title: NPH

status: Public on Mar 31 2022

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

description: S1-L5 (D) and L5-L4 (H) discs

data_processing:
Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the human reference transcriptome (GRCh38), and transcript counts quantified for each annotated gene within every cell.
Assembly: GRCh38
Supplementary files format and content: HDF5 binary data format

source_name: Nucleus pulposus (NP) cells from healthy (H) human Intervertebral disc

extract_protocol:
Human lumbar IVDs were retrieved from spines obtained with familial consent (IRB#s: A04-M53-08B and Tissue Biobank 2019-4896) through the Transplant Quebec Organ Donation Program. Discs dissected from the spinal column were graded according to Thompson grading system and used for tissue and cell isolation. Nucleus pulposus (NP) and inner annulus fibrosis (iAF) cells were isolated separately from degenerating and non-degenerating discs excluding outer AF. 500,000 NP or iAF cells from degenerating or non-degenerating discs were collected by centrifugation, and immediately applied to sc-RNA analysis
10X Chromium Single Cell 3'

value: Human disc tissue

value: Nucleus pulposus (NP) cells

tag: condition

value: healthy


title: Donor1_replicate1

status: Public on Apr 01 2022

type: SRA

city: New York

first: Shane

middle: A.

last: Liddelow

state: NY

address: 435 E. 30th Street

department: Neuroscience Institute

country: USA

institute: NYU Langone Medical Center

library_source: transcriptomic

data_processing:
Basecalling was completed using Illumina NovaSeq 6000 RTA v3.4.4 software.
BCL base call files were converted to FASTQ files using bcl2fastq Conversion software (v2.20).
Using Cell Ranger software suite (v4.0.0) (10X Genomics), FASTQ files were aligned to a premRNA-modified GRCh38 human reference genome (modification steps provided by 10x Genomics), and gene-barcode count matrices were generated for all demultiplexed samples.
Genome_build: premRNA-modified GRCh38
Supplementary_files_format_and_content: We provided both raw sequencing FASTQ files as well as filtered_feature_bc_matrix files (e.g., barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)--the latter which may be directly imported into R/Seurat for analysis.

molecule: polyA RNA

organism: Homo sapiens

source_name: Prefrontal cortex

extract_protocol:
Processing of tissue was completed on ice or at 4°C for the entirety of the protocol. In brief, ~100 mg of postmortem frozen human prefrontal cortex per donor was homogenized in 2 mL homogenization buffer (10 mM Tris pH 8, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X100, 1% RNasin Plus, 1X Protease inhibitor, and 0.1 mM DTT in DNase- and RNase-free water) using a Wheaton Dounce tissue grinder (10 strokes with loose pestle, followed by 10 strokes with the tight pestle). Then, the homogenized tissue was filtered through 30 mm pre-separation filters to remove major debris. Samples were then centrifuged at 900 xg for 10 minutes at 4°C. Nuclei were then immunolabeled for LIM/Homeobox protein (LHX2) and NeuN, and LHX2-positive/NeuN-negative nuclei were collected using a MoFlo XDP sorter with a 100 mm nozzle at 4°C. Collected nuclei were processed using the Single Cell 3’ Gene Expression kit v3 (10x Chromium) according to manufacturer’s instructions, and libraries were sequenced an Illumina NovaSeq 6000.
Sequencing libraries were prepared using the Single Cell 3’ Gene Expression kit v3 (10x Chromium) according to manufacturer’s instructions.

tag: tissue

value: Prefrontal cortex

tag: disease state

value: Non-symptomatic

tag: Sex

value: Male

tag: age


title: Control

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Fastq files were generated either with CellRanger (5.0.1) "mkfastq".
Alignment and counting were performed with CellRanger (5.0.1) "count".
Normalization, scaling, dimensional reduction and clustering of the single-cell transcriptomes were performed using Seurat v4 (detailed in Methods).
Single-cell transcriptomes were classified with a custom neural network (Ozel et al. 2021).
Cluster markers were calculated using Seurat v4.
Assembly: ENSEMBL-release-88-BDGP6
Supplementary files format and content: Seurat object (.rds format) provided includes raw, normalized and scaled expression values for each cell classified as Tm1/2/4/6 or T2 neurons for both conditions. Library of origin as well as identities determined using different methods, as detailed in the paper, are included as metadata fields.

organism: Drosophila melanogaster

source_name: P50 optic lobe

growth_protocol: Standard Drosophila rearing protocols.

extract_protocol: Chromium™ Single Cell 3’ Reagent Kit v3.1 (10X Genomics)

treatment_protocol: No treatments.

tag: genotype

value: UAS-Stinger/+; R71F05-Gal4/+

value: female


title: UAS-pdm3


title: AFD

country: Canada

description: S1-L5 (D) and L5-L4 (H) discs

molecule: total RNA

source_name: Anuulus fibrosis (AF) cells from degenerate (D) human Intervertebral disc

tag: cell type

value: Anuulus fibrosis (AF) cells

value: degenerate intervertebral disc


title: Control Rep1 (Overexpression Study)

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

data_processing:
Data was subjected to quality control check by FastQC_v0.11.8
Reads were mapped to H37Rv genome by TopHat v2.1.1
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Genome_build: ASM19595v2 (H37Rv)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for MazF6 overexpression study.

organism: Mycobacterium tuberculosis

source_name: Microbe

growth_protocol: For overexpression studies, early log phase cultures were induced were anhydrotetracycline addition for 24 hrs. For deletion strains, total RNA was isolated from mid log phase culture grown in 7H11 media.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy minikit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: pTetR-Int Vector only


title: NPD

description: S1-L5 (D) and L5-L4 (H) discs


title: AFH

description: S1-L5 (D) and L5-L4 (H) discs

source_name: Anuulus fibrosis (AF) cells from healthy (H) human Intervertebral disc


title: LDH KO3

city: Boston

first: Tatsuya

last: Kobayashi

state: MA

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

description: LDH KO3

data_processing:
Low quality reads were filtered with adaptors and reads with unknown bases with software SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05 -A 0.25. Mapped clean reads to mm9 reference using HISAT2 V. 2.0.4 with the parameters, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and read count

organism: Mus musculus

source_name: primary rib chondrocytes RNA from P5 mouse

growth_protocol: Primary rib chondrocytes were isolated by O/N digestion with 0.02%  collagenase II.  After removing collagenase by spinning, cells were resuspended in 10% FCS-containing DMEM and cultured for an additional day.

extract_protocol:
Cells were lysed in Trizol.  RNA was extracted by BGI, and quality was checked before sequencing
Libraries were made BGI's platform.
BGI-seq library construction method: mRNA molecules were purified from total RNA using oligo(dT) attached magnetic beads. mRNA molecules were fragmented into small pieces using fragmentation reagent. First and Second Strand cDNA synthesis. Prepare the end repair & add "A", adaptor ligation and PCR.

treatment_protocol: KO (knockout) and C (Control) were isolated from littermates

value: rib chondrocytes

value: C57BL/6-dominant mixed

tag: developmental stage

value: LDH KO


title: Active Motif 39133 1/100 13 PCR column

city: London

first: Monika

last: Moissidis

address: New Hunt's House, Newcomen St

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

description: Bam files were downsampled to the same read depth, duplicates removed, and peaks called with SEACR.

library_source: genomic

data_processing:
Sequenced on HiSeq 4000 (PE75); bcl2fastq used for basecalling.
Sequenced reads were 1) trimmed for adaptor sequences using TrimGalore 0.6.6; 2) mapped to hg19 whole genome using bowtie v2.2.9 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700; 3) duplicate reads were removed with picard v2.6.0 ; 4) deduplicated sam files were converted to bam format using samtools v1.3.1, keeping mapped read pairs. Where applicable bam files were downsampled with samtools v1.3.1
bam files were converted to fragment bed files with bedtools v2.25.0. Fragment bed files were converted to fragment bedgraph files with bedtools v2.25.0
MACS2 peaks were called on bam files with parameters -f BAMPE -g hs -q 1e-5 --keep-dup all –nolambda --nomodel. To call H3K27me3 peaks, the --broad flag was also used.
SEACR peaks were called on fragment bedgraph files with parameters 0.01 non stringent. To call H3K27me3 peaks, a threshold of 0.1 was used.
Assembly: hg19
Supplementary files format and content: bed files with called peaks
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Bench top CUT&Tag was performed as previously described (https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6) using 500,000 exponentially growing K562 cells per experiment. Following tagmentation, either SDS- or column- based DNA extraction was conducted. SDS-based DNA extraction: PCR tubes were placed on a magnetic rack and solution allowed to clear. Supernatant was removed and beads resuspended in 50 μL TAPS Buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA) at RT. Tubes were returned to a magnetic rack and supernatant removed. 5 μL SDS Release Buffer (10 mM TAPS pH 8.5, 0.1% SDS) was added to each tube at RT. After a quick spin, samples were incubated at 58°C for 1 hour. Next, 15 μL SDS Quench Buffer (0.67% Triton-X 100 in Molecular grade H2O) was added at RT. Column-based DNA extraction: 1.68 μL 0.5M EDTA, 0.5 μL 10% SDS, 0.44 μL 10 mg/mL Proteinase K were added to each 50uL sample. Samples were incubated at 55°C for 1 hour and spun quickly. Sample tubes were then placed on a magnetic rack and solutions allowed to clear. Supernatant was transferred to a new microcentrifuge tube and processed according to the ChIP DNA Clean & Concentrator (Zymo Research D5205) protocol.
For library amplification in PCR tube format, 21 μL DNA was combined with 2 μL of universal i5 and uniquely barcoded i7 primer where a different barcode was used for each sample that was intended to be pooled together. 25 μL NEBNext HiFi 2× PCR Master mix was added, then the sample was gently mixed through and spun down. The sample was placed in a Thermocycler with heated lid following these conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 11-15 cycles of 98°C for 10 s and 63°C for 30 s; final extension at 72°C for 1 min; and hold at 4°C. Following PCR, bead cleanup was conducted by addition of 1.1x Ampure XP beads (Beckman Coulter). Library and beads were mixed thoroughly, then spun down and incubated at RT for 10-15 min. Beads were gently washed twice with freshly prepared 80% ethanol using a magnetic rack, then the library was eluted with 20-30 μL 10 mM Tris-HCl pH 8.0 at RT.

tag: cell line

tag: histone mark

tag: antibody

value: Active Motif 39133

tag: antibody dilution

tag: tsa

value: No TSA

tag: dna extraction method

value: column

tag: pcr cycles


title: Abcam-ab4729 1/100 13 PCR column


title: CST9733 1/100 13 PCR SDS

value: SDS


title: Abcam-ab177178 1/100 13 PCR SDS


title: Abcam-ab4729 1/100 13 PCR SDS


title: Diagenode C15410196 1/50 13 PCR SDS

value: Diagenode C15410196


title: Active Motif 39133 1/100 13 PCR SDS


title: Abcam-ab177178 1/100 13 PCR column


title: Diagenode C15410196 1/50 11 PCR column


title: CST9733 1/100 11 PCR column


title: Abcam-ab4729 1/100 11 PCR column


title: Diagenode C15410196 1/50 11 PCR SDS


title: Active Motif 39133 1/100 11 PCR column


title: CST9733 1/100 11 PCR SDS


title: Abcam-ab4729 1/100 11 PCR SDS


title: Abcam-ab177178 1/100 11 PCR column


title: Active Motif 39133 1/100 11 PCR SDS


title: Diagenode C15410196 1/50 15 PCR SDS +TSA

description: Peak files called with SEACR, without duplicates.

