title: hESC-CM control rep3

city: Montreal

first: Guillaume

last: Lettre

address: 5000 Belanger

institute: Montreal Heart Institute

description: bulk RNAseq

data_processing:
RNAseq were pseudoaligned to Gencode v32 using Kallisto with the options quant -b 100 --rf-stranded. Transcripts counts were aggregated by genes.
Assembly: hg38
Supplementary files format and content: Tab separated values matrix files

source_name: hESC-CM

extract_protocol:
The H1-dCas9-KRAB hESC lines were infected with Non-Targeting Control (NTC) and LINC01629 gRNAs, then differentiated into cardiomyocytes and matured for 60 days before harvesting for bulk RNAseq and differential expression analysis. RNA was isolated using the Direct-Zol RNA Miniprep kit.
Total RNA library preparations were prepared using TruSeq Stranded Total RNA Library Prep HMR kit (Illumina, 20020596) and respective cDNA libraries were prepared by Macrogen Asia Pacific Pte. Ltd. RNA libraries were sequenced on HiSeq 4000 Illumina sequencing platform to achieve a sequencing depth of at least 50 million paired-end reads per biological sample.

value: hESC-CM

value: control


title: hESC-CM control rep1

status: Public on Jul 09 2024

type: SRA

state: Quebec

country: Canada

description: bulk RNAseq

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: treatment


title: hESC-CM control rep2

description: bulk RNAseq


title: LNCaP, R1881, 0.1 nM, 24 hours, Input, Rep2

city: Durham

first: Xiaodi

last: Qin

address: 2424 Erwin Road

country: USA

institute: Duke Cancer Institute

library_source: genomic

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39.
Trimmed ChIP-seq reads were aligned to GRCh38/hg38 using BWA v0.7.17. Reads that were unaligned, multi-mapped, failed platform quality checks or had mapping quality less than 30 were removed.
Peaks were called and narrowPeak files were generated using MACS v2.2.7.1 with --pvalue 0.01, --keep-dup all, --call-summits, and -f BAMPE
BigWig files were generated using bamCoverage v3.5.1 from Deeptools suite, with --normalizeUsing RPGC, --binSize 10, --minFragmentLength 40, --effectiveGenomeSize 2701495761.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

molecule: genomic DNA

source_name: Prostate

growth_protocol: LNCaP cells (2,000,000 cells/dish) were seeded in 15 cm tissu culture dish in RPMI 1640  supllemented with 8% charcoal dextran treated FBS(CFS). 5 millions cells were collected per condition. For VCaP cell line (5,000,000 cells/dish), cells were seeded in 15 cm tissu culture dish  in DMEM (8% CFS). 48 hrs later, cells were treated with R1881 for an additional 24 hrs

extract_protocol:
Cells were fixed using a final concentration of 1% methanol-free formaldehyde in PBS at for 10 min and quenched with 125mM glycine for 5 min. Cells were then washed twice in PBS Wash Buffer (Active Motif #53046), pelleted, and stored at -80˚C. For sonication, cells were thawed and resuspended in ice cold Buffer LB1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail (ThermoFisher #78446) on a rotator at 4˚C for 10 minutes. Cells were then centrifuged, liquid decanted, and resuspended in Buffer LB2 (10mM Tris-HCL pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail. Cells were then centrifuged, liquid decanted and resuspended in ice cold Buffer LB3 (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-laurylsarcosine) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail. This nuclear resuspension was transferred into Covaris microtube 130 AFA Fiber pre-Slit snap-cap tubes (Covaris #520045) at a maximum concentration of 3 million cells per 130µL and sonicated using the following parameters on a Covaris ME220 according to the manufacturer’s recommendations (Duration (s) = 360, Peak Power = 75, Duty Factor = 5.0, Cycles/Burst = 1000). Following sonication, 10µL of chromatin was removed for analysis of resulting DNA size and concentration. Briefly, 10µL of sonicated chromatin was incubated with 20µg RNase A (Thermo Scientific #EN0531) in TE pH 8 for 30 minutes at 37˚C in a thermal cycler. 20µg of Proteinase K (Thermo Scientific #EO0491) in Active Motif Elution Buffer AM4 (Active Motif #103926) was then added and the sample was incubated for 30 minutes at 55˚C followed by 90 minutes at 65˚C in a thermal cycler. Samples were then cooled to room temperature and DNA was purified using SPRIselect beads (Beckman #B23318) at a bead:sample ratio of 1.4:1 and eluted in 10µL of 10 mM Tris, 0.1 mM EDTA.
Chromatin corresponding to 1 million cells was diluted with 200µL in Active Motif ChIP Buffer and incubated with pre-clearing Protein G agarose beads. After pre-clearing, agarose beads were pelleted and transferred to a new microcentrifuge tube containing 4µg of antibody specific to the target protein (AR: Abcam ab236225). IPs were then incubated overnight on a rotator at 4˚C. Protein G Agarose beads prepared the previous day according to Active Motif’s Low Cell ChIP kit were added to the antibody-bound chromatin and incubated for 4 hours on a rotator at 4˚C. IPs were then transferred to ChIP filtration columns, washed, and eluted in 80µL according to Active Motif’s Low Cell ChIP kit and DNA purified using SPRIselect beads at a bead:sample ratio of 1.4:1. After SPRI cleanup, ChIP samples and reverse crosslinked input DNA was made into sequencing Illumina libraries using Swift NGS 2S Plus (Swift Biosciences #21096) and indexed using Single Indexed Adapters with MIDs (Swift Biosciences #279384).  ChIP-seq libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit with UMIs.

treatment_protocol: LNCaP and VCaP cells were tretaed with either vehicle, or increasing concentrations of low-dose (0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hours

value: Prostate

tag: cell line

value: LNCaP

tag: cell type

value: epithelial

tag: chip antibody

value: Input

tag: compound

tag: dose

tag: time

value: 24 hours


title: hESC-CM linc01629-KD rep3

description: bulk RNAseq

value: linc01629 knockdown


title: RPE/choroid/sclera complex, IF+NaIO3-2

city: xu zhou

first: Jingzhen

last: Li

address: huang shan road

department: Life science

country: China

institute: xuzhou medical university

data_processing:
In the process of comparison (align) with the reference group, we  choose the reference genome of the species or known transcriptome data (e.g., full-length transcriptome spliced by three-generation technology). The comparison tool was chosen to be HISAT2, which uses a modified BWT algorithm.
The analysis was quantified using the StringTie tool based on the positional information of the gene ratio on the reference genome, thus counting the number of reads covered by each gene from the start to the end range.
To screen the samples for genes with significantly different expression levels in different states.Differential expression analysis was performed by DESeq2 (with duplicate samples) or edgeR (without duplicate samples), and the input data were the reads count expression quantified by StringTie. DESeq2 is divided into three main parts.1) firstly, the original readcount is normalized, mainly for the correction of sequencing depth; 2) then the statistical model is used to calculate the probability of hypothesis testing (pvalue); 3) finally, multiple hypothesis testing is performed.3) Finally, multiple hypothesis testing correction is performed to obtain the FDR value (false discovery rate, padj is its common form). The conventional criteria for screening differential genes are |log2(FoldChange)| > 1 & padj<0.05, and if the number of differential genes is too small under this screening threshold, |log2(FoldChange)| >0.5 & pvalue<0.05 were chosen. both are commonly used screening criteria, and the screening criterion for the current project was |log2( FoldChange)| > 1 & padi<0.05.
We used clusterProfiler software to perform GO function enrichment analysis, KEGG pathway enrichment analysis, etc. on the differential gene sets. The enrichment analysis results are enriched for all differential gene sets, up-regulated differential gene sets, and down-regulated differential gene sets for each differential comparison combination.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: RPE/choroid/sclera complex

extract_protocol:
Total RNA was extracted from eye cup utilizing the Trizol/chloroform method according to standard RNA extraction procedure.
RNA libraries for RNA-seq was prepared using TIANSeq Stranded RNA-Seq Kit (Illumina), follwing manufacturers' protocol
Illumina HiSeq PE150

value: RPE/choroid/sclera complex

tag: genotype

value: wild type

value: intermittent fasting, Intraperitoneal injection of NaIO3


title: LNCaP, Vehicle_CFS, 0, 24 hours, AR, Rep2

value: AR


title: RPE/choroid/sclera complex, IF+NaIO3-3


title: LNCaP, R1881, 10 nM, 24 hours, AR, Rep1

value: 10 nM


title: RPE/choroid/sclera complex, IF+NaIO3-1


title: RPE/choroid/sclera complex, AL+NaIO3-3

value: ad libitum, Intraperitoneal injection of NaIO3


title: LNCaP, R1881, 0.1 nM, 24 hours, Input, Rep1


title: hESC-CM linc01629-KD rep2

description: bulk RNAseq


title: 14_D3_I_474

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.  After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with Version 17 of Entrezgene CDF brain array.

label: Biotin

label_protocol: 50 ng of total RNA is reverse transcribed following the Ovation PicoSL WTA System V2 (Nugen).  After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

growth_protocol: monocytes were isolated from blood of healthy donors and grown for 11 days in the presence of 10 ng/ml of rhGM-CSF

extract_protocol: RNA was extracted using RNeasy® Plus mini kit (Qiagen)

treatment_protocol: in vitro differentiated macrophages were infected with HIV-1 ADA (I) or not NI) for 8 days and then incubated or not (NCO) with Salmonella typhimurium 4/74 (4 74) or D23580 (D23)

tag: infection

value: HIV-1 ADA

tag: incubation

value: Salmonella typhimurium 4/74


title: 12_D2_NI_NCO

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G


title: 18_D3_NI_NCO


title: 13_D3_I_D23

value: Salmonella typhimurium D23580


title: 11_D2_NI_474


title: 10_D2_NI_D23


title: 15_D3_I_NCO


title: 16_D3_NI_D23


title: 9_D2_I_NCO


title: LNCaP, R1881, 0.1 nM, 24 hours, AR, Rep2


title: 17_D3_NI_474


title: hESC-CM linc01629-KD rep1

description: bulk RNAseq

value: hESC-CM


title: 8_D2_I_474


title: RPE/choroid/sclera complex, AL+NaIO3-1


title: LNCaP, R1881, 0.06 nM, 24 hours, Input, Rep2


title: LNCaP, R1881, 0.1 nM, 24 hours, AR, Rep1


title: BALI9, BAL

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

library_source: transcriptomic single cell

data_processing:
The CellRanger v7.0.0 pipeline (mkfastq and count) was used to demultiplex the raw sequencing reads from the single-cell libraries and align them to the GRCh38 reference genome (CellRanger 2020-A).
To demultiplex the mixed samples from Chicago, the fastq files corresponding to the whole-exome sequencing data of these samples were aligned to the CellRanger reference fasta file (refdata-gex-GRCh38-2020-A/genome.fa) using bwa-mem. The resulting .sam files were converted to .bam files using picard. Picard was also used to sort, mark duplicates in, and build indices for the .bam files. The Genome Analysis Toolkit (GATK)’s Best Practices for Germline Short Variant Discovery were followed. These .vcf files were filtered for common single nucleotide polymorphisms (SNPs) with a 5% minor allele frequency cutoff. Demuxlet, implemented in the Demuxafy framework, was used to demultiplex these samples based on their common SNPs [25]. Only samples that had a posterior likelihood of >0.95 were kept.
The feature-barcode matrices for each patient sample were loaded into R and converted into a Seurat (v4.0) object. Cells with fewer than 200 features and those expressing greater than 20% of mitochondrial genes were filtered out to remove dead and dying cells. Samples with fewer than 500 cells were removed to eliminate low-quality samples. The filtered gene expression matrix was normalized using Seurat's NormalizeData function with default settings. Genes with high cell-to-cell variation were identified using the FindVariableFeatures function with the “vst” method. The data was integrated on an assay level (5’ v1 versus v2) using reciprocal PCA to reduce 10X assay-specific effects, and no significant batch effects were noted after this integration. The data were then scaled and centered using the ScaleData function, and the top 3,000 variable features were used for Principal Component Analysis. The top 30 principal components (PCs) were selected based on the elbow plot generated by the ElbowPlot function. Graph-based clustering was performed using the FindNeighbors and FindClusters functions with the selected 30 PCs.
Assembly: Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: For each sample, processed data include Cell Ranger Count filtered outputs: cell barcodes (barcodes.tsv.gz), genes (features.tsv.gz) and count matrix (matrix.mtx.gz).
Supplementary files format and content: demuxlet-outputs.zip (Chicago Mix A10, B10, C10, etc. include barcodes for multiple samples that were multiplexed together in a single 10X lane. demuxlet-outputs.zip contains the demuxlet.best files for each mix, which are the outputs the demultiplexing software demuxlet, that link each barcode to a specific sample (e.g. A10-demuxlet.best links each barcode to a sample). )

