title: Post_P012_t (ATAC-Seq)

first: Yuanyuan

last: Zhang

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking Univerisity

description: 10X Genomics platform

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level, identify TCR sequences and quantify ATAC-seq peaks .
Genome_build: GRCh38 for RNA expression,TCR data and ATAC peaks.

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated with HISTOPAQUE-1077 (Sigma-Aldrich) solution. In brief, 3 ml fresh peripheral blood was collected at baseline, 4 weeks after treatment initiation and disease progression in EDTA anticoagulant tubes and subsequently layered onto HISTOPAQUE-1077. Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco) with 10% FBS (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-µm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library, and 10x Chromium Single cell ATAC-seq Library

treatment_protocol: Half of 22 TNBC patients were treated with paclitaxel monotherapy and the other half were treated with paclitaxel plus atezolizumab as first-line treatment

tag: disease state

value: TNBC patient

tag: group

value: Post-treatment


title: Prog_P013_t (ATAC-Seq)

status: Public on Sep 15 2021

type: SRA

city: Beijing

country: China

description: 10X Genomics platform

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: liver

value: Progression

tag: treatment

value: Chemo


title: Pre_P020_t (ATAC-Seq)

description: 10X Genomics platform

value: breast

value: Pre-treatment


title: Liver High fat/cholic acid diet-fed WSB strain rep1

city: Davis

first: Brian

middle: J

last: Bennett

state: CA

address: 430 West Health Sciences Drive

department: Obesity and Metabolism

country: USA

institute: Western Human Nutrition Research Center, ARS

library_source: transcriptomic

data_processing:
Raw read data was filtered using HTStream (version 1.1.0, https://github.com/ibest/HTStream), which included screening for contaminants (such as PhiX and rRNA), PCR deduplication readout, quality-based trimming, adapter trimming, and overlapping paired-end reads.
For deep sequenced two B6 and two CAST samples, we randomly took 50% of the reads from samples. contaminants (such as PhiX and rRNA), PCR deduplication readout, quality-based trimming, adapter trimming, and overlapping paired-end reads
STAR (version 2.7.0f) was used to align the processed data to custom reference mouse genomes constructed by incorporating genetic variants of eight founder strain into reference mouse genome GRCm38 using g2gtools (https://github.com/churchill-lab/g2gtools).
Log2 transformed count per million (CPM) were calculated. Custom R code was then used for read and alignment quality assessment as well as collating counts into a single table for downstream analysis  .
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2CPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and Total RNA was extracted from frozen liver samples with the Maxwell 16 LEV simplyRNA Tissue Kit according to the manufacturer’s protocol. The RNA-seq libraries were constructed from total RNA following the Illumina TruSeq RNA library construction protocol. The size of the adapted fragments in the libraries was determined by running an Agilent DNA 1000 Chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: WSB/EiJ

tag: age

value: 24 weeks

tag: genotype

value: wild type

value: High fat/cholic acid diet

tag: Sex

value: Female


title: okae bts5-150357

city: Vienna

first: Giovanni

last: Sestini

address: Dr.-Bohr-Gasse 3, 1030 Wien

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

data_processing:
Smart-Seq transcriptome sequencing experiments were analyzed using genome sequence and gene annotation from Ensembl GRCh38 release 103 as reference. For gene expression quantification RNA-seq reads were first trimmed using trim-galore v0.6.6 and thereafter aligned to the genome using hisat2 v2.2.1. Uniquely mapping reads in genes were quantified using htseq-count v0.13.5 with parameter -s no. TPM estimates were obtained using RSEM v1.3.3 with parameter --single-cell-prior. Further analysis was performed in R v4.0.3 with Seurat v4.0.1. Based on initial evaluation of per-cell quality control metrices and outlier identification using the median absolute deviation algorithm, cells with <= 2000 detected genes or >= 12.5% mitochondrial gene percentage were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: tsv of read counts per gene

molecule: polyA RNA

source_name: stem cells

extract_protocol:
Smart-Seq2 protocol
Smart-Seq2


title: Liver AIN-93M diet-fed NZO strain rep3

value: NZO/HILtJ

value: AIN-93M diet


title: okae bts5-150355


title: Liver AIN-93M diet-fed NZO strain rep2


title: okae bts5-150352


title: okae bts5-150351


title: okae bts5-150350


title: okae bts5-150356


title: Pre_P023_t (ATAC-Seq)

description: 10X Genomics platform


title: okae bts5-150366


title: Pre_P012_t (ATAC-Seq)

description: 10X Genomics platform


title: Liver AIN-93M diet-fed NZO strain rep1


title: okae bts5-150353


title: okae bts5-150354


title: Prog_P010_b

description: 10X Genomics platform

value: blood


title: Prog_P008_b

description: 10X Genomics platform


title: okae bts5-150344


title: okae bts5-150343


title: okae bts5-150347


title: Prog_P016_b

description: 10X Genomics platform


title: okae bts5-150349


title: Liver AIN-93M diet-fed NOD strain rep2

value: NOD/ShiLtJ


title: Liver AIN-93M diet-fed NOD strain rep3


title: okae bts5-150341


title: Prog_P002_b

description: 10X Genomics platform


title: okae bts5-150348


title: Prog_P013_t

description: 10X Genomics platform


title: Liver AIN-93M diet-fed NOD strain rep1


title: okae bts5-150345


title: Prog_P013_b

description: 10X Genomics platform


title: Liver AIN-93M diet-fed 129 strain rep3


title: okae bts5-150342


title: Prog_P007_t

description: 10X Genomics platform

value: brain


title: okae bts5-150337


title: okae bts5-150340


title: okae bts5-150339


title: okae bts5-150338


title: okae bts5-150346


title: okae bts5-150336


title: Liver AIN-93M diet-fed B6 strain rep3


title: Liver AIN-93M diet-fed B6 strain rep2


title: okae bts5-150335


title: Liver AIN-93M diet-fed B6 strain rep1


title: Liver AIN-93M diet-fed 129 strain rep1


title: okae bts5-150334


title: okae bts5-150333


title: Liver AIN-93M diet-fed 129 strain rep2


title: Post_P005_t

description: 10X Genomics platform

value: TNBC patient


title: Liver AIN-93M diet-fed AJ strain rep3

value: A/J


title: Post_P008_b

description: 10X Genomics platform

value: Post-treatment


title: Prog_P007_b

description: 10X Genomics platform

value: Progression


title: okae bts5-150332


title: okae bts5-150331


title: Liver AIN-93M diet-fed AJ strain rep2

value: liver


title: okae bts5-150330


title: Post_P017_t

description: 10X Genomics platform


title: okae bts5-150328


title: Liver AIN-93M diet-fed AJ strain rep1


title: okae bts5-150327


title: okae bts5-150326


title: Post_P010_b

description: 10X Genomics platform


title: Liver High fat/cholic acid diet-fed PWK strain rep3

value: PWK/PhJ


title: okae bts5-150324


title: Post_P017_b

description: 10X Genomics platform


title: Post_P020_t

description: 10X Genomics platform

value: breast

value: Chemo


title: Liver High fat/cholic acid diet-fed PWK strain rep2

value: 24 weeks


title: okae bts5-150319


title: Liver High fat/cholic acid diet-fed CAST strain rep2

value: CAST/EiJ

value: wild type


title: okae bts5-150318


title: Liver High fat/cholic acid diet-fed CAST strain rep3

value: High fat/cholic acid diet

value: Female


title: Post_P020_b

description: 10X Genomics platform


title: okae bts5-150322


title: Post_P011_b

description: 10X Genomics platform


title: Liver High fat/cholic acid diet-fed PWK strain rep1


title: Post_P019_t

description: 10X Genomics platform


title: okae bts5-150320


title: Post_P005_b

description: 10X Genomics platform


title: okae bts5-150317


title: Liver High fat/cholic acid diet-fed CAST strain rep1


title: okae bts5-150316


title: Post_P019_b

description: 10X Genomics platform


title: okae bts5-150329


title: okae bts5-150321


title: okae bts5-150315


title: okae bts5-150314


title: okae bts5-150325


title: Liver High fat/cholic acid diet-fed AJ strain rep3


title: okae bts5-150312


title: Post_P022_b

description: 10X Genomics platform


title: okae bts5-150323


title: okae bts5-150313


title: Liver High fat/cholic acid diet-fed NZO strain rep3

value: NZO/HILtJ


title: Post_P022_t

description: 10X Genomics platform


title: okae bts5-150310


title: Liver High fat/cholic acid diet-fed NZO strain rep2


title: Post_P025_t

description: 10X Genomics platform


title: primed H9-150308


title: primed H9-150309


title: Liver High fat/cholic acid diet-fed NZO strain rep1


title: primed H9-150306


title: Post_P025_b

description: 10X Genomics platform

value: blood


title: primed H9-150307


title: Post_P016_t

description: 10X Genomics platform


title: Liver High fat/cholic acid diet-fed NOD strain rep3

value: NOD/ShiLtJ


title: primed H9-150304


title: primed H9-150303


title: okae bts5-150311


title: Post_P016_b

description: 10X Genomics platform


title: primed H9-150300


title: Liver High fat/cholic acid diet-fed NOD strain rep1


title: primed H9-150302


title: Liver High fat/cholic acid diet-fed AJ strain rep2


title: Post_P024_b

description: 10X Genomics platform


title: Liver High fat/cholic acid diet-fed 129 strain rep3


title: Post_P001_b

description: 10X Genomics platform


title: Liver High fat/cholic acid diet-fed NOD strain rep2


title: primed H9-150297


title: Post_P018_t

description: 10X Genomics platform


title: primed H9-150299


title: Liver High fat/cholic acid diet-fed 129 strain rep2


title: primed H9-150296


title: primed H9-150305


title: primed H9-150295


title: Liver High fat/cholic acid diet-fed 129 strain rep1


title: primed H9-150293


title: primed H9-150294


title: Post_P018_b

description: 10X Genomics platform


title: Post_P002_t

description: 10X Genomics platform


title: Liver High fat/cholic acid diet-fed B6 strain rep3


title: primed H9-150291


title: primed H9-150292


title: primed H9-150290


title: primed H9-150289


title: Post_P013_t

description: 10X Genomics platform


title: primed H9-150288


title: primed H9-150301


title: Liver High fat/cholic acid diet-fed B6 strain rep2


title: Liver High fat/cholic acid diet-fed B6 strain rep1


title: Post_P013_b

description: 10X Genomics platform


title: primed H9-150298


title: primed H9-150286


title: Liver High fat/cholic acid diet-fed AJ strain rep1


title: primed H9-150287


title: Post_P023_b

description: 10X Genomics platform


title: primed H9-150285


title: Post_P023_t

description: 10X Genomics platform


title: primed H9-150283


title: PD-L1 KO mice 2 months after MAC infection 3

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).
Genome_build: mm10
Supplementary_files_format_and_content: CPM, fold-change