value: TSA


title: Abcam-ab177178 1/100 11 PCR SDS


title: Abcam-ab4729 1/100 15 PCR SDS +TSA


title: CST9733 1/100 13 PCR column


title: Diagenode C15410196 1/50 13 PCR column


title: Diagenode C15410196 1/50 15 PCR SDS

description: Peak files called with SEACR or MACS2 without duplicates.


title: Abcam-ab177178 1/100 15 PCR SDS +TSA


title: Diagenode C15410196 1/100 15 PCR SDS


title: Diagenode C15410196 1/100 15 PCR SDS +TSA


title: Abcam-ab177178 1/100 15 PCR SDS


title: CST9733 1/100 15 PCR SDS


title: Abcam-ab4729 1/100 15 PCR SDS


title: Active Motif 39133 1/100 15 PCR SDS


title: SH-SY5H cells, cadmium 20 micromolars, replicate 2

type: RNA

city: Milan

first: Chiara

last: Urani

address: Piazza della Scienza, 1

department: Dep. Earth and Environmental Sciences

country: Italy

institute: University of Milano-Bicocca

hyb_protocol: cRNA from each labeling reaction (with a specific activity above 9.0) was hybridized using the Gene Expression Hybridization Kit (Agilent) to the Agilent Whole Human Genome Microarray (Agilent).

scan_protocol: The slices were scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The images were read on the green channel using limma (version 3.46), background substracted using normexp with an offset of 20, normalized using quantile and replicated probes were averaged  to obtain the normalized signal intensity matrix

source_name: cadmium 20 micros replicate 2

label_protocol: All sample-labeling, hybridization, washing, and scanning steps were conducted following the manufacturer’s specifications. Cy3-labeled cRNA was generated from 500 ng input total RNA using Quick Amp Labeling Kit, One-color (Agilent).

growth_protocol: SH-SY5Y cells were cultured in Eagle Minimum Essential Medium (EMEM) and F12 medium (1:1) supplemented with 10% fetal bovine serum and 1% antibiotics at 37°C under a humified atmosphere of 5% CO2 in air.

extract_protocol: RNA was purified using the RNeasy Plus kit (Qiagen), quantified and the integrity assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies Inc.)

treatment_protocol: Neuronal cells (SH-SY5Y) were treated 24 hours after seeding at 10 and 20 µM Cd for 24 hours. Neuronal cells cultured in complete medium under the same conditions were used as controls.

value: SH-SY5H cells

tag: gender

tag: treatment

value: 20 micromolars cadmium treated cells


title: WT1-Treg cells (ATAC-seq)

city: shang hai

first: Qi

last: Liu

address: 280 S. Chongqing Road

country: China

data_processing:
Trimmomatic software were used to remove adapter and low quality reads.
Quality distribution plot and base content distribution were generated by FASTQC.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: CD4+CD25+YFP+Treg cells

growth_protocol: All mice were maintained in the animal facility of Shanghai Jiao Tong University School of Medicine under specific pathogen-free conditions

extract_protocol:
50,000 CD4+CD25+YFP+ Tregs were isolated from 7-week-old chimeric female WT and cKO mice by FACS and washed once with 50 μl cold PBS buffer. Supernatant was discarded by centrifugation at 500 g, 4oC for 5 min. Lysed the cell pellet in 50 μl cold lysis buffer (10 mM NaCl, 10 mM pH7.4 Tris-HCl; 0.5%NP-40 and 3mM MgCl2) and centrifuge immediately at 500g, 4°C for 10 min.
Transposition reaction and purification PCR amplification were performed using Nextera XT DNA Library Preparation Kit (Illumina, Cat. #FC-131-1096) and Qiagen MinElute PCR Purification Kit (Qiagen, Cat. #28004). Illumina Novaseq 6000 was used for sequencing.

treatment_protocol: no treatment

value: post natal 7-week-old

tag: tissue

value: Mus spleen and lymph node

value: isolated CD4+CD25+YFP+ Treg cells from Foxp3cre/+ female mouse by flow cytometery

value: wild type


title: SH-SY5H cells, cadmium 20 micromolars, replicate 1

source_name: cadmium 20 micros replicate 1

value: female


title: Impurity L

city: Beijing

first: Miaoqing

last: Zhang

state: Please Select

address: No. 1, TianTan XiLi, Dong-cheng district

institute: Institute of Medicinal Biotechnology

data_processing:
FastQC software used for basecalling.
Sequences were aligned by using Hisat2/Topha software
Data were filtered using the fastp software,In short, filter the original data, delete the reads that do not meet the analysis criteria, and obtain clean reads that can be used for alignment, statistics and analysis.
Genome_build: Danio_rerio.GRCz11.dna.toplevel.REF.fa
Supplementary_files_format_and_content: tab-delimited text files include gene enrichment analysis for each Sample

organism: Danio rerio

source_name: liver

extract_protocol:
Total RNA were extracted from dissected liver of larvae by using TRIzol reagent, RNA was quantified by using Agilent 2100 BioAnalyzer
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra RNA Library Prep Kit (NEB #E7530S/L)

treatment_protocol: Wild-type AB strain zebrafish (Danio reio) were reared in a standard laboratory environment with a 14 h light/10 h dark cycle at 28±1°C,3 days postfertilization (3 dpf) zebrafish larvae were exposed to azithromycin and its different structural impurities solutions at the same concentration (2 mmol/L) for 72 hours.

value: liver

value: larvae

value: Wild-type AB

value: impurities


title: SH-SY5H cells, cadmium 20 micromolars, replicate 3


title: Sample D

city: Guangzhou

first: XInwei

last: Lin

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Stomatology

institute: Sun Yat-sen University

description: one sample from patients with common chronic apical periodontitis

data_processing:
Raw sequencing reads were demultiplexed by bcl2fastq software to convert them into 150-bp paired-end reads and stored in the FASTQ format.
Genome_build: GRCh38 human reference genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: inflammatory periapical tissue from patients with common chronic apical periodontitis

extract_protocol:
Once the inflammatory periapical tissue of the three teeth was carefully scraped off, the collected samples were immediately placed in an ice-cold preservation solution and then transported to the laboratory to maintain viability.
Using the manufacturer's protocol (10x Single Cell 3' Reagent Kits v2 manual, USA) (10X Genomics, 2016), the prepared cell suspensions were loaded onto barcoded scRNA-seq. In brief, the generation of gel beads in emulsions (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were performed.

tag: disease state

value: chronic apical periodontitis

value: Female

tag: tooth position

value: Mandible posterior teeth at right

tag: chief complaint

value: Demand for restorations of residual crown

value: periapical tissue


title: Impurity S

tag: age


title: SH-SY5H cells, cadmium 10 micromolars, replicate 2

source_name: cadmium 10 micros replicate 3

value: 10 micromolars cadmium treated cells


title: SH-SY5H cells, cadmium 10 micromolars, replicate 3

value: SH-SY5H cells


title: SH-SY5H cells, cadmium 10 micromolars, replicate 1

source_name: cadmium 10 micros replicate 1


title: Sample E

value: Mandible posterior teeth at left

value: Appearance of gingival abscess after post-core and crown restoration more than one year


title: Impurity F


title: cadmium 20 micros replicate 3

source_name: cadmium 20 micros replicate 3

growth_protocol: A549 cells were cultured in Opti-MEM medium (Gibco, Thermo Fisher) supplemented with 10% fetal bovine serum, and 1% antibiotics at 37°C under a humified atmosphere of 5% CO2 in air.

treatment_protocol: Pulmonary  cells (A549) were treated 24 hours after seeding at 10 and 20 µM Cd for 24 hours. Pulmonary cells cultured in complete medium were used as controls.

value: A549 cells

value: male

value: 20 micromolars cadmium treated cells


title: cadmium 10 micros replicate 1


title: cadmium 20 micros replicate 1


title: control, replicate 1

source_name: control, replicate 1

value: control cells


title: SH-SY5H cells, control, replicate 2

source_name: control, replicate 2

value: female


title: cadmium 10 micros replicate 2

source_name: cadmium 10 micros replicate 2


title: Impurity R

value: liver

value: larvae


title: Impurity J

value: Wild-type AB

value: impurities


title: Impurity Q


title: SH-SY5H cells, control, replicate 1


title: Mesenchymal stromal cells - P15

first: kai

last: lin

address: Dongdan three Dongcheng District No. 5

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences

description: mRNA from single MSC

data_processing:
The Cell Ranger software pipeline (version 2.1.0) provided by 10x Genomics was used to process data generated by using the 10x Chromium platform.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.tar archives include matrix.mtx (gene-barcode counts), genes.tsv (genes), and barcodes.tsv (cell barcodes) files.

source_name: Mesenchymal stromal cells

extract_protocol:
MSCs were digested into individual cells, and 10x Genomics was used for the construction of sequencing libraries.
RNA libraries were prepared with Chromium Single cell 3' Reagent v2 kits according to the manufacturer's protocol.

value: Adipose

tag: cell type

value: Mesenchymal stromal cells


title: control, replicate 2


title: Mesenchymal stromal cells - P0

description: mRNA from single MSC


title: cadmium 20 micros replicate 2


title: cKO1-Treg cells (ATAC-seq)

institute: Shanghai Jiao Tong University School of Medicine

source_name: CD4+CD25+YFP+ Treg cells

tag: strain

value: post natal 7-week-old

value: Mus spleen and lymph node

value: isolated CD4+CD25+YFP+ Treg cells from Foxp3cre/+ TKTfl/fl female mouse by flow cytometery

tag: genotype

value: Treg specific TKT knockout


title: Mesenchymal stromal cells - P10

description: mRNA from single MSC

tag: developmental stage


title: Azithromycin

value: azithromycin


title: MIAMI IFNg+CQ_rep2

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2,  and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Only genes that had more than 0 raw counts in all samples in at least one group were used for further analysis. Raw counts from HTSeq and STAR were imported into Bioconductor/R package edgeR, normalized, and tested for differential gene expression. This analysis was done separately for the files produced by each aligner.
Genes that showed differential expression after analysis of the files from at least two aligners were selected for further analysis. Criteria for differential expression FDR < 0.05, fold change larger than 2 in either direction.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text files containing genes raw count
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 0 in all samples in at least one group

source_name: Subtype of bone marrow MSCs

growth_protocol: MIAMI cells were cultured in DMEM-GlutaMAX™, 3% FBS, lipids, 1× Antibiotic-Antimycotic Solution, and 100 μM Ascorbic Acid 2-Phosphate (Sigma). The cells were grown in 10 ng/ml fibronectin-coated flasks at a density of 400 cells/cm2 at 3% O2/5% CO2/92% N2.

