kidney cells

value: pb-NHIP-eGFP


title: PBMCs, YUROD, BCR scVDJ-seq

value: YUROD

value: Blood


title: A108572


title: A107049


title: PBMCs, YUNANCY, TCR scVDJ-seq

description: Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v5.0.1

value: YUNANCY

value: Female

value: B


title: NF-Input


title: HEK293T cell transient overexpressed NHIP 1


title: HEK293T cell transient negative control 3

value: control plasmid


title: DCM3-H3K27me3_ChIPseq

value: Dilated cardiomyopathy

tag: antibody


title: PBMCs, YUHONEY, TCR scVDJ-seq

value: YUHONEY

value: Melanoma

value: Male

value: Combination


title: A106498

value: TD

value: Cord Blood


title: DCM2-H3K27me3_ChIPseq

value: male


title: PBMCs, YUALOE, TCR scVDJ-seq

value: YUALOE


title: A106425


title: HEK293T cell transient negative control 2

value: Human Embryonic Kidney cells


title: HEK293T cell transient negative control 1


title: A106109


title: DCM1-H3K27me3_ChIPseq


title: control 21

source_name: Brain

value: Brain


title: NF2-H3K27me3_ChIPseq

value: Non-failing


title: PBMCs, YUTORY, TCR scVDJ-seq

value: YUTORY

value: Blood

value: Single-cell discovery

value: A


title: control 1065


title: A106031

value: ASD


title: PBMCs, YUTHEA, TCR scVDJ-seq

value: YUTHEA


title: NF1-H3K27me3_ChIPseq


title: HEK293T cell transient overexpressed NHIP 2

value: pb-NHIP-eGFP


title: A105874


title: A105730


title: PBMCs, YUTAUR, TCR scVDJ-seq

value: YUTAUR

value: Melanoma


title: PBMCs, YUCARD, BCR scVDJ-seq

value: YUCARD

value: Male

value: Combination


title: DCM3-H3K4me1_ChIPseq

value: Dilated cardiomyopathy

value: male


title: autism 6294


title: autism 5173


title: PBMCs, YUROD, TCR scVDJ-seq

value: YUROD


title: A105701

value: Cord Blood


title: PBMCs, YUPIXEL, TCR scVDJ-seq

value: YUPIXEL


title: autism 4925

value: Brain


title: A105308


title: DCM1-H3K4me1_ChIPseq


title: A105075

value: TD


title: PBMCs, YUKEND, TCR scVDJ-seq

value: YUKEND

value: Blood

value: Female

value: Single-cell discovery


title: autism 4899

value: ASD


title: autism 3924


title: PBMCs, YUVARDO, TCR scVDJ-seq

value: YUVARDO

value: A


title: NF2-H3K4me1_ChIPseq

value: Non-failing


title: A104851


title: NF1-H3K4me1_ChIPseq


title: PBMCs, YUHERN, TCR scVDJ-seq

value: YUHERN

value: Melanoma


title: control 812


title: A104594


title: PBMCs, YUGRUS, TCR scVDJ-seq

value: YUGRUS

value: Combination


title: DCM3-H3K4me3_ChIPseq

value: Dilated cardiomyopathy

value: male


title: control 738


title: PBMCs, YUFURL, TCR scVDJ-seq

value: YUFURL

value: Male


title: A104551

value: TD

value: Cord Blood


title: DCM2-H3K4me3_ChIPseq


title: PBMCs, YUFUB, TCR scVDJ-seq

value: YUFUB

value: Blood


title: control 602

value: Brain


title: DCM1-H3K4me3_ChIPseq


title: A104289

value: ASD


title: control 1377


title: PBMCs, YUENZO, TCR scVDJ-seq

value: YUENZO

value: Single-cell discovery


title: A104277


title: control 1297


title: PBMCs, YUCARD, TCR scVDJ-seq

value: YUCARD

value: A


title: A104267


title: DCM2-H3K4me1_ChIPseq


title: NF1-H3K4me3_ChIPseq

value: Non-failing


title: DCM3-H3K27ac_ChIPseq


title: control 1104


title: A103664


title: A104034


title: control 1135


title: DCM2-H3K27ac_ChIPseq


title: DCM1-H3K27ac_ChIPseq


title: A103636


title: autism B5144


title: NF2-H3K27ac_ChIPseq


title: A103633


title: NF1-H3K27ac_ChIPseq


title: autism 7041


title: autism 6337


title: PBMCs, H-5, bulk RNA-seq

description: RNA was extracted with the RNAeasy kit, prepared with the TruSeq RNA exome kit, and sequenced on an illumina HiSEQ 2500 instrument

data_processing:
Raw reads were quantified using Salmon v0.12.0 and GENCODE v29, with gene levels normalized to transcripts per million (TPM) using tximport v1.18.0
Genome_build: Gencode v29 (GRCh38.p12)
Supplementary_files_format_and_content: TPM expression matrix

extract_protocol:
Cryopreserved PBMC suspensions were thawed, RNA was extracted using the RNeasy PowerLyzer Tissue & Cells kit (Qiagen, Hilden, Germany), and quality was assessed with a 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA).
Samples were prepared using the TruSeq RNA Exome kit (Illumina, San Diego, CA), per the manufacturer’s instructions. Following hybrid capture, complementary DNA libraries were pooled and sequenced on a HiSeq 2500 instrument (Illumina, San Diego, CA) using 2 x 150 bp paired-end reads.

value: Healthy control

tag: therapy type

value: D


title: autism 5569


title: A103067


title: A103418


title: PBMCs, H-4, bulk RNA-seq


title: autism 4849


title: NF2-H3K4me3_ChIPseq

tag: protocol


title: autism 4721


title: PBMCs, H-2, bulk RNA-seq

tag: patient


title: PBMCs, H-3, bulk RNA-seq


title: autism 4671

tag: genotype


title: A102092

tag: tissue


title: PBMCs, H-1, bulk RNA-seq

tag: diagnosis


title: JLYZ0089 [WGBS]

data_processing:
Raw sequencing files were preprocessed, aligned to the human reference genome and converted to CpG methylation count matrices with the default parameters in CpG_Me. Reads were trimmed to remove adapters and methylation bias on both 5’ and 3’ end.  After trimming, reads were aligned to human reference genome hg38, and filtered for PCR duplicates. Cytosine methylation reports were generated using all covered sites CpG methylation. Quality control was examined for each sample. Libraries with CHH methylation greater than 2% were excluded as incomplete bisulfite conversion. The CpG_Me workflow incorporates Trim Galore, Bismark, Bowtie2, SAMtools, and MultiQC.
Genome_build: hg38
Supplementary_files_format_and_content: CpG methylation count matrices (Bismark cytosine reports) for each Sample

extract_protocol:
The placental samples were frozen within 4 hours after birth. DNA was extracted from placenta tissue with the Gentra Puregene kit (Qiagen, Hilden, Germany) and quantified with the Qubit DNA Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA).
DNA was bisulfite converted with the EZ DNA Methylation Lightning kit (Zymo, Irvine, CA, USA). WGBS libraries were prepared from bisulfite-converted DNA using the TruSeq DNA Methylation kit (Illumina, San Diego, CA, USA) with indexed PCR primers and a 14 cycle PCR programs.

value: Placenta


title: autism 1182


title: JLYZ0090 [WGBS]


title: JLYZ0091 [WGBS]


title: JLYZ0087 [WGBS]


title: JLYZ0189 [WGBS]


title: PBMCs, YUADD, bulk RNA-seq

value: YUADD

value: Melanoma

tag: Sex

value: Bulk cohort 2

value: C


title: JLYZ0088 [WGBS]


title: PBMCs, YUTRIL, bulk RNA-seq

value: YUTRIL

value: Male


title: PBMCs, YUDNA, bulk RNA-seq

value: YUDNA

value: Blood


title: JLYZ0085 [WGBS]

value: ASD


title: JLYZ0086 [WGBS]


title: PBMCs, YUWHEY, bulk RNA-seq

value: YUWHEY


title: JLYZ0184 [WGBS]

value: NonTD


title: JLYZ0084 [WGBS]


title: JLYZ0187 [WGBS]

value: TD


title: JLYZ0186 [WGBS]


title: PBMCs, YUCEVO, bulk RNA-seq

value: YUCEVO

value: Female


title: control 1027

value: Brain


title: PBMCs, WUPALO, bulk RNA-seq

value: WUPALO


title: C2C12 Am80

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

description: Am80 treated

data_processing:
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

organism: Mus musculus

source_name: C2C12 myotube

growth_protocol: C2C12 myoblasts (ATCC CRL-1772) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin. Myogenic differentiation was induced in DMEM supplemented with 5% horse serum and 1% penicillin-streptomycin at 37C under 5% CO2.

extract_protocol: Nuclei were extracted from approximately 50,000 cells. After transposase reactions, cellular DNA was immediately purified. The DNA was amplified for 14 cycles using Nextera primer Ad1 and a unique Ad2.n barcoding primer with NEBNext High-Fidelity 2XPCR Master Mix (NEB). The resulting libraries were size selected to 175-225 bp, purified.

treatment_protocol: Microgravity conditions were produced using a 3D-Clinorotation apparatus (Gravite®, Space Bio-Laboratories Co., Ltd.). This device produces an environment similar to that of outer space (0.001 G) by rotating a sample around two axes, integrating a gravity vector with a temporal axis. This is accomplished by rotation of a chamber at the center of the device, which results in uniform dispersion of the gravity vector within a spherical volume, with a constant angular velocity. Within 8 min, these conditions produced a simulated environment of 10-3 G, measured with a gravity acceleration sensor, which was defined as simulated microgravity. Differentiated C2C12 myotubes were cultured in a cell culture flask (T-75, Corning) filled with differentiation media for 8, 24, and 48 hours under simulated microgravity at 37C. As a control, C2C12 myotubes cultured in the same cell culture flask under the ground condition were used. 100 nM Am80 was added to the culture media as a compound that suppresses myotube atrophy (PNAS 118: e2102895118) to assess effects of this compound on the atrophy-associated changes in chromatin accessibility.

