title: Single cell TCR sequencing of CD4+ Tcells from the intestinal epithelium 5

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Library strategy: Amplicon-seq
Raw fastq files derived from our RNA-seq libraries were processed with cellranger count (v3.1.0) using the 10x Genomics prebuilt mouse reference (v3.0.0 mm10). Our libraries were processed independently and merged into a single experiment at the analysis level using Seurat (v3.1.1) (Stuart et al., 2019). Quality control was performed by removing cells with high (> 5%) mitochondrial UMI content. Cells having more than 4000 or less than 200 genes were excluded from our analysis. TCR contigs and annotation were performed with the Cellranger vdj workflow from 10x Genomics and the prebuild mouse reference (v3.1.0 mm10). Paired TCR clones were defined by the V, (D), J and CDR3 nucleotide composition for alpha and beta chains. TCR clone sharing was assigned to cells expressing identical V, (D), J, and CDR3 nucleotide and amino acid sequences.
Raw fastq files were processed by using the mouse transcriptome (gencode M23) with the kallisto (v0.46) software (Bray et al., 2016). Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R (Pimentel et al., 2017). Shortly, we modeled batch effect and our experimental design using the sleuth_fit function and detected differentially expressed genes between all groups by the likelihood ratio test (lrt). To spot significantly expressed genes between group pairs, we used the wald-test function. Genes with false discovery rate less than 0.05 and 1 log2 fold-change were used in downstream analysis. Gene set enrichment analysis (GSEA) was performed by using signature gene sets in gmt format and a pre-ranked gene list by log2 fold-change between two groups as input for the fgsea package/R (Korotkevich et al., 2019). Gene ontology (GO) analysis was executed by comparing all detected genes as our background and the lists of differentially expressed genes against the biological processes gene sets by using topGO/R (Alexa and Rahnenfuhrer, 2019; Carlson M, 2019).
For Miseq data, fastq files were de-multiplexed and paired-end reads were assembled at their overlapping region using PANDASEQ (Masella et al., 2012) and FASTAX toolkit. Demultiplexed and collapsed reads were assigned to wells according to barcodes. Fasta files from both Sanger and Miseq sequences were aligned and analyzed on IMGT (imgt.org/HighV-QUEST) (Brochet et al., 2008). Cells with identical TCRb CDR3 nucleotide sequences were considered as the same clones. Clonality was confirmed by sequencing TCRa of the expanded clones as assessed by TCRb sequencing for mice shown in Figure S2F and H. Clonality was assigned based on paired TCRab for mice shown in Figure 2 and S2C. Only in frame junction sequences of TCRb were included in the analysis. For fixed-Vb6 mice shown in Figure 2 and S2, each TCRa CDR3 was considered a clone.
Genome_build: mm10

source_name: Intraepithelial lymphocytes (IELs)

extract_protocol:
Single cells were index-sorted using a FACS Aria into 96-well plates containing 5μL of lysis buffer (TCL buffer, Qiagen 1031576) supplemented with 1% β-mercaptoethanol) and frozen in -80°C prior to RT-PCR.
RNA and RT-PCRs for TCRa and TCRb were prepared as previously described (Dash et al., 2011). PCR products for TCRa and TCRb were either subjected to Sanger sequencing or multiplexed with barcodes and submitted to MiSeq sequencing (Han et al., 2014) using True Seq Nano kit (Illumina).

value: Foxp3eGFP-CreERT2 Rosa26|s|-td-Tomato


title: Single cell TCR sequencing of CD4+ Tcells

status: Public on Oct 02 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: CD4 T Cells

tag: strain


title: Single cell TCR sequencing of CD4+ Tcells from the intestinal epithelium 3

value: Foxp3eGFP-CreERT2 Rosa26|s|-td-Tomato and Foxp3-RFP Nur77-GFP


title: CTRL05_re-analyzed

type: genomic

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

description:
methylation profiling using bisulfite converted
GSM3927209

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing:
Data was analysed using R version 3.6.1 (2019-07-05). Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘Champ’ R package (v. 2.16.2), with quality control options set as default. The quality control step retained 736048 probes, which were used for further analysis. Probes overlapped with SNP (96368) and with a detection pvalue < 0.01 (3456), beadcount <3 in at least 5% of samples in one or more samples (10453) were eliminated. X or Y chromosomes probes (16664), non-cg probes (2918), and probes aligning to multiple locations (11) and unannotated probes were also removed from analysis. No background correction was carried out. BMIQ normalisation was applied, with the deafult ‘method’ option”. The BMIQ normalized samples were assigned with respective genome coordinates based on probe name and manifest file B4 annotation (Illumina Inc., USA). Batch correction was performed using Combat function from sva package. The BMIQ normalized and batch corrected matrix has also been submitted here and are represented in the sample data tables. The file Matrix_processed.txt.gz includes the non-normalized Average Beta values.
Matrix_signal_intensities.txt.gz includes:Unmethylated signal (B) and methylated signal (A) intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

tag: tissue

value: peripheral blood

tag: sample status

value: Re-analyzed control

tag: gender

value: Male

tag: disease state

value: Control

tag: batch

tag: ethnicity

value: European


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C6_ad007

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age


title: Mouse astrocytes HER2CA Day 15 repB [exp1]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description:
astro_YT_doxy_day15_repB
Gene expression data from control astrocytes, 15 days after inducing HER2CA expression.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt

data_processing:
Reads quality was checked using FastQC.
Reads were mapped to the mouse reference genome (mm10 build) using STAR (v2.5.3a).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (v1.22.3) and the UCSC gene annotation (mm10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: astro_YT_exp1_expressionMatrix_counts.txt: Tab-delimited expression matrix (raw gene counts).

source_name: Mouse astrocytes + HER2CA Day 15

growth_protocol: Mouse astrocytes with HER2CA are cultured in DMEM-F12, 1% GLN, 1% PS, 1% N-2 supplement, 20 ng/ml mouse EGF, 20 ng/ml mouse bFGF, 1µg/µL Doxycycline. Gliomasphere are cultured in suspension in the same medium. Control mouse astrocytes are cultured in DMEM-F12, 1% GLN, 1% PS,1% N-2 supplement, 20 ng/ml mouse EGF, 20 ng/ml mouse bFGF, without Doxycycline.

extract_protocol:
RNA extraction from cells was performed with NucleoSpin 8 RNA Core Kit (Macherey-Nagel) according to the manufacturer’s instructions, using an automated system (Freedom EVO, Tecan).
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep (Illumina), according to manufacturer’s instructions.

treatment_protocol: HER2CA-transformed mouse astrocytes were treated for 15 days with 1µM 4OH TAM or left untreated.

tag: cell type

value: HER2CA-expressing mouse astrocytes

tag: strain/background

value: C57BL/6J; Yapf/f;Tazf/f

tag: experimental condition

value: Doxycycline and DMSO


title: LPS/IFNg treated Yap/Taz knockout_rep2

city: Singapore

first: Manvendra

middle: Kumar

last: Singh

state: Singapore

address: 8 College Road

department: Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Alignment using STAR version=STAR_2.5.1b
Mapping reads counting : featureCounts (Rsubread R package)
Genome_build: NCBI RefSeq annotation for mm10 (build 38.1) is used
Supplementary_files_format_and_content: RawReadCounts_WtKo_UntLps.txt.gz:  format - ".txt", Content - Raw read counts file from featureCount

source_name: Bone-marrow-derived macrophage (BMDM)

growth_protocol: BMDMs were isolated from the femurs and tibiae of control and YAP/TAZ-dKO mice. Femurs and tibiae were collected by cutting off the hind legs at the hip joint with sterile scissors, ensuring that joints were kept intact, and placed in sterile cold PBS. The excess muscle was removed carefully by leaving the bone with no muscle. Using sharp scissors soaked in 95% ethanol, the ends of the bones were cut. The bone cavity containing BMDMs was flushed out with 5 ml of sterile cold PBS. Cells were then centrifuged at 1000 rpm for 10 minutes for pellet collection. Pellets were resuspended and plated in 20 ml of macrophage medium [Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, catalog no. 11965092) containing 20% L929-conditioned medium, 1% penicillin/streptomycin and 10% FBS]. On day 3, an additional 15 ml of macrophage medium was added and on day 6, all the media were replaced with fresh macrophage media. On day 7, cells were detached using trypsin (Gibco, catalog no. 25200056) for 30 minutes to 1 hour at 4ÅãC. Cells were then washed, centrifuged, resuspended and seeded (1 Å~ 106 cells/well) in a 6-well tissue culture plates using the culture medium (DMEM containing 10% FBS and 1% penicillin/streptomycin).

extract_protocol:
Total RNA was prepared from BMDMs of 2-3 months old control and YAP/TAZ-dKO mice using either Favorgen RNA extraction kit (Favorgen Biotech, catalog no. FATRK 001-2) or PureLink RNA Mini Kit (Thermo Fisher, catalog no. 12183018A).
To perform the RNAseq, total RNA was prepared from BMDMs of 2-3 months old control and YAP/TAZ-dKO mice using either Favorgen RNA extraction kit (Favorgen Biotech, catalog no. FATRK 001-2) or PureLink RNA Mini Kit (Thermo Fisher, catalog no. 12183018A). Subsequently, strand-specific poly(A) RNAseq libraries were generated using NEBNext. Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, catalog no. E7765S) and sequenced on Hiseq2000 sequencer.

treatment_protocol: We performed RNAseq analysis on BMDMs isolated from 2-3 months old control and YAP/TAZ-dKO mice and treated them with or without LPS/IFNg (LPS 100ng/ml + IFNγ 10ng/ml) for 12 hours.