extract_protocol:
Following the treatments, medium was aspirated from cells, and cells were detached from wells by RNAzol and stored at − 80 °C until RNA isolation. RNA was purified using RNAzol according to the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA kit was used for library preparation. 150 base paired-end read sequencing was performed using Illumina NextSeq500. All procedures were performed according to the manufacturer’s instructions. Quality control assessment was done using Illumina RNAseq pipeline to estimate genomic coverage, percent alignment, and nucleotide quality. Raw sequencing data were transformed to fastq format.

treatment_protocol: MIAMI cells were seeded in fibronectin-coated 6-well plates at a density of 1 × 105 cells/well and treated with 5uM of TX, 109 uM of CQ or 500 units of IFNg for 4 days.

value: Bone marrow

value: IFN gamma 500 units+chloroquin 10 microM

tag: cell line

value: BM-MSC


title: MIAMI IFNg+TX_rep2

value: IFN gamma 500 units+tamoxifen 5 microM


title: cadmium 10 micros replicate 3

value: A549 cells

value: male

value: 10 micromolars cadmium treated cells


title: MIAMI IFNg+TX_rep3


title: MIAMI IFNg+CQ_rep3


title: MIAMI CQ_rep1

value: chloroquin 10 microM


title: MIAMI IFNg+TX_rep1


title: MIAMI IFNg_rep1

value: IFN gamma 500 units


title: MIAMI CQ_rep2


title: MIAMI CQ_rep3


title: MIAMI Control_rep1

value: vehicle


title: MIAMI TX_rep2

value: tamoxifen 5 microM


title: MI_VFC_KO_M913

city: Chicago

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Genome_build: mm10

source_name: Heart - Left Ventricle

extract_protocol:
Infarcted left ventricular tissue was collected from Vegfc f/f;LysMCre mice and LysMCre mice 9 days post-MI. In naïve animals, equivalent left ventricle of same approximate mass and anatomical area were also collected. RNA was extracted by column-based solid phase extraction RNeasy Plus mini kit (Qiagen) and the quality and quantity assessed using an Agilent bio-analyzer and Quibit fluorometer, respectively.
Libraries were  constructed according to TruSeq® Stranded mRNA Library Prep protocol

treatment_protocol: The left interior descending coronary artery was permanently ligated at a site 2mm distal to its emergence from under the left atrium. MI was verified by the onset of blanching or pale discoloration of the anterior wall of the LV.

value: Vegfc fl/fl ; LysMCre

value: Myocardium Left Ventricle

value: MI


title: Naiive_VFC_KO_M149

value: Naive


title: MI_Cntrls_M006

value: Vegfc fl/fl


title: MI_VFC_KO_M900


title: MIAMI IFNg_rep2


title: MI_Cntrls_M38


title: MIAMI TX_rep3


title: MIAMI TX_rep1


title: MIAMI Control_rep3


title: MIAMI Control_rep2


title: MIAMI IFNg_rep3


title: Naiive_VFC_KO_M150


title: Naiive_Cntrls_M45


title: Naiive_VFC_KO_M34


title: MI_VFC_KO_M35


title: aSyn 3 [Sample_3]

city: Hannover

first: Matthias

last: Hoellerhage

address: Klinik für Neurologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: replicate 3

hyb_protocol: not provided

scan_protocol: Standard Illumina scanning protocol

data_processing: Background corrected intensity values were forced postive by adding a fixed offset based on the smallest observed value and subsequentially variance was stabililized by log2 transformation. Data normalisation was done via quantile normalization. Filtering was done based on detection p values and an additional unspecific variance filtering step. Summarization was done based on median probe intensities. multiple mappings and and unmappable entries were removed if appropriate.

label: biotin

source_name: LUHMES cells, transduced with adenoviral vector serotype 5

label_protocol: not provided

extract_protocol: RNA was extracted using β-mercaptoethanol activated RLT buffer (Qiagen) within the Rneasy Mini kit according to the manufacturer's instructions

treatment_protocol: Two days after the initiation of differention, LUHMES cells were transduced with adenoviral vectors to overexpress wild-typ alpha-synuclein or GFP under a CMV promoter

value: LUHMES cells

tag: genotype/variation

value: overexpression of wild-type alpha-synuclein


title: Chronic Therapeutic_TG3

city: Denton

first: Dayna

middle: Loyd

last: Averitt

state: Texas

address: 1000 Old Main Circle

department: Biology

institute: Texas Woman's University

data_processing:
Original data was transformed to sequenced reads (raw data) by CASAVA base recognition (Base calling). Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
The clusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each sample
Supplementary_files_format_and_content: Matrix table with fpkm values for every gene and every sample

organism: Rattus norvegicus

source_name: Trigeminal Ganglia tissue

extract_protocol:
Total RNA was extracted from the trigeminal ganglia collected from the hormone treated rats using the Qiagen RN-easy kit protocol. RNA was quantified using a Nanodrop™ spectrophotometer (ThermoFisher Scientific, Waltham, MA). RNA quality was confirmed by A260/280 ratio and only the samples that had a ratio of ≥2 and a concentration > 20 ng/µL were sent for sequencing to Novogene. Novogene confirmed the RNA purity and integrity of the samples using a NanoPhotometer™ spectrophotometer and the RNA Nano 6000 Assay Kit (Bioanalyzer 2100 system), respectively. Samples with RNA integrity number (RIN) > 8 were used for library preparation and sequencing on an Illumina platform (HWI-ST1276).
A total amount of 1 μg RNA per sample was used for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: 1 week capsule implants

value: Sprague Dawley

tag: sex

value: female

value: Therapeutic level E2 (40%)


title: GFP 1 [Sample_4]

description: replicate 1

value: overexpression of GFP


title: Chronic High_TG1

value: Proestrus level E2 (20%)


title: Chronic High_TG2


title: MI_Cntrls_M40


title: Chronic High_TG3


title: aSyn 2 [Sample_2]

description: replicate 2


title: Naiive_Cntrls_M44


title: Chronic Therapeutic_TG2


title: Chronic Veh_TG3

value: Vehicle (100% cholesterol)


title: Chronic Therapeutic_TG1


title: GFP 3 [Sample_6]

description: replicate 3


title: KLF15-3xFLAG_rep4

city: Pittsburgh

first: Erica

middle: Kai Yan

last: Fan

state: Pennsylvania

address: 3471 Fifth Ave

institute: University of Pittsburgh

data_processing:
Initial quality check and adaptor trimming was performed with Trim Galore (0.6.5) for ChIP-seq data (https://www.bioinformatics.babraham.ac.uk/publications.html)
The ENCODE transcription factor ChIP-seq pipeline  was used for alignment to the mm10 genome using bowtie2 (2.4.2) and peak calling using MACS2.
Deduplicated and uniquely mapped reads were used for peak calling analysis after excluding black-list regions following current ENCODE standardized guidelines.
Called peaks for each biological replicate were processed using bedtools for intersections: overlapping peaks in at least two replicates were used for downstream analysis
Assembly: mm10
Supplementary files format and content: We provide bigWig files for each sample that were used for analysis for distribution of transcription factors, feature distibution, and peak visualization.

source_name: Skeletal muscle cell

growth_protocol: N/A, cells from mice and plated

extract_protocol:
For 100,000-150,000 cells, 5uL of anti-FLAG (Cell Signaling Technologies, #8146) or anti-PPARb/d (F-10, Santa Cruz Biotechnology, sc-74517) antibodies were added to 25uL Protein A/G-coupled Dynabeads (Bimake, B23202) in PBS with 0.5% BSA and incubated for 4hr at 4 degrees. Cells were sonicated for 12 cycles of 30s on/30s off on high power using a Bioruptor Pico (Diagenode). Triton-X-100 (final concentration: 1%) and 50x cOmplete protease inhibitor (final concentration: 1x) were added to neutralize the SDS. Samples were incubated at RT for 10min and 5% of the aliquots were saved for preparation of input controls. Antibody-coated Dynabeads were washed with PBS, mixed with cell lysate, and incubated overnight at 4 degrees with rotation. Immunoprecipitated chromatin was washed with 150ul low-salt buffer, high-salt buffer, and LiCl buffer, followed by two washes with TE buffer and two washes with ice cold Tris/HCl (pH 8, 10mM)
Bead-bound chromatin was resuspended in 30ul of tagmentation buffer. 1ul of transposase (Nextera, Illumina) was added and samples were incubated at 37 degrees for 10min, followed by two washes with low-salt buffer. For standard reverse crosslinking: chromatin complexes were diluted with 200ul ChIP elution buffer and 2ul of 20ug/ml proteinase K (Thermo Scientific), vortexed, and incubated overnight at 65 degrees. After reverse crosslinking, 1 ul 20ug/ml RNase (Sigma) was added and incubated at 37 degrees for 30min. DNA purification was carried out using Qiagen MinElute PCR Purification Kit, and libraries were amplified and library cleanup was done using Agencourt AmPureXP beads (Beckman Coulter) at a ratio of 1:1. DNA concentrations in purified samples were measured using the Qubit dsRNA HS Kit (Invitrogen). Libraries were pooled and single-end sequenced (50 cycles) using the NextSeq500 platform (Illumina).

value: Skeletal muscle

tag: chip antibody

value: anti-FLAG

value: 10 weeks


title: KLF15KO_rep3

value: anti-PPARb/d


title: KLF15KO_rep2


title: KLF15KO_rep1


title: KLF15-3xFLAG_rep2


title: MyoCre_rep3

value: MyoCre


title: Chronic Low_TG1

value: Diestrus level E2 (5%)


title: Chronic Low_TG3


title: Chronic Low_TG2


title: Chronic Veh_TG2


title: InVitro_24hr_NB4_API

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NB4, 24hr, Apigenin, 50 μmol/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The AML cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cells were then treated with the indicated concentration of apigenin for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell

value: AML cell line


title: InVitro_24hr_HL60_None

source_name: HL-60, 24hr, no treatment


title: InVitro_24hr_NB4_None

source_name: NB4, 24hr, no treatment


title: InVitro_24hr_HL60_API

source_name: HL-60, 24hr, Apigenin, 20 μmol/L


title: ZF_rep2_RNA

city: Sapporo

first: FAN

last: WEIHONG

state: Hokkaido

address: Kita 8, Nishi 5, Kita-ku

department: Graduate School of Agriculture

institute: Hokkaido University

data_processing:
Illumina Casava1.7 software used for basecalling.
The high-quality sequences filtered by fastp were mapped to the mouse reference genome (mm10) by Bowtie2 (v2.0.0.5) and Tophat (v2.0.0).
Then, the mapping readings were assembled and GTF files were generated by StringTie (v2.2.0). The GTF files were then merged into one file by Cuffmerge, from which the counts of each gene were extracted.
The library size (count) was calculated using cheepelev et al. 's protocol, Nucleic Acid Research, 2009. In short, the exons of all the isomers of a gene are combined into a meta-transcript. The number of declining reads in the exon of this meta-transcript is counted according to the meta-transcript size and the library size.TPM was calibrated against raw reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Placenta

growth_protocol: ICR female mice at 8 weeks of age were used for IVF, after 2-cell stage for the zona removal and cultured until blastocyst.

