title: breast cancer tissue_T1


title: S66_IL17_100_D6

status: Public on Aug 20 2021

type: SRA

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

description:
input_data_CPM_IL17
input_data_Count_IL17

library_source: transcriptomic

data_processing:
Reads from files in the FASTQ format were mapped to the hg19 human reference genome using HISAT 2.2.0, with default parameters. Raw read counts mapped to genes were measured using the BAM format file in HTSeq version 0.12.3, to quantify transcript abundance. The coding genes were selected, and raw read counts were normalized to the trimmed mean of M-values. Differential expression analysis of RNA-seq experiments was conducted with edgeR (version 3.28.1). Unsupervised hierarchical clustering analysis with the Euclidean distance and complete linkage algorithm was used to create a heatmap with the associated dendrogram.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include raw read counts for samples

molecule: total RNA

organism: Homo sapiens

source_name: small intestinal organoid (enteroid)

growth_protocol: Human intestinal organoids was constructed as a previous described method. In brief, we obtained small intestinal mucosa specimens using endoscopic biopsy from the three patients without any mucosal lesions in small intestine, who underwent single-balloon enteroscopy (SBE) at the Samsung Medical Center, Seoul, Korea, after receiving informed consent. Control patients underwent SBE due to small bowel submucosal tumor (heterotopic pancreas and gastrointestinal stromal tumor) and unexplained abdominal pain. This study was approved by the institutional ethical committee of the Samsung Medical Center (IRB No. 2016-02-022).  The intestinal crypts were isolated from endoscopic biopsy specimens using 10 mM EDTA (Thermo Scientific, San Jose, CA, USA) and 1 mM DTT (Thermo Scientific) chelation. The isolated crypts were resuspended into Matrigel (Corning) and plated in 48-well culture plates (Corning). The 250 μl of maintenance medium (50 % Wnt3a-conditioned medium (ATCC#CRL-2647, Manassas, VA, USA) + 50 % 2× basal medium (Basal medium: advanced DMEM/F12 (Thermo Scientific) supplemented with antibiotic–antimycotic solution (Thermo Scientific), 10 mmol/L HEPES (Thermo Scientific), GlutaMAX (Thermo Scientific), 1× N2 (Thermo Scientific), 1× B27 (Thermo Scientific), and 1 mmol/L N-acetylcysteine (Sigma–Aldrich, St. Louis, MO, USA)), supplemented with 50 ng/ml recombinant human epidermal growth factor (Sigma–Aldrich), 100 ng/ml recombinant human noggin (R&D Systems, Minneapolis, MN, USA), 500 ng/ml recombinant human R-spondin 1 (PeproTech, Cranbury, NJ, USA), 10 mM nicotinamide (Sigma–Aldrich), 10 μM p160ROCK inhibitor (Y27632, Selleckchem, Houston, TX, USA), 10 μM p38 MAP kinase inhibitor (SB202190, Sigma–Aldrich), and 10 nM Prostaglandin E2 (PGE2, Cayman Chemical, Ann Arbor, MI, USA) were added. GSK3 inhibitor (CHIR99021, Stemgent, Cambridge, MA, USA) was added to the medium during the first 2 days.   After culturing the organoids for 7 days, the organoids in Matrigel were disrupted mechanically via pipetting, and chemically using TrypLE Express Enzyme (Thermo Scientific). The cell pellet was resuspended in Matrigel and plated in 48-well culture plates (Corning). The medium was changed every 2 days, and organoids were passaged at a ratio of 1:2 – 1:4 on 7 days after crypt plating. To recapitulate the structure and function of the intestinal epithelium, the intestinal organoids (enteroids) were cultured in a differentiation medium (maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2). The differentiation medium was changed every 2 days.

extract_protocol:
After 7th day after embedding (5th days after treatment with IL-17), total RNA was extracted from enteroids using an RNeasy Mini Kit (QIAGEN, Hilden, Germany).
Total RNA was extracted from enteroids using RNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA sequencing was conducted using total RNA samples with >10 μg of RNA and an integrity number > 8. Reverse transcription reactions were performed with 2 μg of isolated total RNA, poly(dT) primers, and SuperScript™ II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA). cDNA libraries were prepared via complementary DNA amplification, end repair, 3'-end adenylation, adapter ligation, and amplification. The libraries were sequenced with HiSeq2500 using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

treatment_protocol: To evaluate the IL-17-induced responses in the enteroids, the intestinal organoids were cultured in a maintenance medium for 2 days to obtain a stable number of organoids, before inducing organoid differentiation and treatment with concentrations of human recombinant IL-17A (R&D Systems). Then, the maintenance medium was replaced with a differentiation medium every 2 days. Different concentrations of human recombinant IL-17 were added to the culture medium every 24 hours.

tag: tissue

value: small intestine (jejunum)

tag: disease

value: control (no small intestinal lesions)

tag: status

value: conventional organoid culture condition with differentiation medium & 100 ng/ml IL-17


title: N2_IL17_0_D6

value: conventional organoid culture condition with differentiation medium


title: patient 1 kidney rep 1

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The raw RNAseq data was aligned to the hg38 genome using the STAR(v2.7.3a) mapper.
Aligned data were annotated using GENCODE v35 gene annotations and counted using featureCounts(v1.6.3).
Genes with fewer than 50 counts across all samples were excluded from the analysis, and the counts were subsequently log2-transformed for differential gene expression analysis using DESeq2. A pairwise comparison between infected tissues (lung, nasopharynx) and uninfected tissues (olfactory bulb, prefrontal cortex, oropharynx, salivary gland, tongue, heart, liver, kidney) with an adjusted p-value < 0.05 for differentially expressed (DE) genes.
Gene Set Enrichment Analysis (clusterProfiler) was performed to probe for Gene Ontology (GO) categories that were significantly overrepresented and statistically different in infected versus non-infected tissues.
Genome_build: hg38
Supplementary_files_format_and_content: featureCount tsv file summarizes raw counts from featureCounts for each sample.
Supplementary_files_format_and_content: DESeq csv file contains DE genes found by DESeq2.
Supplementary_files_format_and_content: GSEA csv file contains GESA results for GO categories.

source_name: kidney autopsy tissue

extract_protocol:
Total RNA was extracted from the autopsy tissues by first flash freezing each tissue in liquid nitrogen and then using the CryoPREP Tissue Disruption System (Covaris) to pulverize the tissue into a fine powder. The powder was then immediately resuspended in cell lysis buffer and RNA was extracted using the ReliaPrep RNA Tissue Miniprep System (Promega, #Z6112) by following the manufacturer’s instructions. A DNase digestion was also performed during the RNA extraction workflow to remove any potential contamination from carryover genomic DNA (reagents included in the kit). The extracted RNA was then purified using 1.8X RNAClean XP beads (Beckman Coulter) to remove any molecular impurities.
Stranded total RNA libraries were generated according to the manufacturer's instructions, using the TruSeq Stranded Total RNA Gold kit for Illumina sequencing
RNAseq, 2x100 PE reads, Illumina NovaSeq 6000

tag: replicate type

value: technical replicate 1

tag: viral rna detected?

value: no


title: patient 1 heart rep 2

source_name: heart autopsy tissue

value: technical replicate 2


title: dHD1_rec_wnt3a_1

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

description: Response to canonical Wnt signaling

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

organism: Mus musculus

source_name: Breast cancer cells

growth_protocol: Tumor-derived trasgenic cell lines with different genotypes were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from all samples at the same time using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. RNA quality control was performed using RNA ScreenTape on an Agilent 4200 TapeStation, and RNA concentration was measured using Quanti-iT RiboGreen RNA assay Kit (Life Technologies).
Library preparation was performed, starting from 200ng total RNA, using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical) revealing excellent quality of libraries (average concentration was 129±14 nmol/L and average library size was 350±11 base pairs). Samples were pooled to equal molarity. The pool was quantified by Fluorometry using the QuantiFluor ONE dsDNA System (Cat# E4871, Promega, Madison, WI, USA). Libraries were sequenced Single-reads 101 bases (in addition: 8 bases for index 1 and 8 bases for index 2) using the NovaSeq 6000 instrument (Illumina) and the S1 Flow-Cell loaded at 400pM and including 1% PhiX. Primary data analysis was performed with the Illumina RTA version V3.4.4. Two Novaseq S1 Flow-Cells runs were performed to compile enough reads (on average per sample: 34.8±3.2 millions pass-filter reads).

treatment_protocol: Established epithelial tumor cell line from above were plated at the same time for no, Wnt3a or TGF-beta tratments. A day after cell plating, we treated cells with no cytokine (only growth medium), TGF-beta (2 ng/ml, 4 days) or Wnt3a (100 ng/ml, 3 days). We changed cytokines every second day and for controls only with growth medium. Total RNA is isolated from all samples at the same time. For biological replicates we used two transgenic cell lines drived from two different mice with the same genotype.

tag: strain

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

tag: transgene

value: Bcl9/Bcl9L_deltaHD1/-, MMTV-PyMT

tag: time point

tag: treatment


title: adjacent non-tumor tissue_N4

type: RNA

city: Lanzhou

first: HongLei

last: Wang

state: Gansu

address: 1 Donggang West Road

department: Department of Galactophore

country: China

institute: The First Hospital of Lanzhou University

description: circRNA expression in breast cancer and adjacent non-tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified . Differentially expressed circRNAs between two samples were identified through Fold Change filtering.

source_name: adjacent non-tumor tissue

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

treatment_protocol: Five cancer tissues and paired adjacent non-cancerous tissues from primary breast cancer patients were used for circRNA microarray. Tissues specimens were obtained during surgery and immediately flash frozen with liquid nitrogen and then frozen at -80℃ until further use.