tag: cell line

tag: strain

tag: cell type

value: Myotube


title: A107825

value: Cord Blood


title: JLYZ0183 [WGBS]

value: Placenta


title: PBMCs, WULOUIS, bulk RNA-seq

value: WULOUIS

value: Melanoma

tag: age

tag: highest irae grade

value: Bulk cohort 2


title: JLYZ0083 [WGBS]


title: JLYZ0182 [WGBS]


title: JLYZ0079 [WGBS]


title: C2C12 Ctrl

description: Control for Am80


title: JLYZ0178 [WGBS]


title: JLYZ0078 [WGBS]


title: JLYZ0075 [WGBS]


title: PBMCs, YUSONG, bulk RNA-seq

value: YUSONG

value: Male

tag: cohort

value: C


title: PBMCs, YUDUAR, bulk RNA-seq

value: YUDUAR

value: Blood

tag: sequencing batch


title: C2C12 Low Oxygen

description: Control for clinorotation

tag: treatment

value: Low oxygen


title: C2C12 Clino

description: Clinorotation

value: Clinorotation


title: JLYZ0188 [WGBS]

value: ASD


title: JLYZ0176 [WGBS]

value: TD


title: PBMCs, YUZIRG, bulk RNA-seq

value: YUZIRG

value: A


title: PBMCs, YUSTE, bulk RNA-seq

value: YUSTE

value: Female


title: JLYZ0174 [WGBS]

value: Placenta


title: JLYZ0071 [WGBS]


title: PBMCs, YUCOT, bulk RNA-seq

value: YUCOT


title: JLYZ0081 [WGBS]


title: JLYZ0169 [WGBS]


title: JLYZ0073 [WGBS]


title: 7B3 IAA 500mg/L rep3

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

description:
Flaws_GeneResults_combined_IAA_2021-11-11.txt
Flaws_rawCounts_2021-11-11.txt
IAA.500_vs_CTRL.html
IAA.500_vs_IAA.10.html

data_processing:
All reference files were downloaded from NCBI’s ftp site. The Mus musculus transcriptome file “GCF_000001635.27_GRCm39_rna.fna.gz” from Annotation 109 from NCBI was used for quasi-mapping and count generation. This transcriptome is derived from genome GRCm39; Since the quasi-mapping step only uses transcript sequences, the gene model file “GCF_000001635.27_GRCm39_genomic.gff.gz” was solely used to generate transcript-gene mapping table (“txID2GeneID”) for obtaining gene-level counts.
Quality check FASTQC (version 0.11.8) on individual samples completed. Average per-base read quality scores are over 30 in all samples and no adapter sequences were found indicating those reads are high in quality. Thus, we skipped the trimming step and directly proceed to transcripts mapping and quantification.
Salmon version 1.2.0 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed using the decoy-aware method in Salmon with the entire genome file “GCF_000001635.27_GRCm39_genomic.fna.gz” as the decoy sequence. Then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates and --validateMappings and --recoverOrphans to help improve the accuracy of mappings. Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package.
Percentage of reads mapped to the transcriptome ranged from 73.5 to 88.4%. The unmapped reads were discarded while the number of remaining reads (range: 39.9 - 67.5 million per sample) were kept for further analysis.
The TMM (trimmed mean of M values) normalization in the edgeR package used to determine TMM normalization factors.
We set the detection threshold at 0.25 cpm (counts per million) in at least 4 samples, which resulted in 21,084 genes being filtered out, leaving 18,169 genes to be analyzed for differential expression that contain 99.96% of the reads. After filtering, TMM normalization was performed again and normalized log2-based count per million values (logCPM) were calculated using edgeR’s7 cpm() function with prior.count = 2 to help stabilize fold-changes of extremely low expression genes.
Limma-trend modeling with remove unwanted variation (RUV) method used to fit a model of treatment with 5 RUV factors to make all 3 pairwise comparisons. Adjustments for multiple testing correction completed with a “global” FDR correction across p-values for all comparisons together.
All analyses from summation of counts to the gene level were done on a laptop in R version 4.1.2 (2021-11-01).
Genome_build: GRCm39 Annotation 109
Supplementary_files_format_and_content: Text file of genes and fold changes comparing treatment groups
Supplementary_files_format_and_content: Html file with interactive plots of log fold change and average log CPM
Supplementary_files_format_and_content: Text file of genes and raw counts

source_name: ovarian antral follicles

growth_protocol: CD-1 mice at 40 days of age were given ad libitum drinking water only (control), drinking water with IAA 10mg/L, or drinking water with IAA 500mg/L for 35 consecutive days.

extract_protocol:
On the morning of collection, estrous cyclicity was determined and ovaries were collected from mice in diestrus. Immediately after euthanasia, antral follicles were meticulously dissected from the ovaries based on size (220–400 µm) using watchmaker’s forceps. Antral follicles (30-40 follicles per mouse) were dissected, snap frozen in liquid nitrogen, and then stored at –80 °C for RNA sequencing. Total RNA was isolated from the antral follicles using a RNeasy Micro kit (Qiagen, Inc., Valencia, California) following the manufacturer's instructions.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one SP lane for 101 cycles from one end of the fragments on a NovaSeq 6000. Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used the first 33nt for adaptor trimming). Adaptor sequence in read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index).

value: ovary

value: IAA 500mg/L

value: adult - 75 days old


title: 8B1 IAA 500mg/L rep4

treatment_protocol: ad libitum drinking water only (control), drinking water with IAA 10mg/L, or drinking water with IAA 500mg/L for 35 consecutive days


title: JLYZ0170 [WGBS]


title: JLYZ0070 [WGBS]


title: JLYZ0074 [WGBS]


title: PBMCs, YUARGE, bulk RNA-seq

value: YUARGE

value: Melanoma

value: Male

value: Bulk cohort 2


title: JLYZ0177 [WGBS]


title: PBMCs, YUVITZ, bulk RNA-seq

value: YUVITZ

value: Blood


title: 7B1 IAA 500mg/L rep2


title: 6B3 IAA 500mg/L rep1


title: PBMCs, YUHONEY, bulk RNA-seq

value: YUHONEY

value: Combination

value: C


title: JLYZ0067 [WGBS]

value: ASD


title: JLYZ0062 [WGBS]

value: TD


title: 8B3 IAA 500mg/L rep5


title: 4A3 control rep10

description:
Flaws_GeneResults_combined_IAA_2021-11-11.txt
Flaws_rawCounts_2021-11-11.txt
IAA.500_vs_CTRL.html
IAA.10_vs_CTRL.html

value: vehicle control


title: JLYZ0168 [WGBS]

value: Placenta


title: JLYZ0175 [WGBS]


title: JLYZ0167 [WGBS]


title: JLYZ0066 [WGBS]


title: PBMCs, YUDEBIT, bulk RNA-seq

value: YUDEBIT

value: A


title: JLYZ0164 [WGBS]


title: PBMCs, YUPESO, bulk RNA-seq

value: YUPESO


title: JLYZ0061 [WGBS]


title: JLYZ0060 [WGBS]


title: 4A1 control rep8

value: ovary

value: adult - 75 days old


title: PBMCs, YUBLIT, bulk RNA-seq

value: YUBLIT

value: Melanoma


title: 2A2 control rep7


title: 1A3 control rep6


title: JLYZ0163 [WGBS]


title: JLYZ0058 [WGBS]


title: JLYZ0057 [WGBS]


title: JLYZ0162 [WGBS]


title: JLYZ0160 [WGBS]


title: JLYZ0056 [WGBS]


title: PBMCs, YUSMAL, bulk RNA-seq

value: YUSMAL

value: Female

value: Bulk cohort 2


title: 8D2 IAA 10mg/L rep5

description:
Flaws_GeneResults_combined_IAA_2021-11-11.txt
Flaws_rawCounts_2021-11-11.txt
IAA.10_vs_CTRL.html
IAA.500_vs_IAA.10.html

value: IAA 10mg/L


title: 7D2 IAA 10mg/L rep4


title: PBMCs, YURIDA, bulk RNA-seq

value: YURIDA

value: Blood

value: Male


title: PBMCs, YUPOGER, bulk RNA-seq

value: YUPOGER

value: Combination


title: JLYZ0158 [WGBS]

value: NonTD

value: Placenta


title: JLYZ0055 [WGBS]

value: ASD


title: JLYZ0166 [WGBS]

value: TD


title: 4A2 control rep9

value: ovary

value: vehicle control


title: 6D3 IAA 10mg/L rep2

value: adult - 75 days old


title: JLYZ0052 [WGBS]


title: PBMCs, YUPRETE, bulk RNA-seq

value: YUPRETE

value: Melanoma

value: A


title: PBMCs, YULAMB, bulk RNA-seq

value: YULAMB

value: Female

value: Bulk cohort 2


title: JLYZ0051 [WGBS]


title: JLYZ0157 [WGBS]


title: PBMCs, YUFROZE, bulk RNA-seq

value: YUFROZE

value: Blood


title: JLYZ0050 [WGBS]


title: JLYZ0156 [WGBS]


title: PBMCs, YUCADA, bulk RNA-seq

value: YUCADA


title: 6D2 IAA 10mg/L rep1

value: IAA 10mg/L


title: 3C3 control rep5

description:
Flaws_GeneResults_combined_IAA_2021-11-11.txt
Flaws_rawCounts_2021-11-11.txt
IAA.10_vs_CTRL.html
IAA.500_vs_CTRL.html


title: JLYZ0154 [WGBS]

value: NonTD


title: PBMCs, YUBROMO, bulk RNA-seq

value: YUBROMO

value: Male

value: Combination


title: JLYZ0049 [WGBS]

value: TD

value: Placenta


title: 3C2 control rep4

value: ovary

value: vehicle control

value: adult - 75 days old


title: JLYZ0153 [WGBS]

value: ASD


title: JLYZ0046 [WGBS]


title: 2C2 control rep3


title: PBMCs, YUGRAPH, bulk RNA-seq

value: YUGRAPH

value: Melanoma

value: A


title: PBMCs, YUAMIGO, bulk RNA-seq

value: YUAMIGO

value: Bulk cohort 2


title: JLYZ0045 [WGBS]


title: JLYZ0152 [WGBS]


title: PBMCs, YUTACI, bulk RNA-seq

value: YUTACI

value: Blood

value: Bulk cohort 1

value: B


title: JLYZ0148 [WGBS]

value: NonTD


title: JLYZ0159 [WGBS]


title: 7D1 IAA 10mg/L rep3

value: IAA 10mg/L


title: JLYZ0044 [WGBS]


title: PBMCs, YUPARK, bulk RNA-seq

value: YUPARK

value: Female


title: 1C3 control rep1

value: ovary


title: JLYZ0145 [WGBS]

value: Placenta


title: JLYZ0043 [WGBS]

value: TD


title: PBMCs, YUJADE, bulk RNA-seq

value: YUJADE

value: Male


title: JLYZ0144 [WGBS]


title: JLYZ0042 [WGBS]

value: ASD


title: PBMCs, YUHIMO, bulk RNA-seq

value: YUHIMO

value: Melanoma


title: JLYZ0138 [WGBS]


title: PBMCs, YUGIRL, bulk RNA-seq

value: YUGIRL


title: JLYZ0137 [WGBS]


title: PBMCs, YUDIME, bulk RNA-seq

value: YUDIME


title: JLYZ0136 [WGBS]


title: JLYZ0041 [WGBS]


title: CD8 T cells, KO1

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

country: China

institute: xian jiaotong university

data_processing:
Illumina Hiseq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the raw reads were trimmed by using Trim Galore (version 0.5.0_dev, Cutadapt version 1.15) with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10), and quantified by using Salmon5. The transcript-level quantification results were converted to the gene-level quantities with tximport R package.
DESeq2 R package was used to normalize the gene-level quantities and followed by differential expression analysis between selected samples with the same package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD8 T cells from the spleen of Zfp335 deficient mice