extract_protocol:
Total RNA samples were prepared from two independent experiments (ZI and ZF groups) using ISOGEN II (Nippon Gene, Tokyo, Japan).
The sequencing libraries were constructed following the  MGI Library Prep Kits Guide using DNBSEQ-G400RS PE150 (MGI, China).

treatment_protocol: E3.5 blastocyst were performed the embryo transfer: zona intact group (ZI, n = 3), and zona free group (ZF group, n = 3).

value: ICR

value: Placenta

value: At birth

value: E3.5 ZF blastocyst by performing embryo transfer


title: Chronic Veh_TG1

value: Sprague Dawley


title: aSyn 1 [Sample_1]

description: replicate 1

value: LUHMES cells

value: overexpression of wild-type alpha-synuclein


title: GFP 2 [Sample_5]

description: replicate 2

value: overexpression of GFP


title: KLF15-3xFLAG_rep3


title: MyoCre_rep1


title: KLF15-3xFLAG_rep1


title: MyoCre_rep2


title: NOD TETpos 3 [WT-3-TET]

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

country: Australia

institute: University of Western Australia

data_processing:
Library strategy: TCR-seq
Agilent TapeStation for quality control of DNA integrity.
Paired-end (2 × 300 bp) high-throughput sequencing was performed using the Illumina MiSeq platform.
Data processing, aggregation of UMIs and alignment of CDR3 sequences to the IMGT/V-QUEST reference genome were performed using repertoire analysis software based on MIGEC and MiXCR pipelines. Only sequences with UMIs were aligned.
TCRβ clones (defined by the CDR3 amino acid sequence) were excluded if they were less than 8 or greater than 20 amino acids in length, included a stop codon or a frameshift.
Assembly: IMGT/V-QUEST reference genome
Supplementary files format and content: txt files
Supplementary files format and content: clonotype tables

source_name: Peripheral lymphoid organs

extract_protocol:
Sorted cells were stored at -80C. RNA was extracted from frozen cells using the RNeasy Plus Micro Kit.
TCRβ amplicon libraries were generated with 5’Rapid Amplification of cDNA Ends (5’RACE) technology. RNA was transcribed to cDNA with a TCRβ constant region primer and a modified SMARTerIIA primer (Integrated DNA Technologies), with 9nt long unique molecular identifiers (UMI) added to individual TCRβ cDNA sequences. TCRβ locus was amplified by nested PCR with an additional TCRβ constant region primers, and a universal primer to SMARTerIIA, with the final PCR adding sequencing adaptors and barcodes to the TCRβ libraries. Products after each PCR were purified using AMPure XP AgenCourt Beads (Beckman Coulter).
TCRβseq (300-base pair paired-end on Illumina MiSeq platform)

treatment_protocol: Single cell suspensions from peripheral lymphoid organs (PLO), (pooled spleen and non-draining lymph nodes) were stained with 8 nM IGRP206–214 (VYLKTNVFL) H-2Kd tetramer (ImmunoID, Parkville, VIC, Australia), washed, and stained with anti-PE MicroBeads (Miltenyi Biotec). Magnetic separation was performed using an AutoMACSpro system (Miltenyi Biotec) to collect IGRP-tetramer positive CD8+ T cells and non-tetramer CD8+CD44+ T cells (flow through cells that did not bind tetramer).

value: wild type NOD

value: Peripheral lymphoid organs

value: IGRP-tetramer positive CD8+ T cells

tag: timepoint

value: 125 days old


title: ZI_rep2_RNA

value: E3.5 ZI blastocyst by performing embryo transfer


title: ZF_rep1_RNA


title: NOD CD8 2 [WT-2-CD8]

value: non-tetramer CD8+CD44+ T cells


title: ZF_rep3_RNA


title: NOD CD8 1 [WT-1-CD8]


title: NOD TETpos 1 [WT-1-TET]


title: Ifngr1 TETpos 1 [GKO-1-TET]

value: Ifngr-1-mutant NOD


title: Ifngr1 TETpos 3 [GKO-3-TET]


title: ZI_rep3_RNA


title: THP1_KO_VSV_24h

first: Lili

last: Cao

address: datun Road

institute: Chinese Academy of Sciences

description:
promoter(<1kb); Promoter (1-2kb); Promoter (2-3kb); 3'UTR; 5'UTR
chromatin accessibility

data_processing:
all libraries were adapted for high-throughput sequencing (75 bp paired-end) on an Illumina NextSeq 500
Raw sequencing data are collected. After filtering data through sequencing data quality assessment, clean reads are further obtained.
After removing adapter sequences and low-quality reads, high-quality reads are processed for further analysis.
The peak calling reads are mapped to the human genome and accessible chromatin regions, such as promoters, 3’ UTR and 5’ UTR.
Assembly: mm9
Supplementary files format and content: bw

source_name: THP-1 cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 100 U/mL Penicillin-Streptomycin.

extract_protocol:
DNA was purified with Magen DNA purify kit
DNA was amplified with primers containing barcodes by using the TruePrep DNA Library Prep Kit (TD501-01)

treatment_protocol: without or with 0.1 MOI VSV infection for 6 hours

tag: agent

value: VSV infection

tag: time point

value: 24 hours


title: THP1_WT_VSV_24h


title: NOD CD8 3 [WT-3-CD8]

tag: tissue


title: NOD TETpos 2 [WT-2-TET]


title: ZI_rep1_RNA

value: ICR

tag: treatment


title: NOD CD8 4 [WT-4-CD8]


title: Impurity I

source_name: liver

value: liver

value: larvae

value: Wild-type AB

value: impurities


title: Skin_Pla2g4e_KO_P0

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression in KO skins at P0

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Mouse GE 4x44K v2 Microarray  for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: KO skin at P0

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted from P0 newborns was purified using a RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

value: Skin


title: Ifngr1 TETpos 4 [GKO-4-TET]


title: THP1_WT_VSV_0h

value: Mock


title: THP1-FLAG-RGG-Mock

description: chromatin accessibility

value: Flag-tagged Del-RGG


title: KO_24h

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: mm9
Supplementary files format and content: peak text files

extract_protocol:
purify DNA with QIA quick PCR purification kit (Magen, D211102) and elute with 50 mL elution buffer
The library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: without or with 0.1 MOI VSV infection for 6 hours or 24 hours

tag: antibody

value: H3K32Ac antibody

value: VSV infection for 24 hours


title: Ifngr1 CD8 4 [GKO-4-CD8]

value: Peripheral lymphoid organs


title: Skin_Pla2g4e_WT_P0

description: Gene expression in WT skins at P0

source_name: WT skin at P0


title: Ifngr1 CD8 2 [GKO-2-CD8]

value: 125 days old


title: THP1_KO_VSV_6h

value: 6 hours


title: Ifngr1 TETpos 2 [GKO-2-TET]

value: IGRP-tetramer positive CD8+ T cells


title: THP1_KO_VSV_0h


title: MIAMI IFNg+CQ_rep1

value: Bone marrow

value: IFN gamma 500 units+chloroquin 10 microM

value: BM-MSC


title: KO_0h

value: H3K30Ac antibody


title: Ifngr1 CD8 3 [GKO-3-CD8]

value: Ifngr-1-mutant NOD

value: non-tetramer CD8+CD44+ T cells


title: WT_0h

value: H3K27Ac antibody


title: Ifngr1 CD8 1 [GKO-1-CD8]


title: THP1_WT_VSV_6h

value: VSV infection


title: THP1-FLAG-WT-VSV

description: chromatin accessibility

value: VSV infection for 6 hours

value: Flag-tagged SAFA


title: THP1-FLAG-RGG-VSV

description: chromatin accessibility

value: Flag-tagged Del-RGG


title: WT_24h

value: H3K29Ac antibody


title: THP1-FLAG-WT-MOCK

description: chromatin accessibility

value: Mock


title: WT_8h

value: H3K28Ac antibody

value: VSV infection for 8 hours


title: KO_8h

value: H3K31Ac antibody


title: T298_38

status: Public on Mar 30 2022

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

description: library of 96 WT TEC cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Assembly: ENCODE VM9
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Thymus

growth_protocol: Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.

extract_protocol:
Thymic stromal cell isolation was done with slight modifications as described earlier (Rode et al., 2015). In contrast to the published method, minced thymi were directly subjected to digestion without discarding any fractions, and lymphoid cells (anti-CD45 beads, Miltenyi Biotec) and erythrocytes (anti-Ter119 beads, Miltenyi Biotec) were manually depleted using MACS technology.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)

treatment_protocol: No Treatment was performed.

value: WT

value: Thymus

tag: gender

value: female


title: T283_45

description: library of 96 WT UEA1+ TEC cells

tag: age


title: T285_43

description: library of 96 WT TEC cells

value: P28 bc

tag: individual

value: female #875


title: T286_42

description: library of 96 WT TEC cells

tag: strain


title: T269_3

description: library of 96 WT Ly51+ TEC cells


title: T284_44

description: library of 96 WT TEC cells


title: T282_46

description: library of 96 WT UEA1+ TEC cells


title: T266_6

description: library of 96 WT TEC cells


title: T267_5

description: library of 96 WT TEC cells


title: T107

description: library of 96 WT TEC cells


title: T268_4

description: library of 96 WT Ly51+ TEC cells


title: T271_1

description: library of 96 WT Ly51+ TEC cells


title: T287_41

description: library of 96 WT TEC cells


title: T300_36

description: library of 96 WT TEC cells


title: T296_40

description: library of 96 WT TEC cells


title: T297_39

description: library of 96 WT TEC cells


title: T270_2

description: library of 96 WT Ly51+ TEC cells


title: T281_47

description: library of 96 WT UEA1+ TEC cells


title: T280_48

description: library of 96 WT UEA1+ TEC cells


title: T265_7

description: library of 96 WT TEC cells


title: T29

description: library of 96 WT TEC cells


title: T254_10

description: library of 96 WT TEC cells


title: T255_9

description: library of 96 WT TEC cells


title: hMSC-derived adipocytes Cadmium rep3

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

country: Switzerland

institute: University of Lausanne

description:
Cd_6_3
Gene expression data.

hyb_protocol: Biotinylated cDNA were hybridized for 16 hr at 45°C on Human Clariom S arrays. Arrays were washed and stained on the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were acquired and processed with GeneChip Command Console (GCC), Expression Console and Transcriptome Analysis Console (TAC).