value: 2-3 months


title: Single cell TCR sequencing of CD4+ Tcells from the intestinal epithelium 2

value: Foxp3-RFP Nur77-GFP


title: CTRL04_re-analyzed

description:
methylation profiling using bisulfite converted
GSM3927208

value: Female


title: BmN4_crosslinked_H3K9me3_2

city: Paris

first: Ines Anna

last: Drinnenberg

address: 26 Rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Adapter-trimmed chIP-seq reads were aligned to the B. mori genome assembly or T. ni genome assembly using Bowtie2- 2.2.9 Alignment files (sam) were converted to bam, sorted, indexed. Duplicates were removed using Picard Tools (v 2.6.0). ChIp-seq scores were visualized in IGV as bigwig files representing average log2 ratio of (IP/Input) in genome-wide 1 kb windows generated using Deeptools bamCompare function.
Adapter trimmed mRNA-seq reads were aligned to the B. mori genome assembly or T. ni genome assembly using STAR-2.7.0a. Alignment files (sam) were converted to bam, sorted, indexed and used to generate 1 kb resolution BPM-normalized bigwig tracks using Deeptools bamCoverage function. Unique, multimapping and duplicate reads were included.
Genome_build: Bombyx mori: genome assembly downloaded from Silkbase: http://silkbase.ab.a.u-tokyo.ac.jp
Genome_build: Trichoplusia ni: GenBank Assembly Accession: GCA_003590095.1
Supplementary_files_format_and_content: ChIP-seq: bigwig files generated using RPKM-normalized Bam files for IP and Input using Deeptools bamCompare function. Each bigwig fille represents average log2 ratio of IP/Input in genome-wide 1kb windows.
Supplementary_files_format_and_content: mRNA-seq: bigwig files genrated using Deeptools bamCoverage function. Each bigwig file represents bins per million mapped reads (BPM) in genome-wide 1 kb windows.

organism: Bombyx mori

source_name: ovary-derived cells

growth_protocol: Cultured silkworm ovary-derived BmN4 and T. ni Hi5 cell lines were maintained in Sf-900 II SFM medium supplemented with (BmN4,) or without (Hi5) 10% fetal bovine serum , antibiotic-antimycotic and 2mM L-glutamine at 27°C.

extract_protocol:
ChIP-seq: DNA-protein complexes (either cross-linked with formaldehyde or not) were isolated with specific antibody after chromatin solubilization using MNase and sonication. isolated DNA was purified using phenol/chloroform/isoamyl alcohol extraction method.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
mRNA-seq: Total RNA was extracted from cells using Trizol reagent.
All steps of Illumina library preparation and sequencing were carried out at the Curie Institute’s sequencing platform using TruSeq ChIPseq protocol or TruSeq Stranded mRNA protocol.
ChIP-seq or mRNA-seq

treatment_protocol: For 20E-related eperiments, BmN4 cells were treated with 20E for 48 hours (for treated samples), or DMSO for 48 hours (for control samples). For 20-washout experiment, BmN4 cells were treated with 20E for 48 hours and then grown in conditioned medium without 20E for an additional 5 days (for mRNAseq) or an additional 10 days (for CENP-T ChIP-seq).

value: ovary-derived cells


title: Mouse astrocytes HER2CA Day 15 repA [exp1]

description:
astro_YT_doxy_day15_repA
Gene expression data from control astrocytes, 15 days after inducing HER2CA expression.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C5_ad004


title: CTRL02_re-analyzed

description:
methylation profiling using bisulfite converted
GSM3927206


title: BmN4_native_H3K9me3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C6_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C5_ad008


title: LPS/IFNg treated Yap/Taz knockout_rep3


title: CTRL03_re-analyzed

description:
methylation profiling using bisulfite converted
GSM3927207


title: H3K4me1_MEFs

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA.
Reads forming adapter dimers were removed using an in-house script.
Reads were mapped to the mouse genome (mm9) using Bowtie with the following arguments: -m 1 --strata --best -y -S –l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: WIG track files were generated using WigMaker. Scores represent tag numbers per total uniquely mapped reads.

growth_protocol: MEFs are grown in glutamine and pyruvate containing DMEM, supplemented with 10% serum, 1% penicillin-streptomycin.

extract_protocol:
Lysates were clarified from cross-linked and sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared and sequenced on the Illumina Hiseq 2500 as single-end 50 bp reads following Illumina's instructions.

tag: strain background

tag: genotype/variation

value: wild type

value: E10.5 embryos

value: Mouse embryonic fibroblasts (MEFs)

tag: chip antibody

value: Rabbit polyclonal anti-H3K4me1 (Abcam, ab8895)


title: 9-PG

description: methylation profiling using bisulfite converted

value: peripheral blood

value: Sister of Proband 4

value: Normal

value: Current study


title: BmN4_crosslinked_Input_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C5_ad012

value: CA


title: BmN4_crosslinked_Input_1


title: Single cell TCR sequencing of CD4+ Tcells from the intestinal epithelium 4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad012

value: male


title: Untreated Yap/Taz knockout_rep3


title: BmN4_native_Input


title: BmN4_crosslinked_H3K4me3_rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad007


title: CTRL06_re-analyzed

description:
methylation profiling using bisulfite converted
GSM3927210

value: Re-analyzed control

value: Control

value: European


title: Untreated control_rep3

value: 2-3 months


title: 10-PM


title: 4-AM

value: Mother of Proband3


title: Untreated control_rep2


title: Untreated Yap/Taz knockout_rep2


title: BmN4_native_H3.3-3X-FLAG


title: Untreated Yap/Taz knockout_rep1


title: Untreated control_rep1


title: 7-PM

value: Mother of Proband 4

value: Female


title: Single cell TCR sequencing of CD4+ Tcells from the intestinal epithelium 1

source_name: Intraepithelial TCR Va2+Vb6+ CD4 Tcells


title: BmN4_crosslinked_H3K9me3_1

value: ovary-derived cells


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad006


title: CTRL01_re-analyzed

description:
methylation profiling using bisulfite converted
GSM3927205

value: Male


title: BmN4_crosslinked_H3K9me2_1


title: PHx, 96h rep2

city: Durham

first: Anna Mae

last: Diehl

address: Research Drive

institute: Duke University

description: 96h post-PHx surgery

data_processing:
FASTQ files were processed according to the pipeline developed by the Kundaje lab
Bam and peak files of each biological replicate were generated and analyzed as described above
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files contain the peak calling results for pre- and post-PHx samples, respectively.

source_name: liver hepatocytes

growth_protocol: Mice were fed with normal diet

extract_protocol:
Hepatocytes were isolated using two-step collagenase perfusion method
ATAC-seq libraries were prepared for sequencing according to Kaestner lab protocol with Tn5 enzymes purchased from Illumina

treatment_protocol: 10-12 weeks old mice underwent partial hepatectomy surgery

value: liver

value: 10-12 weeks old

tag: time point

tag: protocol

value: PHx surgery


title: BmN4_crosslinked_H3K9me2_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad004

tag: strain


title: BmN4_CENP-T_WT_45min_rep2


title: 6-AM

tag: tissue

value: peripheral blood

tag: sample status

value: Brother of Proband 3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad001


title: BmN4_crosslinked_H3K4me3_rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad010


title: BmN4_Input_WT_45min_rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad001


title: PHx, 72h rep1

description: 72h post-PHx surgery


title: PHx, 72h rep2

description: 72h post-PHx surgery


title: BmN4_native_H3K36me3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad012


title: Lcn2 knockout mice CCl4-treated replicate 4

type: RNA

city: Pittsburgh

first: Ramon

last: Bataller

state: PA

address: 200 Lothrop St

institute: Pittsburgh Liver Research Center

hyb_protocol: Followed manufacture's manual

scan_protocol: Followed manufacture's standard protocol

data_processing:
Raw intensity values were read and processed using the limma package for the R programming language (Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015), Nucleic Acids Research, 43(7), e47)
Data were background corrected using the normexp method followed by quantile normalization between arrays

source_name: Lcn2 knockout mice CCl4-treated

label_protocol: Adjust 10 to 200 ng of total RNA in a final volume of 1.5 µL. Add 2 µL of diluted Spike Mix to each tube. Add T7 Primer mix, cDNA master mix and Transcription master mix (including Cyanine 3-CTP). Purify and quantify the cRNA.

growth_protocol: Male BALB/c wild type and Lcn2-/- mice grew to six- to eight-week-old on regular chow diet

extract_protocol: Total RNA was collected using RNeasy mini kit (Qiagen, 74104) with on-column DNase digestion.

treatment_protocol: Mice were subjected to CCl4 which diluted into corn oil (1:5) intraperitoneal injection for 4 weeks at dose of 0.5ml/kg body weight twice a week. Mice were sacrificed 48 hours after last dose of CCl4 administration.