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and KO CD8+ T cells were sorted from the spleens of recipient mice 7 days after LM-OVA infection in the co-transfer model.

value: Zfp335 deficient

value: Spleen

value: CD8 T cells


title: CD8 T cells, WT3

source_name: CD8 T cells from the spleen of WT mice

value: WT


title: JLYZ0037 [WGBS]


title: JLYZ0135 [WGBS]


title: JLYZ0036 [WGBS]


title: CD8 T cells, KO3


title: PBMCs, YUBUMP, bulk RNA-seq

value: YUBUMP

value: Blood

value: Bulk cohort 1

value: B


title: 2C1 control rep2

value: ovary

value: vehicle control

value: adult - 75 days old


title: CD8 T cells, WT2


title: JLYZ0134 [WGBS]

value: TD

value: Placenta


title: JLYZ0035 [WGBS]

value: ASD


title: JLYZ0133 [WGBS]

value: NonTD


title: JLYZ0034 [WGBS]


title: Neg_AM3

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.9, Picard v2.23.1, Samtools v1.10, Preseq v2.0.3, BEDTools v2.29.2, BAMTools v2.5.1, deepTools v3.4.3)
Trimming and alignment (Trim Galore! V0.6.4_dev, BWA v0.7.17-r1188)
Identifying and Counting peaks (MACS2 v2.2.7.1, featureCounts v2.0.1)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited file (txt) for raw hit counts, pseudo hit counts, and cross comparisons

source_name: Tissue Derived Alveolar Mac

extract_protocol:
Genomic DNA
Sorted cells were lysed in buffer (10mM Tris-HCl, 10mM NaCl 3mM MgCL2 and 0.1% IGEPAL) for 15 minutes at 4C, then centrifuged and re-suspended with transposase reaction mix (2x tagmented DNA buffer, transposase [Ilumina Nextera]), and nuclease-free water) and incubated for 30 min at 37 degrees. Cells were then added to MinElute column (Qiagen) and PCR amplified in KAPA HiFi 2x mix (Kapa Biosystems) with barcoding primers(Buenrostro et al., 2013) at 98C for 45 sec (45s) + 5 x at (98C for 15s + 63C for 30s + 72C for 30s) + 72C for 1 min. PCR products were cleaned with MinElute columns and size exclusion was performed with magJet NGS Cleanup and Size Selection kit (Thermo Fisher). Q-PCR library amplification test and PCR library amplification was performed as previously described(Buenrostro et al., 2015).
Paired end strand-specific ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Infected s.c with N. Brasilienses

value: N. brasiliensis day 7


title: PBMCs, YUROSA, bulk RNA-seq

value: YUROSA

value: Melanoma

value: Female


title: JLYZ0131 [WGBS]


title: JLYZ0033 [WGBS]


title: CD8 T cells, KO2

value: Zfp335 deficient

value: Spleen

value: CD8 T cells


title: JLYZ0030 [WGBS]


title: PBMCs, YUPRAF, bulk RNA-seq

value: YUPRAF

value: Blood


title: PBMCs, YUFROME, bulk RNA-seq

value: YUFROME

value: Male

value: Bulk cohort 1

value: B


title: Neg_AM1

growth_protocol: Sorted cells were lysed in buffer (10mM Tris-HCl, 10mM NaCl 3mM MgCL2 and 0.1% IGEPAL) for 15 minutes at 4C, then centrifuged and re-suspended with transposase reaction mix (2x tagmented DNA buffer, transposase [Ilumina Nextera]), and nuclease-free water)


title: PBMCs, YUEVRY, bulk RNA-seq

value: YUEVRY


title: JLYZ0122 [WGBS]

value: Placenta


title: JLYZ0128 [WGBS]


title: PBMCs, YURAISE, bulk RNA-seq

value: YURAISE

value: Combination


title: Pos_AM3

source_name: Monocyte Derived Alveolar Mac

value: N. brasiliensis day 7


title: PBMCs, YURICA, bulk RNA-seq

value: YURICA


title: CD8 T cells, WT1

value: WT


title: JLYZ0028 [WGBS]

value: TD


title: PBMCs, YUBIFO, bulk RNA-seq

value: YUBIFO

value: Melanoma


title: Neg_AM4


title: JLYZ0117 [WGBS]


title: JLYZ0026 [WGBS]


title: PBMCs, YUQIP, bulk RNA-seq

value: YUQIP

value: Female


title: JLYZ0119 [WGBS]

value: NonTD


title: Pos_AM2


title: JLYZ0027 [WGBS]

value: ASD


title: PBMCs, YUMEDIC, bulk RNA-seq

value: YUMEDIC

value: Blood


title: JLYZ0110 [WGBS]


title: Neg_AM2


title: Pos_AM1


title: Naive_AM4

source_name: Naive Alveolar Mac

value: Naive control


title: JLYZ0023 [WGBS]


title: JLYZ0130 [WGBS]


title: JLYZ0039 [WGBS]


title: JLYZ0105 [WGBS]


title: PBMCs, YUMAXI, bulk RNA-seq

value: YUMAXI

value: Male

value: Bulk cohort 1

value: B


title: Naive_AM3


title: JLYZ0029 [WGBS]

value: Placenta


title: Pos_AM4

value: N. brasiliensis day 7


title: PBMCs, YUGRUE, bulk RNA-seq

value: YUGRUE

value: Combination


title: JLYZ0022 [WGBS]

value: TD


title: JLYZ0021 [WGBS]


title: PBMCs, YUCUSK, bulk RNA-seq

value: YUCUSK

value: Melanoma


title: JLYZ0020 [WGBS]


title: Naive_AM1


title: INPUT_C49-SEM_2hr_WCE_K79

city: Palo Alto

first: Tanja

middle: A

last: Gruber

address: 1000 Welch Road Suite 300

department: Pediatrics

description: INPUT match to H3K79me2 samples

data_processing:
Single-end reads of 50bp were mapped human genome hg19(GRCh37-lite) and fruit fly genome dm6(D. melanogaster, UCSC BDGP Release 6) hybrid by BWA (version 0.7.12-r1039, default parameter)
Duplicated reads were then marked with biobambam (version v2.0.87)
Bam files were then split by either human or fruit fly spike-in. For spike-in bam files, we counted the non-duplicated reads by samtools. For human bam files, only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2)
Encode quality guidelines were met for all samples so we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks for visualization
The bigwig tracks for IP were normalized to 1M uniquely mapped spike-in reads, bigwig for INPUT were normalized to 15M uniquely mapped human reads
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: cell line

growth_protocol: SEM cells were cultured in IMDM supplemented with 20% FBS at 37°C; Drosophila S2 cells were cultured in complete Schneider's Drosophila Medium at room temperature.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: SEM cells were treated with 50nM bortezomib or media for 0, 2, 4, and 6 hours at 37°C; Drosophila S2 cells were not treated

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell

tag: spike-in

value: Drosophila melanogaster embryos S2 cell late stage (20–24 hours old)

value: bortezomib 50nM 2 hour exposure

tag: chip antibody


title: PBMCs, YUGIM, bulk RNA-seq

value: YUGIM

tag: therapy type


title: INPUT_C51-SEM_6hr_WCE_K79

description: INPUT match to H3K79me2 samples

value: bortezomib 50nM 6 hour exposure


title: INPUT_C50-SEM_4hr_WCE_K79

description: INPUT match to H3K79me2 samples

value: bortezomib 50nM 4 hour exposure


title: PBMCs, YUBRET, bulk RNA-seq

value: YUBRET

value: Blood


title: INPUT_C48-SEM_0hr_WCE_K79

description: INPUT match to H3K79me2 samples

value: untreated


title: JLYZ0018 [WGBS]

value: ASD


title: Naive_AM2

value: Naive control


title: INPUT_C59-SEM_6hr_WCE

description: INPUT match to H2Bub samples


title: PBMCs, YUKEID, bulk RNA-seq

value: YUKEID

value: Female

value: Bulk cohort 1

value: B


title: Oocyte maturation in vivo rep1

city: Beijing

first: Hao

last: Qin

address: 49 North Garden Rd.,Haidian District

institute: Peking University Third Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter.
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method. RSEM v1.3.3 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
All AS events in the IVM and IVO groups were detected by the replicate multivariate analysis of transcript splicing (rMATS) statistical method (Shen et al., PNAS, 2014.). Only isoforms that were similar to the reference or consisted of novel splice junctions were considered, and splicing differences were detected in five major forms (exon inclusion, exclusion, alternative 5’, 3’, and intron retention events).
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Oocyte

extract_protocol:
Metaphase II stage oocytes for each group were directly lysed with Reaction Buffer containing RNase Inhibitor and used for cDNA synthesis using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio).
Total RNA were extracted from MII oocytes obtained via both IVM and IVO and used to construct a eukaryotic microlibrary. Specifically, we used a SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) to obtain full length cDNA in accordance with the manufacturer’s instructions. cDNA synthesis and amplification were validated by an Agilent 2100 Bioanalyzer (Agilent Technologies) and a High Sensitivity DNA Kit (Agilent Technologies) in accordance with the manufacturer’s instructions. Then, the Nextera XT DNA Library Preparation Kit (Illumina) was used to construct a library that was suitable for sequencing. Finally, a paired-end RNA-seq library was performed on the Illumina NovaSeq 6000 system (2 × 150bp read length).