source_name: Lung tissue

extract_protocol:
Lung tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 500 ng total RNA was used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420). Illumina NextSeq500 was used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PD-L1 KO

tag: agent

value: M. avium


title: Post_P002_b

description: 10X Genomics platform

value: TNBC patient


title: Post_P014_b

description: 10X Genomics platform

value: Post-treatment


title: PD-L1 KO mice 2 months after MAC infection 2


title: primed H9-150281


title: primed H9-150278


title: primed H9-150279


title: PD-L1 KO mice 2 months after MAC infection 1


title: PD-1 KO mice 2 months after MAC infection 3

value: PD-1 KO


title: Post_P012_b

description: 10X Genomics platform


title: primed H9-150277


title: Post_P012_t

description: 10X Genomics platform


title: primed H9-150284


title: Post_P007_b

description: 10X Genomics platform


title: PD-1 KO mice 2 months after MAC infection 2


title: primed H9-150273


title: primed H9-150274


title: Post_P003_t

description: 10X Genomics platform


title: primed H9-150275


title: Wildtype mice 2 months after MAC infection 3

value: WT mice 2 months after MAC infection 3


title: Pre_P008_b

description: 10X Genomics platform

value: Pre-treatment


title: primed H9-150272


title: primed H9-150271


title: PD-1 KO mice 2 months after MAC infection 1


title: primed H9-150269


title: Pre_P005_t

description: 10X Genomics platform

value: liver


title: primed H9-150268


title: Wildtype mice 2 months after MAC infection 1

value: WT


title: primed H9-150266


title: primed H9-150276


title: Pre_P005_b

description: 10X Genomics platform


title: primed H9-150270


title: primed H9-150267


title: primed H9-150265


title: PD-L1 KO mice control 3

value: saline


title: primed H9-150264


title: primed H9-150263


title: PD-L1 KO mice control 2


title: Pre_P017_b

description: 10X Genomics platform


title: primed H9-150261


title: PD-L1 KO mice control 1


title: Pre_P010_t

description: 10X Genomics platform

value: lung


title: PD-1 KO mice control 3


title: primed H9-150259


title: Pre_P010_b

description: 10X Genomics platform


title: primed H9-150260


title: Wildtype mice 2 months after MAC infection 2

value: WT mice 2 months after MAC infection 2


title: primed H9-150258


title: primed H9-150256


title: primed H9-150255


title: primed H9-150282


title: Pre_P020_b

description: 10X Genomics platform

value: Chemo


title: Pre_P017_t

description: 10X Genomics platform


title: primed H9-150257


title: primed H9-150253


title: PD-1 KO mice control 1


title: Wildtype mice control 3


title: Wildtype mice control 2


title: primed H9-150252


title: primed H9-150262


title: primed H9-150254


title: primed H9-150251


title: Pre_P011_b

description: 10X Genomics platform


title: Pre_P019_t

description: 10X Genomics platform


title: Wildtype mice control 1


title: primed H9-150249


title: Pre_P020_t

description: 10X Genomics platform

value: breast


title: Pre_P019_b

description: 10X Genomics platform


title: primed H9-150246


title: primed H9-150248


title: PD-1 KO mice control 2


title: MKL1_Vehicle_4d

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

data_processing:
Fastq files were aligned with STAR to the human reference genome and featureCounts was used to quantified read count. Gene expressions are calculated in FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM in csv

growth_protocol: MKL1 and MKL2 cell lines (Rosen et al., 1987; Van Gele et al., 2002) were cultured in RPMI medium with 10% fetal bovine serum. The remaining MCC cell lines (UM-MCC9, 13, 29, 31, 32, 34, 35, 40, 565) originated at the University of Michigan and were cultured as previously described (Verhaegen et al., 2014). MCC cell lines UM-MCC47, 50, 52, 58, 66, and 68 were established at a later date (Choi et al., 2019) by the same approach and were confirmed to have comparable expression of KRT20 and ATOH1 to earlier established UM-MCC cell lines, and the cell lines were classified as virus-positive or virus-negative based on LT protein and transcript expression

extract_protocol:
RNA was extracted from cell pellets with the RNeasy Mini Kit (Qiagen), including a QIAshredder spin column homogenization step, followed by DNase digestion. 2 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation using the Illumina Tru-Seq Stranded mRNA Library Prep Kit (San Diego, CA).
RNA-seq libraries was prepared by polyA-selected protocol.

treatment_protocol: All MCC cell lines were screened for mycoplasma contamination using the Mycoprobe Kit (R&D Systems). For 5-aza-2’-deoxyazacitidine (DAC) (EMD Millipore) treatments, cells were treated with DAC (or DMSO vehicle) at 5 mM at seven days, unless otherwise noted. DAC treatments were refreshed daily. For trichostatin A (Cell Signaling), cells were treated with 400 nM trichostatin A or vehicle (ethanol) for 24 hours.

value: Vehicle

tag: time point


title: MKL1_decitabine_4d

value: decitabine


title: Pre_P022_t

description: 10X Genomics platform


title: Pre_P025_t

description: 10X Genomics platform


title: primed H9-150245


title: primed H9-150243


title: primed H9-150250


title: primed H9-150244


title: Pre_P022_b

description: 10X Genomics platform

value: blood


title: Pre_P025_b

description: 10X Genomics platform


title: NN_WYG7-HN WGBS

city: Nanjing, Jiangshu Province

first: Xiaorong

last: Fan

state: Jiangshu

address: Tongwei Road 1

institute: Nanjing Agricultural University

description:
0N0NWT_0NHNWT_gene_intersect_dmr.dataset
0N0NWT_0NHNWT__dmr_zone.bed

data_processing:
After downloading raw data from sequencing machine, in order to avoid alignment error, the raw reads will be filtered and trimmed to obtain clean reads. First, remove polluted adapter reads (remove the reads with the number of contaminants in the base more than 5bp) . Second, remove the reads with base calling quality Qemo), and third, remove reads with the percentage of N >5% (For pair-end sequencing, if one end is removed, both ends will be removed). After filtering, the available data were compared with the reference genome Oryza_sativa.IRGSP-1.0.32 to obtain the alignment results using Bismark (v0.9.0) (K Felix, et al. 2011).  The uniquely mapped reads will be used to call the methylated cytosines(C) in highly enriched regions.Valid coverage of methylated cytosine, i.e. the percentage of methylated C among all C on genome, is associated with methylation level. C sites with read depths less than 5 are eliminated firstly. Then for each C site, valid coverage is calculated by for all C or C within each pattern (CpG, CGH, and CHH). Coverage is the count of C sites with more than 5 depth divided by total number of C site by its pattern. For each C site, the methylation level (%) is calculated by: 100* (reads supportted methylation)/ (total reads depth of this site). For methylated region, methylation level (%) is calculated by: 100*methylation level of all C sites in this region/Total number of C sites in this region. The conversion ratio of  Lambda DNA is around 99.5% to 99.6% in all samples.
DMR for (1) The read coverage of each C locus > 4; (2) The total number of C loci in each DMR > = 5; (3) The length of DMR > = 100bp;(4) The difference of methylation level between groups was greater than or equal to 0.3;(5) The CPG site with p-value less than 1e-10 was reserved as the final DMR.
Based on the results of DMR genome annotation, the number of genes with overlapping promoter (1KB upstream) and gene body region
Genome_build: IRGSP1
Supplementary_files_format_and_content: Processed data were stored in txt files, which included differentially methylated region in dmr_zone file, and  gene name in gene_intersect_dmr file.

organism: Oryza sativa

source_name: DNA methylation of NN_WYG7-HN

growth_protocol: For plants grow in the field, all materials were grown in plots in the Agricultural Experiment Station of Zhejiang University, Changxing, Zhejiang. Changxing is located in a subtropical monsoon climate zone. The pH of the soil is 7.2. Potassium, phosphate was fertilization at usual levels in the fields (225kg/ha and 450kg/ha). Plots size was 2 × 2.5 m and the seedlings planted in a 10 × 10 array.

extract_protocol:
For rice grow in the field, all materials were grown in plots in the Agricultural Experiment Station of Zhejiang University, Changxing, Zhejiang. Samples collected in the mature.
Samples shipped to the Anoroad Genome company(Beijing) for whole-genome bisulfite sequencing(WGBS). WGBS librarie preparation, sequencing and data analysis was described as before (??). WGBS libraries are prepared for subsequent cluster generation starting from sample DNA through adaptor ligation, library purification, and quantification. Input gDNA (5 μg) is fragmented by sonication. The fragments are blunt-ended and phosphorylated, and a single ʹAʹ nucleotide is added to the 3ʹ ends of the fragments in preparation for ligation to a methylated adapter that has a single-base ʹTʹ overhang. The ligation products are purified and size-selected by agarose gel electrophoresis. Size-selected DNA is bisulfite-treated and purified. The treated DNA is PCR-amplified to enrich the fragment that have adapters on both ends. The final purified product is then quantitated prior to cluster generation. The WGBS libraries will be sequenced using Illumina HiSeq2500 /4000 Analyzer according to the manufacturer’s instructions.

treatment_protocol: Plants were plants in the field fertilized at a rate of 300 kg N/ha as HN field, no N fertilizer as NN field and the field without N fertilizer (NN) since 2009.