value: BALB/c

tag: gender

tag: genotype

value: Lcn2 knockout

tag: treatment


title: Lcn2 knockout mice CCl4-treated replicate 3

value: male


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad007

tag: brain region

value: CA


title: PHx, 48h rep1

description: 48h post-PHx surgery


title: PHx, 96h rep1

description: 96h post-PHx surgery


title: BmN4_Input_WT_30min


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C5_ad001

tag: Sex


title: BmN4_CENP-T_WT_30min


title: 1-FM

value: Mother of Proband1 and 2

tag: disease state

value: Normal

tag: batch

value: Current study

tag: ethnicity


title: BmN4_native_H3K27me3

tag: cell type


title: Wild type mice CCl4-treated replicate 4

source_name: Wild type mice CCl4-treated

value: wild type


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C4_ad008

tag: age


title: PHx, 0hr rep1

description: healthy, undamaged liver

value: undamaged liver


title: PHx, 48h rep2

description: 48h post-PHx surgery


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad006


title: PHx, 0hr rep2

description: healthy, undamaged liver


title: Lcn2 knockout mice CCl4-treated replicate 2


title: Lcn2 knockout mice CCl4-treated replicate 1


title: Wild type mice CCl4-treated replicate 3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C2_ad012


title: Lcn2 knockout mice control replicate 3

source_name: Lcn2 knockout mice control

value: control


title: Wild type mice CCl4-treated replicate 5


title: Wild type mice CCl4-treated replicate 2


title: Wild type mice control replicate 2

source_name: Wild type mice control


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad004


title: ffEPSC-singlecell-23

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

country: China

institute: Wuhan University

data_processing:
Sequencing reads were aligned to the human genome build hg38/GRCh38 with the HISAT2 .Raw counts were performed with FeatureCounts using GENCODE v29.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: ffEPSC-singlecell

value: extended pluripotent stem cells

tag: transition/culture system

value: Matrigel-based feeder-free conversion and maintenance system


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad002


title: CNV_H3K9Ac_ChIPSeq_2

city: Cincinnati

first: Theresa

last: Alenghat

state: OH

address: 240 Albert Sabin Way, S5.409

department: Division of Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

data_processing:
Fastq files from Illumina pipeline were aligned to mm10 by bowtie (version 1.2.0 PMID: 19261174) with maximum one allowed error in a sequence and no more than one number of hits was allowed.
MACS2 (version 2.1.1.20160309 PMID: 18798982) were used for peak-calling. MACS2 were used with q-value threshold less than 0.2.
Quality control was conducted in Biowardrobe by comparing  the following parameters across samples: percentages of mapped/unmapped/non-uniquely mapped reads, average fragment length, base frequency and average tag density profiles.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain peak list.

source_name: Intestinal Epithelial Cells

extract_protocol:
Nuclear lysates were sonicated and histone-chromatin complexes were immunoprecipitated with an H3K9Ac antibody.
Libraries were prepared with the ThruPLEX DNA-seq kit (Rubicon) and sequenced on an Illumina HiSeq 2000 sequencing system (Sequencing depth: 20 million reads, sequencing condition: single-end, 50bp)

tag: antibody

tag: tissue location

value: distal intestine

tag: sample type

value: conventionally-housed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C3_ad008

tag: strain


title: ffEPSC-singlecell-22


title: Ecoli_H3K9Ac_ChIPSeq_1


title: ffEPSC-singlecell-25


title: Wild type mice control replicate 4

tag: tissue

value: liver


title: Lcn2 knockout mice control replicate 2


title: Lcn2 knockout mice control replicate 1


title: Ecoli_H3K9Ac_ChIPSeq_2


title: ffEPSC-singlecell-24


title: ffEPSC-singlecell-20


title: Wild type mice CCl4-treated replicate 1


title: ffEPSC-singlecell-19


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C2_ad001


title: Wild type mice control replicate 3


title: CNV_H3K9Ac_ChIPSeq_1


title: ffEPSC-singlecell-16


title: Wild type mice control replicate 1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C2_ad008


title: ffEPSC-singlecell-15


title: 3T3_L1_Day8_3

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were  removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: 3T3 L1 Cell Line

extract_protocol:
DRG were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGIseq500 RNA library kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: adipocytes


title: ffEPSC-singlecell-21


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C2_ad007


title: GF_H3K9Ac_ChIPSeq_2

value: germ-free


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C2_ad010


title: ffEPSC-singlecell-13


title: GF_H3K9Ac_ChIPSeq_1


title: ffEPSC-singlecell-12


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad010


title: ffEPSC-singlecell-11


title: ffEPSC-singlecell-18


title: 3T3_L1_Day4_2


title: ffEPSC-singlecell-8


title: 3T3_L1_Day8_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C2_ad002


title: ffEPSC-singlecell-14


title: 3T3_L1_Day8_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad007


title: LPS/IFNg treated control_rep1

value: 2-3 months


title: 3T3_L1_Day4_3


title: ffEPSC-singlecell-7


title: ffEPSC-singlecell-10


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad008


title: ffEPSC-singlecell-9


title: 3T3_L1_Day0_3


title: ffEPSC-singlecell-5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad004


title: ffEPSC-singlecell-17


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad002


title: 3T3_L1_Day0_1


title: ffEPSC-singlecell-6


title: 3T3_L1_Day4_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad006


title: ffEPSC-singlecell-4


title: Qk-KO rep4 [CPZR8]

city: Houston

first: Jian

last: Hu

state: Texas

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FastQC is used to check the read quality
HiSAT2 (--rna-strandness RF --no-mixed --no-discordant --dta) was used to map the reads to mouse genome (mm10) with transcription annotations (GENCODE vM8 basic).
StringTie  was used to count the gene level reads numbers.
DESeq2 was used to do the differential gene analysis.
rMATS.4.0.2 (-t paired -len 75 -analysis P -libType fr-firststrand) was sued to do the alternative splicing analysis.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 result in text format.

growth_protocol: WT or Qk-KO microglia were freshly isolated from Cx3cr1-CreER;QKLoxP/LoxP (Qk-KO) and Cx3cr1-CreER;QKLoxP/+ (WT) mice.

extract_protocol:
Total RNAs were extracted with Rnasey kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 8 weeks old Cx3cr1-CreER;QKLoxP/LoxP (Qk-KO) and Cx3cr1-CreER;QKLoxP/+ (WT) mice were injected with tamoxifen, then fed with 0.2% Cuprizone for 6 weeks.

tag: strain background

value: FvB/C57BL6 hybrid

tag: genotype/variation

value: Cx3cr1-CreER;QKLoxP/LoxP (Qk-KO)

value: brain

tag: tissue/cell type

value: Microglia from corpus callosum


title: Qk-KO rep3 [CPZR7]

value: Cx3cr1-CreER;QKLoxP/+ (WT)


title: 3T3_L1_Day0_2


title: ffEPSC-singlecell-3


title: WT rep4 [CPZR4]


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad006

tag: brain region

value: CA

value: male


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad004

tag: Sex


title: ffEPSC-singlecell-2


title: WT rep2 [CPZR2]


title: ffEPSC-singlecell-1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad010


title: Qk-KO rep1 [CPZR5]


title: Qk-KO rep2 [CPZR6]


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad007


title: 14566X20 HIV-1-BaL-HSA

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
Human GRCh38 genome and gene feature files were downloaded from Ensembl release 87.
A reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.16.
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: Peripheral blood monocyte-derived macrophages

growth_protocol: Monocytes were plated in tissue culture plates and differentiated for 7 days in human serum

extract_protocol:
Total RNA was isolated 18 h following stimulation using RNeasy minikit (Qiagen). Intact poly(A) RNA was purified from total RNA samples (100 to 500 ng) with oligo(dT) magnetic beads, and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation kit (catalog no. RS-122-2101 and RS-122-2102).
Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection

treatment_protocol: On day 7, macrophages were either untreated, treated with one of four FNs, or infected with HIV-1-BaL-HAS

tag: treatment


title: 14566X21 HIV-1-BaL-HSA

value: Peripheral blood monocyte-derived macrophages


title: WT rep3 [CPZR3]


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C10_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C12_ad001


title: WT rep1 [CPZR1]


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C10_ad006


title: 14566X15 Interferon-lambda

value: Interferon-lambda


title: 14566X14 Interferon-lambda


title: WC4

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

description: RNA expression value derived from Expression Console software; core- gene or -exon analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console v4.0 using default analysis settings for RNA analyses  for  gene default and exon default .CHP files.

label: biotin

label_protocol: 150 ng total RNAwas amplified using the  WT Expression Kit and the WT Terminal Labeling Kit (Thermofisher, Darmstadt, Germany).

growth_protocol: HDAC5 KO mice (McKinsey, T.A. et al.. Nature. 2000 Nov 2;408(6808):106-11) and the corresponding wild type littermate controls were group housed under a 12:12 h light–dark cycle (06:00 h lights on) with ad libitum access to low-fat chow (58% carbohydrates, 33% protein, 9% fat, R/M−H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. All experiments were approved by the Ethics Committee of the State Ministry of Agriculture, Nutrition and Forestry (State of North Rhine-Westphalia, Germany). Affymetrix chip microarray was performed from gastrocnemius muscle obtained from 30-week-old HDAC5 KO and wildtype mice fed on chow diet.

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: no further treatment

tag: genotype

value: HDAC5 WT


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C10_ad004


title: 14566X12 Interferon-gamma

value: Interferon-gamma


title: 14566X13 Interferon-lambda


title: 14566X11 Interferon-gamma


title: 14566X19 HIV-1-BaL-HSA


title: LPS/IFNg treated control_rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C10_ad001


title: WC3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C1_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C10_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C11_ad001


title: 14566X9 Interferon-epsilon

value: Interferon-epsilon


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C1_ad010


title: 14566X8 Interferon-epsilon


title: KC3

value: HADAC5 KO


title: KC4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C1_ad006


title: WC2


title: KC2


title: 14566X7 Interferon-epsilon


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C1_ad002


title: 14566X6 Interferon-alpha

value: Interferon-alpha


title: HS-7-c [T30]

city: WuHan

first: Guosong

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
To evaluate the quality of clean reads , fastqc was used  with default parameters
Trinity was used to assemble the transcriptome and calculate the TMM with default parameters
Genome_build: Ziziphus jujuba ZizJuj_1.1 (https://www.ncbi.nlm.nih.gov/genome/15586?genome_assembly_id=219393 )
Supplementary_files_format_and_content: tab-delimited text files include FPKM values  for each Sample and tab-delimited text files include read  counts  for each Sample and transcriptome fasta file

organism: Ziziphus jujuba

source_name: 7 day of heat stress_leaf

extract_protocol:
Total RNA was extracted using a Plant RNA EASYspin Plus Kit (aidlab, Peking, China) according to the instructions of the manufacturer, and treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm and 280 nm (A260 and A280) using SmartSpec Plus (BioRad, USA). RNA integrity was further verified by electrophoresis using a 1.5% agrose gel. To avoid individual variation, we selected three biological replicates for each sample, and extracted total RNA separately, and then we pooled the replicates together for the following experiments.
Construction of cDNA library was independently prepared using 10 ug of total RNA. Polyadenylated RNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen) before being used for the directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 oC until used for sequencing.