value: ICR

value: In vivo matured metaphase II stage oocytes

value: 42-45 weeks


title: Oocyte maturation in vivo rep2


title: JLYZ0015 [WGBS]

value: Placenta


title: Oocyte maturation in vitro rep3

value: In vitro matured metaphase II stage oocytes


title: JLYZ0014 [WGBS]

value: TD


title: PBMCs, YUDONA, bulk RNA-seq

value: YUDONA

value: Melanoma

value: Male

value: Combination


title: INPUT_C57-SEM_2hr_WCE

description: INPUT match to H2Bub samples

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell

value: Drosophila melanogaster embryos S2 cell late stage (20–24 hours old)

value: bortezomib 50nM 2 hour exposure


title: INPUT_C58-SEM_4hr_WCE

description: INPUT match to H2Bub samples

value: bortezomib 50nM 4 hour exposure


title: Oocyte maturation in vitro rep2


title: JLYZ0013 [WGBS]


title: PBMCs, YUBAIX, bulk RNA-seq

value: YUBAIX

value: Blood


title: JLYZ0019 [WGBS]


title: INPUT_C32-SEM_0hr_WCE

description: INPUT match to H2Bub samples

value: untreated


title: JLYZ0012 [WGBS]

value: ASD


title: JLYZ0011 [WGBS]


title: H3K79me2_C47-SEM_6hr_K79

value: bortezomib 50nM 6 hour exposure

value: H3K79me2 Abcam #ab3594


title: Oocyte maturation in vivo rep3

value: ICR

value: In vivo matured metaphase II stage oocytes

value: 42-45 weeks


title: AA_15 ALB Scramble

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

data_processing:
Library strategy: DNA-seq
Data was processed using a in-house pipeline exploiting BWA-mem, Bedtools, Picard, AWK and Linux Bash commands
Genome_build: mm10
Supplementary_files_format_and_content: text files

source_name: blood

extract_protocol:
Conventional lysis buffer [400mM NaCl, 1% SDS, 20mM TRIS-CL pH 8.0, 5mM EDTA (pH 8.0)] was used for DNA extraction from temporal retinal and RPE. For liver, DNA extraction was performed using either the above-mentioned conventional lysis buffer or using the DNeasy Blood & Tissue kit (QIAGEN, Hilden, Germany).
Libraries were generated following the manufacturer’s instructions for “SureSelectQXT Target Enrichment for Illumina Multiplexed Sequencing, Version E0, April 2018”

treatment_protocol: For some samples GuideRNA was used to target the gene.

value: Scramble

tag: targets

value: ALB


title: PBMCs, YUHEAL, bulk RNA-seq

source_name: Peripheral blood

tag: patient

value: YUHEAL

value: Melanoma

value: Male

value: Bulk cohort 1

value: B


title: AA_16 ALB gRNA

value: gRNA


title: PBMCs, YURADIO, bulk RNA-seq

value: YURADIO

value: Combination


title: PBMCs, YUNANCY, bulk RNA-seq

value: YUNANCY

value: Blood

value: Female

value: Single-cell discovery

value: C


title: PBMCs, YUALOE, bulk RNA-seq

value: YUALOE


title: JLYZ0010 [WGBS]

tag: genotype

value: TD

value: Placenta


title: H3K79me2_C46-SEM_4hr_K79

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell

value: Drosophila melanogaster embryos S2 cell late stage (20–24 hours old)

value: bortezomib 50nM 4 hour exposure

value: H3K79me2 Abcam #ab3594


title: AA_14 ALB gRNA

value: ALB


title: H3K79me2_C44-SEM_0hr_K79

value: untreated


title: AA_13 ALB gRNA

value: gRNA


title: JLYZ0008 [WGBS]

tag: tissue


title: H3K79me2_C45-SEM_2hr_K79

value: bortezomib 50nM 2 hour exposure


title: JLYZ0007 [WGBS]


title: PBMCs, YUHERN, bulk RNA-seq

value: YUHERN

tag: diagnosis

value: Melanoma

value: Combination

value: A


title: JLYZ0006 [WGBS]

value: ASD


title: PBMCs, YUROD, bulk RNA-seq

value: YUROD

value: Blood

tag: Sex

value: Male

value: Single-cell discovery


title: H2Bub_C54-SEM_4hr

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell

value: H2B-ub Millipore #17-650


title: AA_12 ALB Scramble

value: Scramble


title: H2Bub_C55-SEM_6hr

value: Drosophila melanogaster embryos S2 cell late stage (20–24 hours old)

value: bortezomib 50nM 6 hour exposure


title: PBMCs, YUTORY, bulk RNA-seq

value: YUTORY


title: Oocyte maturation in vitro rep1

value: ICR

value: In vitro matured metaphase II stage oocytes

value: 42-45 weeks


title: JLYZ0005 [WGBS]

value: Placenta


title: AA_11 ALB Scramble

value: ALB


title: PBMCs, WUMENLO, bulk RNA-seq

value: WUMENLO

value: Melanoma

value: Combination

value: C


title: JLYZ0003 [WGBS]

value: TD


title: AA_10 ALB gRNA

value: gRNA


title: PBMCs, YUFURL, bulk RNA-seq

value: YUFURL

value: Blood

value: Male

value: Single-cell discovery

value: A


title: ChIP-seq_6__S4_L001

status: Public on Jan 12 2022

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
annotated_h2azac_peaks.txt
h2azac_peaks.bed

data_processing:
Raw sequencing reads from HeLa cell lines were mapped to hg38 using HISAT2.
Only uniquely mapped reads were retained. Alignments were filtered using SAMtools to remove duplicate reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2
Peaks called were annotated using region_analysis software and saved in tab delimited text file.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files.
Supplementary_files_format_and_content: h2azac_peaks.bed: BED file containing peaks called using MACSv2.1.1 on H2AZac ChIP-seq samples.

source_name: HeLa

growth_protocol: HeLa cells were obtained from the American Type Culture Collection (ATCC) and grown in DMEM supplemented with 10% FBS with 100 ug/ml streptomycin and 100 U/ml penicillin, at 37°C in a 5% CO2, 95% humidified incubator.

extract_protocol:
Cells were lysed in 1ml LB1 buffer at 4°C for 15 min, and nuclei were pelleted at 2650 rcf for 5 min. Nuclei were resuspended in 1ml LB2 buffer and incubated rotating at 4°C for 10 min and pelleted at 2650 rcf for 5 min. Nuclei were lysed in 1ml LB3 buffer and sonicated using Covaris for 1.5 hours.
TruSeq ChIP Library Preparation Kit manufacturer’s protocol (Illumina)

treatment_protocol: Cells were detached using a scraper, transferred to a microfuge tube and span down at 1230 rcf for 5 minutes. Cell pellet was resuspended in 940 ul of 1% formaldehyde in PBS and incubated on a low speed rotator for 12 minutes at room temperature. 64 ul of 2M glycine was added and continued incubation for 5 more minutes. Cells were span down at 1230 rcf at 4°C and washed 5 times with ice-cold PBS containing protease inhibitor cocktail (Roche Complete EDTA-free).

tag: sample type

value: IP

tag: cell line

value: HeLa


title: JLYZ0001 [WGBS]


title: AA_9 ALB gRNA


title: H2Bub_C32-SEM_0hr

tag: cell type

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell

value: Drosophila melanogaster embryos S2 cell late stage (20–24 hours old)

value: untreated

value: H2B-ub Millipore #17-650


title: ChIP-seq_2__S1_L001

value: none (input)

value: Input


title: ChIP-seq_3_S3_L001


title: ChIP-seq_8_S8_L001


title: ChIP-seq_7_S7_L001


title: H2Bub_C53-SEM_2hr

value: bortezomib 50nM 2 hour exposure


title: 16_S7_L002_R1_001

data_processing:
All RNA-Seq analyses were performed in R (www.R-project.org). All heat maps and their hierarchical clustering were computed using the pheatmap package. If the number of values to be clustered exceeded 1000, rows were pre-aggregated using k-means clustering.
Genes with over 15 counts in at least 2 samples were retained for further analysis. Normalization factors for library sizes were calculated using the trimmed mean of M-values (TMM) method in the calcNormFactors function (edgeR package). For the purpose of linear modeling, ‘JQ treatment’ and ‘Diagnosis’ were combined into one group variable.
The limma voom function was used to compute weights for heteroscedasticity adjustment by estimating the mean-variance trend for log2 counts. Linear models were fit to the expression values of each gene using the lmFit function: Gene expression ~ group. The coefficients, standard deviations and correlation matrix were then recalculated, using contrasts.fit in terms of the comparisons of interest. Empirical Bayes moderation was applied using the eBayes function to obtain more precise estimates of gene-wise variability. P-values were adjusted for multiple hypotheses testing using false discovery rate (FDR) estimation, and differentially expressed genes were determined as those with an estimated FDR ≤ 5%, unless stated otherwise.
Concordance between differential expression in the tested comparisons and one external dataset (post-mortem (CMC, common mind consortium) was evaluated through Spearman correlation of t-statistics.
Genome_build: hg38
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include counts.

source_name: hiPSC forebrain neurons

extract_protocol:
Cell pellets from vehicle (PBS) and JQ1 treated neurons were homogenized in Trizol (Thermo Fisher; cat#15596026) and processed according to the manufacturer’s instructions. RNeasy Microcolumns (Qiagen; cat#74004) were used to further purify RNA, and a nanodrop spectrophotometer confirmed RNA 260/280 and 260/230 ratios to be >1.8.
Following RNA purifications, RNA-seq libraries were prepared according to Illumina protocols.