source_name: human MSCs differentiated to adipocytes

label_protocol: 100 ng of total RNA were used as input for the preparation of labeled double strand cDNA using the GeneChip Pico reagent kit from Thermofisher Scientific.

growth_protocol: The adipose-derived human Mesenchymal Stem Cells were purchased at Lifeline Cell Technology. Cells were grown in MesenPro RS Medium (Gibco) until they reached confluence and then were induced to differentiate into adipocytes for 2 weeks in StemPro Adipogenesis Differentiation Medium (Gibco), following manufacturer instructions.

extract_protocol: Trizol extraction of total RNA, followed by purification with the RNA Miniprep kit (Zymo Research).

treatment_protocol: After 2 weeks of differentiation, adipocytes were incubated with cadmium chloride (CdCl2, Sigma-Aldrich) solutions in water for 48 hours.

tag: cell type

value: adipose tissue-derived mesenchymal stem cells

value: cadmium


title: hMSC-derived adipocytes Cadmium rep1

description:
Cd_6_1
Gene expression data.


title: T251_13

description: library of 96 WT TEC cells


title: T248_16

description: library of 96 WT TEC cells


title: T250_14

description: library of 96 WT TEC cells


title: T249_15

description: library of 96 WT TEC cells


title: hMSC-derived adipocytes control rep2

description:
CTRL_2
Gene expression data.

value: control


title: hMSC-derived adipocytes control rep1

description:
CTRL_1
Gene expression data.


title: hMSC-derived adipocytes control rep3

description:
CTRL_3
Gene expression data.


title: T252_12

description: library of 96 WT TEC cells


title: T253_11

description: library of 96 WT TEC cells


title: T237_19

description: library of 96 WT TEC cells


title: T238_18

description: library of 96 WT TEC cells


title: T236_20

description: library of 96 WT TEC cells


title: T235_21

description: library of 96 WT TEC cells


title: T106

description: library of 96 WT TEC cells


title: hMSC-derived adipocytes Cadmium rep2

description:
Cd_6_2
Gene expression data.