tag: cultivar

value: leaves of the seedling

value: heat stress

tag: time of treatment

value: 7 day of heat stress


title: LPS/IFNg treated control_rep2

tag: age

value: 2-3 months


title: KC1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad012


title: HS-5-c [T26]

source_name: 5 day of heat stress_leaf

value: 5 day of heat stress


title: 14566X10 Interferon-gamma

tag: cell type


title: HS-5-b [T25]


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad001


title: HS-7-b [T29]


title: WC1


title: 14566X5 Interferon-alpha


title: 14566X4 Interferon-alpha


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad007


title: 14566X3 Mock

value: Mock


title: HS-5-a [T08]


title: 14566X2 Mock


title: 14_Standard culture, Basolateral infection (MOI 20), Replicate 2

city: Mannheim

first: Marie

last: Wiatr

address: Theodor-Kutzer-Ufer 1-3

department: University Children's Hospital Mannheim

institute: Medical Faculty Mannheim, Heidelberg University

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
PCR duplicates were cleaned using TrueQuant technology (UMI) and in-house GenXPro GmbH script.
Reads were aligned to the human reference genome (hg38) using the bowtie2 2.3.4.1 mapping tool.
Gene count data was normalized to account for differences in sequencing depth. Testing for differential gene expression was performed in the statistical programming platform R using the DeSeq2 R/Bioconductor package.
Genome_build: Genome Reference Consortium Human Build 38 (hg38)
Supplementary_files_format_and_content: Comma-delimited text file include raw counts for each sample

source_name: HIBCPP_Standard culture_Infection (MOI 20)

growth_protocol: HIBCPP cells are human cells isolated from a 29 year old woman, suffering from a choroid plexus tumor in the right lateral ventricle (fourth ventricle) (I. ISHIWATA et al., 2010). HIBCPP cells were cultured in a T flask (175 cm2) (Greiner, Germany) in HIBCPP 10% medium consisting of Dulbecco’s modified eagle medium (DMEM)/Ham’s F12 1:1 medium (Life technologies, UK) supplemented with 4 mM L-Glutamine, 5 μg/ml insulin, 10 % fetal calf serum (FCS) (Gibco, USA) and 2.5 % Pen/strep (MP Biomedicals, USA). The medium was changed twice a week. When HIBCPP cells reached confluence, they were rinsed with phosphate buffered saline (PBS)(-/-) and further trypsinized (Trypsin, 0.05 % GIBCO©) for 20 minutes at 37°C/5 % CO2. Once HIBCPP cells detached completely, medium was added to stop the trypsinization, and HIBCPP cells were centrifuged at 500 rpm for 20 minutes. Next, the number of HIBCPP cells was evaluated with Trypan blue (Fluka©, Sigma Aldrich) and quantified using a microscope with a Malassez hemocytometer. HIBCPP cells were concentrated at 106 cells/ml, and further seeded at 80.000 HIBCPP cells on filter inserts (Cell inserts Sarstedt, Germany; pore diameter 5.0 μm, pore density 6.0 × 105 pores/cm2, 0.33 cm2) in the inverted (CytoOne© 12 well plate StarLab, Belgium) or normal (CytoOne© 24 well plate StarLab, Belgium) culture model (Supplemental Fig. 1). After one day, the filters in the inverted culture were flipped, and HIBCPP 10 % medium was added to the upper and bottom compartment of the filter and transferred to a 24 well plate (Supplemental Fig. 1). For the normal culture system, after one day, HIBCPP 10 % medium was added on the upper and on the bottom compartment of the insert filter. After two to three days in culture, HIBCPP cells that reached a TEER of [50 Ω x cm2] were further switched in HIBCPP 1 % medium consisting of DMEM/Ham’s F12 1:1 medium, supplemented with 4 mM L-Glutamine, 5 μg/ml insulin and 1 % heat inactivated FCS. Cells were ready to be used in experiments 24 h after this last medium change. The barrier integrity of the HIBCPP cell layer was evaluated via TEER measurement with a tissue voltohmmeter (Milicell© ERS-2 Ephitelial Volt-Ohm meter, Millipore, Germany). In order to perform experiments, HIBCPP cells had to reach a high TEER [215-775 Ω x cm2].

extract_protocol:
Cell lysates were stored in liquid nitrogen before RNA isolation. Isolation of total RNA from ECs was conducted using the ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s instructions. RNA samples were digested using DNase I and RNA integrity was accessed using automated capillary electrophoresis (RNA pico sensitivity assay, LabChip GX II Touch HT, Perkin Elmer, Villebon-sur-Yvette, France).
Genome-wide gene expression profiling was performed using the MACE-seq method. In general, the procedure follows a modified protocol described in Nold-Petry et al. (2015). In brief, samples with 100 ng of DNase-treated RNA were used for library preparation. Synthesis of cDNA was performed by reverse transcription using oligo (dT) primers following fragmentation of cDNA to an average size of 200 bp using sonification (Bioruptor, Diagenode, Seraing, Belgium). DNA was quantified using a Qubit HS dsDNA assay (Thermo Fisher Scientific). cDNA fragments were ligated to DNA adapters containing TrueQuant unique molecular identifiers included in the kit. Library amplification was done using polymerase chain reaction, purified by solid phase reversible immobilization beads (Agencourt AMPure XP, Beckman Coulter, Brea, CA, USA).

treatment_protocol: Once HIBCPP cells had reached a TEER between [215-775 Ω x cm2], cells were used for experiments. they were infected with a different MOI of E-30. The concentration of the E-30 stock was determined using Quantitative TaqMan real-time PCR analysis. Once HIBCPP cells grown on cell culture inserts in the inverted cell culture model reached TEER values between 220 and 670 Ω x cm2. All experiments were performed in 1% medium. To the upper compartment of the filter, 400μl of 1% medium containing E-30 Bastianni at a MOI of 0.7, 1.4, 2.1, 9.1 or 20 were added and kept throughout the experiments. For uninfected controls, only 1% medium was added to the upper compartment.

value: HIBCPP

value: Human choroid plexus papilloma cell line

tag: culture type

value: Standard culture

tag: infection

value: Infection (MOI 20)


title: 15_Standard culture, Basolateral infection (MOI 20), Replicate 3


title: 14566X1 Mock

value: Peripheral blood monocyte-derived macrophages

value: male


title: 13_Standard culture, Basolateral infection (MOI 20), Replicate 1


title: HS-3-b [T21]

source_name: 3 day of heat stress_leaf

value: 3 day of heat stress


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad010

source_name: C57BL/6J Male P56 Mouse Brain

value: CA


title: HS-3-c [T22]


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad006


title: 12_Standard culture, Basolateral infection (MOI 0.7), Replicate 3

source_name: HIBCPP_Standard culture_Infection (MOI 0.7)

value: Infection (MOI 0.7)


title: HS-3-a [T06]


title: HS-1-c [T18]

source_name: 1 day of heat stress_leaf

value: 1 day of heat stress


title: HS-7-a [T10]


title: 11_Standard culture, Basolateral infection (MOI 0.7), Replicate 2


title: 10_Standard culture, Basolateral infection (MOI 0.7), Replicate 1


title: HS-1-b [T17]


title: 7_Standard culture, Control, Replicate 1

source_name: HIBCPP_Standard culture_No infection

value: No infection


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B8_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B8_ad010


title: HS-0-a [T02]

source_name: 0 day of heat stress_leaf

value: leaves of the seedling

value: 0 day of heat stress


title: 8_Standard culture, Control, Replicate 2


title: 9_Standard culture, Control, Replicate 3


title: HS-0-c [T14]

value: heat stress


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B8_ad004


title: 6_Inverted culture, Apical infection (MOI 0.7), Replicate 3

source_name: HIBCPP_Inverted culture_Infection (MOI 0.7)

value: Inverted culture


title: 5_Inverted culture, Apical infection (MOI 0.7), Replicate 2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B8_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B9_ad002


title: HR-7-c

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
To evaluate the quality of clean reads , fastqc was used with default parameters
Trinity was used to assemble the transcriptome and calculate the TMM with default parameters
Genome_build: Ziziphus jujuba ZizJuj_1.1 (https://www.ncbi.nlm.nih.gov/genome/15586?genome_assembly_id=219393 )
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and tab-delimited text files include read counts for each Sample and transcriptome fasta file

source_name: leaves of the seedling

value: leaf

value: 7 day of heat stress


title: 4_Inverted culture, Apical infection (MOI 0.7), Replicate 1

value: HIBCPP


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B8_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad001


title: HR-7-a


title: HR-5-c

value: 5 day of heat stress


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B8_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad010


title: 3_Inverted culture, Control, Replicate 3

source_name: HIBCPP_Inverted culture_No infection

value: Human choroid plexus papilloma cell line


title: 2_Inverted culture, Control, Replicate 2


title: 1_Inverted culture, Control, Replicate 1


title: FFPE_Human_Liver_normal_rep2

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

institute: New England Biolabs

data_processing:
Library strategy: UniNicE-seq
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Sequenced reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program, then mapped to human (hg38) or mouse (mm10) reference genome using bowtie2 with parameters --dovetail --no-unal --no-mixed --no-discordant --very-sensitive -I 0 -X 1000.
Duplicated reads were then removed using picard tool MarkDuplicates and mitochondrial reads were also discarded using the samtools.
peaks were called using MACS2 with the following parameters: -f BAMPE -m 4 100 --bdg --SPMR
coverage track was generated using deepTools bamCoverage with RPKM (Reads Per Kilobase per Million mapped reads) normalization
Genome_build: human: hg38; mouse: mm10
Supplementary_files_format_and_content: bigWig; RPKM nomalized coverage