value: shoot

value: wild type


title: NN_WYG7-LN WGBS

source_name: DNA methylation of NN_WYG7-LN


title: MKL1_Vehicle_7d


title: MKL1

value: baseline


title: Pre_P016_t

description: 10X Genomics platform

value: TNBC patient


title: HN_Ox1-HN WGBS

description:
HN0N82_HNHN82_gene_intersect_dmr.dataset
HN0N82_HNHN82__dmr_zone.bed

source_name: DNA methylation of HN_Ox1-HN


title: primed H9-150241


title: Pre_P016_b

description: 10X Genomics platform


title: HN_Ox1-LN WGBS

source_name: DNA methylation of HN_Ox1-LN


title: MCC65_decitabine+TSA

value: decitabine+TSA


title: primed H9-150240


title: primed H9-150247


title: HN_WYG7-LN WGBS

description:
HN0NWT_HNHNWT_gene_intersect_dmr.dataset
HN0NWT_HNHNWT_dmr_zone.bed

source_name: DNA methylation of HN_WYG7-LN


title: MKL1_decitabine_7d


title: Pre_P001_b

description: 10X Genomics platform


title: MCC65_decitabine_7d


title: Pre_P024_b

description: 10X Genomics platform


title: HN_WYG7-HN WGBS

source_name: DNA methylation of HN_WYG7-HN


title: primed H9-150239


title: MCC65_TSA

value: TSA


title: primed H9-150238


title: primed H9-150242


title: Pre_P028_b

description: 10X Genomics platform

value: Pre-treatment


title: primed H9-150237


title: primed H9-150236


title: MCC65_Vehicle_7d


title: Pre_P018_t

description: 10X Genomics platform


title: MCC65


title: MCC68_decitabine_4d


title: primed H9-150235


title: Pre_P018_b

description: 10X Genomics platform


title: Pre_P002_t

description: 10X Genomics platform


title: primed H9-150234


title: primed H9-150233


title: MCC68_decitabine_7d


title: Pre_P002_b

description: 10X Genomics platform


title: Pre_P013_t

description: 10X Genomics platform

value: liver


title: Pre_P013_b

description: 10X Genomics platform


title: Fertile Control_18

type: RNA

city: Jinan

first: Junhao

last: Yan

address: No.157 Jingliu Road

institute: Center for Reproductive Medicine

description: CircRNA expression in the luteal-phase endometrium C_18

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 10 out of 18 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: luteal-phase endometrial sample, Fertile Control_18

label_protocol: The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Luteal-phase endometrial samples were obtained by Pipelle biopsy at the implantation window of a monitored natural cycle 7–10 days after ovulation

tag: tissure

value: luteal-phase endometrium

value: Fertile Control

tag: gender

value: female


title: Fertile Control_13

description: CircRNA expression in the luteal-phase endometrium C_13

source_name: luteal-phase endometrial sample, Fertile Control_13


title: Fertile Control_16

description: CircRNA expression in the luteal-phase endometrium C_16

source_name: luteal-phase endometrial sample, Fertile Control_16


title: MCC68_Vehicle_7d


title: primed H9-150232


title: MCC52_decitabine+TSA


title: MCC68


title: Pre_P023_t

description: 10X Genomics platform


title: primed H9-150230


title: primed H9-150229


title: Fertile Control_11

description: CircRNA expression in the luteal-phase endometrium C_11

source_name: luteal-phase endometrial sample, Fertile Control_11


title: MCC68_Vehicle_4d


title: MCC52_TSA


title: primed H9-150231


title: Fertile Control_8

description: CircRNA expression in the luteal-phase endometrium C_8

source_name: luteal-phase endometrial sample, Fertile Control_8


title: Fertile Control_7

description: CircRNA expression in the luteal-phase endometrium C_7

source_name: luteal-phase endometrial sample, Fertile Control_7


title: Pre_P023_b

description: 10X Genomics platform


title: primed H9-150228


title: Pre_P014_b

description: 10X Genomics platform


title: MCC52_decitabine_7d


title: Fertile Control_6

description: CircRNA expression in the luteal-phase endometrium C_6

source_name: luteal-phase endometrial sample, Fertile Control_6


title: Fertile Control_10

description: CircRNA expression in the luteal-phase endometrium C_10

source_name: luteal-phase endometrial sample, Fertile Control_10


title: primed H9-150227


title: MCC52_Vehicle_7d


title: Pre_P012_b

description: 10X Genomics platform


title: Pre_P012_t

description: 10X Genomics platform


title: MCC29_decitabine_7d


title: primed H9-150226


title: Pre_P007_t

description: 10X Genomics platform


title: RIF_32

description: CircRNA expression in the luteal-phase endometrium F_32

source_name: luteal-phase endometrial sample, RIF_32

value: recurrent implantation failure


title: MCC52


title: RIF_22

description: CircRNA expression in the luteal-phase endometrium F_22

source_name: luteal-phase endometrial sample, RIF_22


title: primed H9-150225

source_name: stem cells


title: MCC29_Vehicle_7d


title: MCC29


title: Pre_P007_b

description: 10X Genomics platform


title: primed H9-150223


title: primed H9-150224


title: LCH97_Skin

first: Han

last: He

address: No. 8 Dongdajie

institute: Fifth Medical Center of Chinese PLA General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads from each cell were split by specific barcode sequence attached in Read 2. The template switches oligo (TSO) sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Subsequently, reads with adaptor contaminants or low-quality bases (n > 10%) were discarded. Next, the stripped Read1 sequences were aligned to the hg19 human transcriptome (UCSC) using Hisat2 (version 2.1.0).  Uniquely mapped reads were counted using the HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of distinct UMIs for that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell. The 'sc' number in the cell ID refers to the barcode number. e.g., sc1 = barcode1 in the file GSE151713_barcode_sequence.txt.gz

source_name: LCH patient cells

extract_protocol:
LCH skin samples were obtained with informed consent from patients undergoing diagnostic biopsies. Control epidermal LCs were isolated from discarded skin after the elective circumcisions from patients<18year.   Child skin samples were first incubated in RPMI 1640 medium with 1.2 U/ml dispase II (Roche, Indianapolis, IN) at 4 °C for 8 h prior to separation of the epidermal layer. After separation, the epidermal layer was cut into pieces and digested with 0.25% trypsin-EDTA (Gibco) containing 0.25 mg/ml DNase I (Sigma DN25) for 30 min at 37 °C in a humidified incubator. After neutralization, the epidermal layer was passed through a 70-μm cell strainer by grinding, and then washed with PBS. The following antibodies were used to label the cells: CD45 (BV421, 563879 BD, lot 9066960), 7-amino-actinomycin D (7-AAD) (PerCP-Cy5.5, 00699350 eBioscience, lot 1910559), CD207 antibodies (PE, 564727 BD, lot 8135683) and CD1a antibodies (APC, 559775 Biolegend, lot 8164562).   Blood samples were treated with lysis buffer (BD) to remove erythrocytes, and then were subjected to staining using: CD45 (BV421, 563879 BD, lot 9066960), 7-amino-actinomycin D (7-AAD) (PerCP-Cy5.5, 00699350 eBioscience, lot 1910559), HLA-DR (PE, 307606 Biolegend, lot B289372), CD14 (BV786, 563698 BD, lot 8351911), CD3 (APC-Cy7, 300426 Biolegend, lot B289558), CD19 (APC-Cy7, 557791 BD, lot 9064665), CD56 (APC-Cy7, 362512 Biolegend, lot B281874), CD303/BDCA2 (PE-Cy7, 354214 Biolegend, lot B268476) and CD11c (FITC, 561355 BD, lot 8054660).  After staining for 30min in 4°C, cells were washed and resuspended in PBS, and then  were sorted using an Aria 2 Flow Cytometer (BD Bioscience). Data were analysed using BD FACSDIVA V8.0.1 and Flowjo (V10).
Single-cell capturing and downstream libraries were constructed following a modified single-cell tagged reverse transcription (STRT) protocol as previously reported. Cells in good condition were picked by mouth pipette and transferred to lysis buffer. The reverse transcription reaction was performed using a sample-specific 25-nucleotide (nt) oligo dT primer containing an 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT -XXXXXXXX-DDDDDDDD-T25, where X represents the sample-specific barcode, and D stands for the unique molecular identifier (UMI)). After reverse transcription and second-strand cDNA synthesis, cDNAs were amplified by 16-18 cycles of PCR. Then the barcoded DNAs were pooled together and purified with Agencount AMPure XP beads. Biotinylated pre-indexed primers were used to further amplify the PCR products by another four cycles of PCR to introduce biotin tags into the 3′ ends of the amplified cDNAs. About 300 ng cDNA were ultrasonically processed into 300-bp fragments using Covaris S2 system and enriched with Dynabeads MyOneTM Streptavidin C1 beads. Libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and 150-bp paired-end sequencing was performed on the Illumina Hiseq X Ten platform (Novogene).

value: Skin

value: Female

value: child

value: MS-high risk

tag: diagnosis

value: Langerhans cell histiocytosis

tag: tissue preparation

value: fresh


title: RIF_14

description: CircRNA expression in the luteal-phase endometrium F_14

source_name: luteal-phase endometrial sample, RIF_14


title: MCC66_Vehicle_7d

value: Vehicle


title: primed H9-150222


title: MCC66_decitabine_7d

value: decitabine


title: T10_m6A_IP1.fastq

city: guangzhou

first: hui

last: han

state: guangdong

address: yuexiu

institute: the first affiliated hospital，sun yat-sen university

description: m6A RIP-seq

data_processing:
library strategy: meRIP-seq
For the RNA-seq, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode.
For the m6A RIP-seq，peak calling was done with MACS2
Genome_build: hg38
Supplementary_files_format_and_content: FPKM txt file；peak regions txt file

source_name: esophagus

growth_protocol: TE-10 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37°C.