value: Control

value: hiPSC forebrain neurons


title: 7_S5_L002_R1_001


title: 2_S1_L002_R1_001

value: Vehicle (PBS)


title: 4_S2_L002_R1_001


title: 6_S4_L002_R1_001

value: Schizophrenia


title: 6_S4_L001_R1_001


title: 15_S6_L001_R1_001


title: 5_S3_L002_R1_001


title: 16_S7_L001_R1_001


title: 5_S3_L001_R1_001


title: Peromuscus_maniculatus_x_polionotus_F1_hybrid_control_rep3

city: San Francisco

first: Ryan

last: York

address: 1328 6th Avenue

data_processing:
To compare gene expression both across treatments and species, we first removed low-quality and adaptor sequences using SeqPrep (https://github.com/jstjohn/SeqPrep).
The P. maniculatus genome was masked at sites with SNPs using the perl script MaskReferencefromBED (https://github.com/TheFraserLab/ASEr) to avoid reference genome mapping bias. Reads from all F1 hybrid samples were aligned to this masked genome using STAR v 2.4.2a (Dobin et al., 2013) in 2-pass mode.
We determined ASE at the read-level using the script GetGeneASEbyReads in the ASEr package (https://github.com/TheFraserLab/ASEr).
To test for allele-specific expression differences, we first filtered ASE calls from GetGeneASEbyReads requiring at least 1 count per allele from all genes per sample.
After filtering we computed an ASE ratio for each gene by calculating the log2 ratio of P. maniculatus allelic counts compared to P. polionotus allelic counts. Positive values correspond to a P. maniculatus allelic bias while negative values reflect a P. polionotus bias.
Genome_build: pman 1.0
Supplementary_files_format_and_content: Matrix table with allele counts

organism: Peromyscus maniculatus x Peromyscus polionotus

source_name: Whole brain

growth_protocol: All experimental animals were males and housed in standard polysulfone cages (19.7 x 30.5 cm and 16.5 cm high; Allentown, New Jersey, USA) in same sex and genotype groups, until testing adults at approximately 50-80 days of age. Housing cages contained enrichment as previously described (Lewarch and Hoekstra, 2018). We maintained animals at 22 ºC with a 16:8h light:dark cycle and provided them with standard rodent food and water ad libitum. All procedures were approved by the Harvard University Institutional Animal Care and Use Committee (protocol 27-09-3)

extract_protocol:
To capture behavior-relevant gene expression, we focused on the brain. Therefore, at the conclusion of the test trial, we immediately euthanized animals using CO2 inhalation and rapidly dissected whole brains in chilled PBS, flash-froze the sample in liquid nitrogen, and stored it at -80 °C. Later, we homogenized tissues using a TissueLyser (Qiagen, Venlo, Netherlands) in Trizol (ThermoFisher Scientific, Waltham, MA, USA), and extracted total RNA using 5Prime Phase Lock Gel Tubes Heavy (Quantabio, Beverly, MA, USA), followed by clean-up with RNeasy columns (Qiagen, Venlo, Netherlands).
We prepared RNA-seq libraries with a TruSeq Stranded mRNA Library Prep Kit, following manufacturer’s instructions (Illumina, San Diego, CA, USA), and assessed library quality prior to sequencing using a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: We measured burrowing behavior using large sand-filled (Scott Pharma, Marlborough, MA, USA) enclosures (1.2 x 1.5 x 1.1 m) set up as previously described (Weber et al., 2013). We first ran all experimental animals through two “pretest” trials in the enclosures to allow them to acclimate and to confirm individuals burrowed in a species- (or hybrid-) typical manner. Next, we randomly assigned animals to a test trial cohort, “burrowing” or “control”.

value: Whole brain

tag: condition


title: 7_S5_L001_R1_001


title: Peromuscus_maniculatus_x_polionotus_F1_hybrid_control_rep2


title: ChIP-seq_4_S4_L001


title: 4_S2_L001_R1_001


title: 15_S6_L002_R1_001


title: Peromuscus_maniculatus_x_polionotus_F1_hybrid_control_rep1


title: 2_S1_L001_R1_001


title: HBE FOXA2 ChIP-seq rep2

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: HBE FOXA2 ChIP-seq rep2

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibodies.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

value: Human bronchial epithelial cells

value: FOXA2 (Santa Cruz sc6554x)

tag: growth media

value: DMEM + 10percent FBS


title: Peromuscus_maniculatus_x_polionotus_F1_hybrid_burrowing_rep2

value: Burrowing


title: Peromuscus_maniculatus_x_polionotus_F1_hybrid_burrowing_rep3


title: Peromuscus_maniculatus_x_polionotus_F1_hybrid_burrowing_rep1


title: HBE FOXA2 ChIP-seq rep1

source_name: HBE FOXA2 ChIP-seq rep1


title: HBE FOXA1 ChIP-seq rep2

source_name: HBE FOXA1 ChIP-seq rep2

value: FOXA1 (Abcam 5089)


title: HBE FOXA1 ChIP-seq rep1

source_name: HBE FOXA1 ChIP-seq rep1


title: MCF7 CSKko-2 Fulv_Rep2

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: Replicate 2

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program
Fastq files were aligned to human reference genome (hg38/GRCh38, obtained from ensembl) using STAR v2.7.5b.
Reads in exons were counted using featureCounts v1.5.1 in paired end mode (using flag -p) with hg38/GRCh38 ensembl annotations
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: Tab separated text file containing gene expression values

growth_protocol: MCF-7 cells were routinely grown in DMEM supplemented with 10% FCS and 1% Streptomycin/Penicillin, at 37°C in a 5% CO2 humidified incubator

extract_protocol:
The cells were subsequently harvested and frozen at −80 °C until extraction of RNA using the PureLink RNA mini kit (Invitrogen) including Dnase treatment.
llumina TruSeq Stranded mRNA

treatment_protocol: MCF-7 cells were grown in DMEM or in the presence of 1uM Fulvestrant during 20 days.

tag: disease state

value: ER+ breast cancer

value: CSK k.o. clone 2

value: 1uM Fulvestrant


title: MCF7 CSKko-2 Fulv_Rep3

description: Replicate 3


title: GSH_RADONC_RectalCancer_116

city: Frankfurt

first: Adele M.

last: Nicolas

state: Deutschland (DEU)

address: Paul Ehrlich StraBe 42 44, Frankfurt Main, Frankfurt Main

institute: Georg Speyer Haus

data_processing:
Sequence reads trimmed by Trimmomatic Software v.0.36
Trimmed reads mapped to Homo sapiens GRCh38 genome by STAR aligner v.2.5.2b
Unique gene hit counts calculated by Subread packages v.1.5.2
Supplementary_files_format_and_content: Raw counts in txt file format

extract_protocol:
Qiagen Rneasy FFPE kit (Qiagen; #73504)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FFPE material of Patients with advanced rectal cancer treated with neoadjuvant chemoradiotherapy

tag: time

value: Post-CRT

tag: cancer type

value: Rectal cancer

tag: treatment response pcr vs. non-pcr

value: Non-pCR

tag: disease free survival event

tag: disease free survival time (months)


title: GSH_RADONC_RectalCancer_117

tag: treatment


title: MCF7 CSKko-2 Fulv_Rep1

description: Replicate 1


title: GSH_RADONC_RectalCancer_115


title: MCF7 CSKko-1 Fulv_Rep2

description: Replicate 2

value: CSK k.o. clone 1


title: OCIAML2 ABT-199 Resistant S8 Clone Replicate 3

type: genomic

city: North Chicago

first: Shaun

last: Grosskurth

state: Illinois

address: 1 North Waukegan Road

institute: AbbVie

hyb_protocol: Followed recommendations of Infinium HD Methylation Assay Reference Guide provided by Illumina

data_processing: Illumina EPIC methylation array analyses were conducted with R statistical software. Bead count and detection p-value filtering were performed using the pfilter function from the watermelon R package with defaultsettings. The getQC and plotQC functions from the minfi package were used with default settings to check that all samples had sufficiently high median intensities. EPIC arrays were dasen normalized which performs background adjustment, between-array normalization for the Type I and Type II probes separately, and no dye bias correction. Beta values were calculated using functions in wateRmelon.

label: Cy5 and Cy3

growth_protocol: OCI-AML2 and MOLM-13 AML cell lines were purchased from Deutsche Sammlund von Mikroorganismen und Zellkulturen. MV-4-11 cell lines was purchased from ATCC. All cell lines were cultured in suspension in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Sigma), L-glutamine, and penicillin/streptomycin (Invitrogen).

treatment_protocol: ABT-199 resistance was induced by continuously exposing the parental cells to increasing concentrations of ABT-199, starting at 10 nM and increasing to 1 μM with medium changed every 2 days. After cells achieved stable viability (above 90%) at the current ABT-199 dose, the dose was increased until it reached 1 μM. For single-clone selection, ABT-199 resistant cells were seeded into 96-well plates at 1 cell/well by limited dilution assay. Wells with single-cell clones after 3 days were expanded in 48-well plates for 7 days and then to larger flasks while being maintained in 1 μM ABT-199.