molecule: polyA RNA

source_name: BAL

extract_protocol:
At each sample collection site, PBMCs were separated from the whole blood using density gradient centrifugation, and PBMC and BAL samples were cryopreserved in liquid nitrogen as separate samples for single-cell experiments. The PBMCs were cryopreserved in 1.5 ml cryotubes using 10% DMSO in heat-inactivated FBS and were stored long-term in liquid nitrogen. Initial PBMC sample collection, processing, and storage did not differ significantly among the three patient sample collection sites. In Mexico City, bronchoalveolar lavage samples were collected and stored long-term in liquid nitrogen using 10% DMSO in heat-inactivated FBS.
All patient samples were shipped for processing in New Haven, CT, to minimize technical and batch effects arising from sample processing. Samples were randomized based on age, sex, diagnosis, and smoking history into different batches for sample preparation and single-cell library construction. Sixteen samples were processed at a time to reduce batch effects. The sample preparation protocol used was modified from 10X Genomics with the following modifications. Cryopreserved samples were thawed in a 37 °C water bath, and 1.5 ml of 10% FBS in Dulbecco’s Modified Eagle Medium (DMEM) was added to each tube. The cells were centrifuged, the supernatant was removed, and the cells were resuspended in D-PBS with 0.04% bovine serum albumin (BSA). The sample was passed through a 40 µm cell strainer into a 2-mL microcentrifuge tube. The cell concentration was determined using Trypan Blue solution, and Invitrogen Countess Automated Cell Counter. Samples with isolated single cells were diluted, and these cells were loaded into the chip with an anticipated recovery of 10,000 cells according to the manufacturer’s protocol for Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) (from samples from New Haven and Mexico City only). To further reduce batch effects, Chicago samples were pooled, such that each chip lane was loaded with two or three patient samples, with an anticipated recovery cell of 20,000 cells to 30,000 cells, respectively. Any leftover samples were fixed in 80% methanol and stored at -20C to preserve nucleotide integrity for downstream DNA extraction and whole-exome sequencing to SNP-demultiplex mixed patient samples from Chicago. All subsequent library construction steps were followed precisely, and all cDNA library QC was performed using an Agilent 2100 Bioanalyzer.
The single-cell cDNA libraries were sequenced using an Illumina HiSeq4000 machine at the Yale Stem Cell Genomics Center (samples from New Haven and Mexico City) and from an Illumina NovaSeq X at the Yale Center for Genomic Analysis (samples from Chicago). Samples were sequenced at a depth of 150 million reads per sample to allow for adequate transcriptome capture.

value: BAL

tag: cohort

value: Mexico City

tag: samples multiplexed_(chicago_only)

tag: age (singleton or multiplexed)

tag: sex (singleton or multiplexed)

value: M

tag: disease (singleton or multiplexed)

value: IPF

tag: smoking status

value: Never

tag: dlco


title: RPE/choroid/sclera complex, IF+PBS-3

tag: tissue

tag: treatment

value: intermittent fasting, Intraperitoneal injection of PBS


title: BALI8, BAL


title: 7_D2_I_D23


title: RPE/choroid/sclera complex, AL+NaIO3-2


title: LNCaP, R1881, 0.06 nM, 24 hours, Input, Rep1

value: Prostate

tag: cell line

value: LNCaP

tag: cell type

value: epithelial

value: Input

value: 24 hours


title: BALI7, BAL

value: Former


title: RPE/choroid/sclera complex, IF+PBS-1

value: RPE/choroid/sclera complex

value: wild type


title: 6_D1_NI_NCO


title: 4_D1_NI_D23


title: BALI6, BAL


title: LNCaP, R1881, 0.06 nM, 24 hours, AR, Rep2

tag: chip antibody

value: AR

tag: compound


title: 5_D1_NI_474

value: Salmonella typhimurium 4/74


title: RPE/choroid/sclera complex, AL+PBS-2

value: ad libitum, Intraperitoneal injection of PBS


title: BALI5, BAL

value: BAL

value: F


title: RPE/choroid/sclera complex, AL+PBS-1


title: RPE/choroid/sclera complex, AL+PBS-3


title: LNCaP, R1881, 0.06 nM, 24 hours, AR, Rep1

tag: dose

tag: time


title: RPE/choroid/sclera complex, IF+PBS-2

tag: genotype


title: RWPE1_RNA_ML792-DHT_rep3

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. LNCaP cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 1 U/µl penicillin and 1 µg/ml streptomycin. RWPE1 cells were grown in Keratinocyte SFM supplemented with human recombinant epidermal growth factor and bovine pituitary extract. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: VCaP, LNCaP and RWPE1 cells were treated either with vehicle (EtOH) or 100 nM of dihydrotestosterone (DHT) for 6 h before extraction of RNA. Before EtOH or DHT treatment, the cells were treated either with vehicle (DMSO) or SAE inhibitor (ML792) for 24 h prior extraction.

value: Immortalized human prostatic epithelial cells

value: ML792 + DHT

tag: concentration


title: LNCaP, R1881, 0.03 nM, 24 hours, Input, Rep2


title: BALI4, BAL

tag: cohort

value: Mexico City

value: M

value: IPF


title: LNCaP, R1881, 0.03 nM, 24 hours, Input, Rep1

value: Prostate

value: LNCaP


title: RWPE1_RNA_ML792-DHT_rep2


title: BALI2, BAL

tag: samples multiplexed_(chicago_only)


title: RWPE1_RNA_ML792-DHT_rep1


title: LNCaP, R1881, 0.03 nM, 24 hours, AR, Rep2

value: epithelial


title: 2_D1_I_474

tag: infection

value: HIV-1 ADA

tag: incubation


title: 1_D1_I_D23

value: Salmonella typhimurium D23580


title: LNCaP, R1881, 0.03 nM, 24 hours, AR, Rep1

value: 24 hours


title: BALI1, BAL

tag: age (singleton or multiplexed)

tag: sex (singleton or multiplexed)

tag: disease (singleton or multiplexed)

value: Never


title: 3_D1_I_NCO


title: Cortex, LPS, 3days, astrocyte cKO C1

city: Montréal

first: Platon

last: Megagiannis

state: QC

address: 3801 Rue University

department: Neurology and Neurosurgery

institute: McGill University

data_processing:
Reads were downsampled to an equivalent number of reads per sample using seqtk sample (version 1.2)
Adaptors were trimmed with trimmomatic (version 0.39) [1] with the options ILLUMINACLIP:Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:24
Reads were then aligned to the mouse genome (mm10) with bowtie2 (version 2.4.4) using default parameters
Duplicates were removed with picard through gatk MarkDuplicates (version 4.2.5.0)
Peak detection was performed using macs2 callpeak (version 2.2.7.1) with the parameters “-g mm --qvalue 0.05 --shift 100 --extsize 200 --format BAMPE --keep-dup=all --cutoff-analysis –bdg’’.
Assembly: mm10
Supplementary files format and content: bedgraph data files for each sample

source_name: Cortex

growth_protocol: Mice were co-housed with littermates (2-5 per cage) in a temperature-controlled (22-24 °C) and humidity-controlled (40-60%) environment on a 12-hour light/dark cycle with ad libitum food and water.

extract_protocol:
For adult mouse brains, the Adult Brain Dissociation Kit (Miltenyi Biotec), was used. After myelin removal, total cells were counted to proceed to the MACS step. Cell suspensions containing approximately 1x10E6 cells were labeled with superparamagnetic MicroBeads coupled to antibodies specific for the astrocyte marker ACSA-2 (Anti-ACSA-2 MicroBead Kit, mouse; Miltenyi Biotec). Before antibody labeling, nonspecific binding to the Fc receptor was blocked using the FcR Blocking Reagent, mouse (Miltenyi Biotec). Cells were suspended in PBS with 0.5% BSA and the cell suspension was loaded onto an MS Column (Miltenyi Biotec), which was placed in the magnetic field of a MiniMACSTM Separator (Miltenyi Biotec). The magnetically labeled ACSA-2-positive cells were retained within the column and eluted as the positively selected cell fraction after removing the column from the magnet.
For ATAC-sequencing, approximately 100.000 cells were extracted, and library preparation was performed according to the instructions provided in the ATAC-Seq Kit (Active Motif 53150).

treatment_protocol: Lipopolysaccharide (Sigma, L2880) was injected intraperitoneally into mice between 2 to 3 months old at a dose of 5 mg/kg, diluted in endotoxin-free physiological saline (Teligent). Seventy-two hours post LPS injection, 2-3-month-old mice were transcardialy perfused under deep anesthesia with 1 × PBS, and then the brain was removed, dissected, and rinsed. Cortical and hippocampal tissue was isolated and dissected with the gentleMACS Octo Dissociator (Miltenyi Biotec) according to the manufacturer's instructions.

tag: tissue

value: Cortex

value: astrocyte enriched samples

value: Astrocyte cKO LPS 1

value: Lipopolysaccharide


title: VCaP_input_ML792-DHT_rep4

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding input sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: VCaP

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: VCaP cells were treated either with vehicle (EtOH) or 100 nM of dihydrotestosterone (DHT) for 1 h before the start of ChIPs. Before EtOH or DHT treatment, the cells were treated either with vehicle (DMSO) or SAE inhibitor (ML792) for 24 h prior ChIPs.

value: Vertebral Cancer of the Prostate

value: VCaP

tag: treatment


title: RWPE1_RNA_ML792-EtOH_rep3

value: Immortalized human prostatic epithelial cells

tag: cell line

value: ML792 + EtOH


title: Cortex, LPS, 3days, astrocyte cKO C2

tag: cell type

value: Astrocyte cKO LPS 2


title: Cortex, LPS, 3days, control B3

value: Control LPS 3


title: BALI10, BAL

value: BAL

value: Mexico City

value: F

value: IPF

tag: smoking status

value: Former

tag: dlco


title: VCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep4

data_processing:
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR v2.7.8a
Read count extraction and normalization were performed using R packages DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: LNCaP cells (130,000 cells/well) were seeded in 6-well plates in RPMI 1640  supllemented with 8% charcoal dextran treated FBS(CFS). For VCaP cell line (300,000 cells/well), cells were seeded in 6-well plates in DMEM (8% CFS). 48 hrs later, cells were treated with R1881 for an additional 24 hrs

extract_protocol:
Total RNA were isolated using the Aurum™ Total RNA Mini-Kit according to the manufacturer’s instructions (Bio-Rad).
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit.