source_name: Liver

growth_protocol: HCT116 cell line were routinely grown in DMEM media with 10% fetal bovine serum respectively, media being replaced every 3 days. For human tissue section, we purchased it from US Biomax Inc under the agreement of only research purpose. FFPE slides of the liver sample were also custom ordered from BioChain, USA, with 24-48 hrs formalin fixation

extract_protocol:
After we isolated the nuclei from cultured cell or tissue section, the nuclei was labeling with Nt.CviPII, Biotinylated 5mC-dNTP mixture, decroslinked for O/N at 65 degree, and then genomic DNA was extracted using phenol-chloroform method.
Biotin-labeled open chromatin DNA was captured by streptavidin bead and the beads were washed with high salt buffer for 4 times, and followed the library preparation procedure using NEBNext Ultra II DNA library Prep Kit (E7370S, New England Biolabs, Inc)

value: Adult normal liver

value: FFPE liver tissue

tag: tissue type

value: tissue section

tag: experimental variables

value: 5mC, onBead,fixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad006

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

value: CA

value: male

tag: strain


title: HS-0-b [T13]

tag: tissue


title: HR-5-b


title: HS-1-a [T04]

value: 1 day of heat stress


title: Human_Kidney_Fetal

data_processing:
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Sequenced reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program, then mapped to human (hg38) or mouse (mm10) reference genome using bowtie2 with parameters --dovetail --no-unal --no-mixed --no-discordant --very-sensitive -I 0 -X 1000.
Duplicated reads were then removed using picard tool MarkDuplicates and mitochondrial reads were also discarded using the samtools.
peaks were called using MACS2 with the following parameters: -f BAMPE -m 4 100 --bdg --SPMR
coverage track was generated using deepTools bamCoverage with RPKM (Reads Per Kilobase per Million mapped reads) normalization
genome build: human: hg38; mouse: mm10
processed data files format and content: bigWig; RPKM nomalized coverage
Library strategy: UniNicE-seq

source_name: tissue section

value: Kidney

value: fresh frozen

tag: developmental stage

value: Fetal normal


title: HR-5-a


title: HR-3-c

value: 3 day of heat stress


title: HR-1-c


title: HR-7-b


title: Human_Liver_Fetal

value: Liver


title: FFPE_Human_Liver_normal_rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad004


title: Human_Kidney_Normal

value: Adult Normal Kidney


title: HR-3-b

value: leaf


title: HR-1-b


title: Human_Lung_Fetal

value: Lung


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B6_ad006


title: Human_Liver_Normal

value: Adult Normal Liver


title: HR-1-a


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B6_ad001


title: HR-3-a


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B6_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B6_ad004


title: Human_Lung_Normal

value: Adult Normal lung


title: HR-0-b

value: 0 day of heat stress


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B6_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B6_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B5_ad012


title: HR-0-a


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad002


title: K562_5mC_OnBead

source_name: cell line

value: Blood

value: myelogenous leukemia

tag: cell line

value: 5mC, onBead, 2.5U, fixed


title: K562_C_OnBead

value: C, onBead, 2.5U, fixed


title: B6 SPF_17_19_20

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
The raw data was processed with cellranger
Paired-end reads were mapped to the mm9 genome with cellranger for gene-level read counts
Genome_build: mm9

source_name: Bone Marrow

extract_protocol: Libraries were generted using Genomics Chromium Single Cell ‘3 Solution Kit V2 from 10XGenomics.

tag: markers

value: Bone Marrow

value: Female

value: 3-4 months

tag: subject


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B7_ad008

city: La Jolla

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: brain region

value: CA

tag: Sex

value: male


title: MCF7_C_OnBead

value: Breast

value: breast cancer


title: HCT116_50U_5mC_OnBead

value: Colon

value: Colorectal cancer cells

value: 5mC, onBead, 50U, fixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B5_ad001


title: B6 SPF_16_18


title: B6 CVT_14_15


title: HCT116_25U_5mC_OnBead

value: 5mC, onBead, 25U, fixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B5_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B5_ad010


title: B6 CVT_11_12_13


title: HR-0-c

value: leaf

tag: treatment


title: HCT116_C_offBead

value: C, offBead, 2.5U, fixed


title: B6 CVT_8_9_10


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B5_ad004


title: B6 CVT_6_7


title: HCT116_C_OnBead


title: HCT116_5mC_offBead

value: 5mC, offBead, 2.5U, fixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B4_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B5_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B4_ad012


title: B6 SPF_3_4_5


title: MCF7_5mC_OnBead


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B4_ad010


title: TPR D Cyto rep1

first: Eric

last: Wolf

email: ewolf@neb.com, ericjwolf1@gmail.com

department: RNA Division

data_processing:
Transcript quantification was performed utilizing Salmon utilizing an index built from Gencode v.19 annotated protein-coding and long non-coding sequences (command: quant --validateMappings)
Gene level abundances were computed utilizing Tximport
FPKM calculations and fold changes were calculated utilizing DESeq2
Genome_build: hg19/Ghr37
Supplementary_files_format_and_content: DESeq2 FPKM calcualtions

molecule: polyA RNA

source_name: U2OS cells

growth_protocol: Osteosarcoma cell line (U2OS)  was grown in DMEM media supplemented with 10% FBS and 5% Pen-Strep

extract_protocol:
Control and TPR-depleted cells were harvested, fractionated using detergent, and RNA from these fractions was isolated using TRIZOL and Ambion PureLink kit (ThermoScientific)
RNA was poly(A)+ selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep kit (NEB, E7765S). We used NEBNext Multiplex Oligos for Illumina (Index Primers #1 - #24) (NEB, E7335S and E7500S) as the unique index primers.

treatment_protocol: Two independent lentiviral delivered shRNA (Sigma) was used to depleted TPR in U2OS cells

tag: genotype

value: TPR D Knockdown

tag: fraction

value: Cyto


title: B6 SPF_1_2

tag: age


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B4_ad006

last: Ecker

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B4_ad004


title: TPR D Nuc rep1

value: Nuc


title: Chim2_5

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

description: library of ILCs d15 post NB infection shield chimera host cells & TdTom+ donor cells Experiment2

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters (Li and Durbin, 2010). The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapped by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Lung

growth_protocol: C57BL/6 mice were purchased from Charles River Laboratories. All mice were bred and housed under specific pathogen free conditions at the animal facilities of the University of Würzburg (ZEMM and Institute for Immunology and Virology), Memorial Sloan-Kettering Cancer Center, Max Planck Institute of Immunobiology and Epigenetics, Freiburg and Centre Immunologie Luminy and were used in accordance with institutional guidelines and as approved by the local authorities

extract_protocol:
Lungs were harvested, chopped into small pieces and incubated in digestion buffer DMEM (Gibco 31966021); 0.25 mg/ml LiberaseTM TL (Research Grade 05401020001, Roche); 10mM Hepes (Gipco 1563049) for 45 mins at 37°C on Eppendorf rotator at 120rpm. Digestion was stopped with 20ml RPMI 1640 medium Thermo Fisher Scientific; 31870074) added with 50μM 2-mercaptoethonal (AppliChem, A1108). Cells were meshed through 70um cell strainer (Falcon 3522350) and washed and collected in FACS Buffer or 1× MojoSort buffer (BioLegend; 480017). Bone marrow cells from ilia, femora, and tibiae were isolated by crushing the bones in 1× MojoSort buffer. Bone marrow cells were filtered (CellTrics, 30 μm; Sysmex) and washed and collected in 1x MojoSort buffer.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: C57BL/6 /UbiquitintdT (``Ubow``)

value: Lung

value: 6-8 weeks


title: Chim2_8

institute: Max Planck Institute of Immunobiology and Epigenetics


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B4_ad002

value: CA


title: Chim2_6


title: TPR D Total rep1

value: Total


title: Chim2_7


title: TPR A Nuc rep1

value: TPR A Knockdown


title: HCT116_5mC_OnBead

tag: cell type

value: 5mC, onBead, 2.5U, fixed


title: TPR A Total rep1


title: Chim2_4


title: Chim2_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B3_ad012

value: male


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B3_ad007


title: Chim2_2


title: TPR D Cyto rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B3_ad002


title: TPR D Nuc rep3


title: TPR D Total rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B3_ad008


title: Chim2_1


title: Chim1_8


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B2_ad012


title: Chim1_7


title: TPR A Cyto rep1


title: TPR A Total rep3


title: Chim1_5


title: Chim1_6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B2_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B2_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B2_ad004


title: Chim1_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B3_ad004


title: Chim1_3


title: Control Cyto rep3

value: Control


title: Control Nuc rep3


title: Control Nuc rep1


title: Control Cyto rep1


title: Chim1_2


title: Chim1_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B2_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B12_ad010


title: ChieldD_4


title: Control Total rep3


title: TPR D Cyto rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B12_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B12_ad004


title: ChieldD_3


title: TPR A Cyto rep3


title: TPR A Nuc rep3


title: TPR D Nuc rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B2_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B12_ad002


title: ChieldD_2


title: TPR D Total rep2


title: ChieldD_1


title: d15chim2_4

description: library of ILCs d15 post NB infection shield chimera host cells & TdTom+ donor cells Experiment1


title: TPR A Total rep2


title: d15chim2_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad007


title: d15chim2_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad006


title: Control Cyto rep2


title: d15chim2_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B12_ad001


title: primary hepatocytes_Lipocalin replicate 3

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.17
Reads were mapped to hg38 using kallisto v 0.43.0 with parameters -b 50 -t 6; output data is given in transcripts per million (TPM)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with TPM values for all samples

source_name: human primary hepatocytes

growth_protocol: HepG2 cells were routinely cultured in 10% FBS DMEM and human primary hepatocytes grew in the specified growth medium from Triangle Research Laboratories (Research Triangle Park, NC).