tag: sensitivity state

value: ABT-199 Resistant

tag: population clone

value: S8 Clone

value: male

tag: plate information


title: OCIAML2 ABT-199 Resistant S8 Clone Replicate 1

scan_protocol: Followed recommendations of Infinium HD Methylation Assay Reference Guide provided by Illumina


title: OCIAML2 ABT-199 Resistant S1 Clone Replicate 1

label_protocol: Followed recommendations of Infinium HD Methylation Assay Reference Guide provided by Illumina

value: S1 Clone


title: OCIAML2 ABT-199 Resistant S8 Clone Replicate 2

extract_protocol: Followed recommendations of Infinium HD Methylation Assay Reference Guide provided by Illumina


title: OCIAML2 ABT-199 Resistant S2 Clone Replicate 3

value: S2 Clone


title: OCIAML2 ABT-199 Resistant Population Replicate 2

value: population


title: OCIAML2 ABT-199 Sensitive Parental Replicate 3

value: ABT-199 Sensitive

value: parental population


title: OCIAML2 ABT-199 Resistant Population Replicate 3


title: GSH_RADONC_RectalCancer_113


title: MV411 ABT-199 Resistant Population Replicate 3


title: MV411 ABT-199 Sensitive Parental Replicate 1


title: OCIAML2 ABT-199 Sensitive Parental Replicate 2


title: OCIAML2 ABT-199 Resistant S2 Clone Replicate 1


title: OCIAML2 ABT-199 Resistant S2 Clone Replicate 2


title: OCIAML2 ABT-199 Resistant Population Replicate 1


title: GSH_RADONC_RectalCancer_114


title: OCIAML2 ABT-199 Sensitive Parental Replicate 1


title: MV411 ABT-199 Resistant Population Replicate 1


title: OCIAML2 ABT-199 Resistant S1 Clone Replicate 2


title: MCF7 CSKko-1 Fulv_Rep3

description: Replicate 3

tag: genotype


title: MCF7 CSKko-1 Fulv_Rep1

description: Replicate 1


title: MOLM13 ABT-199 Resistant S6 Clone Replicate 3

value: S6 Clone

tag: Sex


title: MV411 ABT-199 Resistant Population Replicate 2


title: MV411 ABT-199 Sensitive Parental Replicate 3


title: MCF7 WT Fulv_Rep3

description: Replicate 3

value: wild type


title: GSH_RADONC_RectalCancer_112


title: GSH_RADONC_RectalCancer_111


title: MCF7 WT Fulv_Rep1

description: Replicate 1

value: ER+ breast cancer


title: MCF7 WT Fulv_Rep2

description: Replicate 2


title: OCIAML2 ABT-199 Resistant S1 Clone Replicate 3


title: MCF7 CSKko-2 DMSO_Rep3

description: Replicate 3

value: CSK k.o. clone 2

value: DMSO


title: MV411 ABT-199 Sensitive Parental Replicate 2


title: GSH_RADONC_RectalCancer_110

value: Post-CRT


title: MOLM13 ABT-199 Resistant S6 Clone Replicate 1b


title: GSH_RADONC_RectalCancer_109

value: Rectal cancer

value: pCR


title: MOLM13 ABT-199 Resistant S6 Clone Replicate 2


title: MCF7 CSKko-2 DMSO_Rep2

description: Replicate 2


title: MOLM13 ABT-199 Resistant S5 Clone Replicate 3

value: S5 Clone


title: MCF7 CSKko-2 DMSO_Rep1

description: Replicate 1


title: GSH_RADONC_RectalCancer_108

value: Non-pCR


title: GSH_RADONC_RectalCancer_107


title: genomic DNA from 5aza_14d_KirPos_02

first: Christopher

last: OAKES

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended settings

data_processing:
Data were processed using the RnBeads software, using BMIQ normalization
Average Beta
Unmethylated and methylated signal intensities

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated using the Gentra Puregene Blood/cell DNA isolation kit (Qiagen) from fresh-frozen samples or the QIAamp FFPE tissue DNA isolation kit (Qiagen) as indicated according to standard instructions

value: Tumor

tag: sample type

value: ENKTL

tag: dna isolation type

value: fresh-frozen

tag: pdx-derived

value: Yes

tag: pdx treatment

tag: sorted population

value: human CD56/KIR-positive


title: GSH_RADONC_RectalCancer_106


title: genomic DNA from 5aza_14d_KirPos_04

tag: disease state


title: MOLM13 ABT-199 Resistant S5 Clone Replicate 2b

tag: cell line

value: ABT-199 Resistant

value: male


title: genomic DNA from 5aza_14d_KirNeg_01

value: human CD56/KIR-negative


title: MCF7 CSKko-1 DMSO_Rep2

description: Replicate 2

value: CSK k.o. clone 1


title: genomic DNA from 5aza_14d_KirNeg_03


title: genomic DNA from 5aza_7d_KirPos_04


title: MOLM13 ABT-199 Resistant S2 Clone Replicate 3b

value: S2 Clone


title: genomic DNA from 5aza_7d_KirPos_03


title: MCF7 CSKko-1 DMSO_Rep1

description: Replicate 1

value: ER+ breast cancer


title: MOLM13 ABT-199 Resistant S2 Clone Replicate 3a


title: MOLM13 ABT-199 Resistant S2 Clone Replicate 2


title: genomic DNA from 5aza_7d_KirPos_01


title: MOLM13 ABT-199 Resistant S6 Clone Replicate 1a

value: S6 Clone


title: genomic DNA from 5aza_7d_KirNeg_04


title: MCF7 WT DMSO_Rep3

description: Replicate 3

value: wild type

value: DMSO


title: GSH_RADONC_RectalCancer_103

tag: time

value: Pre-CRT

tag: cancer type

value: Rectal cancer


title: MCF7 WT DMSO_Rep2

description: Replicate 2


title: GSH_RADONC_RectalCancer_104

tag: treatment response pcr vs. non-pcr

value: pCR

tag: disease free survival event


title: MCF7 CSKko-1 DMSO_Rep3

description: Replicate 3

tag: treatment


title: genomic DNA from 5aza_7d_KirNeg_02

value: Tumor


title: genomic DNA from 5aza_7d_KirPos_02

value: ENKTL


title: genomic DNA from 5aza_14d_KirPos_01

value: fresh-frozen


title: MOLM13 ABT-199 Resistant Population Replicate 2b

tag: sensitivity state

value: population


title: genomic DNA from 5aza_7d_KirNeg_01

value: Yes


title: GSH_RADONC_RectalCancer_105

value: Non-pCR

tag: disease free survival time (months)


title: GSH_RADONC_RectalCancer_102


title: genomic DNA from 5aza_7d_KirNeg_03


title: genomic DNA from 5aza_07

value: human CD56


title: genomic DNA from 5aza_06


title: GSH_RADONC_RectalCancer_101


title: genomic DNA from 5aza_05


title: 24hpi_C3

city: Qingdao

first: Xianhui

last: Ning

address: 7 Nanhai Road

institute: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences

data_processing:
The adaptor and read quality were filtered with fastp (v0.12.4).
The small RNAs including rRNAs, scRNAs, snoRNAs, snRNAs and tRNAs were trimmed by aligned to small RNAs in GeneBank database and Rfam database via Blastall (v2.2.25) with parameter of identity > 97%, and reference genome of flounder via Bowtie (v1.1.2) with parameters of “-v 0 --best --strata -a”.
The known miRNAs were identified by searching against miRBase (release 21.0), and the novel miRNAs were predicted using software MIREAP (v0.2) with parameters of “-A 18 -B 26 -a 20 -b 24 -c 3 -u 20 -e -18 -d 35 -p 14 -v 4 -s 5 -f 10”
The abundance counts of miRNAs were calculated and normalized to TPM
Genome_build: GCF_001970005.1
Supplementary_files_format_and_content: tab-delimited text file containing read counts of known and novel miRNAs

organism: Paralichthys olivaceus

source_name: spleen

extract_protocol:
Three fish from each group was collected at 6, 12 and 24 hpi, and the spleen was taken aseptically and immediately stored in liquid nitrogen. Total RNA was extracted using Trizol RNA extraction reagent.
The 18 sequencing libraries were constructed using NEBNext Multiplex Small RNA Library Prep Kit following the manufacturer's protocol

treatment_protocol: V. anguillarum was cultured in Luria-Bertani (LB) medium at 28 °C to logarithmic stage and harvested by centrifugation at 2000 g for 5 min. The pellet was washed and suspended in PBS to a final concentration of 5 × 108 colony forming units (CFU) mL-1. Fish in group V were injected intramuscularly with 200 μl V. anguillarum suspension and group C was used as the control group and injected with PBS in the same volume.

tag: tissue

value: spleen

tag: group

value: group C

tag: age

value: 10 month

value: uninfected with Vibrio anguillarum for 24 h


title: 24hpi_C2


title: genomic DNA from 5aza_02

tag: sample type


title: genomic DNA from 5aza_04

tag: dna isolation type


title: GSH_RADONC_RectalCancer_099


title: genomic DNA from 5aza_01

tag: pdx-derived


title: 24hpi_C1


title: MOLM13 ABT-199 Resistant Population Replicate 2a

value: ABT-199 Resistant

tag: population clone

tag: Sex

value: male

tag: plate information


title: MOLM13 ABT-199 Resistant Population Replicate 1a

tag: cell line


title: GSH_RADONC_RectalCancer_100

tag: time


title: genomic DNA from Vehicle_03

tag: disease state

tag: pdx treatment

value: Vehicle

tag: sorted population


title: genomic DNA from Vehicle_02


title: MOLM13 ABT-199 Resistant S5 Clone Replicate 2a

value: S5 Clone


title: MOLM13 ABT-199 Sensitive Parental Replicate 2

value: ABT-199 Sensitive

value: parental population


title: GSH_RADONC_RectalCancer_098

value: Pre-CRT

tag: cancer type

value: Rectal cancer

tag: treatment response pcr vs. non-pcr

tag: treatment

tag: disease free survival event


title: MOLM13 ABT-199 Sensitive Parental Replicate 3

tag: sensitivity state


title: genomic DNA from Vehicle_01

value: Tumor

value: ENKTL

value: fresh-frozen


title: genomic DNA from NKLGL3

value: NKLGL

value: No


title: genomic DNA from 5aza_03

value: Yes

value: human CD56


title: GSH_RADONC_RectalCancer_096

value: Non-pCR

tag: disease free survival time (months)


title: genomic DNA from NKLGL2

tag: sample type


title: MOLM13 ABT-199 Sensitive Parental Replicate 1a


title: MCF7 WT DMSO_Rep1

description: Replicate 1

value: ER+ breast cancer

tag: genotype

value: wild type

value: DMSO


title: genomic DNA from ENKTL8

tag: dna isolation type

tag: pdx-derived


title: GSH_RADONC_RectalCancer_097

value: pCR


title: genomic DNA from 5aza_14d_KirNeg_02

value: human CD56/KIR-negative


title: GSH_RADONC_RectalCancer_094


title: 24hpi_V2

tag: tissue

value: spleen

tag: group

value: group V

tag: age

value: 10 month

value: infected with Vibrio anguillarum for 24 h


title: genomic DNA from DFTL-8005

value: Tumor


title: genomic DNA from NKLGL1


title: 24hpi_V3


title: 12hpi_C3

value: group C

value: uninfected with Vibrio anguillarum for 12 h


title: GSH_RADONC_RectalCancer_095

tag: time

value: Pre-CRT

value: Rectal cancer


title: MOLM13 ABT-199 Resistant Population Replicate 1b

tag: cell line

value: ABT-199 Resistant

tag: population clone

value: population

tag: Sex

value: male

tag: plate information


title: 12hpi_C2


title: genomic DNA from ENKTL6

tag: disease state

value: ENKTL

value: fresh-frozen

value: No

tag: pdx treatment

tag: sorted population


title: MOLM13 ABT-199 Sensitive Parental Replicate 1b

tag: sensitivity state

value: ABT-199 Sensitive

value: parental population


title: 12hpi_C1

value: spleen

tag: treatment


title: GSH_RADONC_RectalCancer_093

tag: cancer type

tag: treatment response pcr vs. non-pcr

value: Non-pCR

tag: disease free survival event

tag: disease free survival time (months)