treatment_protocol: LNCaP and VCaP cells were tretaed with vehicle, increasing concentrations of low-dose (0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hours

value: Prostate

value: epithelial

tag: compound

value: Vehicle

tag: dose

value: 0 nM

value: 24 hours


title: RWPE1_RNA_ML792-EtOH_rep2

tag: time


title: Cortex, LPS, 3days, control B2

value: Cortex

value: astrocyte enriched samples

tag: genotype

value: Control LPS 2

value: Lipopolysaccharide


title: BALHN4, BAL

tag: cohort

value: M

value: NFHP


title: RWPE1_RNA_ML792-EtOH_rep1

value: Immortalized human prostatic epithelial cells

value: ML792 + EtOH

tag: concentration


title: Cortex, LPS, 3days, control B1

value: Control LPS 1


title: Cortex, LPS, 3days, astrocyte cKO C3

value: Astrocyte cKO LPS 3


title: BALHN3, BAL

value: BAL

value: Mexico City

tag: samples multiplexed_(chicago_only)

value: F


title: VCaP, R1881, 10 nM, 24 hours, RNA, Rep4

value: Prostate

value: VCaP

value: epithelial

value: 10 nM


title: BALHN2, BAL

value: Never


title: RWPE1_RNA_DMSO-DHT_rep3

value: DMSO + DHT


title: Cortex, Saline, 3days, control A3

value: Cortex

value: astrocyte enriched samples

value: Control Saline 3


title: BALI3, BAL

value: M

value: IPF

value: Former


title: VCaP, R1881, 10 nM, 24 hours, RNA, Rep2

value: 24 hours


title: RWPE1_RNA_DMSO-DHT_rep2

value: Immortalized human prostatic epithelial cells


title: VCaP, R1881, 10 nM, 24 hours, RNA, Rep1


title: Cortex, Saline, 3days, control A2

value: Control Saline 2

value: Lipopolysaccharide


title: BALHN1, BAL

value: BAL

value: Mexico City

value: F

value: NFHP


title: Cortex, Saline, 3days, control A1

value: Control Saline 1


title: BALHF6, BAL

value: FHP

value: Never


title: Microglia-Cortex, Saline, 3days, cKO Saline Sample C3

data_processing:
Raw reads were trimmed using Trimmomatic. FastQC (Babraham Bioinformatics) was used before and after trimming to assess quality control.
Reads were aligned to the murine reference genome (mm10) using the STAR aligner tool. MultiQC (v1.12) was used to assess the quality of alignment. All aligned samples showed more than 89% uniquely mapped reads.
reads were counted using the FeatureCounts package
Expected gene count quantifications from RSEM analysis were imported into R for differential gene analysis using edgeR (v.3.30.3)
The Goseq tool was used to acquire overrepressented gene categories
Assembly: mm10
Supplementary files format and content: DESeq2 outputed differential gene expression files
Supplementary files format and content: DESeq2 outputed normalized counts

extract_protocol:
For adult mouse brains, the Adult Brain Dissociation Kit (Miltenyi Biotec), was used. After myelin removal, total cells were counted to proceed to the MACS step. Cell suspensions containing approximately 1x10E6 cells were labeled with superparamagnetic MicroBeads coupled to antibodies specific for the astrocyte marker ACSA-2 (Anti-ACSA-2 MicroBead Kit, mouse; Miltenyi Biotec). Before antibody labeling, nonspecific binding to the Fc receptor was blocked using the FcR Blocking Reagent, mouse (Miltenyi Biotec). Cells were suspended in PBS with 0.5% BSA and the cell suspension was loaded onto an MS Column (Miltenyi Biotec), which was placed in the magnetic field of a MiniMACSTM Separator (Miltenyi Biotec). The magnetically labeled ACSA-2-positive cells were retained within the column and eluted as the positively selected cell fraction after removing the column from the magnet. Subsequently, the negatively selected fraction was incubated with Anti-CD11b Magnetic Microbeads (130–093-634, Miltenyi Biotec) in PBS with 0.5% BSA. The cell suspension was loaded onto an MS Column (Miltenyi Biotec), which was placed in the magnetic field of a MiniMACSTM Separator (Miltenyi Biotec). The magnetically labeled CD11b-positive cells were retained within the column and eluted as the positively selected cell fraction after removing the column from the magnet
Library was constructed using the Illumina Stranded mRNA prep, according to the manufacturers instructions

value: Cortex

value: microglia

value: Astrocyte cKO LPS 3


title: VCaP, R1881, 0.06 nM, 24 hours, RNA, Rep4

value: Prostate

value: VCaP

value: epithelial


title: VCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep2

value: Vehicle

value: 0 nM

value: 24 hours


title: BALHF5, BAL

value: Former


title: BALHF4, BAL

value: BAL


title: VCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep1


title: VCaP, R1881, 0.06 nM, 24 hours, RNA, Rep2


title: VCaP, R1881, 0.06 nM, 24 hours, RNA, Rep1


title: RWPE1_RNA_DMSO-EtOH_rep2

value: Immortalized human prostatic epithelial cells

value: DMSO + EtOH


title: BALHF3, BAL

value: Mexico City

value: F


title: RWPE1_RNA_DMSO-EtOH_rep1


title: Microglia-Cortex, Saline, 3days, cKO Saline Sample C1

value: Astrocyte cKO LPS 1

value: Lipopolysaccharide


title: VCaP, R1881, 0.03 nM, 24 hours, RNA, Rep4


title: LNCaP_RNA_ML792-DHT_rep2

source_name: LNCaP

value: Lymph Node Carcinoma of the Prostate

value: LNCaP

value: ML792 + DHT


title: LNCaP_RNA_ML792-DHT_rep3


title: BALHF2, BAL

value: FHP

value: Never


title: BALHF1, BAL

value: M


title: RWPE1_RNA_DMSO-DHT_rep1

value: DMSO + DHT


title: Microglia-Cortex, Saline, 3days, Control LPS Sample B2

value: Cortex

value: microglia

value: Control LPS 2


title: RWPE1_RNA_DMSO-EtOH_rep3


title: VCaP, R1881, 0.03 nM, 24 hours, RNA, Rep1

value: Prostate

value: VCaP

value: epithelial

value: 24 hours


title: Microglia-Cortex, Saline, 3days, Control LPS Sample B1

value: Control LPS 1


title: VCaP, R1881, 0.01 nM, 24 hours, RNA, Rep4


title: IPFM8, PBMC

source_name: PBMC

value: PBMC

value: Mexico City

value: IPF

value: Former


title: IPFM9, PBMC


title: LNCaP_RNA_ML792-EtOH_rep3

value: Lymph Node Carcinoma of the Prostate

value: LNCaP

value: ML792 + EtOH


title: Microglia-Cortex, Saline, 3days, cKO Saline Sample C2

value: Astrocyte cKO LPS 2

value: Lipopolysaccharide


title: LNCaP_RNA_ML792-EtOH_rep2


title: VCaP, R1881, 0.01 nM, 24 hours, RNA, Rep2


title: VCaP, R1881, 0.01 nM, 24 hours, RNA, Rep1


title: LNCaP_RNA_ML792-EtOH_rep1


title: LNCaP_RNA_DMSO-DHT_rep3

value: DMSO + DHT


title: Microglia-Cortex, Saline, 3days, Control LPS Sample B3

value: Cortex

value: microglia

value: Control LPS 3


title: Microglia-Cortex, Saline, 3days, Control Saline Sample A1

value: Control Saline 1

value: Saline


title: IPFM3, PBMC

value: F


title: VCaP, R1881, 0.03 nM, 24 hours, RNA, Rep2

value: Prostate

value: VCaP

value: epithelial

value: 24 hours


title: LNCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep4

value: Vehicle

value: 0 nM


title: Cortex, Saline, 3days, cKO LPS Sample N14

description:
lps_results_df (wt_lps_vs_ko_lps).csv
veh_ko_lps_(ko_vs_ko_lps).csv
veh_wt_lps_results_df_(wt_vs_wt_lps).csv

data_processing:
Adapter sequences, low base call quality (Phred score <30), and reads with fewer than 5 bases, were trimmed from all FASTQ files using Cutadapt (v3.5)
STAR (Dobin et al., Bioinformatics, 2012, DOI: 10.1093/bioinformatics/bts635) aligner was used to align trimmed sequences to the mouse reference genome (GRCm39) with gene annotations from mouse Gencode (vM28)
Gene count quantifications were analyzed using RSEM (RNA-Seq by Expectation Maximization; v.1.3.1)
Expected gene count quantifications from RSEM analysis were imported into R for differential gene analysis using edgeR (v.3.30.3)
Functional pathway analysis was performed using Metascape (Zhou et al., Nature Communications, 2019, DOI: 10.1038/s41467-019-09234-6), gProfiler (Reimand et al., R package version 0.67, 2018; https://cran.r-project.org/web/packages/gProfileR/gProfileR.pdf), and ClusterProfiler
Assembly: GRCm39
Supplementary files format and content: EdgeR outputed differential gene expression files

extract_protocol:
Total RNA was extracted from dissected cortexes of LPS-treated animals from both genotypes, using the RNeasy mini kit (QIAGEN, 74104) following the standard user manual.
Total RNA was isolated from mouse brain tissues and was processed using TruSeq ribodepleted mRNA stranded for library preparation (Illumina, 20020594)

treatment_protocol: Lipopolysaccharide (Sigma, L2880) was injected intraperitoneally into mice between 4 to 6 months old at a dose of 5 mg/kg, diluted in endotoxin-free physiological saline (Teligent). Seventy-two hours post LPS injection, brain tissues from mice were directly harvested and dissected and were kept at -80°C for mRNA and protein assays.