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, 74104) with on-column DNase digestion.
Standard illumina protocol for mRNA stranded libraries

treatment_protocol: Both HepG2 cells and primary human hepatocyte were transduced with adenoviral GFP or LCN2 on day 2.

value: primary hepatocytes

tag: transduction

value: LCN2 overexpression


title: Control Nuc rep2


title: primary hepatocytes_Lipocalin replicate 2


title: primary hepatocytes_Lipocalin replicate 1


title: Control Total rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad012


title: d15chim1_4


title: Control Total rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B11_ad004


title: primary hepatocytes_control replicate 3

value: GFP

value: control


title: primary hepatocytes_control replicate 2


title: TPR A Cyto rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad012


title: d15chim1_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad010


title: primary hepatocytes_control replicate 1


title: d15chim1_1


title: exp2_Para22_8

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor -  Pair2 - Experiment2

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: wt dhpg rpf rep4

city: Worcester

first: Annie

last: Hien

address: 373 Plantation Street

institute: UMass Medical School Worcester

description: ca1.wt.dhpg.rep1-8.ribo.rsem.gene.summary.counts.txt

data_processing:
reads were separated based on sample barcode sequences using in-house codes
known 3’ adapter sequences and low quality bases were removed with Cutadapt(Martin, 2011) using parameters -O 2 -q 15 -a “TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG”
reads mapped to rRNA and tRNA genes were removed using Bowtie2(Langmead and Salzberg, 2012) with parameter -N 1
remaining reads were mapped to the mm10 genome using TopHat2(Kim et al., 2013)
For ribosome profiling, PCR duplicates were removed based on Unique Molecular Identifier sequences using in-house codes.
Uniquely mapped reads were then used as input to RSEM (Li and Dewey, 2011) for quantification of gene expression and mapped to RefSeq (v69) mouse coding sequences (RPF).
We used log transformed TPM expression values to correct for batch effects using ComBat following a null model (Leek et al., 2012) (v3.18.0).
Corrected values were transformed back to read counts using the expected size of each transcript informed by RSEM.
Batch-corrected counts were used to identify differentially translated/expressed genes with DESeq2 (Love et al., 2014, p. 2)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files include a summary of counts from RSEM quantification of all mm10 genes.

source_name: mouse hippocampal slice

growth_protocol: Animals were given ad libitum access to food and water and reared on a 12-hour light-dark cycle. P28-42 male mice were used.

extract_protocol:
Trizol LS was used to extract RNA for library preparation.
Ribosome profiling and RNA-seq libraries were prepared following published protocols (Heyer et al., 2015).

treatment_protocol: Hippocampal slices were treated with DHPG (100 µM) (Tocris) or ACSF (vehicle) for 5 min. Slices were then treated with cycloheximide (100 µg/ml) in ACSF, 4°C, snap-frozen on dry ice/EtOH bath, and stored at -80°C.

value: wild-type

value: DHPG

tag: experiment

value: ribosome profiling


title: HepG2 cells_Lipocalin replicate 3

source_name: HepG2 cells


title: wt dhpg rpf rep3


title: HepG2 cells_Lipocalin replicate 2


title: wt dhpg rpf rep5


title: d15chim1_2

value: C57BL/6 /UbiquitintdT (``Ubow``)


title: exp2_Para22_6

value: Lung


title: wt dhpg rpf rep2


title: HepG2 cells_Lipocalin replicate 1


title: wt dhpg rpf rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad004

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad007


title: HepG2 cells_control replicate 3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad002


title: exp2_Para22_2


title: HepG2 cells_control replicate 1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad008


title: exp2_Para22_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad012


title: wt bas rpf rep4

value: vehicle


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B10_ad001

value: CA


title: wt bas rpf rep5


title: wt bas rpf rep2


title: exp2_Para22_7


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad001


title: wt bas rpf rep3


title: HepG2 cells_control replicate 2


title: exp2_Para21_8

description: library of ILCs d15 post NB infection parabiotic C45.1 host_Cd45.2 donor -  Pair2 - Experiment2


title: exp2_Para21_7


title: exp2_Para22_1


title: wt dhpg rna rep5

description: ca1.wt.dhpg.rep1-8.rna.rsem.gene.summary.counts.txt

value: RNA-seq


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad006


title: exp2_Para22_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad004


title: wt dhpg rna rep3


title: exp2_Para21_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad008


title: wt dhpg rna rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_B1_ad002


title: wt bas rpf rep1


title: exp2_Para21_4


title: post_BRAFi_melanoma_metastasis_from_patient_patB38

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray reader.

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

source_name: post-treament formalin-fixed paraffin embedded melanoma metastasis

label_protocol: According to Illumina whole genome DASL assay

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: individual

tag: disease state

value: metastatic melanoma

tag: metastatic site

value: subcutaneous

value: F

value: Vemurafenib (BRAFi)

tag: time

value: post-BRAFi


title: pre_BRAFi_melanoma_metastasis_from_patient_patB35

source_name: pre-treament formalin-fixed paraffin embedded melanoma metastasis

value: M

value: pre-BRAFi


title: post_BRAFi_melanoma_metastasis_from_patient_patB35


title: exp2_Para21_3

tag: strain

tag: tissue


title: wt dhpg rna rep1


title: exp2_Para21_2


title: wt dhpg rna rep4


title: exp2_Para21_6


title: wt bas rna rep4


title: pre_BRAFi_melanoma_metastasis_from_patient_patB38

value: control


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad001

value: male


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad012


title: post_BRAFi_melanoma_metastasis_from_patient_patB33


title: pre_BRAFi_melanoma_metastasis_from_patient_patB33


title: post_BRAFi_melanoma_metastasis_from_patient_patB30


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad010


title: wt bas rna rep3

value: wild-type


title: wt bas rna rep2


title: exp2_Para12_7

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor -  Pair1 - Experiment2

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: TPR A Nuc rep2

value: TPR A Knockdown

value: Nuc

tag: cell line


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad006


title: wt bas rna rep1


title: exp2_Para12_6

value: Lung


title: exp2_Para12_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad004


title: post_BRAFi_melanoma_metastasis_from_patient_patB16

value: visceral


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad002

value: CA


title: exp2_Para12_4


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 17

city: New York

first: Tiago

last: Castro

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Raw fastq files derived from our RNA-seq libraries were processed with cellranger count (v3.1.0) using the 10x Genomics prebuilt mouse reference (v3.0.0 mm10). Our libraries were processed independently and merged into a single experiment at the analysis level using Seurat (v3.1.1) (Stuart et al., 2019). Quality control was performed by removing cells with high (> 5%) mitochondrial UMI content. Cells having more than 4000 or less than 200 genes were excluded from our analysis. TCR contigs and annotation were performed with the Cellranger vdj workflow from 10x Genomics and the prebuild mouse reference (v3.1.0 mm10). Paired TCR clones were defined by the V, (D), J and CDR3 nucleotide composition for alpha and beta chains. TCR clone sharing was assigned to cells expressing identical V, (D), J, and CDR3 nucleotide and amino acid sequences.
Raw fastq files were processed by using the mouse transcriptome (gencode M23) with the kallisto (v0.46) software (Bray et al., 2016). Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R (Pimentel et al., 2017). Shortly, we modeled batch effect and our experimental design using the sleuth_fit function and detected differentially expressed genes between all groups by the likelihood ratio test (lrt). To spot significantly expressed genes between group pairs, we used the wald-test function. Genes with false discovery rate less than 0.05 and 1 log2 fold-change were used in downstream analysis. Gene set enrichment analysis (GSEA) was performed by using signature gene sets in gmt format and a pre-ranked gene list by log2 fold-change between two groups as input for the fgsea package/R (Korotkevich et al., 2019). Gene ontology (GO) analysis was executed by comparing all detected genes as our background and the lists of differentially expressed genes against the biological processes gene sets by using topGO/R (Alexa and Rahnenfuhrer, 2019; Carlson M, 2019).
For Miseq data, fastq files were de-multiplexed and paired-end reads were assembled at their overlapping region using PANDASEQ (Masella et al., 2012) and FASTAX toolkit. Demultiplexed and collapsed reads were assigned to wells according to barcodes. Fasta files from both Sanger and Miseq sequences were aligned and analyzed on IMGT (imgt.org/HighV-QUEST) (Brochet et al., 2008). Cells with identical TCRb CDR3 nucleotide sequences were considered as the same clones. Clonality was confirmed by sequencing TCRa of the expanded clones as assessed by TCRb sequencing for mice shown in Figure S2F and H. Clonality was assigned based on paired TCRab for mice shown in Figure 2 and S2C. Only in frame junction sequences of TCRb were included in the analysis. For fixed-Vb6 mice shown in Figure 2 and S2, each TCRa CDR3 was considered a clone.
Genome_build: mm10

source_name: Natural IEL (nIEL)

extract_protocol:
Sorted cells (300-800 cells) were lysed in a guanidine thiocyanate buffer (TCL buffer, Qiagen) supplemented with 1% β-mercaptoethanol. RNA was isolated by solid-phase reversible immobilization bead cleanup using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified as described (Trombetta et al., 2014).
Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq500 for a total yield of 400M reads.