title: genomic DNA from ENKTL1_SPL

tag: sample type

tag: dna isolation type

tag: pdx-derived

value: Yes

value: human CD56


title: genomic DNA from BM13_CD34

source_name: Bone marrow

value: Normal

value: HSPC


title: 12hpi_V3

tag: tissue

tag: group

value: group V

tag: age

value: 10 month

value: infected with Vibrio anguillarum for 12 h


title: genomic DNA from BM11_CD34


title: genomic DNA from ENKTL1_BM

value: Tumor


title: genomic DNA from ENKTL1


title: GSH_RADONC_RectalCancer_091

tag: time

value: Pre-CRT

value: Rectal cancer


title: 12hpi_V2


title: genomic DNA from BM10_CD34


title: GSH_RADONC_RectalCancer_090


title: 24hpi_V1

value: infected with Vibrio anguillarum for 24 h


title: genomic DNA from Stage6_blood_G3

value: fresh-frozen


title: genomic DNA from Stage5_blood_G3

value: No


title: GSH_RADONC_RectalCancer_089


title: 6hpi_C3

value: group C

value: uninfected with Vibrio anguillarum for 6 h


title: genomic DNA from Stage4B_blood_G3


title: 12hpi_V1

value: spleen


title: genomic DNA from Stage6_blood_G2


title: 6hpi_C2


title: genomic DNA from Stage4B_blood_G2


title: GSH_RADONC_RectalCancer_088

value: Non-pCR


title: GSH_RADONC_RectalCancer_087


title: genomic DNA from Stage6_blood_G1


title: genomic DNA from Stage5_blood_G1


title: genomic DNA from Stage4B_blood_G1


title: GSH_RADONC_RectalCancer_086


title: 6hpi_V3

value: infected with Vibrio anguillarum for 6 h


title: genomic DNA from Stage4B_tonsil_G3

source_name: Tonsil


title: genomic DNA from Stage5_tonsil_G3


title: 6hpi_C1


title: GSH_RADONC_RectalCancer_085


title: 6hpi_V2


title: GSH_RADONC_RectalCancer_084


title: 6hpi_V1


title: genomic DNA from Stage5_tonsil_G2


title: genomic DNA from Stage4A_tonsil_G3


title: genomic DNA from Stage5_blood_G2


title: genomic DNA from Stage4B_tonsil_G2


title: GSH_RADONC_RectalCancer_083


title: genomic DNA from Stage4A_tonsil_G2


title: GSH_RADONC_RectalCancer_082


title: CKAP4_IP_1

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of CKAP4 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: normal right atrial muscle

extract_protocol:
Atrial tissues were obtained from patients with cardiac valvular disease on operation and were rapidly frozen in liquid nitrogen and stored at −80 °C for protein extraction and RNA isolation. Atrial tissues in normal size from patients without atrial fibrillation were classified as normal group, and those in enlarged size from patients with atrial fibrillation were classified as remodeling group.
The CKAP4-bound RNAs from the immunoprecipitation samples were isolated using TRIzol (Invitrogen). cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KK8541, KAPA Biosystems, Boston, USA) according the manufacturer’s procedure, followed by high-throughput sequencing on an Illumina Xten platform for 150 bp paired-end sequencing.

value: right atrium

tag: origin

value: one patient with cardiac valvular disease.


title: genomic DNA from Stage4B_tonsil_G1

tag: disease state

value: Normal


title: GSH_RADONC_RectalCancer_081


title: CKAP4_input_2

source_name: remodeling fibrotic right atrial muscle

tag: antibody


title: genomic DNA from Stage4A_tonsil_G1

tag: pdx treatment

tag: sorted population


title: GSH_RADONC_RectalCancer_080

tag: treatment


title: genomic DNA from Stage3_tonsil_G1


title: CKAP4_input_1


title: GSH_RADONC_RectalCancer_079

tag: cancer type

value: pCR


title: GSH_RADONC_RectalCancer_077

tag: treatment response pcr vs. non-pcr


title: GSH_RADONC_RectalCancer_078

tag: disease free survival event


title: genomic DNA from Stage3_tonsil_G3


title: CTR rep2

city: Verona

first: Stefano

last: Ugel

address: Piazzale L.A. Scuro, 10

department: Medicine

institute: University and Hospital Trust of Verona

data_processing:
Alignment, barcode processing and UMI counting for each sample was performed using 10x Cell Ranger software v.3.1.0 (cellranger count pipeline)
Genome_build: mm10
Supplementary_files_format_and_content: Feature-barcode matrix for each sample in the format returned by 10x cellranger count pipeline

source_name: PDAC infiltrating immune cells

extract_protocol:
Mice were sacrificed, tumours isolated and processed in order to obtain cell suspensions. Two samples/group (each one composed by a pool of 4 mice), were enriched for CD45 marker on FACS ARIA (BD biosciences) instrument. FACS-sorted cells were resuspended in RPMI with 5% FBS to a final concentration of 1000 cells per μl and processed using the 10x Genomics Chromium Controller and the Chromium NextGEM Single-Cell 3′ GEM, Library & Gel Bead kit v3.1 (Pleasanton, California, United States) following the standard manufacturer’s instructions. In brief, 10,000 live cells were loaded onto the Chromium controller to recover 4,000 single cell GEMs per inlet uniquely barcoded. After synthesis of cDNA, sequencing libraries were generated. Final 10X library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and then sequenced on the Illu-mina NextSeq500 (Illumina, San Diego CA, USA).
After synthesis of cDNA, sequencing libraries were generated. Final 10X library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and then sequenced on the Illu-mina NextSeq500 (Illumina, San Diego CA, USA).

treatment_protocol: Mice bearing 7-days orthotopic B6KPC3 tumours, were treated with either 30 mg/kg/d of AT38 in 1% carboxymethyl cellulose/water (vehicle) or vehicle alone through a double i.p. injection each day for 7 days as indicated above.

tag: strain

value: Pancreas

value: Control


title: AT38 rep1

value: Treated with AT38


title: CTR rep1


title: GSH_RADONC_RectalCancer_075

value: Pre-CRT

tag: disease free survival time (months)


title: GSH_RADONC_RectalCancer_076

value: Rectal cancer


title: MHS PRMT7null

city: München

first: Thomas

last: Conlon

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

description: ATAC-Seq

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Genomic regions with high levels of transposition/tagging events are determined using the MACS2 peak calling algorithm (Zhang et al., Genome Biology 2008, 9:R137). Since both reads (tags) from paired-end sequencing represent transposition events, both reads are used for peak-calling but treated a single, independent reads.
To identify the density of transposition events along the genome, the genome is divided into 32 bp bins and the number of fragments in each bin is determined. For this purpose, reads are extended to 200 bp, which is close to the average length of the sequenced library inserts. In silico extension also helps to smooth the data. This information is stored in a bigWig file.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig. Files with extension *.bw. Show the fragment density for 32-nt bins along the genome

source_name: Alveolar Macrophage Cell Line

growth_protocol: WT and Prmt7null clone MHS macrophage cells were maintained in RPMI-1640 medium (Gibco, Life Technologies) supplemented with 10% fetal bovine serum (Gibco, Life Technologies), 50μM β-mercaptoethanol and 100 U/ml penicillin and streptomycin (both Sigma-Aldrich) at 37°C in 5% CO2.

extract_protocol:
100,000 WT and Prmt7null MHS macrophage cells were sent to Active Motif (Carlsbad, CA) for ATAC-Seq analysis, after cryopreserving the cells as described in the ATAC-Seq sample preparation guidelines supplied by the company
Samples were PCR-amplified and sized using the Agilent 2100 Bioanalyzer. Barcoded libraries were sequenced 42 bp paired-end on NextSeq 500 (Illumina).

value: BALB/c

tag: cell type

value: MHS (ATCC CRL-2019) SV40 transformation of alveolar macrophages

tag: genotype

value: PRMT7null (CRISPR/Cas9)


title: CKAP4_IP_2

tag: tissue


title: GSH_RADONC_RectalCancer_074


title: MHS WT

description: ATAC-Seq

value: WT


title: GSH_RADONC_RectalCancer_073


title: genomic DNA from Stage3_tonsil_G2

city: Columbus

tag: sample type

tag: dna isolation type

value: fresh-frozen

tag: pdx-derived

value: No


title: genomic DNA from Stage5_tonsil_G1


title: GSH_RADONC_RectalCancer_072

tag: time

value: Non-pCR


title: GSH_RADONC_RectalCancer_071


title: genomic DNA from ENKTL12

tag: disease state

value: Tumor

value: ENKTL


title: GSH_RADONC_RectalCancer_069


title: GSH_RADONC_RectalCancer_070


title: GSH_RADONC_RectalCancer_068


title: AT38 rep2


title: GSH_RADONC_RectalCancer_066


title: GSH_RADONC_RectalCancer_065


title: GSH_RADONC_RectalCancer_064


title: GSH_RADONC_RectalCancer_063


title: lrKO 2mo testis, biological replicate 3

type: RNA

city: Clermont-Ferrand

first: Antoine

last: Martinez

address: Faculté de Médecine, CRBC, 28 place Henri Dunant

department: GReD

country: France

institute: CNRS, INSERM, Université Clermont Auvergne

description: gene expression

hyb_protocol: following fragmentation, cDNA were hybridized for 17h at 45°C on GenChip MouseGene2.0 from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GenChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: RMA normalization was performed with R and the BioConductor package.