value: bulk

value: Astrocyte cKO LPS 5


title: LNCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep2

value: LNCaP


title: LNCaP_RNA_ML792-DHT_rep1

value: Lymph Node Carcinoma of the Prostate

value: ML792 + DHT


title: CE10, PBMC

value: PBMC

value: New Haven

value: M

value: Control


title: IPFM10, PBMC

value: Mexico City

value: IPF

value: Former


title: Cortex, Saline, 3days, cKO LPS Sample M13

value: Cortex

value: Astrocyte cKO LPS 4

value: Lipopolysaccharide


title: LNCaP_RNA_DMSO-DHT_rep2

value: DMSO + DHT


title: LNCaP_RNA_DMSO-DHT_rep1


title: LNCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep3

value: Prostate

value: epithelial

value: Vehicle

value: 0 nM

value: 24 hours


title: Microglia-Cortex, Saline, 3days, Control Saline Sample A3

value: microglia

value: Control Saline 3

value: Saline


title: CE8, PBMC

value: PBMC

value: New Haven

value: F


title: CE7, PBMC

value: M

value: Control


title: LNCaP, R1881, 10 nM, 24 hours, RNA, Rep4

value: LNCaP

value: 10 nM


title: Cortex, Saline, 3days, cKO LPS Sample F6

value: Cortex

value: bulk

value: Astrocyte cKO LPS 3

value: Lipopolysaccharide


title: LNCaP, R1881, 10 nM, 24 hours, RNA, Rep3

value: Prostate

value: epithelial


title: IPFM7, PBMC

value: Mexico City

value: IPF

value: Former


title: LNCaP_RNA_DMSO-EtOH_rep3

value: Lymph Node Carcinoma of the Prostate

value: DMSO + EtOH


title: Cortex, Saline, 3days, cKO LPS Sample E5

value: Astrocyte cKO LPS 2


title: LNCaP_RNA_DMSO-EtOH_rep2


title: Microglia-Cortex, Saline, 3days, Control Saline Sample A2

value: microglia

value: Control Saline 2

value: Saline


title: CE6, PBMC

value: PBMC

value: New Haven

value: M

value: Control


title: Cortex, Saline, 3days, cKO LPS Sample D4

value: Cortex

value: bulk

value: Astrocyte cKO LPS 1


title: LNCaP, R1881, 10 nM, 24 hours, RNA, Rep2

value: Prostate

value: LNCaP

value: epithelial

value: 10 nM

value: 24 hours


title: LNCaP_RNA_DMSO-EtOH_rep1

value: Lymph Node Carcinoma of the Prostate

value: DMSO + EtOH


title: CE5, PBMC

value: F


title: Cortex, Saline, 3days, Control LPS Sample L12

value: Control LPS 5

value: Lipopolysaccharide


title: VCaP_RNA_ML792-DHT_rep3

value: Vertebral Cancer of the Prostate

value: VCaP

value: ML792 + DHT


title: LNCaP, R1881, 0.1 nM, 24 hours, RNA, Rep4


title: Cortex, Saline, 3days, Control LPS Sample K11

value: Control LPS 4


title: IPFE10, PBMC

value: PBMC

value: New Haven

value: M

value: IPF

value: Current


title: LNCaP, R1881, 0.1 nM, 24 hours, RNA, Rep2

value: Prostate

value: LNCaP

value: epithelial


title: VCaP_RNA_ML792-DHT_rep2


title: IPFE9, PBMC

value: Former


title: LNCaP, R1881, 0.06 nM, 24 hours, RNA, Rep4

value: 24 hours


title: Cortex, Saline, 3days, Control LPS Sample C3

value: Cortex

value: bulk

value: Control LPS 3


title: LNCaP, R1881, 0.1 nM, 24 hours, RNA, Rep3


title: VCaP_RNA_ML792-EtOH_rep3

value: Vertebral Cancer of the Prostate

value: ML792 + EtOH


title: Cortex, Saline, 3days, Control LPS Sample B2

value: Control LPS 2

value: Lipopolysaccharide


title: IPFE7, PBMC

value: PBMC


title: Cortex, Saline, 3days, Control LPS Sample A1

value: Control LPS 1


title: VCaP_RNA_ML792-EtOH_rep2

value: VCaP


title: Cortex, Saline, 3days, cKO Saline Sample 8

value: Astrocyte cKO Saline 4

value: Saline


title: LNCaP, R1881, 0.06 nM, 24 hours, RNA, Rep3

value: Prostate


title: LNCaP, R1881, 0.06 nM, 24 hours, RNA, Rep2

value: LNCaP


title: IPFE5, PBMC

value: New Haven

value: F

value: IPF

value: Never


title: VCaP_RNA_ML792-EtOH_rep1


title: IPFE6, PBMC

value: M

value: Current


title: Cortex, Saline, 3days, cKO Saline Sample 6

value: Cortex

value: bulk

value: Astrocyte cKO Saline 3


title: LNCaP, R1881, 0.03 nM, 24 hours, RNA, Rep4

value: epithelial

value: 24 hours


title: VCaP_RNA_DMSO-DHT_rep3

value: Vertebral Cancer of the Prostate

value: DMSO + DHT


title: Cortex, Saline, 3days, cKO Saline Sample 4

value: Astrocyte cKO Saline 2


title: VCaP_RNA_ML792-DHT_rep1

value: VCaP

value: ML792 + DHT


title: LNCaP, R1881, 0.03 nM, 24 hours, RNA, Rep3

value: Prostate

value: LNCaP


title: IPFE4, PBMC

value: PBMC

value: New Haven

value: F


title: VCaP_RNA_DMSO-DHT_rep2


title: IPFE3, PBMC

value: M

value: IPF

value: Never


title: IPFE8, PBMC

value: Former


title: Cortex, Saline, 3days, cKO Saline Sample 2

value: Cortex

value: bulk

value: Astrocyte cKO Saline 1

value: Saline


title: VCaP_RNA_DMSO-DHT_rep1

value: Vertebral Cancer of the Prostate

value: DMSO + DHT


title: Cortex, Saline, 3days, Control Saline Sample 7

value: Control Saline 4


title: LNCaP, R1881, 0.03 nM, 24 hours, RNA, Rep2

value: epithelial

value: 24 hours


title: VCaP_RNA_DMSO-EtOH_rep3

value: VCaP

value: DMSO + EtOH


title: VCaP, Vehicle_CFS, 0, 24 hours, Rep4

data_processing:
ATAC-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39.
Trimmed ATAC-seq reads were aligned to GRCh38/hg38 using BWA v0.7.17. Reads that were unaligned, multi-mapped, failed platform quality checks or had mapping quality less than 30 were removed.
Peaks were called and narrowPeak files were generated using MACS v2.2.7.1 with --pvalue 0.01, --keep-dup all, --call-summits, and -f BAMPE
BigWig files were generated using bamCoverage v3.5.1 from Deeptools suite, with --normalizeUsing RPGC, --binSize 10, --minFragmentLength 40, --effectiveGenomeSize 2701495761.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
The OMNI protocol was followed for ATAC-seq: https://doi.org/10.1038/nmeth.4396
ATAC-seq libraries were prepared using Nextera DNA Library Prep Kit.

value: Prostate

value: Vehicle

value: 0 nM


title: IPFE2, PBMC

value: PBMC

value: New Haven

value: M

value: IPF


title: IPFE1, PBMC

value: F

value: Never


title: VCaP, Vehicle_CFS, 0, 24 hours, Rep2


title: HPM9, PBMC

value: Mexico City

value: FHP


title: VCaP_RNA_DMSO-EtOH_rep2

value: Vertebral Cancer of the Prostate


title: Cortex, Saline, 3days, Control Saline Sample 1

value: Cortex

value: bulk

value: Control Saline 1

value: Saline


title: Cortex, Saline, 3days, Control Saline Sample 3

value: Control Saline 2


title: VCaP, Vehicle_CFS, 0, 24 hours, Rep1

value: Prostate

value: VCaP

value: epithelial

value: 24 hours


title: VCaP_input_ML792_rep2

value: ML792 + DHT

tag: chip antibody


title: HPM8, PBMC

value: PBMC

tag: age (singleton or multiplexed)

value: M


title: VCaP_input_ML792_rep1


title: HPM4, PBMC

tag: sex (singleton or multiplexed)

value: F


title: colon, colitis, NPM1KO_3

city: Suzhou

first: Minxuan

last: Sun

address: Keling Road

institute: Chinese Academy of Sciences

data_processing:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: ILC3 sorted from colon of mice with colitis

value: group 3 innate lymphoid cells


title: VCaP, R1881, 10 nM, 24 hours, Rep4

value: 10 nM


title: VCaP, R1881, 10 nM, 24 hours, Rep2


title: VCaP_SUMO2_ML792-DHT_rep2

value: Vertebral Cancer of the Prostate

value: SUMO-2/3 (MBL International, M114-3)


title: HPM1, PBMC

value: Mexico City

tag: disease (singleton or multiplexed)

value: FHP

value: Former


title: VCaP_input_DMSO_rep1

value: DMSO + DHT


title: colon, colitis, NPM1KO_2

tag: tissue


title: HPE9, PBMC

value: New Haven


title: Cortex, Saline, 3days, Control Saline Sample 5

value: Cortex

value: bulk

value: Control Saline 3

tag: treatment

value: Saline


title: VCaP, R1881, 10 nM, 24 hours, Rep1

value: Prostate

tag: cell line

value: VCaP

value: epithelial

value: 24 hours


title: VCaP_SUMO2_ML792-DHT_rep1

tag: cell type

value: ML792 + DHT


title: colon, colitis, NPM1KO_1

value: colon

value: ILC3 sorted from colon of mice with colitis

value: group 3 innate lymphoid cells


title: HPE8, PBMC

value: PBMC

value: F

tag: smoking status

value: Never


title: VCaP_SUMO2_ML792-EtOH_rep2

value: Vertebral Cancer of the Prostate

value: ML792 + EtOH

value: SUMO-2/3 (MBL International, M114-3)


title: VCaP, R1881, 0.06 nM, 24 hours, Rep2


title: colon, colitis, WT_3

value: WT


title: HPE7, PBMC

value: New Haven

value: M

value: FHP

tag: dlco


title: colon, colitis, WT_2


title: VCaP_SUMO2_ML792-EtOH_rep1

value: VCaP


title: VCaP, R1881, 0.06 nM, 24 hours, Rep1

value: Prostate

value: epithelial

tag: compound


title: colon, colitis, WT_1


title: HPE6, PBMC

value: Former


title: VCaP_SUMO2_DMSO-DHT_rep1

value: DMSO + DHT


title: VCaP_SUMO2_DMSO-DHT_rep2


title: HPE5, PBMC


title: VCaP, R1881, 0.03 nM, 24 hours, Rep4

tag: dose

value: 24 hours


title: HPE3, PBMC


title: Tet1, Cortex, RNASeq, KO Rep3

city: Philadelphia

first: Yee Hoon

last: Foong

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Quality of raw reads were assessed using FastQC
Raw reads were quality-trimmed Using Trim Galore (v0.6.7)
Reads were aligned to GRCm39 (mm10) using STAR (v2.7.1a) with default parameters
Properly paired primary alignments were retained for downstream analysis using Samtools (v1.9)
Count matrices were generated using stringtie 2.2.3 against RefSeq gene annotation
Assembly: mm10
Supplementary files format and content: Tet1_count_table.csv

source_name: Adult Cortex

extract_protocol:
Total RNA was extrated using Quick RNA Microprep Kit by Zymo Research from whole cortex
mRNA library was generated using Oligo d(T)25 RNA Magnetic Isolation Module followed by UltraII RNA Library Prep Kit (NEB) following manufacturer's protocol

value: Adult Cortex

value: KO


title: Tet1, Cortex, RNASeq, KO Rep4


title: VCaP_SUMO2_DMSO-EtOH_rep1

value: DMSO + EtOH

tag: time


title: Tet1, Cortex, RNASeq, KO Rep2

tag: genotype


title: HPE2, PBMC

value: PBMC

tag: cohort

value: F

value: Never


title: VCaP, R1881, 0.03 nM, 24 hours, Rep1


title: VCaP, R1881, 0.01 nM, 24 hours, Rep4


title: VCaP, R1881, 0.06 nM, 24 hours, Rep4


title: Tet1, Cortex, RNASeq, KO Rep1


title: VCaP_AR_ML792-DHT_rep2

value: Vertebral Cancer of the Prostate

value: ML792 + DHT

tag: concentration

value: AR (rabbit antiserum; Karvonen et al. 1997)


title: VCaP_AR_ML792-DHT_rep1


title: HPE1, PBMC

value: New Haven

tag: samples multiplexed_(chicago_only)

value: M


title: VCaP, R1881, 0.01 nM, 24 hours, Rep1

value: VCaP


title: VCaP, R1881, 0.03 nM, 24 hours, Rep2

value: Prostate


title: CM10, PBMC

value: Mexico City

value: Control

value: Current


title: CM8, PBMC


title: Tet1, Cortex, RNASeq, HxD Rep3

value: HxD


title: VCaP_AR_DMSO-DHT_rep2

value: DMSO + DHT

tag: chip antibody


title: CM9, PBMC

tag: age (singleton or multiplexed)


title: Tet1, Cortex, RNASeq, HxD Rep2

value: Adult Cortex


title: CM7, PBMC

tag: sex (singleton or multiplexed)


title: VCaP_AR_DMSO-DHT_rep1


title: Tet1, Cortex, RNASeq, HxD Rep1


title: VCaP_ATAC_ML792-DHT_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >6-fold over local background.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.

treatment_protocol: VCaP cells were treated either with vehicle (EtOH) or 100 nM of dihydrotestosterone (DHT) for 1 h before the start of nuclei extraction for tagmentation. Before EtOH or DHT treatment, the cells were treated either with vehicle (DMSO) or SAE inhibitor (ML792) for 24 h prior extraction.