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit

treatment_protocol: TE-10 cells were  transfected with shRNA for stable knockdown of METTL3. TE-10 cells with normal expression of METTL3 were used as control.

tag: cell line

tag: cell type

value: esophageal epithelial cell line

value: normal

tag: merip antibody

value: m6A (202003 - Synaptic Systems)


title: RIF_29

description: CircRNA expression in the luteal-phase endometrium F_29

source_name: luteal-phase endometrial sample, RIF_29


title: primed H9-150221


title: RIF_17

description: CircRNA expression in the luteal-phase endometrium F_17

source_name: luteal-phase endometrial sample, RIF_17


title: T10_m6A_IP2.fastq

description: m6A RIP-seq

value: m6A (202004 - Synaptic Systems)


title: RIF_7

description: CircRNA expression in the luteal-phase endometrium F_7

source_name: luteal-phase endometrial sample, RIF_7


title: Normal skin 2

source_name: healthy children cells

value: Male

value: healthy


title: RIF_6

description: CircRNA expression in the luteal-phase endometrium F_6

source_name: luteal-phase endometrial sample, RIF_6

value: luteal-phase endometrium


title: RIF_5

description: CircRNA expression in the luteal-phase endometrium F_5

source_name: luteal-phase endometrial sample, RIF_5

value: female


title: MCC66

value: baseline


title: T10_Input.fastq

description: m6A RIP-seq

value: non


title: Normal skin 1

value: Skin


title: MCC50_Vehicle_7d


title: primed H9-150220


title: TE10_M3sh2

data_processing:
For the RNA-seq, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM txt file

value: esophageal epithelial cell line TE-10


title: primed H9-150219


title: primed H9-150218


title: TE10_M3sh1


title: primed H9-150217


title: Normal skin 3

value: child


title: LCH80_Skin

value: MS-high risk

value: Langerhans cell histiocytosis


title: MCC47_decitabine_7d


title: Sample 21_post target

value: Peripheral blood

value: Female

value: fresh


title: LCH48_Skin


title: primed H9-150216


title: MCC47


title: MCC50_decitabine_7d

value: decitabine


title: MCC47_Vehicle_7d

value: Vehicle


title: primed H9-150215


title: Sample 21 pre target


title: SnailHI in vivo rep2

city: Cambridge

first: Anushka

last: Dongre

address: 455 Main St

institute: Whitehead Institute

description: rep 2

scan_protocol: Transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) to digitally count transcripts

data_processing: Normalization was performed using DESeq2 from the BioConductor package

source_name: qMes PyMT cell line

growth_protocol: E and qM mammary carcinoma cells were either cultured in vitro or prepared by FACS sorting of GFP-labelled carcinoma cells from their corresponding tumors.

extract_protocol: RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Cell lines were isolated from MMTV-PYMT mice, some of which bear reporter constructs that label all cells expressing endogenous levels of Snail.  Snail HI cells express high levels of Snail, low levels of Epcam and are quasi-mesenchymal. In contrast, Snail LO cells express low levels of Snail, high levels of Epcam and are epithelial. Further details about the establishment of these cell lines and their differential responses to immune checkpoint blockade have been previously published (Dongre et al., 2017 -  https://cancerres.aacrjournals.org/content/77/15/3982)

value: PyMT

tag: phenotype

value: quasi-Mesenchymal cancer cells facs sorted from tumors arising in vivo


title: SnailHI in vivo rep1

description: rep 1


title: MCC50


title: primed H9-150213


title: primed H9-150212


title: SnailLO  in vivo rep2

description: rep 2

source_name: Epithelial PyMT cell line

value: Epithelial cancer cells facs sorted from tumors arising in vivo


title: Sample 5 post target

value: Male


title: Sample 5 pre target


title: SnailLO  in vivo rep1

description: rep 1


title: primed H9-150214


title: MCC40_decitabine+TSA

value: decitabine+TSA


title: LCH78_Skin


title: Sample 3 pre target

value: MS-low risk


title: Sample 3 post target


title: pB2 in vivo


title: primed H9-150211


title: MCC40_TSA

value: TSA


title: TE10_M3NC

value: normal


title: MCC40_Vehicle_7d


title: primed H9-150209


title: MCC40_decitabine_7d


title: SnailHI  in vitro rep3

description: rep 3

value: quasi-Mesenchymal  cell line cultured in vitro


title: pB3  in vivo


title: primed H9-150210


title: Sample 2 post target

value: child


title: MCC35_decitabine_7d


title: MCC40

value: baseline


title: Sample 1 post target

value: MS-high risk

value: Langerhans cell histiocytosis

value: cryopreservation


title: MCC35_Vehicle_7d


title: primed H9-150208


title: Sample 2 pre target

value: Peripheral blood

value: fresh


title: MCC35


title: Sample 1 pre target


title: primed H9-150206


title: LCH80_PB


title: SnailHI  in vitro rep2

description: rep 2


title: primed H9-150205


title: SnailHI  in vitro rep1

description: rep 1


title: SnailLO in vitro rep2

description: rep 2

value: Epithelial cell line cultured in vitro


title: MCC34_TSA


title: LCH78_PB


title: LCH48_PB


title: primed H9-150204


title: SnailLO in vitro rep1

description: rep 1

value: PyMT


title: primed H9-150203


title: primed H9-150202


title: pB3  in vitro rep3

description: rep 3


title: MCC34


title: MCC34_decitabine_7d

value: decitabine


title: LCH38_PB

value: Female

value: SS-low risk


title: primed H9-150207


title: pB3  in vitro rep1

description: rep 1


title: MCC34_Vehicle_7d

value: Vehicle


title: SnailLO in vitro rep3

description: rep 3


title: LCH36_PB

value: Male


title: MCC34_decitabine+TSA

value: decitabine+TSA


title: pB3  in vitro rep2

description: rep 2


title: primed H9-150201


title: primed H9-150200


title: MCC31_TSA

value: TSA


title: MCC31_decitabine+TSA


title: pB2  in vitro rep3

description: rep 3


title: primed H9-150199


title: pB2  in vitro rep2

description: rep 2

treatment_protocol: Cell lines were isolated from MMTV-PYMT mice, some of which bear reporter constructs that label all cells expressing endogenous levels of Snail.  Snail HI cells express high levels of Snail, low levels of Epcam and are quasi-mesenchymal. In contrast, Snail LO cells express low levels of Snail, high levels of Epcam and are epithelial. Further details about the establishment of these cell lines and their differential responses to immune checkpoint blockade have been previously published (Dongre et al., 2017 - https://cancerres.aacrjournals.org/content/77/15/3982)


title: LCH29_PB


title: MCC31_decitabine_7d


title: pB2  in vitro rep1

description: rep 1


title: LCH28_PB

value: MS-low risk


title: primed H9-150198


title: MCC31_Vehicle_7d


title: Hyphae_3

city: Nanjing

first: Yingzhi

last: Luo

address: Meiyuan street

institute: Jinling Hospital

data_processing:
BGISEQ software used for basecalling.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering.
After getting clean reads, we used HISAT to align the clean reads to the reference genome.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Lung tissue cells

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. High-throughput sequencing was performed at the BGISEQ platform.
Qualified RNA samples were digested with DNA I enzyme and then poly (A) containing mRNA was purified using Oligo (dT) containing beads. Next, mRNA was fragmented and reverse transcribed to first- and second-strand. Double-strand DNA ends were repaired and modified. Then DNA was amplified via PCR and the products were thermally denatured into single-stranded and cyclized. After rolling circle amplification and quality control, high-throughput sequencing was performed at the BGISEQ platform.

value: lung

value: hyphal fragments

value: 24 hours after intratracheal inoculation


title: LCH37_PB

value: child

value: Langerhans cell histiocytosis


title: MCC31

value: baseline


title: LCH32_PB

value: Peripheral blood

value: fresh


title: primed H9-150197


title: BR3MK2i

city: Nashville

first: John

middle: William

last: Tierney

state: TN

address: 5824 Stevenson Center

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Illumina Casava software used for basecalling.
Raw reads were filtered to remove reads with adaptors, reads with N>10%, reads with Qscore over 50% bases below 5.
STAR v2.5 software was used to align reads.
Gene expression levels were measured using HTSeq v0.6.1 to calculate FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)
Differential expression was determined using the DESeq2 v2_1.6.3 R package.
Genome_build: hg38

source_name: Primary human coronary artery smooth muscle cells

growth_protocol: Three patient samples of primary HCASMCs were obtained from American Type Culture Collection (ATCC PCS-100-021). HCASMCs were cultured using vascular cell basal medium (ATCC PCS-100-030) supplemented with a vascular smooth muscle cell growth kit (ATCC PCS-100-042) and 20% serum to induce phenotype switching. Cells were passaged when flasks reached ~80% confluence.

extract_protocol:
RNA was extracted from lysates using Qiagen Rneasy Mini Kits
Libraries were prepared according to Novogene protocols.

treatment_protocol: Each biological sample was split into two flasks. One flask of cells was cultured out to passage 5 as an untreated control. The other flask was also cultured out to passage 5 with treatments of 50 µM reconstituted lyophilized MK2i-NPs for 2 hours the day after each passage.

value: 20% serum, 50 µM MK2i nanopolyplexes, cultured out to passage 5

tag: patient source

value: Patient 3

value: Coronary artery smooth muscle cells


title: Conidia_2

tag: tissue

value: conidia


title: Conidia_3

tag: treatment


title: primed H9-150193


title: Hyphae_2

tag: strain


title: LCH24_PB

tag: age


title: primed H9-150195


title: primed H9-150194


title: primed H9-150196


title: BR2MK2i

value: Patient 2


title: LCH15_PB

value: Female

value: MS-high risk

value: cryopreservation


title: LCH27_PB

value: Male


title: Conidia_1

value: lung


title: primed H9-150192


title: primed H9-150191


title: Control_PB_09

value: healthy


title: LCH26_PB


title: BR1MK2i

value: Patient 1


title: Control_PB_07

value: child


title: BR3NT

value: 20% serum, cultured out to passage 5


title: Control_3

value: normal saline

value: 24 hours after intratracheal inoculation


title: Hyphae_1

value: hyphal fragments


title: miR_642, biological replicate C

city: Nedlands

first: Peter

middle: J.

last: Leedman

state: Western Australia

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

data_processing:
Image analysis and base-calling was perfromed by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3
The Illumina bcl2fastq 2.18.0.12 pipeline was used to generate the sequence data
Sequence data were aligned to the Hg19 genome build. The Tophat aligner (v2.0.14) was used to map reads to the genomic sequences.
Raw Gene Counts are generated using featureCounts v1.4.6-p5 and default TMM normalization method of edgeR was used to normalize the counts.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include counts (DGE, digital gene expression) values for each sample.