label: biotin

source_name: lrKO 2-month-old mous testis

label_protocol: biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng of total RNA (following the GeneChip® WT PLUS Reagent Kit Affymetrix).

extract_protocol: total RNA were extracted from whole adrenal glands using RNAII nucleotide extraction kit from Macherey-Nagel. RNA quality was assessed by Agilent Bioanalyzer chips.

value: lrKO 2-month-old mous testis

value: Whole testis

tag: age

value: 2 months


title: GSH_RADONC_RectalCancer_062

value: pCR


title: OS03-390 Control 8

city: Atlanta

first: Ashlyn

middle: G

last: Johnson

state: GA

address: 615 Michael Street NE

department: Neurology

institute: Emory University

description: NA indicates data not available.

hyb_protocol: Samples from each disease group were randomly distributed across two nCounter Human glial profiling panels (NanoString, USA) and run on an nCounter FLEX Analysis System (NanoString, USA), according to manufacturers instructions.

scan_protocol: Raw data were imported into nSolver 4.0 and analyzed via the nCounter Advanced Analysis plugin (version 2.1.134) to perform quality control checks and normalize the data.

data_processing:
Raw data were imported into nSolver 4.0 and analyzed via the nCounter Advanced Analysis plugin (version 2.1.134) to normalize the data and conduct differential expression, pathway scoring , and cell type profiling analyses. Covariates included disease (control, AD, and FTD-tau) and cartridge ID (to control for batch effects). All samples passed the quality control analysis conducted by the Advanced Analysis plugin.  Differential expression was calculated using disease as the predictor variable and the cartridge ID as the confounder variable.
The complete_normalized_data.txt includes boolean value (true/false, in the below.threshold column) indicating whether the gene met the threshold for pruning due to low count data.

source_name: dorsolateral prefrontal cortex

extract_protocol: 30 to 50 milligrams of frozen DLPFC, primarily gray matter, was homogenized in one milliliter of Trizol with a bullet blender. Chloroform and centrifugation were used to obtain an aqueous phase containing RNA. The aqueous phase was mixed 1:1 in 100% ethanol and then processed with the Quick-RNA Miniprep Kit (Zymo Research, USA). RNA was eluted in nuclease free water and stored at -80 ˚C until analysis. Quality of the RNA was determined by the Emory Integrated Genomics Core. All samples had concentrations greater than 20 ng/ul and DV200 values greater than 20%, per manufacturer’s recommendation. Samples from each disease group were randomly distributed across two nCounter Human glial profiling panels (NanoString, USA) and run on an nCounter FLEX Analysis System (NanoString, USA).

tag: Sex

value: Female

tag: race

value: white

tag: cartridge id

tag: post mortem interval

tag: apoe genotype

tag: diagnosis

value: Control

value: dorsolateral prefrontal cortex


title: lrKO 2mo testis, biological replicate 1

description: gene expression


title: lrKO 2mo testis, biological replicate 4

description: gene expression


title: lrKO 2mo testis, biological replicate 2

description: gene expression


title: srKO 2mo testis, biological replicate 4

description: gene expression

source_name: srKO 2-month-old mous testis

value: srKO 2-month-old mous testis


title: E15-66 FTD 8

description: NA indicates data not available.

label_protocol: Samples from each disease group were randomly distributed across two nCounter Human glial profiling panels (NanoString, USA) and run on an nCounter FLEX Analysis System (NanoString, USA), according to manufacturers instructions.

value: FTD


title: E14-06 Control 7

description: NA indicates data not available.

value: Male


title: E12-29 AD 8

description: NA indicates data not available.

value: AD


title: E11-139 AD 7

description: NA indicates data not available.


title: E08-24 FTD 7

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_067

value: Pre-CRT

tag: cancer type

value: Rectal cancer

tag: treatment response pcr vs. non-pcr

tag: treatment

tag: disease free survival event


title: srKO 2mo testis, biological replicate 3

description: gene expression

tag: genotype

tag: tissue


title: srKO 2mo testis, biological replicate 2

description: gene expression


title: srKO 2mo testis, biological replicate 1

description: gene expression


title: prKO 2mo testis, biological replicate 3

description: gene expression

source_name: prKO 2-month-old mous testis

value: prKO 2-month-old mous testis


title: E08-133 FTD 6

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_059

value: Non-pCR

tag: disease free survival time (months)


title: WT 2mo testis, biological replicate 8

description: gene expression

source_name: WT 2-month-old mous testis

value: WT 2-month-old mous testis


title: prKO 2mo testis, biological replicate 2

description: gene expression


title: WT 2mo testis, biological replicate 6

description: gene expression


title: E07-70 FTD 5

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_061


title: GSH_RADONC_RectalCancer_057


title: GSH_RADONC_RectalCancer_056


title: GSH_RADONC_RectalCancer_055


title: E05-87 AD 5

description: NA indicates data not available.


title: E06-155 AD 6

description: NA indicates data not available.


title: E05-74 Control 5

description: NA indicates data not available.

value: black


title: E06-41 Control 6

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_053


title: GSH_RADONC_RectalCancer_060


title: GSH_RADONC_RectalCancer_054


title: GSH_RADONC_RectalCancer_052


title: WT 2mo testis, biological replicate 4

description: gene expression

value: Whole testis


title: WT 2mo testis, biological replicate 5

description: gene expression

value: 2 months


title: WT 2mo testis, biological replicate 7

description: gene expression


title: OS98-06 FTD 4

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_051


title: WT 2mo testis, biological replicate 2

description: gene expression


title: prKO 2mo testis, biological replicate 1

description: gene expression


title: WT 2mo testis, biological replicate 3

description: gene expression


title: WT 2mo testis, biological replicate 1

description: gene expression


title: OS-150716 FTD 3

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_058


title: GSH_RADONC_RectalCancer_050


title: OS-140909 AD 4

description: NA indicates data not available.


title: lrKO 2wk testis, biological replicate 2

description: gene expression

source_name: lrKO 2-week-old mous testis

value: lrKO

value: 2 weeks


title: E17-17 FTD 2

description: NA indicates data not available.

value: Female

value: white


title: lrKO 2wk testis, biological replicate 3

description: gene expression


title: GSH_RADONC_RectalCancer_048

value: pCR


title: E16-45 Control 3

description: NA indicates data not available.

value: Control

value: dorsolateral prefrontal cortex


title: GSH_RADONC_RectalCancer_047


title: E14-123 FTD 1

description: NA indicates data not available.

value: Male

value: FTD


title: lrKO 2wk testis, biological replicate 4

description: gene expression


title: OS02-35 Control 4

description: NA indicates data not available.


title: srKO 2wk testis, biological replicate 4

description: gene expression

source_name: srKO 2-week-old mous testis

value: srKO


title: lrKO 2wk testis, biological replicate 1

description: gene expression


title: scRNA_seq_lambskin_curly

city: Yangzhou

first: Shanhe

last: Wang

address: Wenhui road

institute: Yangzhou University

description: The group information is prefixed with curly in the column of processed data file

data_processing:
We used CellRanger count pipeline 3.0.2 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=7000 \’.
Genome_build: GCF_002742125.1_Oar_rambouillet_v1.0_genomic.fna.gz
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

organism: Ovis aries

source_name: lambskin (d3)

extract_protocol:
Hu sheep from Suzhou sheep breeding farm were used in this study. The experimental animals were healthy and under the same management. According to the wool length and curvature, wavy wool individuals and straight wool individuals were selected to obtain lambskin samples. After infiltration anesthesia through hypodermic injection of 2% lidocaine hydrochloride (10 mg), skin samples approximately 2 cm 2 and 2 mm deep were harvested from the body side of lamb. Subsequently, the wound was sewed up and the sample were divided into two parts, one was fixed with 4% paraformaldehyde (Solarbio, Cat#P1110) and another one was kept in DMEM/F12 medium (Gibco™, Cat#31331093) with penicillin-streptomycin (Gibco™, Cat#15240062) for subsequent analysis.To dissociate lambskin into single cells, skins from wavy wool individuals and straight wool individuals were pooled from each group. In order to ensure the quantity of hair follicle cells for each group, we adopt two strategies for dissociation. For strategies one, single hair follicles were isolated and dissociate into single cells. For strategies two, the whole skin was dissociated into single cells. Finally, single cells from two strategies were mixed as the final example. For hair follicles, skins were cut into small pieces and the hair follicles were isolated via microdissection using stereoscope. Collected hair follicles were incubated with pre-warmed (37 °C) TrypLE (Gibco™, Cat#12604013) for a total of 15 min in a 37 °C incubator on a shaker at 65 rpm for a gentle swirl. During the incubation, the dissociation mixture was agitated every 5 min with gentle pipetting. Then, cold 3% bovine serum albumin (BSA) solution (Sigma-Aldrich, Cat#A1933) was added to the dissociated cell suspension to inactivate TrypLE enzymatic activity. For skin tissues, 2 mg/ml collagenase IV (Sigma-Aldrich, Cat#C4-BIOC) was used to digest skin tissues at 37 °C for 30 min. Then, the products were incubated with pre-warmed (37 °C) TrypLE (Gibco™, Cat#12604013) for a total of 15 min. In this process, the skin tissues were mechanically dissociated into single cell suspension by pipetting. The cell suspensions were then filtered through a 40 μm nylon cell strainer (Sangon Biotech, Cat#12604013). Subsequent, the suspension from hair follicles and skins were mixed. An additional three washes with cold 3% BSA solution were performed. Cells were resuspended in 3% BSA. Viability (live cell percentage) and live cell count was determined using Trypan blue (used at a 1:1 ratio) and Countess II. The final cell concentration was around 1,000 cells/μl, with a cell viability greater than 90%.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

tag: breed

value: Hu Sheep

tag: phenotype

value: waved wool individual

value: skin

tag: developmental stage

value: 3 day


title: GSH_RADONC_RectalCancer_046

tag: time

value: Pre-CRT

value: Rectal cancer

value: Non-pCR


title: scRNA_seq_lambskin_straight

description: The group information is prefixed with straight in the column of processed data file

value: straight wool individual


title: GSH_RADONC_RectalCancer_045


title: GSH_RADONC_RectalCancer_044


title: GSH_RADONC_RectalCancer_092