title: VCaP_SUMO2_DMSO-EtOH_rep2

value: DMSO + EtOH

value: SUMO-2/3 (MBL International, M114-3)


title: Tet1, Cortex, RNASeq, WT Rep4

value: WT


title: LNCaP, Vehicle_CFS, 0, 24 hours, Rep3

value: LNCaP

value: epithelial

value: Vehicle

value: 0 nM

value: 24 hours


title: CM6, PBMC

value: PBMC

value: M

tag: disease (singleton or multiplexed)

value: Never


title: CM5, PBMC

tag: tissue

value: Mexico City

value: F


title: VCaP_ATAC_ML792-EtOH_rep1

value: Vertebral Cancer of the Prostate

value: VCaP

tag: treatment

value: ML792 + EtOH


title: VCaP_ATAC_ML792-DHT_rep1

tag: cell line

value: ML792 + DHT


title: Tet1, Cortex, RNASeq, HxD Rep4

value: Adult Cortex

value: HxD


title: LNCaP, R1881, 10 nM, 24 hours, Rep4

value: Prostate

tag: cell type

value: 10 nM


title: Tet1, Cortex, RNASeq, WT Rep2

value: WT


title: CM4, PBMC

value: Control

tag: smoking status

value: Current


title: LNCaP, Vehicle_CFS, 0, 24 hours, Rep5

value: LNCaP

value: epithelial

value: Vehicle

value: 0 nM

value: 24 hours


title: LNCaP, R1881, 10 nM, 24 hours, Rep3


title: VCaP_ATAC_DMSO-DHT_rep2

value: DMSO + DHT


title: LNCaP, Vehicle_CFS, 0, 24 hours, Rep4


title: CM3, PBMC

value: PBMC

value: Mexico City

value: M

tag: dlco


title: Tet1, Cortex, RNASeq, WT Rep1


title: VCaP_ATAC_DMSO-DHT_rep1

value: Vertebral Cancer of the Prostate

value: VCaP


title: LNCaP, R1881, 0.1 nM, 24 hours, Rep5

tag: compound


title: VCaP_ATAC_DMSO-EtOH_rep2

value: DMSO + EtOH


title: CM2, PBMC


title: Single-cell RNA sequencing of CD45-positive and CD45 negative cells from Trex1-IFNGR1-DKO lungs

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

description: Singleron GEXSCOPE

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Assembly: mmu_ensembl_99
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung

extract_protocol:
After lung digestion, CD45 fluorescent antibody and zombie NIR were labeled and both CD45 positive and negative cells were obtained by flow sorting technique, and the single cell bank was constructed after PBS cleaning.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

value: lung


title: Single-cell RNA sequencing of CD45-positive and CD45 negative cells from cGas-KI/+;Vav-icre lungs

description: Singleron GEXSCOPE

tag: genotyp

value: cGas-KI/+;Vav-icre


title: LNCaP, R1881, 0.1 nM, 24 hours, Rep4

value: Prostate

tag: dose

tag: time


title: VCaP_ATAC_DMSO-EtOH_rep1


title: LNCaP, R1881, 10 nM, 24 hours, Rep5

value: 10 nM


title: VCaP, Vehicle_CFS, 0, 24 hours, Input, Rep2

value: Input


title: Tet1, Cortex, RNASeq, WT Rep3

value: Adult Cortex

tag: genotype

value: WT


title: LNCaP, R1881, 0.1 nM, 24 hours, Rep3

value: LNCaP

value: epithelial


title: LNCaP, R1881, 0.06 nM, 24 hours, Rep5

value: 24 hours


title: PHD2/3 KO HYP 3

city: Brussels

first: Jingjing

last: Zhu

address: Avenue Hippocrate 74

country: Belgium

institute: de Duve Institute/Ludwig Institute for Cancer Research

data_processing:
Fastq files were processed withTrimmomatic-0.38 to remove low quality reads.
hisat2-2.1.0 was used to align reads to the mouse genome (grcm38).
The matrix of raw counts was generated using featureCounts from subread-2.0.0 and Mus_musculus.GRCm38.94.gtf
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: TCRP1A CD8 T lymphocyte

growth_protocol: TCRP1A CD8 T cells were isolated from spleen of TCRP1A female mice using anti-mouse CD8α (Ly-2) MicroBeads, and co-cultured with irradiated L1210.P1A.B7-1 cells at 1:2 ratio in IMDM medium containing b-mercaptoethanol (50 μM), 10% fetal bovin serum, L-Arginine (0.55 mM), L-asparagine (0.24 mM), Glutamine (1.5 mM), 50 U/mL penicillin and 50 mg/mL streptomycin (37°C, 8% CO2).

extract_protocol:
HIF-1αKO, PHD2/3 KO and control TCRP1A CD8 T cells were collected, washed twice in cold PBS. Total RNA was extracted using NucleoSpin RNA kit (Macherey Nagel) according to the manufacturer’s instructions.
Libraries were prepared using TruSeq stranded mRNA libary kit.

treatment_protocol: Alive CD8 T cells were enriched, nucleofecte and then cultured in presence of rhIL-2 (25 U/mL) at 21% or 1% O2 for 48 hours.

value: TCRP1A CD8 T lymphocyte

value: activated and nucleofected CD8 T cell were incubated in  hypoxia  for 48 hours


title: PHD2/3 KO HYP 2


title: Single-cell RNA sequencing of CD45-positive and CD45 negative cells from WT lungs

description: Singleron GEXSCOPE


title: VCaP, Vehicle_CFS, 0, 24 hours, Input, Rep1


title: LNCaP, R1881, 0.06 nM, 24 hours, Rep4


title: VCaP, Vehicle_CFS, 0, 24 hours, AR, Rep2

value: AR


title: VCaP, R1881, 0.01 nM, 24 hours, Rep2


title: LNCaP, R1881, 0.06 nM, 24 hours, Rep3


title: PHD2/3 KO HYP 1


title: HIF1A KO HYP 3


title: LNCaP, R1881, 0.03 nM, 24 hours, Rep5


title: VCaP, R1881, 10 nM, 24 hours, Input, Rep2


title: dpi4_GA_1

city: Rehovot

first: Jacob

middle: Kobi

last: Elkahal

address: Herzl St 234

department: Molecular cell biology

country: Israel

institute: Weizmann Institute od Science

data_processing:
The demultiplexing, barcoded processing and gene counting were made using cellranger
Assembly: mm10
Supplementary files format and content: 10x counts: zipped folder of tab-separated values files and matrix files from cellranger

source_name: Heart Injured area

extract_protocol:
Tissue was dissociated into single-cell suspension using a neonatal dissociation kit (Miltenyi Biotec,130-098-373) and the gentleMACS homogenizer, according to the manufacturer’s instructions.
Library was prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

treatment_protocol: Adult female mice underwent a permanent left anterior descending ligation in the heart's left ventricle. The mice were divided into two groups receiving either GA (2 mg/animal/day) or control (PBS / mannitol) by daily IP injections from day 0 (day of MI) up to 4 days post-injury.

value: Heart Injured area

value: cardiac cells (CD45+ enriched)

value: Glatiramer Acetate

tag: time point

value: 4 day post injury


title: CM1, PBMC

value: PBMC

tag: cohort

value: Mexico City

tag: samples multiplexed_(chicago_only)

value: F

value: Control

value: Current


title: HIF1A KO HYP 2


title: dpi4_GA_2


title: Single-cell RNA sequencing of CD45-positive and CD45 negative cells from Trex1 KO lungs

description: Singleron GEXSCOPE

value: lung


title: VCaP, R1881, 10 nM, 24 hours, Input, Rep1

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39.
Trimmed ChIP-seq reads were aligned to GRCh38/hg38 using BWA v0.7.17. Reads that were unaligned, multi-mapped, failed platform quality checks or had mapping quality less than 30 were removed.
Peaks were called and narrowPeak files were generated using MACS v2.2.7.1 with --pvalue 0.01, --keep-dup all, --call-summits, and -f BAMPE
BigWig files were generated using bamCoverage v3.5.1 from Deeptools suite, with --normalizeUsing RPGC, --binSize 10, --minFragmentLength 40, --effectiveGenomeSize 2701495761.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
Cells were fixed using a final concentration of 1% methanol-free formaldehyde in PBS at for 10 min and quenched with 125mM glycine for 5 min. Cells were then washed twice in PBS Wash Buffer (Active Motif #53046), pelleted, and stored at -80˚C. For sonication, cells were thawed and resuspended in ice cold Buffer LB1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail (ThermoFisher #78446) on a rotator at 4˚C for 10 minutes. Cells were then centrifuged, liquid decanted, and resuspended in Buffer LB2 (10mM Tris-HCL pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail. Cells were then centrifuged, liquid decanted and resuspended in ice cold Buffer LB3 (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-laurylsarcosine) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail. This nuclear resuspension was transferred into Covaris microtube 130 AFA Fiber pre-Slit snap-cap tubes (Covaris #520045) at a maximum concentration of 3 million cells per 130µL and sonicated using the following parameters on a Covaris ME220 according to the manufacturer’s recommendations (Duration (s) = 360, Peak Power = 75, Duty Factor = 5.0, Cycles/Burst = 1000). Following sonication, 10µL of chromatin was removed for analysis of resulting DNA size and concentration. Briefly, 10µL of sonicated chromatin was incubated with 20µg RNase A (Thermo Scientific #EN0531) in TE pH 8 for 30 minutes at 37˚C in a thermal cycler. 20µg of Proteinase K (Thermo Scientific #EO0491) in Active Motif Elution Buffer AM4 (Active Motif #103926) was then added and the sample was incubated for 30 minutes at 55˚C followed by 90 minutes at 65˚C in a thermal cycler. Samples were then cooled to room temperature and DNA was purified using SPRIselect beads (Beckman #B23318) at a bead:sample ratio of 1.4:1 and eluted in 10µL of 10 mM Tris, 0.1 mM EDTA.
Chromatin corresponding to 1 million cells was diluted with 200µL in Active Motif ChIP Buffer and incubated with pre-clearing Protein G agarose beads. After pre-clearing, agarose beads were pelleted and transferred to a new microcentrifuge tube containing 4µg of antibody specific to the target protein (AR: Abcam ab236225). IPs were then incubated overnight on a rotator at 4˚C. Protein G Agarose beads prepared the previous day according to Active Motif’s Low Cell ChIP kit were added to the antibody-bound chromatin and incubated for 4 hours on a rotator at 4˚C. IPs were then transferred to ChIP filtration columns, washed, and eluted in 80µL according to Active Motif’s Low Cell ChIP kit and DNA purified using SPRIselect beads at a bead:sample ratio of 1.4:1. After SPRI cleanup, ChIP samples and reverse crosslinked input DNA was made into sequencing Illumina libraries using Swift NGS 2S Plus (Swift Biosciences #21096) and indexed using Single Indexed Adapters with MIDs (Swift Biosciences #279384).  ChIP-seq libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit with UMIs.