growth_protocol: 22Rv1 prostate cancer cells were obtained from the American Type Culture Collection (ATCC) and cultured at 37˚C / 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA extracted from the samples 24 h post-transfection, using the Isolate II RNA kit (Bioline). The quantity and integrity of extracted RNA was determined using a 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using Illumina's Ribo-zero Gold protocol

treatment_protocol: Triplicate wells of 22Rv1 cells were transfected using Lipofectamine 2000 (Thermo Fisher) with 30 nM miR-642a-5p (hsa miR-642a-5p; Ambion Cat #AM17100, Product ID: PM11477) or a negative control miRNA (miR-NC; Ambion Negative Control #1, Cat# AM17110)

value: prostate cancer cells

value: transfected 30 nM miR-642a-5p


title: BR2NT

value: Coronary artery smooth muscle cells


title: LCH20_PB

value: Peripheral blood

value: MS-low risk

value: Langerhans cell histiocytosis

value: fresh


title: Control_PB_08

value: Female


title: primed H9-150190


title: BR1NT


title: Control_1


title: Control_2


title: primed H9-150189


title: miR_642, biological replicate B


title: primed H9-150188


title: T1_Male_D3_rep2

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

description: processed data file: Male_D3.txt

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -AAGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the mouse genome (mm10, obtained from UCSC) using Hisat2(v2.1.0) with parameters: --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
After that, Mapped reads were subsequently assembled into transcripts guided by the UCSC gff annotation files (mm10) using featureCounts (v1.6.1)
The RNA abundance were calculated and normalized by DEseq2(v1.26.0). The differentially expressed genes were also calculated by DEseq2(v1.26.0).
Genome_build: mm10
Supplementary_files_format_and_content: The RNA abundance were calculated by DEseq2 as described above.
Supplementary_files_format_and_content: Male_D3.txt (Raw counts)
Supplementary_files_format_and_content: Male_8W.txt (Raw counts)
Supplementary_files_format_and_content: Male_D3_DESeq2_norm.txt (Normalized counts)
Supplementary_files_format_and_content: Male_8W_DESeq2_norm.txt (Normalized counts)

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Approximately 1µg total RNA per sample was treated with Ribo-Zero™ Magnetic Kit(Epicentre) to deplete rRNA. The retrieved RNA was fragmented by adding First Strand Master Mix(Invitrogen). First-strand cDNA was generated using random primers reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the cDNA fragments. Then the PCR products are purified with Ampure XP Beads. The final library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The Qualified libraries were sequenced pair end on the Hiseq X-ten platform (BGI-Shenzhen, China).

treatment_protocol: pregnant mice were assigned randomly to IUGR group and normal saline (NS) group. The pregnant mice in IUGR group were injected intraperitoneally with Dexamethasone (1 mg/kg/d) since 14.5 dpc for five consecutive days; the mice in NS group accepted the same volume of NS injection.

value: hippocampus

tag: development stage

value: postnatal day 3

value: male

tag: genotype

value: wildtype

value: Intrauterine growth retardation group (IUGR)


title: Control_PB_04

tag: Sex

value: child

value: healthy


title: miR_642, biological replicate A


title: Control_PB_05

value: Male


title: primed H9-150187


title: T2_Male_8W_rep2

description: processed data file: Male_8W.txt

value: postnatal 8-week


title: C2_Male_8W_rep2

description: processed data file: Male_8W.txt

value: normal saline group (NS)


title: C1_Male_D3_rep2

description: processed data file: Male_D3.txt


title: Control_PB_01/02/03


title: miRNC, biological replicate B

value: prostate cancer cells

value: transfected with negative control miRNA


title: primed H9-150185


title: primed H9-150183


title: Control_PB_06

value: Peripheral blood


title: DD48 (ko12)

city: Erlangen

first: Lars

last: Nitschke

state: Bavaria

address: Staudtstr. 5

department: Biology

country: Germany

data_processing:
trimming by trimmomatic (SE -threads 8 ILLUMINACLIP:TruSeq3-SE.fa:2:30:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
mapping to GRCm38.p6 genome by STAR (--readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate)
# Program:featureCounts v2.0.0; Command:"featureCounts" "-T" "4" "-O" "-M" "--fraction" "--extraAttributes" "gene_name"
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw feature counts of all features and all samples

source_name: Splenic pDCs

extract_protocol:
Splenic single cell suspensions were generated by Collagenase D/DNAse I treatment. PDCs were enriched by anti-PDCA-1 paramagentic beads (Miltenyi). Cells were sort purified and subjected to direct RNA extraction (µRNAeasy, Qiagen). RNA quality was controlled using the BioRAD RNA HiSens Kit on an EXPERION analyzer. cDNA libraries were generated and sequenced at the EMBL Heideberg, Germany.
Total RNA from each sample was used as input for the Illumina TruSeq Stranded messenger RNA LT Sample Prep Kit (Illumina) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and copied into first strand complementary DNA using random primers and reverse transcriptase. Second strand cDNA synthesis was then done using DNA polymerase I, RNase H and substituting dUTP for dTTP. The cDNA was ligated to adapters and enriched with PCR to create the final cDNA library. The library was pooled and sequenced

value: Siglec-H -/-

value: pDCs


title: DD47 (ko10)


title: T2_Male_8W_rep1

description: processed data file: Male_8W.txt


title: Postpartum_Breast_Cancer_09

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
RSEM v1.2.31 for quantification of expressed genes annotated by gencode.v19.annotation.gtf
The default parameters for RSEM with STAR as the alignment
Genome_build: hg19

source_name: Breast Cancer FFPE

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted from recently cut 10 µm FFPE sections using the miRNeasy FFPE kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol, using 1-4 sections (10-40 µm) per case
An input of 75 ng of total FFPE RNA was used with the TruSeq RNA Access Library Prep Kit and were prepared according to manufacturer instructions (Illumina, San Diego, CA)
Illumina TruSeq RNA Access Library utilizes over 2 million targeted oligos to capture gene expression of greater than 98% of known protein coding genes

treatment_protocol: Not applicable

tag: ageatprimarydx

tag: ihc er

value: pos

tag: ihc pr

tag: ihc her2, disc=discordant ihc, na=not available

value: neg

tag: parity at collection

value: Postpartum

value: female

value: Lum B

tag: stageatdx


title: T1_Male_D3_rep1

description: processed data file: Male_D3.txt

value: hippocampus

value: postnatal day 3

tag: gender

value: male

value: wildtype


title: HI576-Nfatc2

city: Madison

first: Shane

middle: P

last: Simonett

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

data_processing:
Illumina Nextera adapters were trimmed with cutadapt (version 2.0) with option “-q 30 --minimum-length 36”.
Paired-end ATAC-seq reads were aligned to the human genome assembly (hg19) with bowtie2 (version 2.3.4.1) with option “-X 800 --no-mixed --no-discordant”.
For each sample, unmapped reads were filtered out by using SAMtools view (version 1.8), with option “-F 4” and mitochondrial reads were removed.
Duplicate reads were removed with Picard tools (version 2.9.2)
In total, 231,232 master ATAC peaks (mean width 663 ± 393 bp) were called for pooled GFP and Nfatc2 samples with MACS2.
We utilized “getCounts()” function in chromVAR to obtain the count matrix of Tn5 cuts.
We then performed differential accessibility analysis with DESeq2 and obtained Nfatc2 opening and closing chromatin.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: csv file of ATAC peaks identified in human islets treated with Ad-GFP or Ad-ca-Nfatc2

source_name: Human pancreatic islets

growth_protocol: All human islets were obtained through the IIDP (Integrated Islet Distribution Program). Upon receipt, all human islets were incubated overnight in RPMI 1640 supplemented with 8.0 mM glucose, 1% antibiotic/antimycotic (Gibco), 5 mM HEPES, and 10% FBS before performing experiments.

extract_protocol:
48 hours after GFP or Nfatc2 adenoviral transduction, 50 average sized human islets were picked into a 1.7 mL tube. The islets were washed with 500 uL of PBS at 4C and pelleted by centrifugation at 100 x g for 1 minute. 300 uL of ATAC Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) was used to resuspend the islets. The islets were incubated for 20 minutes on ice. After incubating, the islets were lysed by trituration with a 25 gauge needle essentially until intact islets were no longer visible. The lysate was centrifuged at 500 x g for 10 minutes at 4C. This generated a crude nuclei pellet and a supernatant. The supernatant was discarded and the nuclei pellet was washed with 100 uL of ATAC Lysis buffer in order to reduce cytoplasm and mitochondrial contamination. This mixture was centrifuged at 500 x g for 10 minutes at 4C and the supernatant was removed. Per ATAC-seq sample, a mixture of 25 uL 2x TDE buffer, 22.5 uL nuclease-free water, and 2.5 uL TDE1 transposase enzyme (Nextera DNA Library Prep kit, Illumina) was applied and incubated for 30 minutes in a 37C water bath. The samples were then purified using a MinElute Reaction cleanup kit (Qiagen) and eluted using two sequential aliquots of 10 uL EB buffer. After purification all ATAC samples were kept at -80C. All ATAC-seq samples were transposed and frozen prior to preparing all libraries.
Libraries were amplified using 20 uL of ATAC sample, 10 uL of unique dual indexes (IDT for Illumina Nextera DNA UD Indexes Set A (96 Indexes, 96 Samples)), and 30 uL of NEBNext High Fidelity 2x PCR Master Mix. Each ATAC sample was amplified by 12 cycles which was determined by qPCR to be saturating for the libraries. The PCR thermocycler was set to 72C for 5 minutes, 98C for 30 seconds, and then 12 total cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute. After amplification the libraries were purified using MinElute PCR purification cleanup kit (Qiagen).

treatment_protocol: Isolated human islets were treated with an adenovirus to overexpress a constitutively active (ca) Nfatc2 protein or GFP. Islets were collected for ATAC-seq 48 hours later.

value: Human pancreatic islets

value: M

tag: expression

value: constitutively active Nfatc2


title: DD46 (ko9)

tag: cell type


title: DD45 (ko8)


title: C2_Male_8W_rep1

description: processed data file: Male_8W.txt

value: postnatal 8-week

value: normal saline group (NS)


title: DD44 (ko4)


title: HI576-GFP

value: Ad-GPF


title: miRNC, biological replicate C

tag: cell line

value: prostate cancer cells

value: transfected with negative control miRNA


title: HI575-Nfatc2

tag: tissue

value: F


title: MV3

last: zhang

address: 2205 Songhu Road

institute: Fudan University

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCm38.p5 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: txt file includes RPKM values for each Sample.

source_name: intestinal epithelia

growth_protocol: All mice of both sexes were of a C57BL/6 background and housed under specific pathogen-free conditions in automated watered and ventilated cages on a 12-h light/dark cycle.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Tissues of the small intestines were dissected into 2-5mm2 fractions, then IECs were collected from incubated with lysis buffer followed by the centrifuged material and washed in cold HEPES (10 mM) buffer.