tag: sequencing batch

tag: experiment batch

tag: cell

tag: tcr

value: NEG


title: pre_BRAFi_melanoma_metastasis_from_patient_patB30

value: metastatic melanoma

tag: Sex

tag: treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C10_ad002

tag: brain region

tag: age


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A9_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A8_ad012


title: exp2_Para12_3


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 16

value: POS


title: exp2_Para12_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A8_ad001


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 15


title: KO3_HL60-RNA

city: Ciudad Real

first: Sara

last: Artigas Jerónimo

state: Ciudad Real

address: Ronda de Toledo 12

department: Sanidad y Biotecnología (SaBio)

country: Spain

institute: Instituto de Investigación en Recursos Cinegéticos (IREC)

data_processing:
HiSeq 2x150 PE HO.
Sequencing reads were trimmed  to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Then, trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the START aligner v.2.5.2b.
Hit counts for genes and exons were generated and compared  separately. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Reads were strand-specifically counted.
Gene hit counts were used for downstream differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with abundance messurements for each gene and sample. The Wald test p-value, the Benjamini-Hochberg adjusted p-value,  log2 fold change and gene ID and name for each gene are included in the same table.

source_name: human Caucasian promyelocytic leukemia HL60 cells

growth_protocol: WT and AKR2 KO HL60 cells were grown and mantained in RPMI 1640 medium (Invitrogen) supplemented with fetal bovine serum (FBS  Gibco) at a concentration of 10%. Cells were grown in a humidifies incubator with 5% carbon dioxide at 37ºC

extract_protocol:
Cells (8 x10e6 cells per biological replicate) were washed with PBS and pelleted by centrifugation. Then, total RNA was isolated using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) and used for sequencing.
RNA-seq library preparation and sequencing were performed by Genewiz's service.

tag: cell type

value: promyelocytic leukemia

tag: genotype

value: AKR2 knock down


title: KO2_HL60-RNA


title: exp2_Para21_1


title: pre_BRAFi_melanoma_metastasis_from_patient_patB08

tag: individual

value: subcutaneous

value: F


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 13


title: exp2_Para11_8

description: library of ILCs d15 post NB infection parabiotic C45.1 host_Cd45.2 donor -  Pair1 - Experiment2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A8_ad008

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56


title: exp2_Para12_1

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor  -  Pair1 - Experiment1


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 14


title: post_BRAFi_melanoma_metastasis_from_patient_patB04

tag: disease state

value: M

value: Vemurafenib (BRAFi)

value: post-BRAFi


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 18


title: post_BRAFi_melanoma_metastasis_from_patient_patB08

tag: metastatic site


title: pre_BRAFi_melanoma_metastasis_from_patient_patB04

value: control

tag: time

value: pre-BRAFi


title: pre_BRAFi_melanoma_metastasis_from_patient_patB16


title: KO1_HL60-RNA


title: exp2_Para11_6

tag: strain

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad001

value: male


title: WT3_HL60-RNA

value: wild type


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad012


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 12


title: WT2_HL60-RNA


title: exp2_Para11_5

tag: tissue

value: Lung


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad007

value: CA


title: WT1_HL60-RNA

tag: cell line


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A8_ad006


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 10

tag: sequencing batch


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad010


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 9

tag: experiment batch

value: NEG


title: BmN4_Input_WT_45min_rep1

city: Paris

first: Ines Anna

last: Drinnenberg

address: 26 Rue d'Ulm

institute: Institut Curie

data_processing:
Adapter-trimmed chIP-seq reads were aligned to the B. mori genome assembly or T. ni genome assembly using Bowtie2- 2.2.9 Alignment files (sam) were converted to bam, sorted, indexed. Duplicates were removed using Picard Tools (v 2.6.0). ChIp-seq scores were visualized in IGV as bigwig files representing average log2 ratio of (IP/Input) in genome-wide 1 kb windows generated using Deeptools bamCompare function.
Adapter trimmed mRNA-seq reads were aligned to the B. mori genome assembly or T. ni genome assembly using STAR-2.7.0a. Alignment files (sam) were converted to bam, sorted, indexed and used to generate 1 kb resolution BPM-normalized bigwig tracks using Deeptools bamCoverage function. Unique, multimapping and duplicate reads were included.
Genome_build: Bombyx mori: genome assembly downloaded from Silkbase: http://silkbase.ab.a.u-tokyo.ac.jp
Genome_build: Trichoplusia ni: GenBank Assembly Accession: GCA_003590095.1
Supplementary_files_format_and_content: ChIP-seq: bigwig files generated using RPKM-normalized Bam files for IP and Input using Deeptools bamCompare function. Each bigwig fille represents average log2 ratio of IP/Input in genome-wide 1kb windows.
Supplementary_files_format_and_content: mRNA-seq: bigwig files genrated using Deeptools bamCoverage function. Each bigwig file represents bins per million mapped reads (BPM) in genome-wide 1 kb windows.

source_name: ovary-derived cells

extract_protocol:
ChIP-seq: DNA-protein complexes (either cross-linked with formaldehyde or not) were isolated with specific antibody after chromatin solubilization using MNase and sonication. isolated DNA was purified using phenol/chloroform/isoamyl alcohol extraction method.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
mRNA-seq: Total RNA was extracted from cells using Trizol reagent.
All steps of Illumina library preparation and sequencing were carried out at the Curie Institute’s sequencing platform using TruSeq ChIPseq protocol or TruSeq Stranded mRNA protocol.
ChIP-seq or mRNA-seq

value: ovary-derived cells


title: exp2_Para11_4


title: exp2_Para11_3


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 8

tag: cell

value: POS


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad006


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 7

tag: tcr


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 6


title: BmN4_FLAG_WT_15min


title: BmN4_CENP-T_WT_45min_rep1


title: exp2_Para11_2


title: exp2_Para11_1


title: Para22_7

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor -  Pair2 - Experiment1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad008

tag: Sex


title: Para22_8


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 4


title: BmN4_Input_WT_15min


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 5


title: Para22_6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad012


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad001


title: Para22_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad010


title: R571-6_6_KO-TCR

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Star/2.6.0b
Reads per gene were counted with HT-Seq/0.9.1
Read counts were normalized with R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads for the  genes

source_name: KO_Splenic naïve CD8 T cells

extract_protocol:
anti-CD3 and anti-CD28 24 hours treated CD8 T cells used for total RNA isolation with Trizol (Invitrogen), and subjected to RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: NIK-CD4Cre-OT-I (KO)

value: 6 to 8-week old

value: spleen

value: Splenic naive CD8 T cells


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 2


title: R571-5_5_KO-TCR


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad004

tag: brain region


title: BmN4_CENP-T_WT_60min


title: Para22_4

tag: age


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A7_ad002


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 1


title: R571-4_4_KO-TCR

tag: cell type


title: Para22_3


title: R571-3_3_WT-TCR

source_name: WT_Splenic naïve CD8 T cells

tag: genotype

value: Wild Type-OT-I (WT)


title: 10x TCR Single cell sequencing of IELs 2

description: TCR.Meta.csv

data_processing:
Library strategy: TCR-seq
Raw fastq files derived from our RNA-seq libraries were processed with cellranger count (v3.1.0) using the 10x Genomics prebuilt mouse reference (v3.0.0 mm10). Our libraries were processed independently and merged into a single experiment at the analysis level using Seurat (v3.1.1) (Stuart et al., 2019). Quality control was performed by removing cells with high (> 5%) mitochondrial UMI content. Cells having more than 4000 or less than 200 genes were excluded from our analysis. TCR contigs and annotation were performed with the Cellranger vdj workflow from 10x Genomics and the prebuild mouse reference (v3.1.0 mm10). Paired TCR clones were defined by the V, (D), J and CDR3 nucleotide composition for alpha and beta chains. TCR clone sharing was assigned to cells expressing identical V, (D), J, and CDR3 nucleotide and amino acid sequences.
Raw fastq files were processed by using the mouse transcriptome (gencode M23) with the kallisto (v0.46) software (Bray et al., 2016). Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R (Pimentel et al., 2017). Shortly, we modeled batch effect and our experimental design using the sleuth_fit function and detected differentially expressed genes between all groups by the likelihood ratio test (lrt). To spot significantly expressed genes between group pairs, we used the wald-test function. Genes with false discovery rate less than 0.05 and 1 log2 fold-change were used in downstream analysis. Gene set enrichment analysis (GSEA) was performed by using signature gene sets in gmt format and a pre-ranked gene list by log2 fold-change between two groups as input for the fgsea package/R (Korotkevich et al., 2019). Gene ontology (GO) analysis was executed by comparing all detected genes as our background and the lists of differentially expressed genes against the biological processes gene sets by using topGO/R (Alexa and Rahnenfuhrer, 2019; Carlson M, 2019).
For Miseq data, fastq files were de-multiplexed and paired-end reads were assembled at their overlapping region using PANDASEQ (Masella et al., 2012) and FASTAX toolkit. Demultiplexed and collapsed reads were assigned to wells according to barcodes. Fasta files from both Sanger and Miseq sequences were aligned and analyzed on IMGT (imgt.org/HighV-QUEST) (Brochet et al., 2008). Cells with identical TCRb CDR3 nucleotide sequences were considered as the same clones. Clonality was confirmed by sequencing TCRa of the expanded clones as assessed by TCRb sequencing for mice shown in Figure S2F and H. Clonality was assigned based on paired TCRab for mice shown in Figure 2 and S2C. Only in frame junction sequences of TCRb were included in the analysis. For fixed-Vb6 mice shown in Figure 2 and S2, each TCRa CDR3 was considered a clone.
Genome_build: mm10

source_name: Intraepithelial lymphocytes (IELs)

extract_protocol:
Tomato+ and Tomato- CD4+ IELs were sorted, counted for viability and immediately subjected to library preparation. The scRNA-seq and scTCR-seq libraries were prepared using the 10x Single Cell Immune Profiling Solution Kit, according to the manufacturer’s instructions at the Genomics core of Rockefeller University.
The single-cell TCR libraries were sequenced on an Illumina NextSeq500 to a minimum sequencing depth of 5,000 reads per cell using read lengths of 150 bp read 1, 8 bp i7 index, 150 bp read 2.

value: Foxp3eGFP-CreERT2 Rosa26|s|-td-Tomato

tag: tomato

value: CD4 cells from intestinal epithelium


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad006


title: Para22_2


title: 10x TCR Single cell sequencing of IELs 1

description: TCR.Meta.csv


title: BmN4_CENP-T_WT_15min


title: Para22_1


title: 10x mRNA Single cell sequencing of IELs 2

description:
RNA.Meta.csv
data.10x.rds

extract_protocol:
Tomato+ and Tomato- CD4+ IELs were sorted, counted for viability and immediately subjected to library preparation. The scRNA-seq and scTCR-seq libraries were prepared using the 10x Single Cell Immune Profiling Solution Kit, according to the manufacturer’s instructions at the Genomics core of Rockefeller University.
 The scRNA libraries were sequenced on an Illumina NextSeq500 to a minimum sequencing depth of 50,000 reads per cell using read lengths of 26 bp read 1, 8 bp i7 index, 98 bp read 2.


title: R571-1_1_WT-TCR


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A6_ad002


title: Para21_8

description: library of ILCs d15 post NB infection parabiotic C45.1 host_Cd45.2 donor -  Pair2 - Experiment1


title: Pos_FH_H2A.Z_MEFs

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

description: The crispr-cas9 system was used to insert DNA element encoding the HA-HA-FLAG-FLAG amino acids in frame with the N terminus of the h2afz1 gene in MEFs.