value: Prostate

value: VCaP

tag: chip antibody

value: Input

value: 10 nM


title: dpi4_Control_2

value: Mannitol


title: LNCaP, R1881, 0.03 nM, 24 hours, Rep4

value: LNCaP

value: epithelial

value: 24 hours


title: dpi4_Control_1

value: Heart Injured area

value: cardiac cells (CD45+ enriched)


title: LNCaP, R1881, 0.03 nM, 24 hours, Rep3


title: VCaP, R1881, 10 nM, 24 hours, AR, Rep2

value: AR


title: SCR HYP 3

value: TCRP1A CD8 T lymphocyte

value: activated and nucleofected CD8 T cell were incubated in  hypoxia  for 48 hours


title: dpi1_GA

value: Glatiramer Acetate

value: 1 day post injury


title: LAA, AF, CF102, snATACseq

description: 10X Genomics

library_source: other

data_processing:
We aligned FASTQ to Cellranger’s GRCh38-2020-A reference using the count function of cellranger-arc-2.0.0 for each sample. We then aggregated all samples using cellranger-arc aggr function. For downstream analyses, we used Seurat v4 and Signac. We kept ATAC peaks present in at least 10 cells. We removed low quality cells using the following thresholds: > 200 detected genes, > 400 detected peaks, <10% mitochondrial reads, > 2 transcription start site enrichment score and > 10% ATAC reads in peaks. We integrated the data using Harmony. We removed doublets using both scDblFinder scores and manual sub-clustering curation. We then re-clustered cells using seurat’s function FindMultiModalNeighbors() with the first 20 PCs of the RNAseq data and PCs 2-20 of the ATACseq data. Finally, we refined ATACseq peaks with cell-type labels using Signac’s CallPeaks function.
Assembly: hg38
Supplementary files format and content: Tab separated values matrix files
Library strategy: Single Cell Multiome ATAC + Gene Expression

molecule: other

source_name: Left atrial appendage

extract_protocol:
Left atrial appendage biopsies were collected before cardiopulmonary bypass and immediately, rinsed of blood, towel-dried and snap-frozen in liquid nitrogen until use for subsequent experiments.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

value: Left atrial appendage

tag: Sex

value: M

tag: rhythm

value: AF


title: VCaP, R1881, 10 nM, 24 hours, AR, Rep1

tag: tissue

value: Prostate

value: VCaP


title: SCR HYP 2

tag: treatment


title: dpi1_Control


title: LAA, AF, CF97, snATACseq

description: 10X Genomics


title: VCaP, R1881, 0.06 nM, 24 hours, Input, Rep2

tag: cell line

value: Input


title: SCR HYP 1

tag: cell type


title: VCaP, Vehicle_CFS, 0, 24 hours, AR, Rep1


title: VCaP, R1881, 0.06 nM, 24 hours, Input, Rep1


title: LAA, AF, CF93, snATACseq

description: 10X Genomics


title: Mafb ko CAMs-03

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description:
N093-43
RawCountTable_N093R0502_Mafb.tsv.gz

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore.
Reads were aligned to GRCm38 reference using HISAT2.
Uniquely mapped reads were counted by featureCounts and UMI duplication was ramoved by using UMI tools.
Assembly: GRCm38
Supplementary files format and content: raw counts, compressed tab separated files (.tsv.gz)

source_name: brain

growth_protocol: 12-20 weeks old mice were bred under SPF conditions.

extract_protocol:
Brains were excised from mice transcardially perfused with PBS and 500 cells each of CD11b+ CD45+ Ly6G- CD206- microglia and CD11b+ CD45+ Ly6G- CD206+ CAMs(CNS associated macrophage) were collected into 30uL of direct lysis buffer (TaKaRa #635013) by CytoFlex SRT(Beckman Coulter, Inc).
Libraries were prepared using 15uL out of 30uL lysate by CEL-Seq2(Hashimshony T et al.) method individually. 10nt of UMI followed by 9nt of cell barcode are in Read1 and 81nt of insert reads are in Read2.

value: brain

value: CNS associated macrophage

value: Mafb-ko


title: Mafb ko CAMs-04

description:
N093-44
RawCountTable_N093R0502_Mafb.tsv.gz


title: PHD2/3 KO NORM 3

value: activated and nucleofected CD8 T cell were incubated in  normoxia  for 48 hours


title: VCaP, R1881, 0.06 nM, 24 hours, AR, Rep2

value: epithelial

value: 24 hours


title: Mafb ko CAMs-02

description:
N093-42
RawCountTable_N093R0502_Mafb.tsv.gz


title: PHD2/3 KO NORM 2


title: LAA, SR, CF91, snATACseq

description: 10X Genomics

value: SR


title: HIF1A KO HYP 1

value: TCRP1A CD8 T lymphocyte


title: LAA, SR, CF89, snATACseq

description: 10X Genomics

value: F


title: PHD2/3 KO NORM 1


title: LAA, SR, CF77, snATACseq

description: 10X Genomics


title: Mafb control CAMs-05

description:
N093-40
RawCountTable_N093R0502_Mafb.tsv.gz

value: Mafb-flox


title: HIF1A KO NORM 3


title: Mafb ko CAMs-01

description:
N093-41
RawCountTable_N093R0502_Mafb.tsv.gz


title: LAA, SR, CF69, snATACseq

description: 10X Genomics


title: Mafb control CAMs-04

description:
N093-39
RawCountTable_N093R0502_Mafb.tsv.gz


title: LAA, AF, CF102, snRNAseq

description: 10X Genomics

molecule: nuclear RNA


title: HIF1A KO NORM 2


title: VCaP, R1881, 0.03 nM, 24 hours, Input, Rep1


title: Mafb control CAMs-03

description:
N093-38
RawCountTable_N093R0502_Mafb.tsv.gz


title: HIF1A KO NORM 1


title: Mafb control CAMs-02

description:
N093-37
RawCountTable_N093R0502_Mafb.tsv.gz


title: VCaP, R1881, 0.03 nM, 24 hours, AR, Rep1

value: AR


title: LAA, AF, CF97, snRNAseq

description: 10X Genomics

value: Left atrial appendage


title: LAA, AF, CF93, snRNAseq

description: 10X Genomics

value: M


title: SCR NORM 3


title: VCaP, R1881, 0.01 nM, 24 hours, Input, Rep2


title: Mafb control CAMs-01

description:
N093-36
RawCountTable_N093R0502_Mafb.tsv.gz


title: SCR NORM 2


title: LAA, SR, CF91, snRNAseq

description: 10X Genomics


title: Mafb ko MG-04

description:
N093-35
RawCountTable_N093R0502_Mafb.tsv.gz

value: microglia


title: VCaP, R1881, 0.03 nM, 24 hours, Input, Rep2

value: Prostate


title: LAA, SR, CF89, snRNAseq

description: 10X Genomics


title: VCaP, R1881, 0.01 nM, 24 hours, Input, Rep1

value: VCaP


title: Mafb ko MG-03

description:
N093-34
RawCountTable_N093R0502_Mafb.tsv.gz


title: SCR NORM 1


title: VCaP, R1881, 0.01 nM, 24 hours, AR, Rep1


title: Mafb ko MG-02

description:
N093-33
RawCountTable_N093R0502_Mafb.tsv.gz


title: MEFs - S6K1/S6K2 DKO Passage 8_SG62

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Primary analysis RTA 2.11.3 and Secondary analysis CASAVA- 2.17
Sequencing was conducted on an Illumina HiSeq 2500 system with 75 base pair single-end reads
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a)
Gene based counting was performed using the STAR aligner (version 2.7.1a) .
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.28.1)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

source_name: Mouse embryonic fibroblasts

extract_protocol:
RNA was then extracted by Trizol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse embryonic fibroblasts

value: Fibroblast

value: S6K1/S6K2 DKO

value: Late passage (P8)


title: VCaP, R1881, 0.03 nM, 24 hours, AR, Rep2


title: VCaP, R1881, 0.01 nM, 24 hours, AR, Rep2


title: MEFs - S6K1/S6K2 DKO Passage 8_SG64


title: LAA, SR, CF77, snRNAseq

description: 10X Genomics


title: Mafb ko MG-01

description:
N093-32
RawCountTable_N093R0502_Mafb.tsv.gz

value: brain

value: Mafb-ko


title: MEFs - S6K1/S6K2 DKO Passage 8_SG61


title: 32-NT-137964

city: HOUSTON

first: Katayoun

last: Rezvani

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description:
BulkATACseq
bulkATAC_rawCount.csv

data_processing:
Cellranger mkfastq v3.01 to generate FASTQ
Cellranger count v3.01 to generate count matrix
Assembly: GRCh38
Supplementary files format and content: [Cellranger files] comprising a MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, features.tsv)

extract_protocol:
Libraries were sequenced  2 x 100 bp on an Illumina NovaSeq6000 to obtain at least 50 million high quality mapping reads per sample.
By applying RNA  and ATAC sequencing, we want to investigate the epigenetic factors that contributing for IL-21-induced memory formation in NK cells

value: CBNK

value: 32-NT-137964 NK cells alone


title: 22RV1 cells, PLEK2 over-expression 3

city: Chicago

first: Xu

last: Han

state: IL

address: 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using "Cutadapt". Then trimmed sequence reads were mapped to GRCh38/hg38 using "STAR". Finally read counts were extracted and normlized.
Assembly: hg38
Supplementary files format and content: xlsx file includes normalized counts for each sample

growth_protocol: 22RV1 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested with TRIzol reagent (Invitrogen). 150ng RNA was used to construct the sequencing library.
RNA libraries for RNA-seq were prepared using Illumina stranded mRNA-seq library prep kit following manufacturer's protocols.

treatment_protocol: PLEK2 over-expression and control plasmids were transfected into 22RV1 cells, and cells were harvested 48 hours after transfection.

value: Prostate cancer cell line

value: PLEK2 OV

value: PLEK2 over-expression


title: 22RV1 cells, PLEK2 over-expression 2


title: Mafb control MG-05

description:
N093-31
RawCountTable_N093R0502_Mafb.tsv.gz

value: Mafb-flox


title: MEFs - S6K1/S6K2 WT Passage 8_SG60

value: S6K1/S6K2 WT


title: 31-CEBPDKO-IL15-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 31-CEBPDKO-IL15-137964 NK cells alone


title: 22RV1 cells, PLEK2 over-expression 1


title: MEFs - S6K1/S6K2 WT Passage 8_SG59


title: Mafb control MG-04

description:
N093-30
RawCountTable_N093R0502_Mafb.tsv.gz

value: microglia


title: 22RV1 cells, Control 3

value: NC

value: Control


title: Mafb control MG-03

description:
N093-29
RawCountTable_N093R0502_Mafb.tsv.gz


title: 30-CEBPDKOIL21-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 30-CEBPDKOIL21-137964 NK cells alone


title: MEFs - S6K1/S6K2 WT Passage 8_SG58

value: Mouse embryonic fibroblasts

value: Fibroblast


title: 29-CEBPD-KI-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 29-CEBPD-KI 137964 NK cells alone


title: 22RV1 cells, Control 2


title: MEFs - S6K1/S6K2 WT Passage 8_SG57

value: Late passage (P8)


title: Mafb control MG-02

description:
N093-28
RawCountTable_N093R0502_Mafb.tsv.gz

value: brain


title: LAA, SR, CF69, snRNAseq

description: 10X Genomics

value: Left atrial appendage

value: F

value: SR


title: 22RV1 cells, Control 1

value: Prostate cancer cell line


title: 28-IL15CEBPD-KI-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: CBNK

value: 28-IL15CEBPD-KI 137964 NK cells alone


title: MEFs - S6K1/S6K2 WT Passage 3_SG48

value: S6K1/S6K2 WT

value: Early passage (P3)


title: Cx3cr1-control-CAMs-03

description:
N093-26
RawCountTable_N093R0502_Irf8.tsv.gz

value: CNS associated macrophage


title: 27-IL15-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 27-IL15-137964 NK cells alone


title: Cx3cr1-control-CAMs-02

description:
N093-25
RawCountTable_N093R0502_Irf8.tsv.gz


title: MEFs - S6K1/S6K2 WT Passage 3_SG50


title: 26-IL21-CEBPD-KI-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 26-IL21-CEBPD-KI-137964 NK cells alone


title: 25-IL21-137964

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 25-IL21-137964 NK cells alone


title: MEFs - S6K1/S6K2 WT Passage 3_SG46

value: Mouse embryonic fibroblasts


title: Cx3cr1-control-MG-03

description:
N093-23
RawCountTable_N093R0502_Irf8.tsv.gz

value: microglia


title: 24-24-NT-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 24-NT-137748 NK cells alone