title: T234_22

description: library of 96 WT TEC cells


title: T223_25

description: library of 96 WT TEC cells


title: T222_26

description: library of 96 WT TEC cells


title: T232_24

description: library of 96 WT TEC cells


title: T233_23

description: library of 96 WT TEC cells


title: T221_27

description: library of 96 WT TEC cells


title: T220_28

description: library of 96 WT TEC cells


title: T105

description: library of 96 WT TEC cells


title: T218_30

description: library of 96 WT TEC cells


title: T216_32

description: library of 96 WT TEC cells


title: T217_31

description: library of 96 WT TEC cells


title: T207_33

description: library of 96 WT TEC cells


title: T205_35

description: library of 96 WT TEC cells


title: T204_36

description: library of 96 WT TEC cells


title: T206_34

description: library of 96 WT TEC cells


title: T202_38

description: library of 96 WT TEC cells


title: T203_37

description: library of 96 WT TEC cells


title: T201_39

description: library of 96 WT TEC cells


title: T104

description: library of 96 WT TEC cells


title: T219_29

description: library of 96 WT TEC cells


title: T191_41

description: library of 96 WT TEC cells


title: T190_42

description: library of 96 WT TEC cells


title: T200_40

description: library of 96 WT TEC cells


title: T189_43

description: library of 96 WT TEC cells


title: T103

description: library of 96 WT TEC cells


title: T187_45

description: library of 96 WT TEC cells


title: T188_44

description: library of 96 WT TEC cells


title: T175_21

description: library of 96 WT TEC cells


title: T185_47

description: library of 96 WT TEC cells


title: T184_48

description: library of 96 WT TEC cells


title: T172_24

description: library of 96 WT TEC cells


title: T99

description: library of 96 WT UEA1+ TEC cells


title: T174_22

description: library of 96 WT TEC cells


title: T299_37

description: library of 96 WT TEC cells


title: T108

description: library of 96 WT TEC cells


title: T97

description: library of 96 WT UEA1+ TEC cells


title: T96

description: library of 96 WT TEC cells


title: T95

description: library of 96 WT TEC cells


title: T186_46

description: library of 96 WT TEC cells


title: T76

description: library of 96 WT TEC cells


title: T93

description: library of 96 WT TEC cells


title: T75

description: library of 96 WT TEC cells


title: T94

description: library of 96 WT TEC cells


title: T171_25

description: library of 96 WT TEC cells


title: T173_23

description: library of 96 WT TEC cells


title: T74

description: library of 96 WT TEC cells


title: T72

description: library of 96 WT TEC cells


title: T73

description: library of 96 WT TEC cells


title: T703

description: library of 96 WT TEC cells

value: Fgf7 tg

value: male


title: T700

description: library of 96 WT TEC cells


title: T98

description: library of 96 WT UEA1+ TEC cells


title: T696

description: library of 96 WT TEC cells


title: T70

description: library of 96 WT TEC cells


title: T701

description: library of 96 WT TEC cells


title: T697

description: library of 96 WT TEC cells


title: T698

description: library of 96 WT TEC cells


title: T702

description: library of 96 WT TEC cells


title: T69

description: library of 96 WT TEC cells


title: T695

description: library of 96 WT TEC cells


title: T170_26

description: library of 96 WT TEC cells


title: T694

description: library of 96 WT TEC cells


title: T699

description: library of 96 WT TEC cells


title: T67

description: library of 96 WT Ly51+ TEC cells

value: female #778


title: T693

description: library of 96 WT TEC cells


title: T68

description: library of 96 WT Ly51+ TEC cells


title: T71

description: library of 96 WT TEC cells


title: T678

description: library of 96 WT TEC cells


title: T692

description: library of 96 WT TEC cells


title: T675

description: library of 96 WT TEC cells


title: T169_27

description: library of 96 WT TEC cells


title: T677

description: library of 96 WT TEC cells


title: T674

description: library of 96 WT TEC cells


title: T679

description: library of 96 WT TEC cells


title: T672

description: library of 96 WT TEC cells


title: T168_28

description: library of 96 WT TEC cells


title: T676

description: library of 96 WT TEC cells


title: T655

description: library of 96 WT TEC cells


title: T659

description: library of 96 WT TEC cells


title: T658

description: library of 96 WT TEC cells


title: T663

description: library of 96 WT TEC cells


title: T66

description: library of 96 WT Ly51+ TEC cells


title: T656

description: library of 96 WT TEC cells


title: T661

description: library of 96 WT TEC cells


title: T654

description: library of 96 WT TEC cells


title: T102

description: library of 96 WT TEC cells


title: T657

description: library of 96 WT TEC cells


title: T652

description: library of 96 WT TEC cells


title: T65

description: library of 96 WT Ly51+ TEC cells


title: T662

description: library of 96 WT TEC cells


title: T653

description: library of 96 WT TEC cells


title: T159_29

description: library of 96 WT TEC cells


title: T673

description: library of 96 WT TEC cells


title: T650

description: library of 96 WT TEC cells


title: T651

description: library of 96 WT TEC cells


title: T660

description: library of 96 WT TEC cells


title: T64

description: library of 96 WT TEC cells


title: T649

description: library of 96 WT TEC cells


title: T648

description: library of 96 WT TEC cells


title: T62

description: library of 96 WT TEC cells


title: T630

description: library of 96 WT TEC cells


title: T631

description: library of 96 WT TEC cells


title: T629

description: library of 96 WT TEC cells


title: T264_8

description: library of 96 WT TEC cells


title: T628

description: library of 96 WT TEC cells


title: T625

description: library of 96 WT TEC cells


title: T627

description: library of 96 WT TEC cells


title: T626

description: library of 96 WT TEC cells


title: T158_30

description: library of 96 WT TEC cells


title: T621

description: library of 96 WT TEC cells


title: T624

description: library of 96 WT TEC cells


title: T620

description: library of 96 WT TEC cells


title: T622

description: library of 96 WT TEC cells


title: T623

description: library of 96 WT TEC cells


title: T61

description: library of 96 WT TEC cells


title: T157_31

description: library of 96 WT TEC cells


title: T63

description: library of 96 WT TEC cells


title: T617

description: library of 96 WT TEC cells


title: T619

description: library of 96 WT TEC cells


title: T618

description: library of 96 WT TEC cells


title: T596

description: library of 96 WT TEC cells


title: T595

description: library of 96 WT TEC cells


title: T599

description: library of 96 WT TEC cells


title: T616

description: library of 96 WT TEC cells


title: T598

description: library of 96 WT TEC cells


title: T592

description: library of 96 WT TEC cells


title: T156_32

description: library of 96 WT TEC cells


title: T594

description: library of 96 WT TEC cells


title: T597

description: library of 96 WT TEC cells


title: T580_20

description: library of 96 WT TEC cells


title: T593

description: library of 96 WT TEC cells


title: T582_18

description: library of 96 WT TEC cells


title: T579_21

description: library of 96 WT TEC cells


title: T578_22

description: library of 96 WT TEC cells


title: T576_24

description: library of 96 WT TEC cells


title: T583_17

description: library of 96 WT TEC cells


title: T577_23

description: library of 96 WT TEC cells


title: T567_25

description: library of 96 WT TEC cells


title: T155_33

description: library of 96 WT TEC cells


title: T563_29

description: library of 96 WT TEC cells


title: T562_30

description: library of 96 WT TEC cells


title: T565_27

description: library of 96 WT TEC cells


title: T239_17

description: library of 96 WT TEC cells


title: T559_33

description: library of 96 WT TEC cells


title: T561_31

description: library of 96 WT TEC cells


title: T566_26

description: library of 96 WT TEC cells


title: T564_28

description: library of 96 WT TEC cells


title: T581_19

description: library of 96 WT TEC cells


title: T154_34

description: library of 96 WT TEC cells


title: T560_32

description: library of 96 WT TEC cells


title: T558_34

description: library of 96 WT TEC cells


title: T553_39

description: library of 96 WT TEC cells


title: T554_38

description: library of 96 WT TEC cells


title: T556_36

description: library of 96 WT TEC cells


title: T555_37

description: library of 96 WT TEC cells


title: T529_47

description: library of 96 WT TEC cells


title: T530_46

description: library of 96 WT TEC cells


title: T526_2

description: library of 96 WT TEC cells


title: T534_42

description: library of 96 WT TEC cells


title: T533_43

description: library of 96 WT TEC cells


title: T552_40

description: library of 96 WT TEC cells


title: T535_41

description: library of 96 WT TEC cells


title: T153_35

description: library of 96 WT TEC cells


title: T532_44

description: library of 96 WT TEC cells


title: T152_36

description: library of 96 WT TEC cells


title: T524_4

description: library of 96 WT TEC cells


title: T525_3

description: library of 96 WT TEC cells


title: T528_48

description: library of 96 WT TEC cells


title: T531_45

description: library of 96 WT TEC cells


title: T523_5

description: library of 96 WT TEC cells


title: T557_35

description: library of 96 WT TEC cells


title: T502_10

description: library of 96 WT TEC cells


title: T521_7

description: library of 96 WT TEC cells


title: T503_9

description: library of 96 WT TEC cells


title: T527_1

description: library of 96 WT TEC cells


title: T501_11

description: library of 96 WT TEC cells


title: T500_12

description: library of 96 WT TEC cells


title: T520_8

description: library of 96 WT TEC cells


title: T143_37

description: library of 96 WT TEC cells


title: T499_13

description: library of 96 WT TEC cells


title: T498_14

description: library of 96 WT TEC cells


title: T522_6

description: library of 96 WT TEC cells


title: T483_21

description: library of 96 WT TEC cells


title: T485_19

description: library of 96 WT TEC cells


title: T486_18

description: library of 96 WT TEC cells


title: T497_15

description: library of 96 WT TEC cells


title: T487_17

description: library of 96 WT TEC cells


title: T480_24

description: library of 96 WT TEC cells


title: T477_27

description: library of 96 WT TEC cells


title: T484_20

description: library of 96 WT TEC cells


title: T142_38

description: library of 96 WT TEC cells


title: T478_26

description: library of 96 WT TEC cells


title: T479_25

description: library of 96 WT TEC cells


title: T101

description: library of 96 WT TEC cells


title: T476_28

description: library of 96 WT TEC cells


title: T474_30

description: library of 96 WT TEC cells


title: T475_29

description: library of 96 WT TEC cells


title: T496_16

description: library of 96 WT TEC cells


title: T473_31

description: library of 96 WT TEC cells


title: T481_23

description: library of 96 WT TEC cells


title: T482_22

description: library of 96 WT TEC cells


title: T453_35

description: library of 96 WT TEC cells


title: T472_32

description: library of 96 WT TEC cells


title: T452_36

description: library of 96 WT TEC cells


title: T141_39

description: library of 96 WT TEC cells


title: T450_38

description: library of 96 WT TEC cells


title: T451_37

description: library of 96 WT TEC cells


title: T448_40

description: library of 96 WT TEC cells


title: T449_39

description: library of 96 WT TEC cells


title: T455_33

description: library of 96 WT TEC cells


title: T447_41

description: library of 96 WT TEC cells


title: T444_44

description: library of 96 WT TEC cells


title: T445_43

description: library of 96 WT TEC cells


title: T446_42

description: library of 96 WT TEC cells


title: T44

description: library of 96 WT TEC cells


title: T422_6

description: library of 96 WT TEC cells


title: T423_5

description: library of 96 WT TEC cells


title: T41

description: library of 96 WT TEC cells


title: T421_7

description: library of 96 WT TEC cells


title: T420_8

description: library of 96 WT TEC cells


title: T42

description: library of 96 WT TEC cells


title: T140_40

description: library of 96 WT TEC cells


title: T443_45

description: library of 96 WT TEC cells


title: T442_46

description: library of 96 WT TEC cells


title: T43

description: library of 96 WT TEC cells


title: T405_15

description: library of 96 WT TEC cells


title: T419_9

description: library of 96 WT TEC cells


title: T139_41

description: library of 96 WT TEC cells


title: T407_13

description: library of 96 WT TEC cells


title: T40

description: library of 96 WT TEC cells


title: T418_10

description: library of 96 WT TEC cells


title: T406_14

description: library of 96 WT TEC cells


title: T417_11

description: library of 96 WT TEC cells


title: T416_12

description: library of 96 WT TEC cells


title: T403_17

description: library of 96 WT TEC cells


title: T440_48

description: library of 96 WT TEC cells


title: T404_16

description: library of 96 WT TEC cells


title: T454_34

description: library of 96 WT TEC cells


title: T441_47

description: library of 96 WT TEC cells


title: T138_42

description: library of 96 WT TEC cells


title: T400_20

description: library of 96 WT TEC cells


title: T401_19

description: library of 96 WT TEC cells


title: T402_18

description: library of 96 WT TEC cells


title: T391_21

description: library of 96 WT TEC cells


title: T390_22

description: library of 96 WT TEC cells


title: T38

description: library of 96 WT TEC cells


title: T389_23

description: library of 96 WT TEC cells


title: T386_26

description: library of 96 WT TEC cells


title: T385_27

description: library of 96 WT TEC cells


title: T388_24

description: library of 96 WT TEC cells


title: T375_29

description: library of 96 WT TEC cells


title: T387_25

description: library of 96 WT TEC cells


title: T374_30

description: library of 96 WT TEC cells


title: T36

description: library of 96 WT TEC cells


title: T39

description: library of 96 WT TEC cells


title: T373_31

description: library of 96 WT TEC cells


title: T365_35

description: library of 96 WT TEC cells


title: T363_37

description: library of 96 WT TEC cells


title: T35

description: library of 96 WT TEC cells


title: T364_36

description: library of 96 WT TEC cells


title: T350_42

description: library of 96 WT TEC cells


title: T372_32

description: library of 96 WT TEC cells


title: T37

description: library of 96 WT TEC cells


title: T348_44

description: library of 96 WT TEC cells


title: T366_34

description: library of 96 WT TEC cells


title: T360_40

description: library of 96 WT TEC cells


title: T137_43

description: library of 96 WT TEC cells


title: T136_44

description: library of 96 WT TEC cells


title: T115_46

description: library of 96 WT TEC cells


title: T33

description: library of 96 WT TEC cells


title: T333_19

description: library of 96 WT Ly51+ TEC cells


title: T351_41

description: library of 96 WT TEC cells


title: T362_38

description: library of 96 WT TEC cells


title: T329_23

description: library of 96 WT TEC cells


title: T361_39

description: library of 96 WT TEC cells


title: T318_26

description: library of 96 WT TEC cells


title: T319_25

description: library of 96 WT TEC cells


title: T349_43

description: library of 96 WT TEC cells


title: T384_28

description: library of 96 WT TEC cells


title: T116_45

description: library of 96 WT TEC cells


title: T344_48

description: library of 96 WT TEC cells


title: T317_27

description: library of 96 WT TEC cells


title: T34

description: library of 96 WT TEC cells


title: T367_33

description: library of 96 WT TEC cells


title: T328_24

description: library of 96 WT TEC cells


title: T316_28

description: library of 96 WT TEC cells


title: T313_31

description: library of 96 WT TEC cells


title: T314_30

description: library of 96 WT TEC cells


title: T303_33

description: library of 96 WT TEC cells


title: T302_34

description: library of 96 WT TEC cells


title: T312_32

description: library of 96 WT TEC cells


title: T347_45

description: library of 96 WT TEC cells


title: T331_21

description: library of 96 WT TEC cells


title: T335_17

description: library of 96 WT Ly51+ TEC cells


title: T31

description: library of 96 WT TEC cells


title: T32

description: library of 96 WT TEC cells


title: T345_47

description: library of 96 WT TEC cells


title: T334_18

description: library of 96 WT Ly51+ TEC cells


title: T332_20

description: library of 96 WT Ly51+ TEC cells


title: T100

description: library of 96 WT UEA1+ TEC cells


title: T301_35

description: library of 96 WT TEC cells


title: N30uM3

city: Hangzhou

first: Jiaqian

last: Pu

address: Xuezheng Str.

institute: Zhejiang Gongshang University

data_processing:
Sequencing of bacterial DNA with 16S rRNA gene regions V3-V4. The sequencing platform is MiSeqPE250 and the sequencing primers are universal primers
The obtained data were screened, optimized and spliced, and then subjected to quality control such as rejection of questionable sequences to obtain high quality sequences
Clustering of high quality sequences at 97% similarity and chimeric filtering to obtain OTUs for species classification
The abundance information in each sample OTU was counted, and the experimental data were tested for normal distribution by the IBM SPSS Statistics 19.0 software ANOVA-LSD test and the non-parametric Mann-Whitney test
Assembly: NC8
Supplementary files format and content: OUT

source_name: Feces

growth_protocol: Volunteers ate a healthy diet for the previous two months and did not take medications such as antibiotics

extract_protocol:
Bacterial DNA extraction from faecal samples and fermentation samples using QIAamp® PowerFecal® DNA kit
The Illumina sequencing platform was used to perform high-throughput sequencing of 16S rRNA (V3-V4 high-variance region) in 10 groups of microbial communities in faecal samples. The data obtained were screened, optimized and spliced, and then quality-controlled to obtain high-quality sequences, and the high-quality sequences were clustered at 97% similarity and chimerically filtered to obtain OTUs for species classification

treatment_protocol: Each sample was fermented with manure worker for 24h

tag: pathological status

value: Healthy

tag: tag

value: Feces

value: treated with NC830 for 24 hours


title: N30uM9


title: N30uM2


title: N30uM4


title: T113_48

description: library of 96 WT TEC cells

tag: genotype/variation


title: N30uM7


title: N30uM6


title: T330_22

description: library of 96 WT TEC cells


title: N3uM8

value: treated with NC83 for 24 hours


title: T346_46

description: library of 96 WT TEC cells


title: T114_47

description: library of 96 WT TEC cells


title: T315_29

description: library of 96 WT TEC cells


title: N3uM5


title: T30

description: library of 96 WT TEC cells


title: F7

value: untreated


title: F8


title: N30uM8


title: N30uM5


title: F4


title: F3


title: IELp Ctrl_rep_2

city: Bethesda

first: Jia

last: Nie

state: Maryland

address: Building 37, Room 3016

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Basecalling was performed using RTA 3.7.17
Barcode was demultiplexed with mkfastq in Cellranger 5.0.0
Alignment, tagging and gene counting were done with Cellranger 5.0.0
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files of raw/filtered gene-by-barcode matrces

extract_protocol: Chromium Single Cell V(D)J Reagent Kits (v1.1 Chemistry) per the manufacturer instructions (10X genomics) were used for library. Libraries were pooled and sequenced on NextSeq 500 (Kit V3, 100 cycle, parameter: R1: 26bp, I1: 8bp and R2: 98 bp).

tag: population

tag: genotype

value: Cd4 Cre- lrffl/fl


title: N3uM4


title: F1


title: N30uM10


title: IELp Ctrl

data_processing:
Basecalling was performed using RTA 1.12.4.2
Sequencing reads were demultiplexed using Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger software to produce the fastqfiles
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: barcode file, gene file and gene expression matrix

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics) were used for library. Libraries were pooled and sequenced with paired-end reads of 26x98bp or 26x57bp on a NextSeq500 sequencer (Illumina).

tag: cell population


title: A2

status: Public on Mar 28 2022

city: New York

first: Bin

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics) against the provided GRCh38 reference genome using default parameters, including introns.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Human postmortem brain sample

extract_protocol:
Nuclei were isolated from frozen tissue, as per 10x Genomics’ recommendations, using chilled, 0.1% Nonident P40 lysis buffer with gentle homogenization and washed.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis. Libraries were sequenced using a 2x100PE configuration on a NovaSeq instrument (Illumina, San Diego, CA), targeting a depth of 50,000-100,000 reads per nucleus.