value: breast tissue

tag: gender

value: female

tag: age


title: breast cancer tissue_T3

source_name: breast cancer tissue

value: breast tumor


title: adjacent non-tumor tissue_N3


title: adjacent non-tumor tissue_N2


title: N2_IL17_10_D6

value: small intestine (ileum)

value: conventional organoid culture condition with differentiation medium & 10 ng/ml IL-17


title: forelimb blastema mesenchyme, dmso_rep2

city: Gainesville

first: Malcolm

last: Maden

state: Florida

department: Biology

institute: University of Florida

data_processing:
All reads were evaluated using fastQC [fastqc/0.11.7].
Low quality reads and reads with adapter sequences were trimmed using Trimmomatic [trimmomatic/0.36, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36], and the trimmed read were analyzed again using fastqc.
Reads were aligned to the axolotl genome using HISAT2 [hisat2/2.1.0, -q --dta].
SAM files were converted to BAM files using samtools [samtools/1.8, samtools view -S], sorted [samtools sort], and indexed [samtools index -c].
Novel genes were identified and a transcriptome assembled using StringTie [stringtie/1.3.4d] and gffread [gffread/0.9.8c]
Transcript counts were produced with featureCounts [subread/1.6.2, featureCounts -s 2 -p -t exon -g gene_id].
Differential expression analysis was conducted using edgeR [edgeR/3.26.8, glmQLFit, adjust.method = "BH", p.value = 0.05].
Genome_build: AmexG_v3.0.0
Supplementary_files_format_and_content: am580_featureCounts_raw_counts.txt (Matrix table containing raw gene counts, generated by featureCounts, for all detected genes in all 12 samples)
Supplementary_files_format_and_content: am580_edgeR_abundance.txt (Matrix table containing normalized abundance counts, generated by edgeR, for all detected genes in all 12 samples)
Supplementary_files_format_and_content: am580_transcriptome.fa (Transcriptome containing sequences of all detected genes. Prepared from StringTie gff using gffread.)
Supplementary_files_format_and_content: am580_stringtie_merged.gff (GFF constructed using StringTie)

organism: Ambystoma mexicanum

source_name: forelimb blastema mesenchyme

growth_protocol: Axolotls were maintained in 40% Holtfreter's solution.

extract_protocol:
Total RNA was extracted using a RNeasy Fibrous Tissue Mini Kit (QIAGEN 74704) according to the manufacturer’s protocol.
Illumina TruSeq stranded libraries were constructed via poly-A selection by HudsonAlpha Discovery in Huntsville, Alabama, USA.

treatment_protocol: Axolotl forelimbs were amputated mid-zeugopod and treated 24 hours later with systemic 25 nM Am580 or equal volume DMSO vehicle control for 5 days. The blastemas were collected 24 hours after treatment, the epidermis physically removed, and the mesenchyme tissue stored in RNALater.

value: albino

value: forelimb blastema mesenchyme

value: Dimethyl sulfoxide


title: S66_IL17_10_D6

value: small intestine (jejunum)

value: control (no small intestinal lesions)


title: patient 1 heart rep 1


title: patient 1 tongue rep 2

source_name: tongue autopsy tissue


title: S66_IL17_1_D6

value: conventional organoid culture condition with differentiation medium & 1 ng/ml IL-17


title: S66_IL17_0_D6

value: conventional organoid culture condition with differentiation medium


title: dHD1_fl_wnt3a_2

description: Response to canonical Wnt signaling

value: Bcl9/Bcl9L_deltaHD1/fl, MMTV-PyMT


title: dHD1_fl_wnt3a_1

description: Response to canonical Wnt signaling


title: adjacent non-tumor tissue_N1


title: patient 1 salivary gland rep 2

source_name: salivary gland autopsy tissue

value: technical replicate 2

value: no


title: patient 1 tongue rep 1

value: technical replicate 1


title: dHD1_rec_wnt3a_2

description: Response to canonical Wnt signaling

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

value: Bcl9/Bcl9L_deltaHD1/-, MMTV-PyMT


title: dHD2_rec_no_3

description: Control, no stimulation

value: Bcl9/Bcl9L_deltaHD2/-, MMTV-PyMT

value: no cytokine


title: dHD2_rec_no_1

description: Control, no stimulation


title: vit-5RNAi2

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 2*150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value.The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: Caenorhabditis elegans WBcel235
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

organism: Caenorhabditis elegans

growth_protocol: Worms were maintained on nematode growth media (NGM) and fed with E. coli OP50 at 20°C

extract_protocol:
Bacteria were removed and worms were natural precipitation by M9 buffer , flash frozen on dry ice, and RNA was harvested using Trizol reagent.A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N2 worms were treatment with control L4440 RNAi or vit-5 RNAi at larval stage.  Then the young adult animals were transferred onto the plates and fed with E. coli OP50  at 20°C,and harvesting worms at 5-day-old  .

tag: developmental stage

value: 5-day-old adult worms

tag: genotype

value: vit-5 RNAi


title: vit-5RNAi3


title: Healthy Donor 3 PBMCs

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
demultiplexing with cellranger mkfastq v2.1.1
obtaining read counts with cellranger count v2.1.1
aggregation of count data from both extraction batches with cellranger aggr v2.1.1
differential expression analysis and visualization with Seurat v3
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: space delimited text files containing expression matrix of raw counts and column metadata

source_name: PBMCs

extract_protocol:
We isolated PBMCs from whole blood using BD Vacutainers (BD, Franklin Lakes, NJ, USA) according to the manufacturers’ instructions. We aimed for 6,000 cells per sample.
Libraries were prepared using the Chromium controller (10X Genomics, Pleasanton, CA; USA) in conjunction with the single-cell 3’ v2 kit (1st experiment, stable state) or single-cell 3’ v3 (2nd experiment, stable state; acute state) according to the manufacturer's instructions.

tag: cell type

value: PBMCs

tag: mpo genotype

value: MPO wildtype

tag: individual

value: Healthy Donor 3

tag: extraction batch

value: second batch

tag: disease status

value: healthy


title: patient 1 salivary gland rep 1


title: dHD2_rec_no_2

description: Control, no stimulation

tag: tissue


title: Healthy Donor 1 PBMCs

value: Healthy Donor 1

value: first batch


title: GPP Patient 2 PBMCs

value: MPO-deficient

value: GPP Patient 2

value: diseased


title: Healthy Donor 2 PBMCs

value: Healthy Donor 2


title: vit-5RNAi1


title: patient 1 olfactory bulb rep 2

source_name: olfactory bulb autopsy tissue

value: technical replicate 2

value: no


title: patient 1 nasal pharynx rep 2

source_name: nasal pharynx autopsy tissue

value: yes


title: dHD2_fl_no_1

description: Control, no stimulation

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

value: Bcl9/Bcl9L_deltaHD2/fl, MMTV-PyMT

value: no cytokine


title: dHD1_rec_no_2

description: Control, no stimulation

value: Bcl9/Bcl9L_deltaHD1/-, MMTV-PyMT


title: WTEV1

value: 5-day-old adult worms

value: wild type


title: GPP Patient 1, Sample 1 PBMCs

value: PBMCs

value: GPP Patient 1


title: patient 1 olfactory bulb rep1

value: technical replicate 1


title: WTEV2


title: WTEV3


title: dHD1_fl_no_2

description: Control, no stimulation

value: Bcl9/Bcl9L_deltaHD1/fl, MMTV-PyMT


title: GPP Patient 1, Sample 2 PBMCs

value: MPO-deficient

value: second batch


title: dHD1_fl_no_1

description: Control, no stimulation


title: dHD2_fl_no_2

description: Control, no stimulation


title: patient 1 prefrontal cortex rep 2

source_name: prefrontal cortex autopsy tissue


title: 42: non-responder RNA-seq

city: St. Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

data_processing:
 mRNA sequencing via polyA selection
Bioinformatics analysis workflow using Genewiz standard package

molecule: polyA RNA

source_name: Pretreatment biopsy

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Biopsied tumors were immediately snap frozen and stored in vapor phase in liquid nitrogen tank until analysis

value: tumor

tag: drug treatment

value: Alisertib + Nab-Paclitaxel

tag: drug response

value: non-responder


title: 34: non-responder RNA-seq


title: patient 1 oral pharynx rep 1

source_name: oral pharynx autopsy tissue

tag: replicate type

tag: viral rna detected?

value: no


title: contronl brain pool from multiple donors rep 2

source_name: brain tissue

value: technical replicate 2


title: uterine leiomyoma cell treated with 32.0 μmol/L NP

city: haikou

first: Feng

middle: Tao

last: Zhang

state: hainan

address: 58 Renmin Avenue, Meilan District

department: School of  Life and  Pharmaceutical Sciences

institute: Hainan University

library_source: genomic

data_processing:
Gene expression information and the differential H3K27ac peaks for the identified BPA-responsive differentially expressed genes were integrated to reveal correlations between H3K27ac (hUP or hDN) and gene expression (gUP or gDN) using R scripts. BETA was used to integrate ChIP-seq and RNA-seq data.
BETA runs function prediction, target detection and binding motif analysis step by step. BETA uses a Rank Product algorithm to screen for target genes of histone modification based on both the proximity of the modification to the transcription start site（TSS） of the gene and the differential expression level of the gene.
BPA-responsive differentially expressed genes with differential H3K27ac peaks (FDR < 0.05) within ±200bp of the TSS of the BPA-responsive differentially expressed genes were identified by the BETA. In order to find the target genes of transcription factor, We use FIMO to scan motif matching sequence in the 2-kb promoters region of the direct target gene obtained by BETA（P < 0.0001）
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tab-delimited text files includes peak values for each sample
Supplementary_files_format_and_content: tab-delimited text files with raw peak values all samples

molecule: genomic DNA

source_name: uterine leiomyoma cell lines

growth_protocol: The third generation of uterine leiomyoma cells was chosen and seeded on three 96-well culture plates at a density of 100 μl/well. The 96-well cell culture plate was incubated at 37 ° C with 5% CO2 for 48 h. Following that, 10μl of CCK-8 reagent(APExBIO, Houston, USA)was added to each well incubated for 2 h at 37 °C.

extract_protocol:
For each sample, approximately 107 cells were washed in FBS-free media then crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched by addition of glycine to a final concentration of 0.15 M for 5 min at room temperature. Crosslinked cells were washed with ice-cold PBS, the supernatant discarded. Then chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein A Dynabeads coupled with 5 μg of antibody.
After immunoprecipitation, beads were recovered using a magnet and washed. DNA was eluted and cross‐links reverted at 65°C for 4 hours then purified with QIAGEN Kit. DNA was quantitated using the Qubit® dsDNA HS assay and a Qubit® 2.0 Fluorimeter (Invitrogen). For ChIP-Seq, 5ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten.

treatment_protocol: Three representative primary cultured cell lines were selected, and cells were treated with 10.0 μmol/L BPA (Sigma) and 0.1% Dimethyl sulfoxide（DMSO，D2650, Sigma）for 48h before H3K27ac ChIP sequencing.

tag: disease state

value: uterine leiomyoma

value: treated with 32.0 μmol/L NP for 48h

value: female


title: 40: responder RNA-seq

value: responder


title: uterine leiomyoma cell treated with 10.0 μmol/L BPA

value: treated with 10.0 μmol/L BPA for 48h


title: patient 1 prefrontal cortex rep 1


title: uterine leiomyoma cell treated with 0.1% DMSO

value: treated with 0.1% DMSO for 48h


title: 27: responder RNA-seq


title: patient 1 nasal pharynx rep 1

value: yes


title: contronl brain pool from multiple donors rep 1


title: dHD1_rec_no_1

description: Control, no stimulation

tag: strain

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

tag: transgene

value: Bcl9/Bcl9L_deltaHD1/-, MMTV-PyMT

tag: time point

value: no cytokine


title: patient 1 oral pharynx rep 2


title: 31: responder RNA-seq


title: 12day_cultured_human_myoblasts_rep3

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description:
Tn5-transposed chromatin
results_d0_vs_d12_human_ATACseq.xlsx

data_processing:
Mapping. Reads were then mapped to the human (hg38) or mouse (mm10) genome using Bowtie2 (parameters -I 38 -X 2000 --local --dovetail --no-mixed --no-discordant) and filtered to remove mitochondrial reads and PCR duplicates. Peaks were identified using MACS2.1.1 (parameters --nomodel --nolambda --keep-dup all --call-summits -q 0.05 -B).
Differential analysis. Analysis of differential accessibility was performed by generating a list of peaks representative of all samples using the peak summits identified by MACS2. Each summit was extended 50bp in both directions and the resulting lists of peaks were combined, sorted and merged to obtain a dataset of unique and non-overlapping loci. For each differential analysis, the respective list was then used to extrapolate the sequencing depth coverage from each sample bedGraph file using Bedtools map. Coverage files were then analyzed using DEseq2 to identify loci with differential chromatin accessibility. Loci in human and murine activated satellite cells vs cultured cells were selected based on q-value<0.01 (False Discovery Rate) and absolute log2FoldChange>3.
Analysis of the chromatin accessibility landscape in murine freshly-isolated satelite cells employed additional datasets from GSE89977 (GSM2394780 ATAC-seq Satellite cells).
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files represent the output of the comparisons freshly-isolated satellite cells (d0) vs cultured cells (d12 for human and d4-d10 for mouse) analysis using DESeq2. Each row represent one of the loci (100bp window around the summit) idenfied in the ATAC-seq samples (human or mouse), and includes genomic coordinates, log2FC and adjusted p-value (among the other).

source_name: vastus lateralis muscle

growth_protocol: Human and murine satellite cells were isolated from the muscle mononuclear fraction obtained following tissue enzymatic digestion. More specifically, dissected muscles or sample biopsies were minced into fragments of 1-3mm size using a razor blade, transferred into a conical tube and incubated with a Collagenase II digestion solution (2mg/ml Collagenase II in DMEM high glucose and 1% penicillin/streptomycin) for 75 minutes (60 minutes for human tissue) at 37°C in a shaker set at 200rpm. Human biopsies (between 50-100mg) were incubated with 3ml of digestion solution in a 15ml tube; for murine tissues, 15ml of digestion solution were used to digest the muscles dissected from one hindlimb (using a 50ml tube). After digestion, tubes were then centrifuged at 1000g for 7 minutes at 4°C and, after aspirating the top 50% of the digestion solution, the remaining was washed with 2 volumes of Rinsing Solution (10% Horse Serum (Hyclone), 1% Penicillin/Streptomycin and 0.1?M HEPES in Ham's/F-10 media - Hyclone) and then centrifuged at 1000g for 7 minutes at 4°C, repeating this procedure twice. After the second wash, the pellet was further shredded with the help of a glass pipette (resuspending 5-7 times) and centrifuged at 1000g for 7 minutes at 4°C. The resulting supernatant was carefully aspirated (leaving approximately 3-4mm of volume above to not disturb the pellet), resuspended in a Dispase-Collagenase II digestion solution (0.1 mg/ml collagenase II and 0.5 mg/ml dispase in rinsing solution), vortexed for 20 seconds and incubated 30 minutes (20 minutes for human tissue) at 37°C in a shaker set at 200rpm. Following the second digestion, tubes were vortexed for 20 seconds and then further homogenized using a syringe equipped with a 16 gauge (G) followed by 18 G needle. The homogenate was then filtered through a 40µm filter and then centrifuged at 1000g for 7 minutes at 4°C. Before centrifuge, the tube used for the digestion was washed twice using 3ml of rinsing solution and each wash was applied to the 40µm filter, thus combining it to the original homogenate volume. After carefully aspirating the supernatant, the resulting pellet represented the mononuclear muscle fraction. In general, due to the small size of the biopsy, human samples were devoid of red cells. If necessary, cell pellets were incubated with ACK lysis buffer (Thermoscientific) following the manufacturers' instructions. Human samples were resuspended in 1ml of MACS buffer supplemented with 10µl of human Fc-Block (Miltenyi Biotec), incubated 5 minutes on ice and then supplemented with 10µl of PE-conjugated anti-CD82 (clone ASL-24 - Biolegend) and 10µl of APC-conjugated anti-CD56 (clone 5.1H11 - Biolegend) followed by a 30-minute incubation on ice. Cells were washed with 10ml of sterile PBS, centrifuged for 7 minutes at 4°C and resuspended in 1ml of MACS buffer (Miltenyi Biotec) supplemented with Propidium Iodide (PI). Human satellite cells were identified as CD56+CD82+. Sorted human cells were collected in human myoblast culture media (described below). Murine samples were obtained from 8-12 week old Pax7-ZsGreen reporter mice. In this case, cell pellets were resuspended in MACS buffer supplemented with PI (4ml for each hindlimb-derived fraction) and then processed for FACS. Murine satellite cells were identified as ZsGreen+. Sorted murine cells were collected in murine myoblast culture media (described below). All cell sorting experiments were performed using a FACS AriaII instrument (BD Biosciences).

extract_protocol:
Chromatin accessibility studies were performed following the protocol described by Buenrostro and colleagues (Buenrostro et al., 2015). Except for freshly isolated human cells, which isolation yield ranged between 5,000 and 10,000 cells, all other samples consisted of 50,000 cells (freshly sorted mouse cells, cultured mouse and human cells). Briefly, cells were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes.
Transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10µl Elution Buffer. Primer extension followed by PCR amplification using Illumina-compatible adapter-barcodes and final library preparation were performed at the University of Minnesota Genomic Center.

treatment_protocol: Sorted human and murine satellite cells were plated onto 0.1% gelatin coated plates maintained in a humidified incubator at 37°C, 5% CO2, 5% O2. 500-1000 human satellite cells were plated in a 24-well plate following each isolation. Human cells were cultured using human myoblast culture media: Ham's/F-10 media (Hyclone) supplemented with 20% FBS (Sigma Aldrich), 1% penicillin/streptomycin (Thermoscientific), 500nM dexamethasone (Cayman Chemical), 2ng/ml basic fibroblast growth factor (Peprotech), 143µM ?-mercaptoethanol (Sigma Aldrich). Murine satellite cells were cultured using murine myoblast culture media: DMEM/F12 medium (Thermoscientific) supplemented with 20% FBS, 5ng/ml basic fibroblast growth factor, 1% penicillin/streptomycin, and 0.25% chick embryonic extract (US Biological). All cells were sub-cultured when density reached 40-50%.

value: skeletal muscle

value: in vitro cultured muscle cells

tag: days in culture

tag: clinical state

value: healthy muscle


title: CM12

city: Mannheim

first: Mahak

last: Singhal

address: Ludolf-Krehl-Straße 13-17

institute: European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University

description: LP-CM-processed-data.txt

data_processing:
Sequencing strategy: NovaSeq 6K SR 100bp Single-End.
RTA v3.4.4
The sequenced reads were aligned to the human reference transcriptome (hg19) using Kallisto (version 0.43.1). Average fragment length of 300 and standard deviation 100 were provided as additional parameters.
Paired t-test was used to determine the p-values.
Genes with TPM>=1 for all 8 samples were considered for further analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: LP-CM-processed-data.txt: Tab-delimited text file

source_name: Lung

growth_protocol: Lung pericytes (LP) were cultured in complete pericyte media from ScienCell Research Laboratories. LLC tumor cells either over expressing Lrg1 or control vector were cultured in complete DMEM media.

extract_protocol:
Total RNA was isolated with GeneElute Mammalian total RNA isolation kit (Sigma).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer’s protocol.

treatment_protocol: 500000 LLC cells (either control cells or cells with Lrg1-overexpression) were seeded in 10-cm dish. After 2 days, cells were incubated in 0% DMEM to collect conditioned media (CM) for 24h. Simultaneously, 100000 LP were seeded in 6-well dishes. Next day, LP were incubated in 1:1 mixture of 0% pericyte media and tumor CM for 3h.

value: Lung

value: Pericytes

tag: treatment

value: Tumor CM- Lrg1


title: 12day_cultured_human_myoblasts_rep1

tag: cell type


title: 32: non-responder RNA-seq

value: tumor

value: Alisertib + Nab-Paclitaxel

value: non-responder


title: 1-1

data_processing:
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 4.0.3) and selected according to the following criteria: cells with > 200 genes and < 20% of mitochondrial gene expression in UMI counts. Cells that passed the filtering criteria were integrated and clustered. The canonical cell type marker genes that are conserved across conditions were identified in the cluster. The annotation of the intestinal epithelial cell type to the cell cluster depended on the display of the significant expression of the cell marker obtained from the single cell database.22 When multiple different cell markers were expressed in a single cluster, the cell type was assigned based on the number of expressing cell markers or well-established marker expressions. DEGs focused on the gene related to IL-17 signaling and cell death modality between the conditions was evaluated for each cell type.
A total of 12,926 individual cell transcriptomes were recovered from IL-17-free enteroids (7,337 cells) and IL-17-treated enteroids  (5,619 cells)
Genome_build: GRCh38

source_name: small intestinal organoid (enteroid)

extract_protocol:
After 7th day after embedding (5th days after treatment with IL-17), 3different enteroids treated with and without 100 ng/ml IL-17 were mechanically disrupted by vigorous pipetting and then enzymatically digested into single cell suspension using TrypLE Express. Single cell suspensions of IL-17-free enteroids and the single cell suspensions of IL-17-treated enteroids were combined, respectively.
Bar-coded sequencing libraries were prepared using Chromium Next GEM Single Cell 3p RNA library v3.1 (10X Genomics, Pleasanton, CA, USA) and sequenced on a HiSeq X Ten system, targeting 10,000 per each sample of IL-17-free and -treated enteroids. Reads were aligned to a human reference genome (GRCh38-3.0.0) and processed using the CellRanger 3.1.0 pipeline (10X Genomics).

value: small intestine

tag: disease

value: control (no small intestinal lesions)

tag: status

value: conventional organoid culture condition with differentiation medium & 100 ng/ml IL-17


title: CM24

description: LP-CM-processed-data.txt


title: CM3

description: LP-CM-processed-data.txt


title: 1

value: conventional organoid culture condition with differentiation medium


title: CM9

description: LP-CM-processed-data.txt


title: Daudi cells - BioMag - H3K4me3_rep2

city: Bunkyo-ku

first: Yasuhiro

last: Fujiwara

address: 1-1-1 Yayoi

department: IQB

country: Japan

institute: The University of Tokyo

data_processing:
library strategy: CUT&Tag
CUT&Tag reads were aligned to the hg19 genome assembly using Bowtie version 1.3.0.
peaks were called using MACS2 version 2.2.7.1 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files and peal files with quantitative data

source_name: Daudi cells - BioMag - H3K4me3

growth_protocol: Daudi cells were routinely generated by re-plating (typically 1 × 10^6 cells) on a uncoated 10 cm plastic dish in RPMI1640 medium (189-02025, Wako) with 20% FBS, Pen Strewp(1540-22, Gibco), and GlutaMAX (35050-061, Gibco).

extract_protocol:
Cells bound to magnetic beads were treated with Digitonine, antibody, then pA-Tn5 fusion transposase. Genomic DNA was isolated and purifired using phenol-Chloroform.
Libraries were prepared according to previously reported method (PMID: 31036827). Briefly,  the adapter sequence-tagmented DNA fragments were amplified by PCR using Universal i5 and uniquely barcoded i7 primers and NEBNext High-Fidelity 2x PCR Master mix (New England BioLabs, M0541S) with 14 PCR cycles. The PCR products were purified by using Ampure XP beads, and cleaned with 80 % ethanol. The size distribution of libraries was confirmed by an Agilent 2100 Bioanalyzer Instrument (Agilent Technologies) and High Sensitivity DNA Chips (5067-4626) (Agilent Technologies). The barcoded libraries were quantified by KAPA Library Quantification Kit, Complete kit for ABI Prism, Illumina Platform (KK4835, 07960204001, Roche). The Paired-end sequencing of DNA libraries were sequenced on Illumina HiSeq X sequencer (Illumina) following the manufacturer's protocols.

value: B lymphoblast

tag: tissue source

value: Peripheral blood

tag: antibody


title: fresh_human_sat_cell_rep2

tag: tissue

value: freshly-isolated satellite cells


title: Daudi cells - BioMag - IgG_rep2

source_name: Daudi cells - BioMag - IgG

value: IgG


title: Daudi cells - BioMag - H3K4me3_rep1


title: CM23

description: LP-CM-processed-data.txt

value: Tumor CM- ctrl


title: 12day_cultured_human_myoblasts_rep2

value: skeletal muscle

value: in vitro cultured muscle cells


title: OG12

city: Changzhou

first: Xia

last: Yi

address: 21 Gehu Middle Road

institute: Changzhou University

data_processing:
Paired reads were aligned to a reference genome of S. cerevisiae S288c (NCBI accession no. GCA_000146045.2).
We evaluated the differentially expressed genes (DEGs) according to the absolute value of the log2 ratio ≥ 2.0 and the significant DEGs combining the absolute value of the log2 ratio ≥ 2.0 and false discovery rate (FDR) < 0.001.
Gene ontology (GO) and KEGG pathway analysis were separately analyzed using DAVID (Database for Annotation, Visualization, and Integrated Discovery) and IPA (Ingenuity pathway analysis).
Genome_build: The reference genome S. cerevisiae S288c
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae XH7

extract_protocol:
The cultures were separately kept at ice-water mixture and 50 oC heat shock for 1 h, and then the cells were centrifuged at 12,000 × g at 4 ℃ for 10 min. All samples were stored at -80 oC. The total RNA was isolated from the above cell samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the instructions. The purified RNA prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEBNext, New England) was qualified by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and stored at -80 oC.
The complementary DNA (cDNA) libraries were prepared using NEBNext Ultra RNA Library Prep kit (NEBNext, New England) and processed by Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

tag: condition

value: Control strain at 50 oC


title: Daudi cells - BioMag - IgG_rep1


title: OC12

value: Control strain at 30 oC


title: Daudi cells - T1 - H3K4me3_rep1

source_name: Daudi cells - T1 - H3K4me3


title: fresh_human_sat_cell_rep1

value: healthy muscle


title: OG11


title: CM11

description: LP-CM-processed-data.txt

value: Lung

value: Pericytes


title: CM8

description: LP-CM-processed-data.txt


title: Daudi cells - T1 - H3K4me3_rep2


title: AG13

source_name: Saccharomyces cerevisiae Z100

value: Adaptive strain at 50 oC


title: Daudi cells - T1 - IgG_rep1

source_name: Daudi cells - T1 - IgG


title: iN-VO, No Induction

city: La Jolla

first: Udit

last: Parekh

state: CA

address: 9500 Gilman Drive, Room 353, Powell-Focht (EBU3A)

department: Bioengineering

institute: University of California, San Diego

data_processing:
Samples were sequenced on an Illumina NovaSeq 6000 platform
Fastq files were aligned, and cell barcodes and UMIs processed using cellranger count (Cell Ranger version 3.0.0). The reference human genome used was GRCh38
Lists of barcodes and features, and the feature-barcode matrix were generated by Cell Ranger v3.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is comprised of three zipped, tab-separated files: list of cell barcodes (barcodes.tsv.gz), list of genes/features (features.tsv.gz) and a feature-barcode matrix file (matrix.mtx.gz)

source_name: Blood vessel organoid

growth_protocol: Blood vessel organoids were generated using a protocol published by Wimmer et al., Nature Protocols, 14, 3082–3100 (2019). For all types of neuro-vascular organoids, the standard organoid medium was supplemented with BDNF and NT-3 from day 15 onward. For organoids where NEUROD1 expression was induced, 1 ug/ml doxycycline was added to the medium for the specified number of days.

extract_protocol:
To dissociate organoids for single cell RNA-seq, 5-6 organoids were incubated in a 1 mL 20 U/mL Papain solution (Worthington, LS003126) for 30 minutes, passed through a 40 𝜇m filter, spun down at 300 rcf for 5 minutes, and resuspended in 0.04% BSA solution. Cells were then loaded into the Chromium Chip B (10x Genomics).
Libraries were constructed using the standard Chromium Single Cell 3ʹ Reagent Kits v3 workflow (10x Genomics).

value: Human embryonic stem

tag: cell line

tag: cell line modification

value: Integration of doxycycline inducible NEUROD1-P2A-GFP overexpression cassette

tag: integration method

value: PiggyBac transposon

value: Day 45 organoids with no NEUROD1 induction


title: iN-VO, 15 Days Induction

value: Day 45 organoids with 15 days of NEUROD1 induction


title: CM2

description: LP-CM-processed-data.txt


title: human_AF_2

city: Beijing

first: Jian

last: He

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

data_processing:
10X Genomics CellRanger version 4.0.0 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 4.0.0) with default mapping arguments.
Genome_build: GRCh38
Supplementary_files_format_and_content: loom files include UMI values for each cell

source_name: human IVD cells

extract_protocol: Chromium Single cell 3’ Library and Gel Bead Kit V3 (10X Genomics, PN-1000075) was used for scRNA-seq libraries construction

value: annulus fibrosus

value: IVD cells

tag: age

value: 31 year-old


title: AG12

tag: strain


title: PK44 cells in Yolk sac 2

first: Gong

last: Yandong

data_processing:
For scRNA-seq data from modified STRT-seq, raw reads of each cell were first split by specific barcode sequence attached in Read 2. The template switch oligo (TSO) sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Subsequently, reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Next, the stripped Read1 sequences were aligned to mm10 mouse transcriptome (UCSC) using Hisat2 (version 2.1.0) (Kim et al., 2015). Uniquely mapped reads were counted by HTSeq package (Anders et al., 2015) 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 the distinct UMIs of that gene.
Supplementary_files_format_and_content: comma-delimited csv files include UMI values and cell annotation for each cell

source_name: PK44 cells

extract_protocol: Sequencing libraries were constructed following a modified  single-cell tagged reverse transcription (STRT) protocol as previously  reported35–37. The cells were first judged by morphology under  a microscope to assess their condition, with cells in good condition  being picked by mouth pipette and directly placed into 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, the cDNAs were amplified by 16 cycles  of PCR. The barcoded DNAs were then pooled together and purified  using Agencount AMPure XP beads. Biotinylated pre-indexed primers  were used to further amplify the PCR product by an additional  four cycles of PCR to introduce biotin tags to the 3′ ends of the amplified  cDNAs. Approximately 300 ng cDNA was sonicated into 300-bp  fragments using the Covaris S2 system and enriched with Dynabeads  MyOneTM Streptavidin C1 beads. Libraries were constructed using a  Kapa Hyper Prep Kit (Kapa Biosystems) and were then submitted to  150-bp paired-end sequencing on an Illumina Hiseq X Ten platform  (Novogene).


title: human_AF_1


title: iN-VO, 45 Days Induction

value: Day 45 organoids with 45 days of NEUROD1 induction


title: AG11


title: human_CEP_1

value: cartilage endplate


title: OC11


title: human_CEP_2


title: AC12

value: Adaptive strain at 30 oC


title: AC13


title: PK44 cells in Yolk sac 1


title: human_NP_2

value: nucleus pulposus


title: human_NP_3


title: MSR1_Term

city: Bayreuth

first: Cornelius

middle: Nicolas

last: Riese

address: Universitätsstraße 30

department: Microbiology

institute: University of Bayreuth

data_processing:
The sequencing reads were trimmed for low quality bases prior to mapping.
Afterwards, reads were mapped to the M. gryphiswaldense genome (Accession No. CP027526) by using bowtie2 with default settings for single-end read mapping (Langmead and Salzberg, 2012).
TSS were automatically detected using the Cappable-tools with standard parameters as in Ettwiller et al., 2016.
The identified TSS were classified by the location in the genome into four groups: primary TSS (pTSS), intragenic TSS in sense orientation (iTSS), or antisense orientation (asTSS), and TSS positioned in the antisense direction in the intergenic regions were classified as "other" (oTSS).
Afterwards, the putative TSS in the major magnetosome biosynthesis clusters were curated manually by combining the information from the Cappable-seq and whole transcriptome datasets.
Putative trasncription termination sites (TTS) were curated manually depending on the respective increase in read coverage, deacrease of read coverge in the whole transcriptome dataset and their location within a the genome.
Genome_build: CP027526
Supplementary_files_format_and_content: XLSX-file with all identified TSS in the genome
Supplementary_files_format_and_content: XLSX-file with the identified TSS in the major magnetosome clusters
Supplementary_files_format_and_content: XLSX-file of identified transcription termination sites in the major magnetosome clusters

organism: Magnetospirillum gryphiswaldense

source_name: Bacteria, WT

growth_protocol: Cells of M. gryphiswaldense were cultivated in 5 L screw-capped bottles at 25°C to mid-growth phase (OD565 = 0.2).

extract_protocol:
Cells were harvested by centrifugation at 4°C and flash frozen with liquid nitrogen prior total RNA isolation. RNA isolated from biological duplicates using the mirVana RNA isolation kit (Thermo Fisher Scientific, Waltham, USA) including DNase treatment was pooled and subsequently used for library preparation.
For the enrichment of primary 5’-ends, a modified version of the Cappable-sequencing technique  was used (Ettwiller et al., 2016). Briefly, 5’-fragment enriched cDNA libraries of the pooled RNA-samples were produced by first capping 5' triphosphorylated with 3’-desthiobiotin-TEG-guanosin 5' triphosphate (DTBGTP) (New England Biolabs, Ipswitch, USA) using the vaccinia capping enzyme (VCE). Subsequently, biotinylated RNA was captured on streptavidin beads and eluted to obtain the 5' fragment of the primary transcripts. For elimination of unspecific binding to the column matrix, an uncapped control was treated the same way as the capped sample. The Cappable-enriched fragments were poly(A)-tailed and 5' Illumina TrueSeq sequencing adapters were ligated to 5' mono-phosphate groups of the transcripts. The 5'triphosphate groups were then converted into 5' monophosphate ends by a CapClip Acid Pyrophosphatase (Cellscript, Medison, USA) and 5' Illumina TrueSeq sequencing adapters were ligated to the new 5' mono-phosphate groups of the transcripts. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/µl using a high-fidelity DNA polymerase. For Illumina sequencing, 100 – 400 bp long 5'-fragments were isolated from the full-length cDNA. For this purpose, the cDNA preparation was fragmented using dsDNA Fragmentase (New England Biolabs, Ipswitch, USA) and the 5'-cDNA fragments were then bound to streptavidin magnetic beads. The cDNA was blunted, and the 3' Illumina sequencing adapter was ligated to the 3' ends of the cDNA fragments. The bead bound cDNA was finally PCR-amplified . For the whole transcriptome and 3’-end dataset rRNA was depleted from the pooled RNA sample using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina, San Diego, USA). The remaining mRNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics, Chaska, USA) and analyzed by capillary electrophoresis. Fragmentation of mRNA, reverse transcription, adapter ligation and PCR amplification were performed according to TrueSeq Standard mRNA library instructions (Illumina). Single-end sequencing for the two libraries was performed on an Illumina NextSeq 500 system using 1x75 bp read length. For the 3’-end library preparation a 3' Illumina sequencing adapter was ligated to the 3'-OH ends and paired-end sequenced on an Illumina NextSeq 500 system using 2x75 bp read length.

tag: genotype

value: wild type

tag: protocol

value: 3'-end library


title: MSR1_RWTSS

value: Ribo-depleted whole transcriptome shotgun sequencing library


title: AC11


title: MSR1_TSS

value: 5'-end enriched library


title: human_NP_1

value: 18 year-old


title: PEDV infected porcein intestinal organoids rep2

status: Public on Aug 19 2021

city: Shanghai

first: Changlong

last: Liu

state: Shanghai

address: 518 Ziyue Road, Minhang

institute: Shanghai Veterinary Research Institute

description:
2x150 paired-end sequence reads
PEDV2

data_processing:
Quality of FASTQ file were evaluated by FastQC software
Raw reads were filtered with Cutadapt sofware with parameters of 10 bp overlap, 20% base mismatch
Reas were mapped to sus scrofa genome Sus_scrofa.Sscrofa11.1.dna.toplevel.fa with Bowtie2 with default parameter
Raw counts were generated using Htseq with Sus_scrofa.Sscrofa11.1.dna.toplevel.fa annotation file
Gene differential expression was analyzed by Deseq2 software using genes raw counts
Genome_build: Sus_scrofa.Sscrofa11.1.dna.toplevel.fa
Supplementary_files_format_and_content: csv files include raw reads counts and FPKM values for each Sample ...

organism: Sus scrofa

source_name: small intestine

growth_protocol: Porcein intestinal organoids were incubated at 37°C in 5% CO2 and grown in porcine intestinal organoids medium, which contains Advanced DMEM/F12, 100 µg/ml primocin, 2 mM GlutaMax, 10 mM HEPES, 1 × N2, 1 × B27, 1 mM N-Acetyl-Cysteine, 10 mM Nicotinamide, 50% L-WRN conditioned medium, 50 ng/ml human EGF, 500 nM A83-01 and 3 μM SB202190

extract_protocol:
Total RNA were isolated with miRNeasy MiniKit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Porcein intestinal organoids were infected with 0.1 MOI of transmissible gastroenteritis virus (TGEV),  porcine epidemic diarrhea virus (PEDV) or DMEM as control

tag: agent

value: Infected with PEDV


title: TGEV infected porcein intestinal organoids rep2

description:
2x150 paired-end sequence reads
TGEV2

value: Infected with TGEV


title: pulmonary tumor (mesenchymal tumor)

city: Kobe

first: Masato

last: Komatsu

state: Hyogo

address: 7-5-2 Kusunoki-Cho, Chuo-Ku

department: Diagnostic Pathology

institute: Kobe University Hospital

description: FFPE-derived RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
We use internal software SOAPnuke to filter reads, followed as:1) Remove reads with adaptors;2) Remove reads in which unknown bases(N) are more than 10%;3) Remove low quality reads (we define the low quality read as the percentage of basewhich quality is lesser than 15 is greater than 50% in a read).Software information [SOAPnuke:version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1 -Q 2(website: https://github.com/BGI-flexlab/SOAPnuke)]
We use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the  HISAT2 mapping step. Software information [HISAT2 version: v2.0.4, Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000]  (Website: http://www.ccb.jhu.edu/software/hisat)
For gene expression analysis, We mapped clean reads to reference using Bowtie2, and then calculate gene  expression level with RSEM. Software information [Bowtie2 :Version: v2.2.5, Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --nomixed  --no-discordant -p 1 -k 200 (Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml) RSEM :Version: v1.2.12 Parameters: default]
SOAPfuse software was used for identifying  gene rearrangement. Software infromation [SOAPfuse Version: v1.18 Parameters: -fs 1 -tp 9 -fm]
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of sample
Supplementary_files_format_and_content: tab-delimited text files include candidate fusion genes of sample

source_name: A 56-years-old male

extract_protocol:
Tumor was surgically removed and fixed in 10% formarin.Total RNA was extracted from three pieces  of a 10‐μm‐thick FFPE section of the tumor using the RNAstorm FFPE RNA extraction kit (CellData Sciences, Fremont,CA, USA)
A sequencing library was prepared using the TruSeq RNA Access Library Prep kit (Illumina, San Diego,CA, USA) according to the manufacturer's instructions

value: lung


title: 160 organoid LEP rep 1

city: Duarte

first: Rosalyn

middle: W.

last: Sayaman

address: 1500 E Duarte Rd

description:
Cells isolated from primary breast organoid
33689_160_org_LEP_S32

data_processing:
Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle. Real-time analysis (RTA v2.2.38) software was used to process the image analysis.
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic [Bolger et al., 2014]. The processed reads were mapped back to the human genome (hg19) using TOPHAT2 software [Kim et al., 2013].
HTSeq [Anders and Huber, 2010] and RSeQC [Wang et al., 2012] software were applied to generate the count matrices and strand information, respectively with default parameters.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Matrix table of raw counts for 120 samples encompassing 34,623 transcripts mapped to Ensembl IDs.

source_name: Primary breast organoid

growth_protocol: Primary HMECs were established from organoids isolated from collected breast tissue samples. HMECs were maintained and grown to 4th passage according to previously reported protocol using M87A medium containing cholera toxin and oxytocin at 0.5 ng/ml and 0.1nM, respectively [LaBarge et al., 2013, Garbe et al., 2009].

extract_protocol:
KAPA mRNA Hyper prep kit
Total RNAs were isolated from enriched LEPs and MEPs with Quick-RNA Microprep Kit (Zymo Research, R1050). For RNA-seq, isolated RNAs were submitted to Integrative Genomic Core at City of Hope (IGC at COH) for library preparation and sequencing.
RNA sequencing libraries were prepared with Kapa RNA mRNA HyperPrep Kit (Kapa Biosystems, Cat KR1352) or KAPA stranded mRNA-seq (Kapa Biosystems, Cat KK8420) according to the manufacturer's protocol. 100 ng of total RNA from each sample was used for polyA RNA enrichment. The enriched mRNA underwent fragmentation and first strand cDNA synthesis. The combined 2nd cDNA synthesis with dUTP and A-tailing reaction generated the resulting ds cDNA with dAMP to the 3’ ends.  The barcoded adaptors were ligated to the ds cDNA fragments. A 10-cycle of PCR was performed to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.

treatment_protocol: LEP and MEP enrichment was performed across multiple studies (Sayaman, Miyano et al., 2021, Shalabi et al., 2021, Todhunter et al., 2021). Enrichment was conducted by FACS or EasySEP Cell Separation (Stem Cell Technologies) using well-established LEP-specific cell-surface markers: CD227 (anti-human CD227-FITC, BD Biosciences, clone HMPV) or CD133 (anti-human CD133-PE, BioLegend, clone7), and MEP-specific cell-surface marker: CD271 (anti-human CD271-APC, BioLegend, clone ME20.4). Protocols were validated and found to sort similar populations regardless of antibody combination and enrichment methodology. Breast epithelial cells were stained following standard flow cytometry protocol.

value: breast

value: Not Reported

tag: chemotherapy

value: No chemo

value: Reduction Mammaplasty

value: RM

value: Luminal epithelial cells

value: LEP

value: organoid

value: FACS (BD FACSAriaIII)

value: Mark A. LaBarge

tag: institution

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: 237 organoid LEP rep 1

department: Population Sciences, Beckman Research Institute

institute: City of Hope Comprehensive Cancer Center

description:
Cells isolated from primary breast organoid
33691_237_org_LEP_S33


title: PEDV infected porcein intestinal organoids rep1

description:
2x150 paired-end sequence reads
PEDV1


title: TGEV infected porcein intestinal organoids rep1

description:
2x150 paired-end sequence reads
TGEV1


title: MOCK infected porcein intestinal organoids rep2

description:
2x150 paired-end sequence reads
NC2

value: Control


title: 160 organoid MEP rep 1

description:
Cells isolated from primary breast organoid
33688_160_org_MEP_S31

value: Myoepithelial cells

value: MEP


title: MOCK infected porcein intestinal organoids rep1

description:
2x150 paired-end sequence reads
NC1


title: 96L organoid LEP rep 1

description:
Cells isolated from primary breast organoid
33693_96L_org_LEP_S34


title: 124 organoid LEP rep 1

description:
Cells isolated from primary breast organoid
33685_124_org_LEP_S26


title: 112R organoid MEP rep 1

description:
Cells isolated from primary breast organoid
33686_112R_org_MEP_S29


title: 124 organoid MEP rep 1

description:
Cells isolated from primary breast organoid
33684_124_org_MEP_S25


title: healthy control_4

city: Paris

first: Charles

last: Cassius

address: 1 avenue Claude Vellefaux

department: Dermatologie

country: France

institute: Hôpital Saint-Louis

hyb_protocol: hybridazation protocol was made according to manufacturer protocol https://www.nanostring.com/wp-content/uploads/2021/03/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

data_processing: normalization was performed as follows: the scaling factor for a sample was defined as the ratio of the average across all geometric means and the geometric mean of the sample. For each sample, all gene counts were multiplied by the corresponding scaling factor. After normalization, background level was re-computed as 54 normalized counts. Genes with no values above background levels, as well as positive, negative control and housekeeping genes were removed from subsequent analyses. Normalized counts were log10-transformed for all subsequent analyses

source_name: skin

label_protocol: we analyzed 100 ng (5 μl) of total RNA from each sample using the Nanostring Human Immunology kit v2

extract_protocol: From a lesional dermal-epidermal skin biopsy, 10 formalin-fixed paraffin-embedded (FFPE) sections, each 10-μm-thick, were taken. Total RNA was automatically extracted from tissue samples using the Maxwell RSC RNA FFPE kit protocol (Promega, Charbonnières-les-bains, France).

value: healthy control


title: healthy control_3


title: healthy control_2


title: 51L organoid MEP rep 1

description:
Cells isolated from primary breast organoid
33682_51L_org_MEP_S23


title: seasonal chilblain_2

value: seasonal chilblain


title: seasonal chilblain_4


title: 195L organoid MEP rep 1

description:
Cells isolated from primary breast organoid
33680_195L_org_MEP_S21


title: 51L organoid LEP rep 1

description:
Cells isolated from primary breast organoid
33683_51L_org_LEP_S24


title: seasonal chilblain_1


title: 163 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
33666_163_MEP_S5

source_name: Human Mammary Epithelial Cells

value: HMEC 4p


title: chilblain like lesion COVID 19_8

value: chilblain like lesion COVID 19


title: 195L organoid LEP rep 1

description:
Cells isolated from primary breast organoid
33681_195L_org_LEP_S22

value: breast

value: Not Reported


title: 163 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
33667_163_LEP_S6

value: No chemo

value: Reduction Mammaplasty


title: chilblain like lesion COVID 19_9


title: 112R organoid LEP rep 1

description:
Cells isolated from primary breast organoid
33687_112R_org_LEP_S30

value: RM

value: Luminal epithelial cells


title: seasonal chilblain_3


title: chilblain like lesion COVID 19_7


title: healthy control_1


title: 112R HMEC 4p LEP rep 3

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
33665_112R_LEP_S4

value: LEP


title: 112R HMEC 4p MEP rep 3

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
33664_112R_MEP_S3

value: FACS (BD FACSAriaIII)


title: 240L HMEC 4p MEP rep 4

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
33662_240LB_MEP_S1

value: Mark A. LaBarge


title: chilblain like lesion COVID 19_6


title: 429ER HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27019_429ER_LEP_S22

value: FACS (Bio-Rad S3 Cell Sorter)

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: chilblain like lesion COVID 19_3


title: chilblain like lesion COVID 19_4


title: chilblain like lesion COVID 19_2


title: chilblain like lesion COVID 19_10


title: 153L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27017_153L_LEP_S37


title: 29 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27018_29_LEP_S38


title: chilblain like lesion COVID 19_1


title: 117R HMEC 4p LEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27016_117R_LEP_S36


title: 112R HMEC 4p LEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27015_112R_LEP_S35


title: 240L HMEC 4p LEP rep 4

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
33663_240LB_LEP_S2


title: MBC_day50_1: Memory B cells day 50 after immunization

city: Solna

first: Taras

last: Kreslavsky

address: Nks Bioclinicum, J7:30, Visionsgatan 4

department: Department of Medicine, Solna (MedS)

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads were aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using RNA STAR (Dobin et al., 2012) (usegalaxy.eu; Galaxy Version 2.7.8a (Afgan et al., 2018)). The calculation of RNA expression values was all based on the RefSeq database, which was downloaded from UCSC on January 10th, 2014. The annotation of immunoglobulin and T cell receptor genes was incorporated from the Ensembl release 67 (Cunningham et al., 2015). Genes with overlapping exons were flagged and double entries (i.e. exactly the same gene at two different genomic locations) were renamed. Genes with several transcripts were merged to consensus-genes consisting of a union of all underlying exons using the fuge software (I. Tamir, unpublished), which resulted in 25,726 gene models. The data sets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 2014). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Genome_build: MM9
Supplementary_files_format_and_content: Excel table with TPM values for all samples, see ‘data processing step’ for details.

source_name: Splenic B cells

extract_protocol:
Single cell lysis kit
NEBNext Ultra II

value: Igh B1-8hi/+

tag: cell preparation

value: Ex vivo, FACS-sorted from spleens

tag: cell sorting strategy

value: Igκ- CD4- CD8- F4/80- CD3- Ter119 -CD11c- CD45.1+ CD19+ Igλ+ CCR6+ GL7int/lo

tag: cell type

value: Splenic B cells


title: 168R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27013_168R_LEP_S33

value: HMEC 4p


title: PB_day4_1: Plasmablasts day 4 after immunization


title: 184D HMEC 4p LEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27014_184D_LEP_S34


title: chilblain like lesion COVID 19_5

tag: disease

value: chilblain like lesion COVID 19


title: GCBC_day4_4: Germinal center B cells day 4 after immunization


title: GCBC_day4_3: Germinal center B cells day 4 after immunization


title: 356E HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27012_356E_LEP_S32

value: breast


title: GCBC_day4_1: Germinal center B cells day 4 after immunization


title: GCBC_day4_2: Germinal center B cells day 4 after immunization


title: 240L HMEC 4p LEP rep 3

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27010_240L_LEP_S29

value: Not Reported


title: 48R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27011_48R_LEP_S30

value: No chemo


title: AP_MBC_day4_4: Activated precursors/memory B cells day 4 after immunization


title: 429ER HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27009_429ER_MEP_S28

value: Reduction Mammaplasty

value: Myoepithelial cells

value: MEP


title: 29 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27008_29_MEP_S21

value: RM


title: AP_MBC_day4_3: Activated precursors/memory B cells day 4 after immunization


title: AP_MBC_day4_2: Activated precursors/memory B cells day 4 after immunization


title: 153L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27007_153L_MEP_S20


title: MBC_day50_2: Memory B cells day 50 after immunization


title: 117R HMEC 4p MEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27006_117R_MEP_S27


title: AP_MBC_day4_1: Activated precursors/memory B cells day 4 after immunization


title: AP_MBC_day2.5_4: Activated precursors/memory B cells day 2.5 after immunization


title: 112R HMEC 4p MEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27005_112R_MEP_S26


title: PB_day4_2: Plasmablasts day 4 after immunization


title: 184D HMEC 4p MEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27004_184D_MEP_S25


title: AP_MBC_day2.5_2: Activated precursors/memory B cells day 2.5 after immunization


title: AP_MBC_day2.5_3: Activated precursors/memory B cells day 2.5 after immunization


title: 168R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27003_168R_MEP_S24


title: AP_MBC_day2.5_1: Activated precursors/memory B cells day 2.5 after immunization


title: 240L HMEC 4p MEP rep 3

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27000_240L_MEP_S10


title: 356E HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27002_356E_MEP_S19


title: 48R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
27001_48R_MEP_S11


title: 184D HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25481_184D_LEP_S35

value: Luminal epithelial cells

value: LEP


title: RL3_muscle

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

institute: University of Basel

description:
WGBS from adult tissue
RL_m_n2_50bpmean_SNPcorr.bw

data_processing:
RNAseq reads were mapped to MZ_UMD2a and gene expression values were calculated using kallisto (see SUPP methods)
WGBS reads were mapped to mapped to SNP-corrected genomes (based on MZ_UMD2a) and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see SUPP Methods). Methylation at CG sites with ≥5 ≤100 non-clonal seq reads averaged across 50bp-long non-slidding windows per species were performed to produce bw files.
Species-specific high-confidence SNP-corrected genome (fa file) was generated for each of the species studied in this study by using published whole genome sequencing dataset (Malinsky et al 2018); see Methods.
DMRs were called using DSS (see SUPP Methods). P<0.05, minimal overall methylation difference across any DMR between any species was >25% (d25pc), ≥4 CpG, ≥50bp and pvalue<0.05 (p005). For DMR calling, all CG sites were used independent of sequencing coverage following DSS recommandations (improved DMR calling).
Genome_build: Maylandia zebra MZ_UMD2a  and SNP-corrected genomes
Supplementary_files_format_and_content: tpm for RNAseq (tsv) generated using kallisto, mCG/CG (bigwig) generated using bismark, SNP-corrected genomes (fa)

organism: Rhamphochromis longiceps

source_name: homogenised adult skeletal muscle

extract_protocol:
Genomic DNA extracted using phenol/chlorophorm approach (see SUPP methods)
DNA strand-specific library using methylated adaptor (NEB) followed by bisulfite conversion (Imprint, Sigma), according to manusfacturer's instructions. WGBS libraries contain lambda genome spike-in control (0.2% w/w).

value: skeletal muscle

tag: Sex

value: male

tag: type

value: wild-caught


title: RL2_muscle

tag: tissue


title: RL1_mC_liver

description:
WGBS from adult tissue
RL_l_n2_50bpmean_SNPcorr.bw

source_name: homogenised adult liver tissue

value: liver


title: RL3_mC_liver


title: PG3_mC_muscle_run2

description:
WGBS from adult tissue
PG_m_n2_50bpmean_SNPcorr.bw

organism: Petrotilapia genalutea


title: PG3_mC_muscle_run1


title: RL2_mC_liver


title: PG1_mC_muscle_run2


title: PG1_mC_muscle_run1


title: 184D HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25480_184D_MEP_S34

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: 240L HMEC 4p LEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25430_RNA_240L_LEP_S4

value: HMEC 4p

value: EasySEP Cell Separation (Stem Cell Technologies)


title: C019C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25428_RNA_C019C_LEP_S2

value: breast

tag: bmi

value: Premenopause

value: Family History

value: Contralateral-to-Tumor

value: CLTT


title: PG1_mC_liver

description:
WGBS from adult tissue
PG_l_n3_50bpmean_SNPcorr.bw


title: 169L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25423_RNA_169L_MEP_S33

value: Not Reported

value: No chemo

value: Reduction Mammaplasty

value: RM

value: Myoepithelial cells

value: MEP


title: PG3_mC_liver

value: liver

value: male

value: wild-caught


title: 006 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25422_RNA_006_LEP_S32

value: Luminal epithelial cells

value: LEP

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: PG2_mC_liver


title: 124 HMEC 4p MEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25425_RNA_124_MEP_S35

value: breast

value: HMEC 4p

value: FACS (BD FACSAriaSORP)


title: 006 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25421_RNA_006_MEP_S31

value: Not Reported


title: 117R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25420_RNA_117R_LEP_S30

value: No chemo


title: MZ2_mC_liver

description:
WGBS from adult tissue
MZ_l_n3_50bpmean_SNPcorr.bw

organism: Maylandia zebra


title: MZ3_mC_liver


title: DL2_mC_muscle_run2

description:
WGBS from adult tissue
DL_m_n2_50bpmean_SNPcorr.bw

organism: Diplotaxodon limnothrissa

value: skeletal muscle


title: C019C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25427_RNA_C019C_MEP_S1

value: Premenopause

value: Family History

value: Contralateral-to-Tumor

value: CLTT


title: DL1_mC_muscle_run2

value: male


title: 240L HMEC 4p MEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25429_RNA_240L_MEP_S3

value: Reduction Mammaplasty

value: RM

value: Myoepithelial cells

value: MEP

value: EasySEP Cell Separation (Stem Cell Technologies)


title: DL1_mC_muscle_run1

value: wild-caught


title: MZ1_mC_liver

value: liver


title: 030 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25417_RNA_030_MEP_S27

value: breast

value: HMEC 4p

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: C039C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25416_RNA_C039C_LEP_S26

value: PALB2 VUS, APC VUS

value: Menopause

value: Chemo

value: Luminal epithelial cells

value: LEP


title: 030 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25418_RNA_030_LEP_S28

value: Not Reported

value: No chemo

value: Reduction Mammaplasty


title: 124 HMEC 4p LEP rep 2

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25426_RNA_124_LEP_S36

value: RM

value: FACS (BD FACSAriaSORP)


title: 169L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25424_RNA_169L_LEP_S34


title: 117R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25419_RNA_117R_MEP_S29

value: Myoepithelial cells

value: MEP


title: DL1_mC_liver

description:
WGBS from adult tissue
DL_l_n3_50bpmean_SNPcorr.bw

value: liver

value: male

value: wild-caught


title: DL2_mC_liver


title: C017L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25412_RNA_C017L_LEP_S22

value: breast

value: Premenopause

value: Family History

value: Prophylactic Mastectomy

value: PM

value: HMEC 4p

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge


title: Huh7 sh2-1

first: Guangyan

last: Zhangyuan

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: Huh7 sh2-1

data_processing:
Basecalls performed using bcl2fastq2 version 2.19.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic v0.36, then mapped to mm10 whole genome using bowtie2 v2.2.6。
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RSEM v1.1.17
Differential expression genes were calculated using edgeR v3.18.1 and DESeq2 v1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

source_name: Huh7 sh2

growth_protocol: Huh7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (GIBCO, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen, CA, USA) in a humidified 37℃ incubator supplemented with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and VersicanV1 knockdown lentivirus generated from 293T cells using calcium phosphate precipitation, and transfected into Huh7 cell lines mediated by polybrene (8 ug/ml) for 6 – 8 hours.

tag: cell line

value: liver cancer cell line

tag: genotype/variation

value: transfected with VersicanV1 knockdown lentivirus


title: Huh7 sh2-2

description: Huh7 sh2-2


title: C039C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25415_RNA_C039C_MEP_S25

tag: age

value: PALB2 VUS, APC VUS

value: Menopause

value: Chemo

value: Contralateral-to-Tumor

value: CLTT

value: EasySEP Cell Separation (Stem Cell Technologies)

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: DL3_mC_liver

value: liver

value: male

value: wild-caught


title: C014R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25410_RNA_C014R_LEP_S20

value: breast

value: Family History

value: No chemo

value: Prophylactic Mastectomy

value: Luminal epithelial cells

value: LEP


title: Huh7 shNC-3

description: Huh7 shNC-3

source_name: Huh7 shNC

value: liver cancer cell line

value: transfected with contol lentivirus


title: Huh7 sh2-3

description: Huh7 sh2-3

value: transfected with VersicanV1 knockdown lentivirus


title: C017L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25411_RNA_C017L_MEP_S21

value: Premenopause

value: PM

value: Myoepithelial cells

value: MEP

value: HMEC 4p

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge


title: C018C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25414_RNA_C018C_LEP_S24

value: No Family History

value: Chemo

value: Contralateral-to-Tumor

value: CLTT

value: EasySEP Cell Separation (Stem Cell Technologies)

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: DL2_mC_muscle_run1

value: skeletal muscle

value: male

value: wild-caught


title: C020C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25408_RNA_C020C_LEP_S18

value: breast

value: Luminal epithelial cells

value: LEP


title: C014R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25409_RNA_C014R_MEP_S19

value: Menopause

value: Family History

value: No chemo

value: Prophylactic Mastectomy

value: PM

value: Myoepithelial cells


title: C063C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25406_RNA_C063C_LEP_S16

value: Not Reported

value: No Family History

value: Chemo

value: HMEC 4p

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge


title: C018C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25413_RNA_C018C_MEP_S23

value: Premenopause

value: Contralateral-to-Tumor

value: CLTT

value: MEP

value: EasySEP Cell Separation (Stem Cell Technologies)

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Huh7 shNC-1

description: Huh7 shNC-1

value: liver cancer cell line

value: transfected with contol lentivirus


title: Tom+ LCMV-specific TRM cells day >30 - SI IEL - rep 3

city: Amsterdam

first: Klaas

last: van Gisbergen

state: Select one

address: Plesmanlaan 125

department: Department of Hematopoiesis

country: Netherlands

institute: Sanquin Research and Landsteiner Laboratory

description: Tom+ LCMV-specific TRM cells

data_processing:
Barcodes were removed using the fastx_barcode_splitter script from the fastx toolkit v0.0.14
Read mapping was performed using STAR(v2.5.3a) against mouse genome mm10.
Read count quantification was done with featureCounts (v1.5.2) using Ensembl’s v92 annotation with a minor modification to correct for incorrect intron/exon boundaries in Zfp683 (Hobit) locus.
Read count normalization was done using the cmp() function of EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: All mice were maintained under specific pathogen-free (SPF) conditions

extract_protocol:
SI IEL and LPL preparations were obtained from the small intestine. After removal of residual fat tissue, Peyer’s patches, and feces, small intestine tissue was cut into pieces of 1 cm and incubated in Hanks’ balanced slat solution (HBSS, Gibco) with 10% fetal calf serum (FCS), 5 mM EDTA, and 1 mM dithiothreitol (DTT) for 30 min at 37°C. After repeated vortexing, the IEL fraction was released from the tissue and isolated by filtering over a 70 μm cell strainer. Subsequently, IEL-depleted intestine pieces were washed in HBSS supplemented with 2% FCS and enzymatically digested for 30 min at 37 °C with 375 U ml-1 Collagenase Type I (Worthington) and 0.15 mg ml-1 DNase I (Roche, from bovine pancreas, grade II) in RPMI 1640 (supplemented with 10% FCS) to isolate the LPL fraction. Similarly, kidneys were cut into pieces of 1 mm3, which were enzymatically digested for 30 min at 37 °C with 750 U ml-1 Collagenase Type I (Worthington) and 0.31 mg ml-1 DNase I (Roche, from bovine pancreas, grade II) in RPMI 1640 (supplemented with 10% FCS). Single cell suspensions from the LPL fraction of small intestine, kidney, spleen, LNs and liver were prepared by mechanical disruption via passing over a 70 μm cell strainer. The isolated lymphocytes from liver, kidney, SI IEL and LPL were purified by density centrifugation on a 60% / 40% Percoll gradient (GE Healthcare). Contaminating erythrocytes were removed using red blood cell lysis buffer (155mM NH4Cl, 10mM KHCO3, 0,1mM EDTA).
Library construction was performed by Single Cell Discoveries (The Netherlands) using the CEL-Seq protocol as published in Hashimshony et al. Cel Rep 2012 (doi:j.celrep.2012.08.003).

treatment_protocol: Mice were infected intraperitoneally with 10^5 plaque-forming units (PFU) of LCMV Armstrong obtained from EVAg, or with 10^4 PFU of replication sufficient rLCMV OVA

value: Tissue-resident memory CD8+ T cells

value: small intestine

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: C063C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25405_RNA_C063C_MEP_S15

value: breast

value: Not Reported

value: Myoepithelial cells


title: C020C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25407_RNA_C020C_MEP_S17

value: No Family History

value: Chemo

value: HMEC 4p


title: Tom+ LCMV-specific TRM cells day >30 - SI IEL - rep 2

description: Tom+ LCMV-specific TRM cells


title: C008C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25402_RNA_C008C_LEP_S12

value: Menopause

value: Luminal epithelial cells

value: LEP

value: FACS (Bio-Rad S3 Cell Sorter)

value: Mark A. LaBarge


title: C003R2 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25404_RNA_C003R2_LEP_S14

value: Premenopause

value: No chemo

value: Prophylactic Mastectomy

value: PM

value: EasySEP Cell Separation (Stem Cell Technologies)

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: C008C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25401_RNA_C008C_MEP_S11

value: breast

value: Contralateral-to-Tumor

value: CLTT

value: MEP


title: C009R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25400_RNA_C009R_LEP_S10

value: No Family History


title: Tom- LCMV-specific TEM cells day >30 - Kidney - rep 1

description: Tom‒ LCMV-specific TEM cells

source_name: kidney

value: Effector memory CD8+ T cells

value: kidney

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: Tom+ LCMV-specific TRM cells day >30 - Kidney - rep 3

description: Tom+ LCMV-specific TRM cells

value: Tissue-resident memory CD8+ T cells


title: Huh7 shNC-2

description: Huh7 shNC-2

value: liver cancer cell line

value: transfected with contol lentivirus


title: Tom- LCMV-specific TEM cells day >30 - Kidney - rep 2

description: Tom‒ LCMV-specific TEM cells


title: C009R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25399_RNA_C009R_MEP_S9

value: Premenopause

value: Myoepithelial cells

value: HMEC 4p

value: Mark A. LaBarge


title: Tom+ LCMV-specific TRM cells day >30 - Kidney - rep 2

description: Tom+ LCMV-specific TRM cells


title: Tom+ LCMV-specific TRM cells day >30 - Liver - rep 2

description: Tom+ LCMV-specific TRM cells

source_name: liver

value: liver


title: Tom+ LCMV-specific TRM cells day >30 - Liver - rep 1

description: Tom+ LCMV-specific TRM cells


title: Tom+ LCMV-specific TRM cells day >30 - SI IEL - rep 1

description: Tom+ LCMV-specific TRM cells

value: small intestine


title: C001R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25396_RNA_C001R_LEP_S6

value: breast

value: Menopause

value: Family History

value: No chemo

value: Prophylactic Mastectomy

value: PM

value: Luminal epithelial cells

value: LEP

value: FACS (Bio-Rad S3 Cell Sorter)

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Tom- LCMV-specific TEM cells day >30 - Liver - rep 3

description: Tom‒ LCMV-specific TEM cells

value: Effector memory CD8+ T cells

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: Tom+ LCMV-specific TRM cells day >30 - Kidney - rep 1

description: Tom+ LCMV-specific TRM cells

value: Tissue-resident memory CD8+ T cells

value: kidney


title: C003R2 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25403_RNA_C003R2_MEP_S13

value: Premenopause

value: No Family History

value: Myoepithelial cells

value: MEP

value: HMEC 4p

value: EasySEP Cell Separation (Stem Cell Technologies)

value: Mark A. LaBarge


title: C023R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25393_RNA_C023R_MEP_S3

value: breast

value: Not Reported

value: Family History

value: No chemo

value: Prophylactic Mastectomy


title: C002R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25392_RNA_C002R_LEP_S2

value: Menopause

value: PM

value: Luminal epithelial cells

value: LEP

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: C002R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25391_RNA_C002R_MEP_S1


title: Tom- LCMV-specific TEM cells day >30 - Spleen - rep 3

description: Tom‒ LCMV-specific TEM cells

source_name: spleen

value: Effector memory CD8+ T cells

value: spleen

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: Tom- LCMV-specific TEM cells day >30 - Liver - rep 1

description: Tom‒ LCMV-specific TEM cells

value: liver


title: Tom- LCMV-specific TEM cells day >30 - Spleen - rep 2

description: Tom‒ LCMV-specific TEM cells


title: C004R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25397_RNA_C004R_MEP_S7

value: No Family History

value: Chemo

value: Myoepithelial cells

value: MEP

value: HMEC 4p

value: FACS (Bio-Rad S3 Cell Sorter)


title: Tom- LCMV-specific TEM cells day >30 - Kidney - rep 3

description: Tom‒ LCMV-specific TEM cells

value: kidney


title: C004R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25398_RNA_C004R_LEP_S8

value: breast

value: Prophylactic Mastectomy

value: Mark A. LaBarge


title: 90P HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14923_90P_LEP_RNA_CAGATC

extract_protocol:
KAPA stranded mRNA-seq kit
Total RNAs were isolated from enriched LEPs and MEPs with Quick-RNA Microprep Kit (Zymo Research, R1050). For RNA-seq, isolated RNAs were submitted to Integrative Genomic Core at City of Hope (IGC at COH) for library preparation and sequencing.
RNA sequencing libraries were prepared with Kapa RNA mRNA HyperPrep Kit (Kapa Biosystems, Cat KR1352) or KAPA stranded mRNA-seq (Kapa Biosystems, Cat KK8420) according to the manufacturer's protocol. 100 ng of total RNA from each sample was used for polyA RNA enrichment. The enriched mRNA underwent fragmentation and first strand cDNA synthesis. The combined 2nd cDNA synthesis with dUTP and A-tailing reaction generated the resulting ds cDNA with dAMP to the 3’ ends.  The barcoded adaptors were ligated to the ds cDNA fragments. A 10-cycle of PCR was performed to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.

value: Not Reported

value: Peripheral-to-Tumor

value: PTT

value: Luminal epithelial cells

value: FACS (BD FACSVantage)


title: 353P HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14924_353P_MEP_RNA_GATCAG

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Tom- LCMV-specific TEM cells day >30 - Liver - rep 2

description: Tom‒ LCMV-specific TEM cells

value: Effector memory CD8+ T cells

value: liver

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: C023R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25394_RNA_C023R_LEP_S4

value: Family History

value: No chemo

value: PM

value: LEP

value: EasySEP Cell Separation (Stem Cell Technologies)


title: Tom- LCMV-specific T cells day 8 - SI IEL - rep 3

description: Tom‒ LCMV-specific effector T cells

value: small intestine


title: C001R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
25395_RNA_C001R_MEP_S5

value: breast

value: Menopause

value: Prophylactic Mastectomy

value: Myoepithelial cells

value: MEP

value: HMEC 4p

value: FACS (Bio-Rad S3 Cell Sorter)


title: 90P HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14922_90P_MEP_RNA_GCCAAT

value: Not Reported

value: Peripheral-to-Tumor

value: PTT

value: FACS (BD FACSVantage)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: 215C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14921_215C_LEP_RNA_ACAGTG

value: Contralateral-to-Tumor

value: CLTT

value: Luminal epithelial cells