title: MEFs - S6K1/S6K2 WT Passage 3_SG47

value: Fibroblast


title: Cx3cr1-control-CAMs-01

description:
N093-24
RawCountTable_N093R0502_Irf8.tsv.gz

value: brain


title: MEFs - S6K1 KO Passage 8_SG27

value: S6K1 KO

value: Late passage (P8)


title: 23-CEBPDKOIL15-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 23-CEBPDKOIL15-137748 NK cells alone


title: MEFs - S6K1 KO Passage 8_SG25


title: Cx3cr1-control-MG-01

description:
N093-21
RawCountTable_N093R0502_Irf8.tsv.gz


title: 22-22-CEBPDKOIL21-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 22-CEBPDKOIL21-137748 NK cells alone


title: Irf8 ko CAMs-05

description:
N093-20
RawCountTable_N093R0502_Irf8.tsv.gz


title: 21-CEBPD-KI-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: CBNK

value: 21-CEBPD-KI 137748 NK cells alone


title: MEFs - S6K1 KO Passage 8_SG24


title: Mafb control MG-01

description:
N093-27
RawCountTable_N093R0502_Mafb.tsv.gz

value: Mafb-flox


title: MEFs - S6K1 WT Passage 8_SG23

value: S6K1 WT


title: VCaP, R1881, 0.06 nM, 24 hours, AR, Rep1

value: Prostate

value: VCaP

value: epithelial

value: AR

value: 24 hours


title: 20-IL15CEBPD-KI-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 20-IL15CEBPD-KI-137748 NK cells alone


title: 19-IL15-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 19-IL15-137748 NK cells alone


title: MEFs - S6K1 WT Passage 8_SG22

value: Mouse embryonic fibroblasts

value: Fibroblast


title: Irf8 ko CAMs-04

description:
N093-19
RawCountTable_N093R0502_Irf8.tsv.gz

value: brain

value: CNS associated macrophage


title: Irf8 ko CAMs-03

description:
N093-18
RawCountTable_N093R0502_Irf8.tsv.gz


title: Post 7

city: Pittsburgh

first: Jing

middle: Hong

last: Wang

address: 5117 Centre Ave, Suite 2.35

department: Department of Medicine

institute: University of Pittsburgh

description: Adaptive Biotechnologies’ ImmunoSEQ platform

data_processing:
Processed data file from Immunoseq data analyzer for each sample is submitted
Assembly: mm10
Supplementary files format and content: Processed data files from Immunoseq data analyzer

source_name: Blood

growth_protocol: Cultured C-225 cells were resuspended in sterile PBS and Matrigel in a 1:1 ratio.  Subsequently, 2 million tumor cells were injected subcutaneously into the flank regions of each mouse.

extract_protocol:
PBMCs were isolated from peripheral blood samples collected from C-225 tumor-bearing mice (n=7) on day 102 (pre-PBMC) and day 116 (post-PBMC) after the first tumor inoculation. Each mouse has 2 samples sequenced including pre- and post-PBMC, tumor rechallenge was on day 109.  RBC was lysed and genomic DNA was purified.
ImmunoSEQ mmTCRB Service (Survey)

value: Blood

value: PBMC


title: MEFs - S6K1 WT Passage 8_SG21

value: Late passage (P8)


title: MEFs - S6K1 WT Passage 8_SG19


title: R986-32-32-NT-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

extract_protocol:
Libraries were prepared using Illumina next generation RNA sequencing .
By applying RNA  and ATAC sequencing, we want to investigate the epigenetic factors that contributing for IL-21-induced memory formation in NK cells

value: CBNK

value: 32-NT-137964 NK cells alone


title: 18-18-IL21CEBPD-KI-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 18-IL21CEBPD-KI-137748 NK cells alone


title: Post 4


title: Irf8 control CAMs-05

description:
N093-15
RawCountTable_N093R0502_Irf8.tsv.gz


title: R986-30-30-CEBPDKOIL21-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 30-CEBPDKOIL21-137964 NK cells alone


title: MEFs - S6K1 WT Passage 3_SG05

value: S6K1 WT

value: Early passage (P3)


title: Irf8 control CAMs-04

description:
N093-14
RawCountTable_N093R0502_Irf8.tsv.gz


title: Irf8 ko CAMs-01

description:
N093-16
RawCountTable_N093R0502_Irf8.tsv.gz


title: MEFs - S6K1 WT Passage 3_SG03


title: Irf8 control CAMs-03

description:
N093-13
RawCountTable_N093R0502_Irf8.tsv.gz


title: Post 6


title: MEFs - S6K1 WT Passage 3_SG04


title: R986-29-29-CEBPD-KI-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 29-CEBPD-KI 137964 NK cells alone


title: R986-31-31-CEBPDKO-IL15-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 31-CEBPDKO-IL15-137964 NK cells alone


title: Irf8 ko CAMs-02

description:
N093-17
RawCountTable_N093R0502_Irf8.tsv.gz


title: Post 2


title: Post 3


title: Irf8 control CAMs-02

description:
N093-12
RawCountTable_N093R0502_Irf8.tsv.gz


title: R986-28-28-IL15CEBPD-KI-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 28-IL15CEBPD-KI 137964 NK cells alone


title: MEFs - S6K1_2_KO3_RAS_S40

data_processing:
Primary analysis RTA 2.11.3 and Secondary analysis CASAVA- 2.17
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a)
Gene based counting was performed using the STAR aligner (version 2.7.1a) .
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.28.1)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

value: S6K1/S6K2 DKO

value: Constitute RAS expression


title: Post 1


title: Post 5


title: Pre 7


title: R986-27-27-IL15-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 27-IL15-137964 NK cells alone


title: 17-IL21-137748

description:
BulkATACseq
bulkATAC_rawCount.csv

value: 17-IL21-137748 NK cells alone


title: Cx3cr1-control-MG-02

description:
N093-22
RawCountTable_N093R0502_Irf8.tsv.gz

value: brain

value: microglia


title: Pre 6

value: Blood

value: PBMC


title: Pre 4


title: R986-26-26-IL21-CEBPD-KI-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: CBNK

value: 26-IL21-CEBPD-KI-137964 NK cells alone


title: R986-24-24-NT-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 24-NT-137748 NK cells alone


title: Pre 5


title: MEFs - S6K1 WT Passage 3_SG02

value: Mouse embryonic fibroblasts

value: Fibroblast


title: Irf8 ko MG-03

description:
N093-08
RawCountTable_N093R0502_Irf8.tsv.gz


title: MEFs - S6K1_2_WT3_ EV_S31

value: S6K1/S6K2 WT

value: Empty vector


title: R986-23-23-CEBPDKOIL15-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 23-CEBPDKOIL15-137748 NK cells alone


title: MEFs - S6K1_2_WT2_RAS_S36


title: R986-25-25-IL21-137964

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 25-IL21-137964 NK cells alone


title: Irf8 control MG-05

description:
N093-05
RawCountTable_N093R0502_Irf8.tsv.gz


title: MEFs - S6K1_2_WT3_RAS_S37


title: Irf8 ko MG-01

description:
N093-06
RawCountTable_N093R0502_Irf8.tsv.gz


title: MEFs - S6K1_2_WT1_RAS_S35


title: Pre 2


title: Irf8 ko MG-04

description:
N093-09
RawCountTable_N093R0502_Irf8.tsv.gz


title: Pre 3


title: R986-21-21-CEBPD-KI-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 21-CEBPD-KI 137748 NK cells alone


title: MEFs - S6K1_2_WT1_ EV_S29


title: Irf8 control MG-04

description:
N093-04
RawCountTable_N093R0502_Irf8.tsv.gz


title: Irf8 ko MG-05

description:
N093-10
RawCountTable_N093R0502_Irf8.tsv.gz


title: MEFs - S6K1_2_WT2_ EV_S30


title: Irf8 control CAMs-01

description:
N093-11
RawCountTable_N093R0502_Irf8.tsv.gz

value: CNS associated macrophage


title: R986-22-22-CEBPDKOIL21-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 22-CEBPDKOIL21-137748 NK cells alone


title: MEFs - S6K1_2_KO2_RAS_S39

value: S6K1/S6K2 DKO

value: Constitute RAS expression


title: R986-20-20-IL15CEBPD-KI-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 20-IL15CEBPD-KI-137748 NK cells alone


title: Pre 1

value: Blood


title: MEFs - S6K1_2_KO1_RAS_S38


title: Irf8 ko MG-02

description:
N093-07
RawCountTable_N093R0502_Irf8.tsv.gz

value: brain

value: microglia


title: MEFs - S6K1_KO3_RAS_S16

value: S6K1 KO


title: Irf8 control MG-03

description:
N093-03
RawCountTable_N093R0502_Irf8.tsv.gz


title: R986-19-19-IL15-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: CBNK

value: 19-IL15-137748 NK cells alone


title: H3K4me3-sgMEN1-M53

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg38 genome assembly using bwa/0.7.2 with default configurations.
\peaks were called using MACS/2.1.2 with the following setting: --extsize 1 -q 0.01 -f BAMPE -B --SPMR -g hs.
bigWig file were generated using bedGraphToBigWig from ucsctools/378. Peak text files were generated using MACS/2.1.2
Genome_build: hg38
Supplementary_files_format_and_content: bed; bw

source_name: A549 cell line

growth_protocol: A549 cells were cultured in RPMI-1640 and supplemented with 10% fetal bovine serum (FBS).

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

treatment_protocol: MEN1 was knockout by lenti-guide virus.

value: lung

tag: growth

value: in vitro

tag: antibody

value: Anti-Histone H3 (tri methyl K4) (Abcam, ab8580).


title: H3K4me3-sgMEN1-M12_input


title: Irf8 control MG-02

description:
N093-02
RawCountTable_N093R0502_Irf8.tsv.gz


title: Irf8 control MG-01

description:
N093-01
RawCountTable_N093R0502_Irf8.tsv.gz


title: R986-17-17-IL21-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 17-IL21-137748 NK cells alone


title: H3K4me3-sgLac_input


title: R986-18-18-IL21CEBPD-KI-137748

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 18-IL21CEBPD-KI-137748 NK cells alone


title: MEFs - S6K1_KO1_RAS_S14

value: Mouse embryonic fibroblasts

value: Fibroblast


title: R986-15-15-CEBPDKOIL15-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 15-CEBPDKOIL15-138265 NK cells alone


title: MEFs - S6K1_WT2_RAS_S12

value: S6K1 WT


title: H3K4me3-sgMEN1-M12


title: MEFs - S6K1_KO2_RAS_S15

value: Constitute RAS expression


title: WT_tdT_2

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Wildtype + astrocyte tdTomato control with DCZ treatment

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: WT + tdTomato control

extract_protocol:
Brain tissue was lysed with lysis buffer and the RNA was extracted with the Qiagen RNAeasy kit.
Libraries were prepped using the Illumina Truseq stranded RNA (100ng) + Ribozero Gold Library prep kit.

treatment_protocol: Mice were microinjected in the striatum with either tdTomato AAV or hM4Di AAV.