tag: stain

value: Mst4 KO

value: small intestine

value: intestinal epithelia

value: post natal week 8


title: Nulliparous_Breast_Cancer_07

value: pos

value: neg

value: NULLIP

value: female

value: Lum B


title: miRNC, biological replicate A

tag: treatment


title: Postpartum_Breast_Cancer_08

value: equiv

value: Postpartum


title: DD42 (wt11)

value: Siglec-H +/+

value: pDCs


title: C1_Male_D3_rep1

description: processed data file: Male_D3.txt

value: hippocampus

value: postnatal day 3

value: male

tag: strain

value: wildtype

value: normal saline group (NS)


title: MV2

value: Mst4 KO

value: small intestine

tag: age


title: Nulliparous_Breast_Cancer_06

value: Lum A


title: HI575-GFP

value: Human pancreatic islets

value: F

value: Ad-GPF


title: MV1

tag: genotype

value: intestinal epithelia

value: post natal week 8


title: Postpartum_Breast_Cancer_07

value: pos

value: discord

tag: Sex

value: female


title: Postpartum_Breast_Cancer_06

tag: ageatprimarydx

value: neg

value: Postpartum


title: primed H9-150182

data_processing:
Smart-Seq transcriptome sequencing experiments were analyzed using genome sequence and gene annotation from Ensembl GRCh38 release 103 as reference. For gene expression quantification RNA-seq reads were first trimmed using trim-galore v0.6.6 and thereafter aligned to the genome using hisat2 v2.2.1. Uniquely mapping reads in genes were quantified using htseq-count v0.13.5 with parameter -s no. TPM estimates were obtained using RSEM v1.3.3 with parameter --single-cell-prior. Further analysis was performed in R v4.0.3 with Seurat v4.0.1. Based on initial evaluation of per-cell quality control metrices and outlier identification using the median absolute deviation algorithm, cells with <= 2000 detected genes or >= 12.5% mitochondrial gene percentage were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: tsv of read counts per gene

source_name: stem cells


title: DD41 (wt7)

value: Siglec-H +/+

value: pDCs


title: HI574-GFP


title: 17738X24 Young Male CHZ-28

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

data_processing:
To analyze RNA sequencing data, human GRCh38 FASTA and GTF files were downloaded from Ensembl release 98 and the reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads
Mapped reads were assigned to annotated genes in the GTF file using featureCounts v1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCount output files combined into a single matrix

source_name: Primary Muscle Cells

extract_protocol:
RNA was extracted from myoblasts using miRNeasy Mini Kit (Qiagen #217004), DNase treated (TURBO DNase, Thermofisher #AM2238) and cleaned using Zymo RNA Clean & Concentrator-5 columns (#11-325).
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583), and average RIN was 8.3.  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.  Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664).

treatment_protocol: Myoblasts were isolated from muscle biopsied from healthy community dwelling older (4m/4f, 69y) adult participants before (pre) and after (post) the metformin ingestion period. Myoblasts were harvested from young participants (4m/4f, 27y) to serve as a “youthful” comparator.

value: myoblasts

tag: subject

value: Young

tag: time point

value: Male


title: Postpartum_Breast_Cancer_05

tag: ihc er

tag: ihc pr

tag: ihc her2, disc=discordant ihc, na=not available


title: M3

value: WT

value: small intestine


title: DD40 (wt6)


title: DD43 (ko3)

value: Siglec-H -/-


title: M2


title: Nulliparous_Breast_Cancer_05

value: equiv

tag: parity at collection

value: NULLIP

value: Lum B

tag: stageatdx


title: HI574-Nfatc2

value: Human pancreatic islets

value: F

tag: expression

value: constitutively active Nfatc2


title: DD39 (wt5)

tag: cell type


title: Postpartum_Breast_Cancer_04

value: pos

value: female


title: M1

tag: tissue

value: intestinal epithelia

value: post natal week 8


title: 17738X23 Young Male CHZ-20


title: 17738X22 Young Male CHZ-21


title: 17738X21 Young Male CHZ-18


title: DD38 (wt1)

value: Siglec-H +/+

value: pDCs


title: DRG-CPIP_rep4

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

data_processing:
Primary sequencing data produced by RNA-Seq (raw reads) were subjected to quality control (QC).
Raw reads were filtered into clean reads by internal software SOAPnuke (version 1.5.2), followed by: Remove reads in which unknown bases (N) are more than 10%; Remove reads with adaptors; Remove low quality reads (we define the low quality read as the percentage of base which quality is < 15 and > 50% in a read).
QC of alignment was performed to determine if re-sequencing was needed. If the alignment result passed QC, downstream analysis including gene expression, differentially expressed genes, cluster analysis, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA) analysis, etc. was then performed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Dorsal root ganglia

growth_protocol: Rats were randomly allocated, and 5 rats were housed per cage(12 hour light–dark cycles and 24 ± 2 ℃). Food and water were provided ad libitum.

extract_protocol:
At day 7, rats were deeply anesthetized with sodium pentobarbital (50 mg/kg) and were perfused transcardially with 200 mL 0.9% saline (4℃). After the perfusion, the left (contralateral) side L4-6 DRG segments were collected and were immediately preserved in the RNA later solution (Thermo Fisher, USA). Total RNA was extracted using the Trizol reagent (Thermo Fisher, USA) following the manufacturer’s instructions.  DNase I was used to degrade contaminating DNA. The purity and concentration of the samples was assessed by Nanodrop Spectrophotometer (NanoDrop Products, USA) and the RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
The fragments were enriched by PCR amplification to construct a library ready for sequencing using BGISEQ-500 by BGI Group (Shenzhen, China).

value: Sprague Dawley

value: L4-6 DRG

value: chronic post-ischemic pain (CPIP)


title: Postpartum_Breast_Cancer_03

value: neg

value: Postpartum


title: Nulliparous_Breast_Cancer_04

value: equiv

value: Lum A


title: DRG-CPIP_rep3


title: 72_CD62L_lo_3

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description: mouse Tcells Activation

data_processing:
Read were trimmed using homerTool
Alignment was done to the genome concatenate with mature tRNA (Chan, P.P. & Lowe, T.M. (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucl. Acids Res. 44(Database issue):D184-D189.) using Bowtie2 with parameters --very-sensitive-local. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were assigned by ratio of valid readsof the possible mapping location.
Read count was done using BedTools-coverage count.
Genome_build: mm10
Supplementary_files_format_and_content: read counts of mature tRNA and sum of read per anticodon of all samples

source_name: activated CD4 T-cells, 72 hours after activation, low CD62L

growth_protocol: Naïve cells were extracted from six spleens of B6 mice using the StemCell CD62L+CD44+ kit (female, 7 weeks, 6-9% naive). Each two spleens were pooled to a total of 3 samples extracted separately. A portion from the naïve state was taken to FASC sorted for live cells followed by RNA extraction. The remaining naive cells were activated by addition of anti-CD3/anti-CD28 activation bead (1:1 bead:cell ratio, thermoFisher Scientific Cat#11131D)    Cells were grown at 0.25 cell/ml in 24 wells, and were collected at 20h, 48h, and 72h after activation. At 20h only live cells were sorted. At 48 and 72 h cells were sorted into CD62L+CD44+ (memory T-cells) and CD62L-CD44+(effector T-cells). The cells were stained as followed, and analyzed using ARIAIII FACS:

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

treatment_protocol: cells were centrifuged at 12,000 rpm for 1 min, frozen in liquid nitrogen and stored at -80 ̊C until RNA extraction.

value: B6 mice

tag: activation stage

value: 72 hours

value: CD4 T-cells

tag: rna population

value: tRNA


title: 17738X19 Young Female CHZ-12

value: myoblasts

value: Young

value: Female


title: 72_CD62L_lo_1

description: mouse Tcells Activation

tag: strain

value: female


title: 17738X20 Young Female CHZ-17

tag: age


title: Postpartum_Breast_Cancer_02

value: pos


title: Nulliparous_Breast_Cancer_03

value: NULLIP


title: 17738X17 Young Female CHZ-14


title: 72_CD62L_lo_2

description: mouse Tcells Activation


title: 17738X18 Young Female CHZ-08


title: DRG-CPIP_rep1

value: Sprague Dawley

tag: treatment


title: 72_CD62L_hi_3

description: mouse Tcells Activation

source_name: activated CD4 T-cells, 72 hours after activation, high CD62L

tag: Sex


title: Nulliparous_Breast_Cancer_02

tag: ageatprimarydx

value: Lum B


title: 72_CD62L_hi_2

description: mouse Tcells Activation


title: DRG-Con_rep4

value: L4-6 DRG

value: control


title: 17738X16 Old Post Female METF028

tag: subject

value: Old

value: Post


title: 17738X15 Old Post Female METF026

tag: time point


title: DRG-Con_rep2


title: DRG-Con_rep3


title: Nulliparous_Breast_Cancer_01

tag: ihc er

value: neg


title: 72_CD62L_hi_1

description: mouse Tcells Activation

value: B6 mice


title: 48_CD62L_lo_3

description: mouse Tcells Activation

source_name: activated CD4 T-cells, 48 hours after activation, low CD62L

value: 48 hours


title: 17738X14 Old Post Female METF017


title: DRG-CPIP_rep2

value: chronic post-ischemic pain (CPIP)


title: DRG-Con_rep1


title: INV 3D 2

city: New York

first: Nathaniel

middle: R

last: Campbell

state: NY

institute: Memorial Sloan Kettering Cancer Center

data_processing:
quality control with FASTQC (Babraham Bioinformatics)
trimming with TRIMMOMATIC
reads were aligned to GRCz10 (Ensembl version 81) using STAR with --quantMode GeneCounts
quality control via SeQC
Differential expression was calculated with DESeq2
Genome_build: GRCz10, Ensembl version 81
Supplementary_files_format_and_content: CSV file with raw counts from STAR

organism: Danio rerio

source_name: Melanoma

growth_protocol: ZMEL1 was grown in Corning Ultra-Low Attachment 6-well plates (#3471) at 28ºC in a humidified incubator in DMEM (Gibco #11965) supplemented with 10% FBS (Seradigm), 1X penicillin/streptomycin/glutamine (Gibco #10378016), and 1X GlutaMAX (Gibco #35050061)

extract_protocol:
Total RNA was extracted with the RNeasy Plus Mini kit with QiaShredder (Qiagen)
Purified RNA was delivered to GENEWIZ (South Plainfield, NJ) for mRNA preparation with the TruSeq RNA V2 kit (Illumina)