value: Substanstia nigra

tag: disease state

value: Unaffected Control

tag: brain bank donor id

value: HctYH

value: Female

tag: race

value: White

tag: ethnicity

value: Hispanic

tag: postmortem interval hours

tag: braak stage


title: N30uM1

tag: treatment


title: N3uM10


title: NK_young

status: Public on Mar 25 2022

city: Hefei

first: mingming

last: wu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

description:
gender composition: F/M=2/2
scRNA for NK cells

data_processing:
Sequences were aligned using Cell Ranger version 1.3.1 from 10x Genomics with default parameters.
Quality control and dimensionality reduction were performed in R v3.6.3 using the Seurat package. For the initial QC step, we created Seurat objects for the young and elderly groups and filtered out the cells that expressed <400 genes, >3000 genes or > 10% mitochondrial genes. The gene expression count matrix for each cell was normalized using the “pp.normalize_total” function of Scanpy and log-transformed to the product (base e) after the addition of a pseudocount of 1.
parameter setting: CD45+ lymphocyte clustering: CCA=20, PCA=25, resolution=0.29; Lin-CD7+ NK cell clustering: CCA=25, PCA=25, resolution=0.5; NK cell clustering from COVID-19 and HD samples: CCA=25, PCA=25, resolution=0.5
Assembly: hg19
Supplementary files format and content: UMI count for each cell in mtx format and cell barcodes/genes in tsv format

source_name: NK cells

extract_protocol:
For the scRNA-seq analysis of human blood lymphocytes and NK cells, lymphocytes were sorted as CD45+ cells, and NK cells were sorted as CD3/CD19/CD20/CD14−CD7+ cells using FACS (SONY SH800S); the purity was above 95%. The cells from 4 elderly individuals were pooled in one tube and the cells from 4 young individuals were pooled in another tube. We then counted and resuspended the pooled cells at a concentration of 1000 cells/μL, aiming for an estimated 6000 cells per library, following the instructions of the single-cell 3ʹ solution v3 reagent kit (10X Genomics).
Single-cell libraries were constructed strictly according to the manufacturer’s standard protocols. Each sequencing library was generated with a unique sample index. Libraries were sequenced on the Illumina NovaSeq 6000 system.

value: healthy

value: NK cells

tag: Sex

value: pooled male and female

tag: mean age (years)

tag: age sd


title: Lym_young

institute: University of Science and Technology of China

description:
gender composition: F/M=2/2
scRNA for Lymphocytes

source_name: Lymphocytes

tag: cell type

value: Lymphocytes


title: N3uM7

tag: pathological status


title: N3uM9

tag: tag


title: N3uM3


title: N3uM2


title: 10 weeks_Ctrl_mouse205

status: Public on Mar 24 2022

city: Frankfurt

first: Nadine

last: Biesemann

state: Hessen

address: Industriepark Hoechst H824

institute: Sanofi

data_processing:
FASTQ files were pre-processed by RNA-Seq Analysis Snakemake Workflow (RASflow).
Raw read quality was evaluated using FastQC. Reads were trimmed for adaptors and sequence quality using Trim Galore.
Trimmed reads were aligned to mouse GRCm39 reference genome using HISAT2.
Paired reads were counted by using featureCounts at the gene level.
Genome_build: GRCm39 reference genome
Supplementary_files_format_and_content: A matrix table with raw counts for genes on all samples.

source_name: Paw homogenate

extract_protocol:
For mouse paws, frozen tissues were homogenized in 1.2 ml of QIAzol Lysis Reagent (Qiagen) per sample using a TissueLyser (Qiagen) for 2 x 5 min at 30 Hz, 4°C. The lysates were centrifuged for 5 min at 12,000 g, 4°C to remove debris. 250 µl of supernatant was used for RNA isolation using the Direct-zol-96 RNA kit (Zymo Research) by following the manufacturer’s instructions.
For mouse paws, 1 µg of total RNA was used as an input material for library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The libraries were multiplexed and paired-end sequenced (2 × 75 bp) on NextSeq 550 instrument (Illumina) using the NextSeq 500/550 High Output Kit (150 cycles).

treatment_protocol: Chicken type II collagen (CII, MD Bioproducts) was dissolved overnight in 0.1 M acetic acid (Fulka) at 4°C. The solution was then emulsified with an equal volume of Complete Freund’s adjuvant (CFA, Sigma) in an ice-cold water bath. The male DBA1 mice (age between 10 to 12 weeks, ENVIGO) were intradermally injected with 50 μl of this emulsion (containing 100 μg CII/mouse) at the base of the tail (day 0). On day 21 animals were boosted with 50 μl emulsion of CII in Incomplete Freund’s adjuvant (IFA, Sigma).

tag: strain

value: male

tag: tissue

value: Right hind paw

value: Ctrl

tag: time point

value: 10 weeks


title: N3uM1

value: Healthy

value: Feces

value: treated with NC83 for 24 hours


title: 10 weeks_Ctrl_mouse201


title: 8 weeks_Ctrl_mouse195

value: 8 weeks


title: F6

value: untreated


title: 6 weeks_Ctrl_mouse192

value: 6 weeks


title: F9


title: 6 weeks_Ctrl_mouse190


title: F5


title: IELp LRF KO_rep_2

tag: population

tag: genotype

value: Cd4 Cre+ lrffl/fl


title: 8 weeks_Ctrl_mouse188

tag: disease state


title: N3uM6


title: F2


title: 7 weeks_Ctrl_mouse186

value: 7 weeks


title: 7 weeks_Ctrl_mouse187


title: IELp LRF KO

tag: cell population


title: C1

last: Zhang

value: Substanstia nigra

value: Unaffected Control

tag: brain bank donor id

value: HctZP

tag: age

tag: gender

value: Male

tag: race

value: White

tag: ethnicity

value: Not Hispanic


title: 7 weeks_Ctrl_mouse183

tag: Sex

value: male

value: Right hind paw


title: 8 weeks_Ctrl_mouse198

value: Ctrl


title: NK_elder

value: healthy

value: NK cells

value: pooled male and female

tag: mean age (years)

tag: age sd


title: 4 weeks_Ctrl_mouse179

value: 4 weeks


title: F10

tag: pathological status

value: Healthy

value: Feces

tag: treatment

value: untreated


title: Lym_elder

tag: cell type

value: Lymphocytes


title: 8 weeks_Ctrl_mouse197

tag: strain

tag: tissue

value: 8 weeks


title: 3 weeks_Ctrl_mouse176

tag: time point

value: 3 weeks


title: 10 weeks_Ctrl_mouse204

value: 10 weeks


title: 3 weeks_Ctrl_mouse173


title: 10 weeks_Ctrl_mouse206


title: 3 weeks_Ctrl_mouse171


title: 2 weeks_Ctrl_mouse169

value: 2 weeks


title: 8 weeks_Ctrl_mouse200


title: 2 weeks_Ctrl_mouse167


title: 2 weeks_Ctrl_mouse168


title: 10 weeks_Ctrl_mouse202


title: 6 weeks_Ctrl_mouse193

value: 6 weeks


title: 6 weeks_Ctrl_mouse194


title: 6 weeks_Ctrl_mouse189


title: 2 days_Ctrl_mouse160

value: 2 days


title: 2 days_Ctrl_mouse159

value: male


title: 2 days_Ctrl_mouse163

value: Right hind paw


title: 2 days_CIA_mouse157

value: CIA


title: 2 days_Ctrl_mouse162

value: Ctrl


title: 7 weeks_CIA_mouse158

value: 7 weeks


title: 6 weeks_CIA_mouse156


title: 4 weeks_Ctrl_mouse178


title: 3 weeks_Ctrl_mouse174


title: 7 weeks_CIA_mouse152


title: 7 weeks_Ctrl_mouse185


title: 4 weeks_Ctrl_mouse182


title: 2 days_CIA_mouse153


title: 4 weeks_Ctrl_mouse180


title: 2 weeks_Ctrl_mouse170


title: 7 weeks_Ctrl_mouse184


title: 4 weeks_Ctrl_mouse181


title: 4 weeks_CIA_mouse145


title: 3 weeks_Ctrl_mouse172


title: 2 weeks_Ctrl_mouse165


title: 3 weeks_CIA_mouse140


title: 2 days_Ctrl_mouse164


title: 2 weeks_Ctrl_mouse166


title: 2 days_Ctrl_mouse161


title: 8 weeks_CIA_mouse155


title: 4 weeks_CIA_mouse151


title: 2 weeks_CIA_mouse143


title: 8 weeks_CIA_mouse132


title: 2 days_CIA_mouse135


title: 3 weeks_Ctrl_mouse175


title: 2 weeks_CIA_mouse154


title: 6 weeks_CIA_mouse139


title: 7 weeks_CIA_mouse141


title: 4 weeks_CIA_mouse144


title: 2 weeks_CIA_mouse148


title: 10 weeks_CIA_mouse149


title: 2 days_CIA_mouse131


title: 2 weeks_CIA_mouse121


title: 8 weeks_CIA_mouse117


title: 2 days_CIA_mouse122


title: 8 weeks_CIA_mouse119


title: 3 weeks_CIA_mouse124


title: 7 weeks_CIA_mouse125


title: 7 weeks_CIA_mouse127


title: 3 weeks_CIA_mouse147


title: 8 weeks_CIA_mouse112


title: 4 weeks_CIA_mouse114


title: 10 weeks_CIA_mouse109


title: 6 weeks_CIA_mouse104


title: 10 weeks_CIA_mouse133


title: 7 weeks_CIA_mouse130


title: 8 weeks_CIA_mouse142


title: 3 weeks_CIA_mouse123


title: 10 weeks_CIA_mouse128


title: 2 weeks_CIA_mouse137


title: 3 weeks_CIA_mouse99


title: 2 days_CIA_mouse90


title: 4 weeks_CIA_mouse91


title: 6 weeks_CIA_mouse96


title: 8 weeks_CIA_mouse86


title: 6 weeks_CIA_mouse87


title: 3 weeks_CIA_mouse120


title: 6 weeks_CIA_mouse82


title: 7 weeks_CIA_mouse84


title: 2 days_CIA_mouse129


title: 2 weeks_CIA_mouse106


title: 3 weeks_CIA_mouse108


title: 10 weeks_CIA_mouse118


title: 6 weeks_CIA_mouse78


title: 3 weeks_CIA_mouse89


title: 10 weeks_CIA_mouse116


title: 2 days_CIA_mouse105


title: 7 weeks_CIA_mouse103


title: 4 weeks_CIA_mouse115


title: 2 days_CIA_mouse98


title: 8 weeks_CIA_mouse95


title: 3 weeks_CIA_mouse75


title: 8 weeks_CIA_mouse73


title: 6 weeks_CIA_mouse81


title: 4 weeks_CIA_mouse72


title: 8 weeks_CIA_mouse79


title: 8 weeks_CIA_mouse71


title: 6 weeks_CIA_mouse69


title: 2 weeks_CIA_mouse66


title: 2 weeks_CIA_mouse64


title: 6 weeks_CIA_mouse85


title: 2 days_CIA_mouse80


title: 10 weeks_CIA_mouse60


title: 4 weeks_CIA_mouse62


title: 2 days_CIA_mouse77


title: 4 weeks_CIA_mouse113


title: 2 weeks_CIA_mouse102


title: 2 weeks_CIA_mouse97


title: 6 weeks_CIA_mouse59


title: 7 weeks_CIA_mouse58


title: 8 weeks_CIA_mouse55


title: 10 weeks_CIA_mouse88


title: 10 weeks_CIA_mouse54


title: 10 weeks_CIA_mouse53


title: 2 weeks_CIA_mouse50


title: 2 days_CIA_mouse63


title: 4 weeks_CIA_mouse74


title: 4 weeks_CIA_mouse49


title: 2 weeks_CIA_mouse68


title: 2 days_CIA_mouse56


title: 10 weeks_CIA_mouse61


title: 6 weeks_CIA_mouse44


title: 3 weeks_CIA_mouse34


title: 2 days_CIA_mouse31


title: 4 weeks_CIA_mouse39


title: 7 weeks_CIA_mouse26


title: 10 weeks_CIA_mouse40


title: 6 weeks_CIA_mouse33


title: 2 days_CIA_mouse51


title: 6 weeks_CIA_mouse22


title: 2 weeks_CIA_mouse37


title: 3 weeks_CIA_mouse38


title: 7 weeks_CIA_mouse21


title: 6 weeks_CIA_mouse41


title: 10 weeks_CIA_mouse76


title: 2 days_CIA_mouse52


title: 8 weeks_CIA_mouse16


title: 8 weeks_CIA_mouse45


title: 7 weeks_CIA_mouse43


title: 3 weeks_CIA_mouse29


title: 7 weeks_CIA_mouse15


title: 2 days_CIA_mouse47


title: 2 weeks_CIA_mouse48


title: 6 weeks_CIA_mouse11


title: 3 weeks_CIA_mouse57


title: 2 days_CIA_mouse30


title: 7 weeks_CIA_mouse12


title: 7 weeks_CIA_mouse9


title: 10 weeks_CIA_mouse7


title: 4 weeks_CIA_mouse2


title: 2 weeks_CIA_mouse17


title: donor 3_unstim

data_processing:
FASTQ files were imported into ArrayStudio (Qiagen).
Raw data quality control was performed and then a filtering step was applied to remove reads corresponding to rRNAs as well as reads having low quality score or shorter than 25 nt.
Reads were further mapped to the Human genome B38 using Omicsoft sequence aligner (OSA, version 4):
Paired reads were counted at the gene level using Ensembl.R96 gene model.
Genome_build: NCBI Human genome B38
Supplementary_files_format_and_content: A matrix table with raw counts for genes on all samples. Ensembl.R96 gene model was used.

source_name: Macrophages

growth_protocol: Human peripheral blood monocytes were isolated from anonymous donors’ prefinal blood using Ficoll density centrifugation, followed by magnetic separation with positive selection (CD14 MicroBeads, Miltenyi Biotec). Monocytes were differentiated into macrophages by culturing in macrophage serum-free medium (Life Technologies) containing 50 ng/ml recombinant human macrophage colony-stimulating factor (Immunotools) for 5 days. Following differentiation, cells were cultured in RPMI 1640 medium supplemented with 10% heat inactivated fetal bovine serum (Thermo Fisher) and maintained at 37°C in a 5% CO2/air environment.

extract_protocol:
Frozen cell pellet from each well was lysed by addition of 350 µl of the TRI Reagent solution included in the Direct-zol-96 RNA kit. Total RNA was then isolated from the lysates using the Direct-zol-96 RNA kit.
60 ng of total RNA was used for library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext rRNA Depletion Kit (New England Biolabs). The libraries were paired-end sequenced (2 × 75 bp) on NovaSeq 6000 instrument (Illumina) using the NovaSeq 6000 S2 Reagent Kit (200 cycles).

treatment_protocol: Macrophages were stimulated with 50 ng/ml lipopolysaccharides from Escherichia coli O111:B4 (Sigma) for 24 hours.

value: Macrophages

value: Unstimulated

tag: donor

value: donor 3


title: donor 4_LPS

value: 50 ng/ml LPS for 24 hours

value: donor 4


title: 10 weeks_CIA_mouse6

tag: disease state


title: donor 1_unstim

value: donor 1


title: ebv Mutu input

status: Public on Mar 18 2022

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

description: DNA input

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605) using bowtie2.
Peak calling was performed using MACS2 with the broadPeaks option and input DNA used as a reference set.
Integrative Genomics Viewer was used for data visualization.
Assembly: Human gammaherpesvirus 4
Supplementary files format and content: reads pileup in bedgraph format

organism: human gammaherpesvirus 4

source_name: MUTU

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

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

treatment_protocol: Chromatin immunoprecipitation with next generation sequencing (ChIP-seq) was performed as described: 2.5×107 cells were crosslinked with 1% formaldehyde for 10 min and chromatin was sonicated with a Qsonica sonicator. 1/10 of the sonicated chromatin was collected and used as input material while the rest of the chromatin was immunoprecipitated using 5 µg of target antibody. DNA fragments of ∼150–300 bp were visualized by agarose gel purification. Immunoprecipitated DNA was ligated to adapter primers using the TruSeq ChIP Library Preparation Kit (Illumina) and then sequenced using the Illumina HiSeq 2500 platform according to the manufacturer’s recommendations (Illumina).

value: B-cells

tag: antibody


title: 3 weeks_CIA_mouse5

value: 3 weeks


title: 7 weeks_CIA_mouse94


title: 4 weeks_CIA_mouse28

value: 4 weeks


title: 8 weeks_CIA_mouse20

value: 8 weeks


title: donor 3_LPS


title: 8 weeks_CIA_mouse18


title: donor 4_unstim


title: 4 weeks_CIA_mouse14


title: donor 1_LPS


title: root tip, col_fullMS_r2

status: Public on Mar 16 2022

city: Perth

first: Ryan

last: Lister

address: 35 Stirling Highway

institute: The University of Western Australia

description:
col_fullMS_r1, col_fullMS_r2, col_halfMS_r1, col_halfMS_r2 were all processed simultaneously
ms_final.rds

data_processing:
Reads were mapped using a modified version of the 10x Genomics CellRanger pipeline. Reads were mapped to a version of the Arabidopsis (TAIR10) genome with ambiguous base codes placed at SNP positions for the genotypes sequenced, as identified by the Arabidopsis 1001 genomes project.
Cells were then genotyped and cell doublets identified by performing density-based clustering on the SNP UMI counts for each genotype
The Seurat v3 R package was used for data normalization, cell filtering, batch correction, dimension reduction, and clustering.
Assembly: TAIR10
Supplementary files format and content: Processed data files are Seurat objects. The root_final.rds object contains all processed wild-type cells: the 'integrated' slot contains the integrated (genotype-corrected) data, and the 'batch_corrected' slot the batch-corrected data. The col_final.rds object contains wild-type col-0 cells only, and batch-corrected data. The scr_final.rds object contains scr-3 data, and the ms_final.rds object contains data from Col-0 cells from seedlings grown on full or half MS and processed simultaneously. The meta data of each object contains different cell annotations.

organism: Arabidopsis thaliana

source_name: root tip (~up to 3 mm) of seedlings at 6dag

growth_protocol: Seedlings were grown vertically on Murashige and Skoog basal medium with vitamins plates supplemented with 1% sucrose for 6-7 dag before root tips were collected

extract_protocol:
For each genotype, root tips were placed in 15ml of protoplasting solution [1.25% w/v cellulase, 0.3% w/v macerozyme, 0.4M D-mannitol, 20mM MES (pH 5.7), 20mM KCl, 10mM CaCl2, 0.5% w/v BSA, and 5mM β-mercaptoethanol in ultrapure water] and incubated at room temperature for 1 hour on a tube rotator. The solution was subsequently filtered through a 70μm and a 40μm cell strainer (Falcon) to separate protoplasts from undissociated tissue. Cells were centrifuged for 5 minutes at 500 x g in a swinging bucket centrifuge. The pellet was resuspended in 15ml of protoplast resuspension buffer [0.4M D-mannitol, 20mM MES (pH 5.7), 20mM KCl, 10mM CaCl2, and 0.5% w/v BSA in ultrapure water] and centrifuged at 500 x g for 5 minutes. Cells were resuspended in the protoplast resuspension buffer, and filtered through a 35μm cell strainer Snap Cap (Falcon). The final concentration was adjusted to 900-1,200 cells/μl. Protoplasts from two Arabdiopsis accessions were mixed in equimolar quantities and barcoded with a Chromium Controller (10X Genomics).
10X Genomics 3' Single Cell Gene Expression v2/v3
scRNA-seq

tag: developmental stage

value: seedlings at 6dag

value: root tip

tag: genotype

value: Col-0 cells

tag: growth medium

value: full MS (1x)


title: donor 2_LPS

value: donor 2


title: 6 weeks_CIA_mouse1

value: male

value: Right hind paw

value: CIA

value: 6 weeks


title: donor 2_unstim

value: Macrophages

value: Unstimulated


title: root tip, ws2_r1

description:
ws-2 cells were mixed with other cells not included in the study, to identify multiplets. Fastq files were subsetted to only keep the reads associated with ws-2 cells
root_final.rds

value: ws-2 cells


title: ebv LCL Lamin B1 ChIP

description: Immunoprecipitated DNA by LaminB1

source_name: LCL


title: 4 weeks_CIA_mouse3


title: root tip, ws2_r2


title: ebv LCL Lamin A/C ChIP

description: Immunoprecipitated DNA by LaminA/C

value: LaminA/C


title: ebv LaminB1 ChIP

description: Immunoprecipitated DNA by LaminB1

value: B-cells


title: root tip, ws2_r3


title: root tip, c24_r2

description:
C24 cells were mixed with other cells not included in the study, to identify multiplets. Fastq files were subsetted to only keep the reads associated with C24 cells
root_final.rds

value: C24 cells


title: ebv LCL input

description: DNA input


title: root tip, col_halfMS_r2

value: half MS (0.5x)


title: root tip, col_fullMS_r1


title: root tip, col0_ler_r4

description:
root_final.rds
col_final.rds

value: mix of Col-0 and Ler cells


title: root tip, col0_c24_r5

description:
root_final.rds
col_final.rds

value: seedlings at 6dag

value: mix of Col-0 and C24 cells


title: 7 weeks_CIA_mouse13

value: 7 weeks


title: root tip, col_halfMS_r1

value: root tip

value: Col-0 cells


title: root tip, col0_cvi0_r2

description:
root_final.rds
col_final.rds

value: mix of Col-0 and Cvi cells

value: full MS (1x)


title: root tip, col0_cvi0_r3

description:
root_final.rds
col_final.rds


title: root tip, col0_cvi0_r1

description:
root_final.rds
col_final.rds