value: WT

tag: condition

value: tdT


title: H3K4me3-sgLac


title: MEFs - S6K1_WT1_RAS_S11


title: WT_tdT_1


title: R986-16-16-NT-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 16-NT-138265 NK cells alone


title: MEFs - S6K1_WT3_RAS_S13


title: WT_tdT_3


title: WT_tdT_4


title: R986-13-13-CEBPD-KI-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 13-CEBPD-KI-138265 NK cells alone


title: R986-14-14-CEBPDKO-IL21-38265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 14-CEBPDKO-IL21-138265NK cells alone


title: MEFs - S6K1_WT3_ EV_S7

value: Empty vector


title: sgMEN1_53_MLL_rep2

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg38 genome assembly using bwa/0.7.2 with default configurations.
\peaks were called using MACS/2.1.2 with the following setting: --extsize 1 -q 0.01 -f BAMPE -B --SPMR -g hs.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file were generated using bedGraphToBigWig from ucsctools/378. Peak text files were generated using MACS/2.1.2

value: KMT2A/MLL antibody (Abcam, ab272023),


title: H3K4me3-sgMEN1-M53_input

value: lung


title: WT_hM4D_4

description: Wildtype + astrocyte hM4Di activation with DCZ treatment

source_name: KO + astrocyte hM4Di activation


title: R986-12-12-IL15-CEBPD-KI-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: CBNK

value: 12-IL15-CEBPD-KI-138265 NK cells alone


title: sgMEN1_53_MLL_rep1

value: in vitro


title: MEFs - S6K1_WT2_ EV_S6


title: WT_hM4D_3


title: sgMEN1_53_IgG


title: MEFs - S6K1_WT1_ EV_S5


title: R986-11-11-IL15-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 11-IL15-138265 NK cells alone


title: sgMEN1_53_MEN1_rep2

value: Menin antibody (Bethyl laboratories, A300-115A)


title: WT_hM4D_2


title: Liver - OKO_6

data_processing:
Primary analysis RTA 1.18.64 and Secondary analysis CASAVA- 1.8.4
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to mm9 genome using Tophat 2.0.11
Gene based counting was performed using the Rsubread package.
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.18.1 )
Assembly: mm9
Supplementary files format and content: tab-delimited text file include raw counts for each Sample generated by  Rsubread.

source_name: Liver

extract_protocol:
Livers were flash frozen and RNA was then extracted by Trizol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: S6K1 KO

value: Old age (600 days)


title: Liver - OKO_5


title: R986-8-8-NT-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 8-NT-137961 NK cells alone


title: sgMEN1_53_MEN1_rep1


title: R986-7-7-CEBPDKO-IL15-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 7-CEBPDKO-IL15-137961 NK cells alone


title: sgMEN1_12_MLL_rep2


title: WT_hM4D_1

source_name: WT + astrocyte hM4Di activation

value: WT


title: Liver - OKO_2


title: sgMEN1_12_MLL_rep1


title: R986-9-9-IL21-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 9-IL21-138265 NK cells alone


title: KO_tdT_3

description: SAPAP3 KO + astrocyte tdTomato control with DCZ treatment

source_name: KO + tdTomato control

value: KO

value: tdT


title: sgMEN1_12_IgG


title: sgMEN1_12_MEN1_rep2


title: Liver - OKO_1


title: Liver - OKO_4


title: R986-6-6-CEBPDKO-IL21-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 6-CEBPDKO-IL21-137961 NK cells alone


title: KO_tdT_4


title: KO_tdT_1


title: KO_tdT_2


title: Liver - OWT_10


title: KO_hM4D_4

description: SAPAP3 KO + astrocyte hM4Di activation with DCZ treatment


title: R986-5-5-CEBPD-KI-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 5-CEBPD-KI-137961 NK cells alone


title: R986-10-10-IL21-CEBPD-KI-138265

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 10-IL21-CEBPD-KI-138265 NK cells alone


title: R986-4-4-IL15-CEBPD-KI-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: CBNK

value: 4-IL15-CEBPD-KI-137961 NK cells alone


title: Liver - OWT_7


title: LacZ_IgG

value: lung

value: in vitro


title: KO_hM4D_3


title: R986-3-3-IL15-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 3-IL15-137961 NK cells alone


title: Liver - OWT_5

value: Liver


title: KO_hM4D_2


title: Liver - OWT_4


title: LacZ_MLL_rep2

value: KMT2A/MLL antibody (Abcam, ab272023),


title: R986-2-2-IL21 CEBPD-KI-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 2-IL21 CEBPD-KI-137961 NK cells alone


title: LacZ_MLL_rep1


title: R986-1-1-IL21-137961

description:
BulkRNAseq
bulkRNA_rawCount.csv

value: 1-IL21-137961 NK cells alone


title: Liver - YWT_6

value: Young age (90 days)


title: Liver - OWT_1

value: WT

value: Old age (600 days)


title: KO_hM4D_1

value: KO


title: LacZ_MEN1_rep1

value: Menin antibody (Bethyl laboratories, A300-115A)


title: IL15 CBNK GBM Day 9  coculture 124610 RNA

description:
scRNAseq
rna_IL21_15.RDS

source_name: IL-15 NK cells + GSC20 9 days coculture

extract_protocol:
For sc-RNA seq, single cell capture, barcoding and library preparation were performed following the 10X Genomics Single Cell Chromium 3’ protocols (CG000183, V3.1). Ten libraries were pooled to give a final concentration of 10 nM. Pooled samples underwent further qPCR to determine the final concentration before submission for sequencing with the NovaSeq6000 sequencer using the S2 100 cycles flow cell and sequenced for 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC (Advanced Technology Genomics Core) core at MD Anderson.
By applying RNA  and ATAC sequencing, we want to investigate the epigenetic factors that contributing for IL-21-induced memory formation in NK cells

value: IL-15 NK cells + GSC20 9 days coculture


title: A549_invitro_rep2

description:
processed data file:
A549_invitro_test.gene_summary.txt

data_processing:
MAGeCK and MAGeCK0VISPR softwares were used to analyze CRISPR data.
Raw sequencing data are pre-processed by using MAGeCK to obtain the read counts for each sgRNA. Control sgRNAs are used to normalize the data.
MAGeCK TEST algorithm is used to compare treatment with control samples to obtain the significantly enriched and depleted sgRNAs and genes.
Genes with p value less than 0.001 are canditate hits.
Genome_build: hg38
Supplementary_files_format_and_content: gene_summary.txt

extract_protocol: Genomic DNA was extracted from replicate samples (QIAamp Blood Midi kit) and sgRNA inserts were amplified by PCR. The sgRNAs were designed using the CRISPR-DO tool that accounted for sgRNA specificity and cutting efficiency. sgRNAs were synthesized as 73-mer oligonucleotides (CustomArray, USA), GAAAGGACGAAACACCGNNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGC (N’s denote sgRNA 20 nucleotide target sequence; sense orientation) with a total of 12,472 sequences and amplified by PCR as a pool using the following primers: TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTT GTGGAAAGGACGAAACACCG (Forward) and ACTTTTTCAAGTTGATAACG GACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC (Reverse). The PCR product was purified and cloned in the lentiGuide-Puro vector using BsmBI (NEB). Ligation was performed using the NEBuilder® HiFi DNA Assembly Cloning Kit and transformed into an electrocompetent strain (Stbl4; ThermoFisher, USA) to achieve ~300x coverage. Colonies were scraped off Agar plates using LB medium. Plasmid DNA was extracted using NA0310 Sigma GenElute™ HP Plasmid Maxiprep Kit and adequate library representation of each sgRNA was confirmed by NGS.

treatment_protocol: We inoculated the transduced A549 cells to NOD/SCID mice and harvested xenograft tumors at day 14.


title: Liver - YWT_4


title: E14.5, En1/2 CKO cerebellum, replicate 1

city: New York

first: Alexandra

middle: L.

last: Joyner

state: New York

address: 430 E 67th St

department: Developmental Biology Program

institute: Sloan Kettering Institute

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files.

source_name: tdT+ sorted cells from cerebellum

extract_protocol:
Animals were dissected in ice cold Hank’s balanced salt solution (HBSS) (Gibco) and were pooled together for downstream steps. Two replicate experiments were performed. On ice, cerebella were detached from the rest of the brain using forceps and dissociated in Accutase (Innovative Cell Technologies) at 37°C for 7-10 minutes. Following dissociation, accutase was washed out using neural stem cell (NSC) media (Neurobasal, supplemented with N2, B27 and non-essential amino acids, Gibco). Samples were triturated by pipetting up and down using a P1000, filtered through a 35um cell strainer (Falcon)and then centrifuged at 500g at 4°C for 5 minutes. Cells were washed again in NSC media and were finally filtered into polypropylene round bottom tubes (Falcon) prior to sorting for tdT+ cells. tdT+ cells were sorted into polypropylene round bottom tubes, spun down at 500g at 4°C for 5 minutes and resuspended in NSC media prior to single cell library preparation.
Single cell libraries were prepared using 10X Genomics’ Chromium Next GEM Single Cell 3’ Reagent Kits, v3.1 according to manufacturer’s instructions. Prior to loading the 10X Genomics chip, the limited sample preparation protocol was used. Cell viability was quantified using 0.2% (w/v) Trypan Blue on a hemocytometer, and 7,000 viable cells were targeted per pooled sample.

value: tdT+ sorted cells from cerebellum

value: Atoh1-Cre/+; En1lox/lox, En2lox/lox; R26LSL-tdT/+


title: IL21 CBNK GBM Day 9 coculture 124610 RNA

description:
scRNAseq
rna_IL21_15.RDS

source_name: IL-21 NK cells + GSC20 9 days coculture

value: CBNK

value: IL-21 NK cells + GSC20 9 days coculture


title: Liver - YWT_3


title: IL21 CBNK day 7  124610 (baseline) RNA

description:
scRNAseq
rna_IL21_15.RDS

source_name: IL-21 NK cells alone (baseline)

value: IL-21 NK cells alone (baseline)


title: E14.5, control cerebellum, replicate 2

description: 10X Genomics

value: Atoh1-Cre/+; R26LSL-tdT/+


title: sgMEN1_12_MEN1_rep1

value: lung

value: in vitro


title: A549_invitro_rep1


title: Liver - YWT_2

value: Liver


title: E14.5, control cerebellum, replicate 1

description: 10X Genomics


title: A549_day0_rep2


title: Liver - YWT_1


title: IL21 CBNK GBM Day 3 coculture 124610 RNA

description:
scRNAseq
rna_IL21_15.RDS

source_name: IL-21 NK cells + GSC20 3 days coculture

value: IL-21 NK cells + GSC20 3 days coculture


title: IL15 CBNK day 7  124610 (baseline) RNA

description:
scRNAseq
rna_IL21_15.RDS

source_name: IL-15 NK cells alone (baseline)

value: IL-15 NK cells alone (baseline)


title: LacZ_MEN1_rep2


title: EAS42_4_KI

city: Paris

first: Carole

last: Peyssonnaux

address: 24 rue du Faubourg saint Jacques

institute: INSERM

data_processing:
Libraries were quantified by Q bit and profiles were assessed using the DNA High Sensitivity LabChip kit on an Agilent Bioanalyzer
Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode
After sequencing, a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).
Obtained fastq files were then aligned using STAR algorithm (version 2.5.2b) and quality control of the alignment realized with Picard tools (version 2.8.1).
Reads were then counted using Featurecount (version Rsubread 1.24.1) and the statistical analyses on the read counts were performed with the DESeq2 package version 1.14.1 to determine the proportion of differentially expressed genes between two conditions.
Assembly: Ensembl release 101, GRCm38

source_name: Skin

extract_protocol:
RNA was harvested using trizol.
The libraries were prepared following the Stranded mRNA Prep protocol from Illumina, starting from 250 ng  of high quality total RNA.

value: Skin

value: 5 Hamp1-KI ker


title: IL15 CBNK GBM Day 3 coculture 124610 RNA

description:
scRNAseq
rna_IL21_15.RDS

source_name: IL-15 NK cells + GSC20 3 days coculture

value: IL-15 NK cells + GSC20 3 days coculture


title: E14.5, En1/2 CKO cerebellum, replicate 2

description: 10X Genomics


title: EAS42_3_WT

value: WT


title: A549_xeno_rep4

description:
processed data file:
PDX_A549_test.gene_summary.txt

source_name: A549 xenograft

value: in vivo