tag: cell line

value: Melanoma

tag: culture method


title: INV 3D 3


title: 48_CD62L_lo_2

description: mouse Tcells Activation

value: CD4 T-cells

value: tRNA


title: INV 3D 1


title: 48_CD62L_lo_1

description: mouse Tcells Activation


title: Postpartum_Breast_Cancer_01

tag: ihc pr

tag: ihc her2, disc=discordant ihc, na=not available

tag: parity at collection

value: Postpartum

value: Basal


title: 48_CD62L_hi_3

description: mouse Tcells Activation

source_name: activated CD4 T-cells, 48 hours after activation, high CD62L

value: female


title: 17738X12 Old Post Male METF007

value: myoblasts

value: Male


title: 17738X11 Old Post Male METF006


title: 48_CD62L_hi_2

description: mouse Tcells Activation


title: PRO 3D 2

tag: cell type


title: H8-C1

data_processing:
The human islet RNA-sequencing reads were mapped via bowtie against the refseq hg19 reference.
Gene expression values were then estimated via RSEM.
Expected transcripts per million were normalized using median-by-ratio normalization.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab delimited text file of transcripts per million (TPM)

extract_protocol:
The human islets were lysed with 350 uL of QIAzol Lysis Reagent (Qiagen) and stored at -80˚C before purifying RNA using Mini RNeasy purification kits per manufacturer’s instructions.
Total RNA submitted to the University of Wisconsin-Madison Biotechnology Center was verified for purity and integrity via the NanoDrop2000 Spectrophotometer and Agilent 2100 BioAnalyzer, respectively. Samples that met the Illumina sample input guidelines were prepared according the TruSeq® Stranded Total RNA Sample Preparation Guide (Rev. E) using the Illumina® TruSeq® Stranded Total RNA Sample Prep Gold kit (Illumina Inc., San Diego, California, USA) as directed. For each library preparation, 1ug of total RNA was ribosomally reduced and purified by paramagnetic beads (Agencourt RNA Clean XP beads, Beckman Coulter, Indianapolis IN, USA). Subsequently, each rRNA depleted sample was fragmented using divalent cations under elevated temperature. The fragmented RNA was synthesized into double-stranded cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and RNase H for removal of mRNA. Double-stranded cDNA was purified by paramagnetic beads (Agencourt AMPure XP beads, Beckman Coulter). The cDNA products were incubated with Klenow DNA Polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt DNA fragments. DNA fragments were ligated to Illumina adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end. The adapter-ligated DNA products were purified by paramagnetic beads. Adapter ligated DNA was amplified in a Linker Mediated PCR reaction (LM-PCR) for 10 cycles using PhusionTM DNA Polymerase and Illumina's PE genomic DNA primer set and then purified by paramagnetic beads. Quality and quantity of the finished libraries were assessed using the AATI Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) and BioPlex Synergy 2 Plate Reader (BioTek® Instruments, Winooski, VT, USA), respectively.

treatment_protocol: Isolated human islets were treated with an adenovirus to overexpress a constitutively active (ca) Nfatc2, ca-Nfatc1 or GFP. Islets were collected for RNA-seq 48 hours later.

tag: tissue

value: Human pancreatic islets

value: F

tag: expression

value: constitutively active Nfatc1


title: 17738X10 Old Post Male METF025

value: Old


title: H7-GFP

value: Ad-GPF


title: PRO 3D 1


title: H7-C1


title: INV-6

data_processing:
quality control with FASTQC (Babraham Bioinformatics)
reads were aligned to GRCz10 (Ensembl version 81) using STAR with --quantMode GeneCounts
quality control via SeQC
Differential expression was calculated with DESeq2
Genome_build: GRCz10, Ensembl version 81
Supplementary_files_format_and_content: CSV file with raw counts from STAR

growth_protocol: ZMEL1 was grown at 28ºC in a humidified incubator in DMEM (Gibco #11965) supplemented with 10% FBS (Seradigm), 1X penicillin/streptomycin/glutamine (Gibco #10378016), and 1X GlutaMAX (Gibco #35050061)


title: 20_3

description: mouse Tcells Activation

source_name: activated CD4 T-cells, 20 hours after activation

tag: activation stage

value: 20 hours

tag: rna population


title: H8-C2

tag: age

value: constitutively active Nfatc2


title: H8-GFP


title: 17738X8 Old Pre Female METF028

value: Pre

value: Female


title: H6-GFP


title: 17738X9 Old Post Male METF032

value: Post


title: 17738X13 Old Post Female METF008


title: INV-5

value: Melanoma


title: 20_2

description: mouse Tcells Activation

tag: strain

value: B6 mice

value: CD4 T-cells

value: tRNA


title: 17738X7 Old Pre Female METF026

tag: Sex


title: H6-C2


title: 20_1

description: mouse Tcells Activation

value: female


title: H5-GFP


title: PRO-3


title: 48_CD62L_hi_1

description: mouse Tcells Activation

value: 48 hours


title: 17738X5 Old Pre Female METF008

value: myoblasts


title: Naive_3

description: mouse Tcells Activation

source_name: Naïve CD4 T-cells

value: naive


title: INV-4


title: PRO-2


title: H5-C2

value: Human pancreatic islets

value: F


title: PRO-1


title: 17738X4 Old Pre Male METF007

value: Old

value: Male


title: H7-C2


title: Naive_1

description: mouse Tcells Activation


title: Naive_2

description: mouse Tcells Activation


title: H5-C1

value: constitutively active Nfatc1


title: 17738X2 Old Pre Male METF025


title: 17738X3 Old Pre Male METF006


title: sg_tfap2a/e 2

treatment_protocol: Knockout was performed in ZMEL1-PRO cells using the Alt-R CRISPR-Cas9 system (IDT)

tag: sgrna

value: tfap2a and tfap2e


title: H4-C2

value: M

value: constitutively active Nfatc2


title: macrophage heart with heart failure rep4 [C21S3 IC]

city: PARIS

first: Catherine

last: PAVOINE

address: 91 boulevard de l'hôpital

department: UMR ICAN 1166

country: France

institute: INSERM Sorbonne Université

data_processing:
quality control: Raw sequencing data was quality-controlled with the FastQC program.
Trimmomatic was used to remove adapter sequences, trim low quality reads, and discard reads shorter than 40 bp.
alignment: Reads were aligned to the mouse reference genome (build mm10) with the TopHat2 tool.
quality control: Mapping results were quality-checked using RNA-SeQC.
Aligned reads were counted using the featureCounts at the gene-level.
Genome_build: mm10
Supplementary_files_format_and_content: Normalization and differential analysis were performed with the glm edgeR package.

source_name: macrophage heart with heart failure

extract_protocol:
cell isolation: CD14+/CD64+ cardiac macrophages sorted by FACS
Total RNA from FACS sorted CD64+/CD14+ cells was isolated using the Nucleospin RNA XS kit (Macherey Nagel), according to the manufacturer instructions.
cDNA libraries were generated using total RNA with SMART-Seq v4 Ultra Low Input RNA Kit (TAKARA) and constructed according to manufacturer protocols
Paired end sequencing (2 x 75 bp) was performed by Nextseq 500 machine using High Output kit (150 cycles).

treatment_protocol: mice implanted with saline (control) or  isoproterenol pumps for 14 days (concentric hypertrophy, HCC) or 28 days (Heart failure, IC)

tag: treatment

value: iso pump for 28 days

value: heart

value: CD14+/CD64+ cardiac macrophages


title: macrophage heart with heart failure rep3 [C18S2 IC]


title: 17738X1 Old Pre Male METF032

tag: subject

tag: time point

value: Pre


title: H6-C1


title: 17738X6 Old Pre Female METF017

value: Female


title: sg_tfap2a/e 1

tag: cell line

value: Melanoma


title: macrophage heart with heart failure rep2 [C13S3 IC]


title: H4-GFP

value: Ad-GPF


title: H4-C1


title: macrophage heart with heart failure rep1 [C13S2 IC]


title: sg_scr 3

value: Non-targeting Control


title: macrophage heart with concentric hypertrophy rep4 [C23S2 HCC]

value: iso pump for 14 days


title: H3-GFP

value: Human pancreatic islets


title: sg_scr 2


title: sg_tfap2a/e 3


title: macrophage heart with concentric hypertrophy rep3 [C23S1 HCC]


title: H3-C1


title: H3-C2


title: H2-GFP


title: H2-C2


title: macrophage heart with concentric hypertrophy rep2 [C17S4 HCC]


title: macrophage control heart rep3 [C24S4 CTS]

source_name: macrophage control heart

value: saline pump


title: H2-C1


title: macrophage heart with concentric hypertrophy rep1 [C15S2 HCC]


title: macrophage control heart rep4 [C24S5 CTS]


title: H1-GFP

value: F


title: H1-C2


title: sg_scr 1


title: macrophage control heart rep1 [C19S4 CTS]


title: macrophage control heart rep2 [C19S5 CTS]


title: H1-C1


title: KO-4_98_liver

city: Dresden

first: Triantafyllos

last: Chavakis

address: Fiedlerstraße 42

department: Klinische Pathobiochemie

institute: Medizinische Fakultät der TU Dresden

description:
KO-4_98
processed data file: bfx1090.mm10.e81.txt

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.19.1.
Reads were aligned to the mouse genome assembly (mm10) using GSNAP (2017-03-17; parameters: --gunzip -A sam --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 1 -n 1 -s EnsemblGene-81.ss.mm10.iit) with known splice sites from Ensembl (v81) as support.
Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.1; parameters: -a EnsemblGene-81.mm10.TR.gtf -s 2 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bfx1090.mm10.e81.txt: Tab-delimited counts table from featureCounts with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'.

source_name: liver

extract_protocol:
Livers were removed and stored in -80° C until RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel).
mRNA enrichment and reverse-transcription into cDNA was done with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.

tag: strain/background

tag: genotype

value: HuR KO

value: Liver


title: HI560-input

data_processing:
The raw reads from all samples were aligned to human reference genome (hg19) with Bowtie 2 (version 2.3.1).
We used Bowtie2 default reporting mode with the argument -X 550 --no-mixed --no-discordant being specified.
Picard MarkDuplicates tool (version 2.9.2) was used to remove duplicate reads from the alignment.
We performed peak calling from mapped and properly paired reads with Bioconductor package MOSAiCS (version 3.5).
The peak sets called from the six samples were merged and 8,635 peaks were retained based on the following criteria. We included (i) peaks reproducible in at least two samples and (ii) peaks identified in one sample, whose summit signals are higher than the third quantile of the summit signals of the reproducible peaks.
Peaks in ENCODE DAC blacklist regions were dropped from the peak list.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig files contain the Nfatc2 peaks identified from 6 human islet samples.
Supplementary_files_format_and_content: bigBed file contains the merged peaks used to determine Nfatc2 binding in human islets.

extract_protocol:
~17,000 human IEQs were incubated with 5 mL of 1% formaldehyde (Thermo Scientific, Cat. # 28906) in PBS for 5 minutes at room temperature. To quench the formaldehyde fixative, 256 uL of 2.5 mM glycine was added, incubated for 2 minutes, and then centrifuged (500 x g) to pellet the islets. Islets were washed with 1mL each of PBS, NCP buffer 1 (10 mM HEPES pH 6.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100) and NCP buffer 2 (200 mM NaCl, 10 mM HEPES pH 6.5, 1 mM EDTA, 0.5 mM EGTA). Islets were then lysed in 3 mL of lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% Empigen BB, 1% SDS, 1mM PMSF, and Roche cOmplete Mini EDTA-free Protease Inhibitor Cocktail Tablet). The islets were triturated with a 30-gauge needle ~20 times, and then sonicated using a Branson Digital Sonifier 250 with a double step microtip probe at 30% amplitude for 15 cycles (30 seconds on, 30 seconds off). The sample was then centrifuged (13000 x g, 10 minutes, 4˚C), and supernatant collected for immunoprecipitation. The supernatant was diluted with IP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100) at a ratio 5:2, IP buffer:supernatant; 10% of the supernatant was set aside for ChIP input determination. To the IP buffer/supernatant mixture, 10 uL of anti-HA antibody (Abcam, ab9110) was used to immunoprecipitate HA-tagged Nfatc2/chromatin complexes overnight at 4˚C. The following day 100 uL Protein A/G magnetic beads (Pierce) were supplied to the immunoprecipitated mixture for 2 hours. The magnetic bead complexes were then sequentially washed with 1 mL of wash buffer #1 (2 mM EDTA, 20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 150 mM NaCl), wash buffer #2 (2 mM EDTA, 20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), and wash buffer #3 (1 mM EDTA, 10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% sodium deoxycholate, 1% NP-40 Alternative), followed by 5 washes in TE buffer. The Nfatc2/chromatin complexes were then eluted with elution buffer (200 mM NaCl, 100 mM NaHCO3, and 1% SDS) at 65˚C overnight. Eluted DNA was purified using MinElute PCR purification cleanup kit (Qiagen).
Samples were prepared according the TruSeq ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size-selected for an average insert size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit dsDNA HS Assay Kit, respectively. Libraries were standardized to 2 nM.

treatment_protocol: Isolated human islets were treated with an adenovirus to overexpress a constitutively active HA-tagged Nfatc2 protein. Islets were collected for ChIP-seq 48 hours later.


title: KO-2_1999_liver

description:
KO-2_1999
processed data file: bfx1090.mm10.e81.txt


title: HeLa cell culture - CDT WT - Rep5 [CDTR_5]

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 microarray (8X60K, Design 039494) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 12 out of 15 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 32772 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 26516 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: HeLa cell culture - CDT WT

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: HeLa cells were were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Life Technologies), supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco) and 1% antibiotics (penicillin/streptomycin). Cells were plated at a density of 150000 cells per well in 6 wells plate

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) mRNA were extracted and the quality of these samples was assessed (Agilent RNA 6000 Nano Kit Quick, Agilent Bioanalyzer 2100); RNA Integrity Number (RIN) of these mRNA was superior to 9.8.

treatment_protocol: One day after seeding, cells were exposed to 0.25 ng/ml of WT or HA CDT for 48 H. For chronic exposure, individual clones were selected, the rest of the cells were pooled. CDT was added at each passage (every 2-3 days) for 8 weeks.

value: HeLa

tag: condition

value: CDT WT

tag: exposure time

value: 8 weeks

tag: rna integrity number


title: HeLa cell culture - CDT WT - Rep2 [CDTR_2]


title: HI559-input

tag: tissue

value: M

value: constitutively active Nfatc2


title: HI560-HA-ChIP

tag: expression


title: HeLa cell culture - CDT HA - Rep7 [HA_7]

source_name: HeLa cell culture - CDT HA

value: CDT HA


title: HeLa cell culture - CDT HA - Rep2 [HA_2]


title: KO-3_99_liver

description:
KO-3_99
processed data file: bfx1090.mm10.e81.txt


title: HeLa cell culture - NT - Rep1 [NT_col_1]

source_name: HeLa cell culture - NT

value: NT


title: HeLa cell culture - CDT HA - Rep23478 [HA_pool]


title: KO-1_1998_liver

description:
KO-1_1998
processed data file: bfx1090.mm10.e81.txt


title: HeLa cell culture - NT - Rep2 [NT_2]


title: HeLa cell culture - CDT HA - Rep3 [HA_3]


title: HeLa cell culture - NT - Rep2 [NT_col_2]


title: WT-3_100_liver

description:
WT-3_100
processed data file: bfx1090.mm10.e81.txt

value: HuR WT


title: WT-4_1997_liver

description:
WT-4_1997
processed data file: bfx1090.mm10.e81.txt


title: HI559-HA-ChIP

source_name: Human pancreatic islets


title: HI558-input


title: HeLa cell culture - CDT HA - Rep8 [HA_8]


title: HeLa cell culture - CDT WT - Rep12345 [CDTR_pool]


title: WT-2_1996_liver

description:
WT-2_1996
processed data file: bfx1090.mm10.e81.txt


title: HeLa cell culture - CDT WT - Rep3 [CDTR_3]


title: HI558-HA-ChIP


title: HI557-input


title: WT-1_1995_liver

description:
WT-1_1995
processed data file: bfx1090.mm10.e81.txt


title: HeLa cell culture - CDT WT - Rep1 [CDTR_1]


title: HeLa cell culture - CDT HA - Rep4 [HA_4]


title: Spinalcord_Vehicle_mouse5

city: Barcelona

first: Carmen

last: Espejo

address: Passeig de la Vall d'Hebron, 119-129, Edifici Collserola, Laboratory 149-151

country: Spain

institute: Vall d'Hebron Institute of Research - Centre d'Esclerosi Múltiple de Catalunya

description: Gene expression data from EAE mice treated with vehicle (Clostridia strains culture medium)

hyb_protocol: Following fragmentation, 5.5ug of ds-cDNA were hybridized for 16 h at 45ºC on GeneChip Clariom S mouse array plate. Array plate was washed and stained in the Affymetrix Genetitan Instrument (GeneTitan Multichannel system)

scan_protocol: Array plate was scanned using the Genetitan instrument (GeneTitan Multichannel system)

data_processing: The data were processed and analyzed separately for each tissue. Raw expression values were obtained directly from .CEL files and were processed using the RMA method to get normalized expression values (log2 scale) summarized at the gene level. Different quality checks were performed before and after normalization to ensure that all samples were suitable for differential expression analysis. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis.  Statistical language R (version 3.6.1) and Bioconductor associated packages were used to process and analyze the data.

label: biotin

source_name: Spinal cord, Vehicle, 28 days post-immunization

label_protocol: Biotinylated ds-cDNA were prepared according to the standard Affymetrix (ThermoFisher) protocol from 50 ng total RNA (GeneChip 3' IVT Pico Kit Manual Workflow, user guide).

extract_protocol: Spinal cord: Total RNA was isolated using QIAzol lysis reagent (79306, Qiagen) and RNeasy Mini Kit (74104, Qiagen) with on-column DNase digestion (79254, Qiagen) in order to remove any genomic DNA trace according to the manufacturer's instructions. Spleen: RNeasy Mini Kit together with on-column DNase digestion was also used to isolate splenocyte total RNA according to the manufacturer's instructions.

value: Spinal cord

value: Vehicle (Clostridia strains culture medium)


title: Spinalcord_Vehicle_mouse6


title: HI557-HA-ChIP


title: Spleen 104w

city: Münster

first: Monika

last: Stoll

institute: Institute for Human Genetics, Genetic Epidemiology, University of Muenster

data_processing:
FastQC quality control and read trimmed using trimmomatic
aligned to the mouse reference genome GRCm38 with BWA mem
marking duplicate reads with picard.2.11.0
GATK version 3.7 RNAseq variant calling pipeline: BaseRecalibrator, Haplotypecaller and VariantFiltration (FS > 30.0, QD < 2.0)
Filter for strain 129S1_SvImJ specific variants in hybrid strain mice
Genome_build: GRCm38
Supplementary_files_format_and_content: vcf files with called variants for each sample individually

source_name: Spleen

extract_protocol:
Total DNA was extracted from small intestine, liver and spleen tissues of naturally aged mice of 12 and 104 weeks of age. DNA was extracted using the Quick-DNATM Miniprep Plus Kit (Zymo Research) following the manufacturer’s protocol.
500 ng of the genomic DNA was sheared on the S220 instrument (Covaris) followed by NGS library preparation using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The size of the resulting library was controlled by use of a D1000 ScreenTape (Agilent 2200 TapeStation) and quantified using the NEBNext Library Quant Kit for Illumina (NEB). Equimolar pooled libraries were sequenced in a paired end mode (80 cycles) on the NextSeq 500 System (Illumina) using v2 chemistry yielding in an average QScore distribution of 85% >= Q30 score.

value: 104 weeks

value: Spleen


title: HI556-input

value: Human pancreatic islets


title: 4W_KO_3_A32_1

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

data_processing:
STAR v2.5: Read Alignment
htseq-count: fpkm
DESeq2: Differential expression analysis
Genome_build: mm10

source_name: Liver tissue

extract_protocol: mouse liver tumors were removed, flash frozen on dry ice, and total RNA extracted using the PureLink™ RNA Mini Kit (Thermo Fisher) and subjected to library preparation using Illumina TrueSeq RNA kit V2 according to manufacturer’s protocol with 1 ug of total RNA for the construction of sequencing libraries.

value: mixed B6;129P2 background

value: 4-week post-DEN treatment

tag: genotype/variation

value: knockout