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover v0.9.2 (https://sourceforge.net/projects/dimerremover/). Reads were mapped to the mouse genome (mm9) using Bowtie v1.0.0 with the following arguments: -m 1 --strata --best -y -S –l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: WIG track files were generated using WigMaker. Scores represent tag numbers per total uniquely mapped reads. Bigwig files were generated using Deeptools bamCoverage v2.5.0 (Ramírez et al., 2016) with the following parameters "--MNase --binSize 1 --skipNonCoveredRegions --outFileFormat bigwig --normalizeTo1x 2150570000".

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: MEFs are grown in glutamine and pyruvate containing DMEM, supplemented with 10% serum, 1% penicillin-streptomycin .

extract_protocol:
Sub-confluent MEFs expressing FLAG-HA tagged endogenous H2A.Z were lysed in hypotonic buffer (10 mM Tris-HCl at pH 7.65, 1.5 mM MgCl2, 10 mM KCl) and disrupted by Dounce homogenizer. The cytosolic fraction was separated from the nuclei by centrifugation at 4°C. Nuclei were re-suspended in sucrose buffer (20 mM Tris-HCl at pH 7.65, 15 mM KCl 60 mM NaCl, 0.15 mM spermine, 0.5 mM spermidine) adjusted with high-salt buffer (20 mM Tris-HCl at pH 7.65, 25 % glycerol, 1.5 mM MgCl2, 0.2 mM EDTA, 900 mM NaCl) to get a final NaCl concentration of 300 mM. The nuclear-soluble fraction was recovered by centrifugation at 4°C. The pellet containing chromatin fraction was incubated in sucrose buffer containing 1mM CaCl2, and MNase (2.5U/g of cells) 10 min at 37°C. Digestion was stopped with 4 mM EDTA and mononucleosomes were recovered by centrifugation at 4°C. Tagged nucleosomes were immunoprecipitated with anti-Flag M2-agarose (Sigma), eluted with Flag peptide (0.5 mg/mL), further affinity-purified with anti-HA antibody-conjugated agarose, and eluted with HA peptide (1 mg/mL). The HA and Flag peptides were first buffered with 50 mM Tris-Cl (pH 8.5), then diluted to 4 mg/mL in TGEN 150 buffer (20 mM Tris at pH 7.65, 150 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, 10% glycerol, 0 0.01% NP40), and stored at −20°C until use. Between each step, beads were washed in TGEN 150 buffer. Nucleosomes were submitted to RNase and proteinase K digestion, and DNA was extracted by phenolchloroform.  Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads (for ChIP-seq analysis) or paired-end 50 bp reads (for nucleosome positioning analysis) following Illumina's instructions.

tag: genotype/variation

value: HA-HA-FLAG-FLAG in frame with the N terminus of the h2afz1 gene

value: MEFs were derived from E13.5 embryos

value: Mouse embryonic fibroblasts (MEFs)

tag: chip antibody

value: Double-immunoaffinity purification of native FLAG-HA tagged mononucleosomes


title: Para21_7

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad001

value: male


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad012

value: CA


title: Para21_6

value: Lung


title: FH_H2A.Z_MEFs


title: 10x mRNA Single cell sequencing of IELs 1

description:
RNA.Meta.csv
data.10x.rds


title: WT_SC_biological_rep_3

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Illumina BaseSpace software was used for basecalling.
Sequenced reads were mapped to mm10 whole genome using hisat2 v 2.1.0.
Mapped reads (bam files) were converted to bigwig using bamCoverage (v3.4.0, from deepTools)
Genome_build: mm10

source_name: satellite cells

extract_protocol:
Mouse hindlimb satellite cells were isolated by Fluorescence Activated Cell Sorting (FACS) by selecting for ITGA7+, Hoechst+, Lin- (CD45-, CD11b-, CD31-, SCA1-) cells. 3000 satellite cells per mouse were immediately lysed by sorting directly into reaction buffer (SMART-Seq V4 Ultra Low Input kit, Takara Bio).
RNA from lysed FACS-sorted satellite cells was converted into cDNA libraries using SMART-Seq V4 Ultra Low Input kit (Takara Bio). Illumina sequencing adapters were then added using the Nextera XT DNA library preparation kit (Illumina).

value: wild type

value: 4 weeks

value: satellite cells

tag: gender


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad007

department: Genomic Analysis Laboratory

tag: strain


title: WT_SC_biological_rep_2


title: DMSO rep6

city: Ann Arbor

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

data_processing:
Basecalling was performed by the Illumina HiSeq4000
FastQC was used for FASTQ file quality control
Sequences were aligned to the mm10 transcriptome using Kallisto v0.43.1 with parameters -b 100 --single -l 200 -s 20
Transcripts were counted and converted to genes using Tximport v1.8.0
Genome_build: mm10
Supplementary_files_format_and_content: csv files for TPMs (transcript per million counts) for each sample will be included

source_name: Primary tail fibroblast cell line

growth_protocol: The CCG-HTA-1 cells are grown in DMEM containing high glucose and no sodium pyruvate. This is supplemented with 10% FCS and a penicillin/streptomycin/antimycotic solution.

extract_protocol:
RNA was extracted from cells 48 hours after compound treatment using RNAzol, as per the manufacture, and ribodepleted using [WHAT KIT?????]
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: Cells were cultured in ambient oxygen at 37C with 10% CO2. Cells were added so that they would be approximately 80% confluent at the time of exposure to the chemicals being tested. 24 hours after cells were added the cells had attached and the chemicals were added to the culture media of the cells. After the appropriate time cells were harvested.

tag: agent

value: DMSO rep6

tag: passage

value: Passage 4

value: Mice were 5-8 weeks when cells were collected


title: WT_SC_biological_rep_1


title: DMSO rep5

tag: cell line

value: DMSO rep5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad010


title: Para21_4

tag: tissue


title: Para21_2


title: M_Kidney_nonfix_25K

source_name: tissue

extract_protocol:
After we isolated the nuclei from cultured cell or tissue section, the nuclei was labeling with Nt.CviPII, Biotinylated 5mC-dNTP mixture, decroslinked for O/N at 65 degree, and then genomic DNA was extracted using phenol-chloroform method.
Biotin-labeled open chromatin DNA was captured by streptavidin bead and the beads were washed with high salt buffer for 4 times, and followed the library preparation procedure using NEBNext Ultra II DNA library Prep Kit (E7370S, New England Biolabs, Inc)

value: Kidney

value: Kidney tissue

tag: developmental stage

value: Adult mouse

tag: experimental variables

value: 5mC, onBead, 25K cells, nonfixed


title: DMSO rep3

value: DMSO


title: DMSO rep4

value: DMSO rep4


title: DMSO rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad002

tag: Sex


title: M_Kidney_nonfix_10K

value: 5mC, onBead, 10K cells, nonfixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad006

value: male


title: Para21_1

source_name: Lung

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: M_Kidney_nonfix_5K

value: 5mC, onBead, 5K cells, nonfixed


title: Paral12_8

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor -  Pair1 - Experiment1

value: Lung


title: M_Kidney_nonfix_500

value: 5mC, onBead, 500 cells, nonfixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad012

value: CA


title: M_Kidney_fix_25K

value: 5mC, onBead, 25K cells, fixed


title: DMSO rep1

value: Passage 4


title: R571-2_2_WT-TCR

city: Houston

tag: strain background

value: Wild Type-OT-I (WT)

value: 6 to 8-week old

value: spleen

value: Splenic naive CD8 T cells


title: Para21_5


title: Podofilox rep3

value: Podofilox

value: Mice were 5-8 weeks when cells were collected


title: M_Kidney_nonfix_250

value: Kidney

value: Kidney tissue

value: Adult mouse

value: 5mC, onBead, 250 cells, nonfixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad010

tag: brain region

value: male


title: Podofilox rep2

tag: age


title: Paral12_7

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: Para21_3

value: Lung


title: Paral12_6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad006


title: Bulk_RNA-Sequencing of Wild Type or  Tracf/f mice 11

tag: sequencing batch

tag: experiment batch

tag: cell

tag: tcr

value: POS


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A5_ad008

value: CA


title: Podofilox rep1


title: AEG 3482 rep3


title: Paral12_5


title: Para12_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad002


title: T_Cell_5K

source_name: cells

value: Lymphocyte

tag: cell type

value: T-cell lymphoma

value: 5mC, onBead, 5K cells, fixed


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad004