title: mg132_3h_4

description:
9O
total RNA (ribosomal RNA depleted)


title: bulkRNA-L1-40-1

status: Public on Dec 14 2021

type: SRA

city: Los Angeles

first: Ying

last: Lin

state: California

address: 675 Charles E. Young Drive South

country: USA

institute: University of California, Los Angeles

description: L1 bulk RNA-seq expression.xlsx

library_source: transcriptomic

data_processing:
bulk ATAC-seq: Raw fastq reads files were mapped to FlyBase reference genome (release 6.29) using Bowtie2 (2.2.9) and uniquely mapped genes were kept. All samples were pooled together prior to peak calling. Read start positions were shifted +4 or -5bp and used for peak calling using MACS2 (2.1.1) with parameters “-q 0.01 --nomodel --shift -100 --extsize 200”. Then bedtools multicov (2.27.1) was used to sum the total reads within each peak separately for each sample. Peaks with CPM ≥ 4 were used for counts normalization with edgeR.
bulk RNA-seq: fastq files were mapped to FlyBase reference genome (release 6.29) using STaR (2.6.0) and only uniquely mapped reads were collected. Genes with counts per million (CPM) ≥ 4 in more than 2 samples were used for normalization with R package edgeR (3.26.8). Gene expression was quantified using RPKM units (Reads Per Kilobase of exon per Million reads mapped), calculated based on reads in the sum of exons using customized scripts.
single cell RNA-seq: Fastq files were processed using Cell Ranger (3.1.0) pipeline using default parameters. Reference transcriptome package for Cell Ranger was generated using Drosophila melanogaster genome sequence and gene annotations from FlyBase (release 6.29). DGRP samples were demultiplexed based on parental genotypes using demuxlet (version 2).Downstream analysis including cell-type clustering was performed using Seurat package (3.1.2).
Genome_build: FlyBase 6.29
Supplementary_files_format_and_content: Bulk RNA-seq and bulk-ATAC-seq: abundance measurements in excel sheets; single cell RNA: cell-type cluster and counts in Seurat object.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Maintenance and rearing of fly lines, as well as staging of pupae was done as described in Tan et al 2015

extract_protocol:
FACS-sorted cell suspension
Single cell RNA-seq: FACS-sorted cell suspension were loaded on 10X Genomics Chromium machine for single cell prepration. Single-cell RNA-Seq libraries were generated using Chromium Single Cell Reagent Kit V3 according to the manufacturer's protocol. Bulk RNA-seq: FACS sorted cell suspension were used for library prepration with SMART-seq2 protocol published by Picelli et al, 2014. Bulk ATAC-seq: FACS sorted cell suspension were used to library prep with modified protocol published by Buenrostro et al., 2013

tag: tissue

value: brain

tag: cell type

value: FACS-sorted L1 neurons

tag: age

tag: genotype

value: wild type


title: bulkRNA-L1-72-2

description: L1 bulk RNA-seq expression.xlsx


title: Adult Epcam Negative v2 Mouse Cochlea

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

description: After mincing with a scalpel and washing in PBS, the tissue was incubated in thermolysin (Sigma-Aldrich) at 37°C for 20 minutes. It was then transferred to Accumax (Innovative Cell Technologies) for 35 minutes, with trituration every 5-10 minutes. The dissociated tissue was diluted in PBS with 10% FBS and filtered through a 40 μm cell strainer. Cells were pelleted and dead cells and debris removed using the Dead Cell Removal Kit (Miltenyi Biotec) following the manufacturer’s instructions. When indicated, Epcam positive cells were next enriched in one fraction using CD326 (EpCAM) MicroBeads, mouse (Miltenyi Biotec).

data_processing:
10X Genomics Cell Ranger pipeline
See their website for their proprietary steps
the output matrix files are here and are included for postprocessing for R analysis
The web summaries for the experiments are attached as a guide to how the sequencing results turned out.
Genome_build: Genome_build: mm10 for mouse, and hg19 for human

molecule: total RNA

organism: Mus musculus

source_name: cochlea

extract_protocol:
Cells were loaded onto the Chromium Controller from 10x Genomics for single cell capture.
10x Chromium

value: cochlea

tag: strain

value: Swiss Webster

tag: developmental stage

value: Adult (6 weeks old)

value: wildtype


title: KP1

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

data_processing:
Read trimming (Trimmomatic 0.38)
Alignment into chrimeric genome (STAR 2.6.0a)
Summation (featureCounts, subread 1.6.3)
Genome_build: Homo sapiens (release 94) and Klebsiella pneumoniae (ENSEMBL, release 41)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for six libraries

organism:
Klebsiella pneumoniae
Homo sapiens

source_name: Confluent human epithelial cell line (A549) co-incubated with Klebsiella pneumoniae

growth_protocol: Human epithelial cell line was cultured with no antibiotics into confluence, confluence was maintained for 10 more days before experiment

extract_protocol:
Total RNA isolation based on phenol-chloroform, gDNA treatment using RNase-free DNase
RNA libraries were prepared for sequencing using standard Illumina protocols with rRNA depletion

treatment_protocol: Klebsiella pneumoniae culture was co-incubated into the epithelial cells

value: wildtype strain

tag: human cell line


title: G2_0h_3

city: Mexico City

first: Luis

middle: Alonso

last: Herrera Montalvo

state: Mexico City

address: Periferico Sur 4809, Arenal Tepepan, Tlalpan

department: Unidad de Investigacion Biomedica en Cancer

country: Mexico

institute: Instituto Nacional de Cancerología / Instituto Nacional de Medicina Genómica

description:
8O
total RNA (ribosomal RNA depleted)

data_processing:
Raw sequencing reads were checked for quality with fastqc, adapter removal and quality trimming was performed with cutadapt version 1.18 with parameters --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35
Mapping to the genome (assembly hg38) was performed with STAR aligner (1) version 2.7.1a with special parameters winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 for multimapping reads.
Gene and subfamily repetitive elements quantification was performed with TEcount (version 2.1.3), part of the TEtranscripts package, using gencode v34 annotations for genes and the provided curated repeat annotations for hg38 found in (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF
Genome_build: hg38
Supplementary_files_format_and_content: tab separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts hg38 repeat ids)

organism: Homo sapiens

source_name: Colorectal cancer

growth_protocol: HCT-116 cells (human colon cancer, ATCC CCL-247) were grown in 10% FBS supplemented McCoy's 5A medium at 37°C in 5% CO2 at 95% humidity and subcultured according to the supplier’s instructions.

extract_protocol:
After treatment, cells were washed with PBS, and RNA was extracted with TRIzol (Ambion, 15596018, Carlsbad, CA) according to the manufacturer’s instructions. DNA was digested with a TURBO DNA-Free kit (Ambion, AM1907, Vilnius, Lithuania) according to the manufacturer’s instructions.
TruSeq Stranded Total RNA Library Prep

treatment_protocol: A total of 1.3 x 104 cells per cm2 were seeded on 6-well plates, 24 h before the experiment. We synchronized cells (except the asynchronous controls) with a single, 16 h, 2 mM thymidine block (Sigma T1895, product of China) to obtain G1 cells. The cultures were subsequently incubated in fresh medium for 7 h to obtain G2/M cells. Once synchronized, the cells were treated for 3 h with the indicated drug or drug combination. The drug concentrations were the following: 50 µg/ml α-amanitin (Sigma A2263, product of Germany), 20 µM MG132 (Sigma C2211, product of Israel), and 100 nM bortezomib (Selleckchem, S1013).

tag: cell line

tag: treatment


title: ZP5

data_processing:
Read trimming (Trimmomatic 0.38)
Alignment into chrimeric genome (STAR 2.6.0a)
Summation (featureCounts, subread 1.6.3)
Genome_build: Danio rerio release 94 and pneumococcal genome (NAR, 2018)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for six libraries

organism:
Streptococcus pneumoniae
Danio rerio

source_name: Zebrafish embryo (2dpf) infected by Streptococcus pneumoniae D39V, complemented strain

growth_protocol: Embryo was harvested two days after fertilization and used for infection experiment

treatment_protocol: Bacterial culture was injected into the the brain ventricle

value: complemented


title: ZP6


title: Ctrl_0h_3

description:
6O
total RNA (ribosomal RNA depleted)


title: bulkATAC-L1-72-2

description: L1 bulk ATAC-seq peak level.xlsx

library_source: genomic

molecule: genomic DNA


title: E14.5 Mouse Cochlea

description: Mice were maintained under approval from the Institutional Animal Care and Use Committee at the University of California, San Francisco. The tissue was minced with a scalpel, collected in PBS, and pelleted by centrifugation. It was dissociated in TrypLE Select  (Life Technologies) at 37°C with trituration every five minutes. Once the tissue was dissociated (10-30 minutes), HBSS supplemented with 10% FBS and 2 mM EDTA was added and the suspension was passed through a 30 μm cell strainer. Cells were pelleted and then incubated with SYTOX Blue dead cell stain (Thermo Fisher Scientific) at a 1:1000 dilution for twenty minutes on ice. Cells were washed and then FACS used to collect only live cells. These cells were counted on a Moxi Flow (ORFLO Technologies) and resuspended at 1000 cells/μL in 0.04% BSA in PBS for single cell capture.

value: Embryonic 14.5 days


title: mg132+a-aman_3h_4

description:
10O
total RNA (ribosomal RNA depleted)


title: E16.5 Mouse Cochlea

value: Embryonic 16.5 days


title: bulkATAC-L1-72-1

description: L1 bulk ATAC-seq peak level.xlsx


title: mg132_3h_3

description:
4O
total RNA (ribosomal RNA depleted)


title: E12.5 Mouse Cochlea

value: Embryonic 12.5 days


title: bulkATAC-L1-60-2

description: L1 bulk ATAC-seq peak level.xlsx


title: ZP4


title: Cold_rep2

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Chronic cold

data_processing:
The quality of raw reads were assessed using fastqc.
Ribosomal RNA content was determined by aligning the reads against a set of Mouse rRNA sequences using bowtie2 v.2.3.4.1.
Raw reads were processed and trimmed to remove phiX and adapter sequences, and to remove the first 20 bases from each read.
Processed reads were aligned to GRCm38.p6 primary genome assembly using GENCODE v21 annotation, with STAR v.2.7.0e, to generate counts per gene.
Tables of raw counts and counts-per-million (CPM) normalized counts were generated. Prior to analysis, genes with low expression (defined here as a those with mean CPM less than 0.3) were filtered, leaving 16,206 genes.  Differential expression analyses were conducted using the limma-voom Bioconductor pipeline
Supplementary_files_format_and_content: log fold-change

source_name: iWAT

extract_protocol: Total RNA was extracted from iWAT and purified using Zymo RNA clean & concentrate kit. The purified RNA was analyzed by using Bioanalyzer for quality control and used for library preparation.

value: iWAT


title: ZP3

source_name: Zebrafish embryo (2dpf) infected by Streptococcus pneumoniae D39V, ply mutant strain

value: ply mutant


title: ZP2


title: Cold_rep3

description: Chronic cold


title: G2_0h_2

description:
3O
total RNA (ribosomal RNA depleted)


title: ZP1


title: mg132+a-aman_3h_3

description:
4M
total RNA (ribosomal RNA depleted)


title: Ctrl_0h_2

description:
1M
total RNA (ribosomal RNA depleted)


title: E18.5 Mouse Cochlea

value: Embryonic 18.5 days


title: Cold_rep1

description: Chronic cold


title: bulkATAC-L1-40-1

description: L1 bulk ATAC-seq peak level.xlsx


title: PC9 cells-antagomir_nc_3

city: Shanghai

first: Fang

last: Hu

address: 241 Huaihai West Road, Xuhui District

country: China

institute: Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiaotong University

description: tsRNA-5001a knockdown negative control

data_processing:
quality control, alignment, Gene expression analysis, differentially expressed genes
gene annotation: GO, KEGG
Gene enrichment data analysis
Network data analysis
Genome_build: hg19

source_name: lung adenocarcinoma cells

extract_protocol:
The RNA sequencing samples used are the knockdown group and its control, with 3 samples repeated in each group
The Illumina Xten platform was used for sequencing. After quality control, the original sequencing data were mapped to the reference genome sequence, and the reads mapped to the gene were counted.

value: lung adenocarcinoma

tag: condition

value: tsRNA-5001a knockdown negative control


title: mg132_3h_2

description:
11L
total RNA (ribosomal RNA depleted)


title: b2-3: b2-DHFR - without CHX - Replicate 3

city: Stanford

first: Felix

middle: Christian

last: Boos

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: ribosome footprints

data_processing:
Library strategy: Ribosome Profiling (Ribo-Seq)
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adapter sequences were trimmed using Cutadapt v2.8
rRNA reads were removed by alignment with Bowtie v1.2.3
Remaining reads were aligned to a library of sequences of open reading frames containing 1000 nucleotides up- and downstream of the ORF, obtained from the yeast genome database SGD (genome release R64-2-1).
Each read was assigned to a specific A-site nucleotide by empirically determining a nucleotide offset from the 5' end of each fragment length that displayed three nucleotide periodicity.
Genome_build: R64-2-1
Supplementary_files_format_and_content: Density files contain the read counts for each gene along the sequence in tab-delimited format. Column 1: Systematic gene name; Column 2: Position relative to annotated Start of ORF (0 being the A from the start codon ATG); Column 3: Nucleotide at this position; Column 4: Read count

organism: Saccharomyces cerevisiae

source_name: ribosome preparation

growth_protocol: Cells were grown in minimal selective medium containing 2% lactate as sole carbon source

extract_protocol:
Cells were harvested by fast filtration, flash-frozen in liquid nitrogen and lysed in a Retsch bead mill under cryogenic conditions. Cell powder was thawed and footprints were generated by RNase I digestion. Ribosomes were pelleted through a 25% (w/v) sucrose cushion by centrifugation for 20 min at 72,000 rpm in a Beckman TLA 100.2 rotor. RNA was extracted with hot acid phenol:chloroform.
Ribosome footprints were size selected by TBE-Urea PAGE. rRNA was removed with the Ribo-zero Gold kit (Illumina). RNA footprints were dephosphorylated, ligated to a linker sequence, reverse-transcribed to cDNA and circularized. Illumina sequencing barcodes were added by PCR amplification. Libraries were quantified with qPCR (Kapa Biosystems)

treatment_protocol: Expression of DHFR or b2-DHFR was induced for 4.5 h by addition of 0.5% galactose. For replicate 1, cycloheximide was added to the cultures 2 min prior to harvesting.

tag: replicate

tag: clogger expression

value: b2-DHFR (clogger)

tag: chx treatment

value: no CHX


title: PC9 cells-antagomir_nc_2

description: tsRNA-5001a knockdown negative control


title: Thermoneutral_rep3

description: Thermoneutrality


title: mg132+a-aman_3h_2

description:
4L
total RNA (ribosomal RNA depleted)


title: PC9 cells-antagomir_nc_1

description: tsRNA-5001a knockdown negative control


title: Thermoneutral_rep2

description: Thermoneutrality


title: G2_0h_1

description:
2L
total RNA (ribosomal RNA depleted)


title: b2-2: b2-DHFR - without CHX - Replicate 2

description: ribosome footprints


title: Thermoneutral_rep1

description: Thermoneutrality


title: b2-1: b2-DHFR - with CHX - Replicate 1

description: ribosome footprints

value: 2min before cell lysis


title: bulkATAC-L1-40-2

description: L1 bulk ATAC-seq peak level.xlsx

value: brain

value: FACS-sorted L1 neurons

value: wild type


title: bulkATAC-L1-60-1

description: L1 bulk ATAC-seq peak level.xlsx


title: PC9 cells-antagomir_3

description: tsRNA-5001a knockdown

value: tsRNA-5001a knockdown


title: cyt-3: cyt DHFR - without CHX - Replicate 3

description: ribosome footprints

value: cytosolic DHFR (control)


title: Ctrl_0h_1

description:
1L
total RNA (ribosomal RNA depleted)


title: PC9 cells-antagomir_2

description: tsRNA-5001a knockdown


title: cyt-2: cyt DHFR - without CHX - Replicate 2

description: ribosome footprints


title: P7_Native_EC

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10 Amistad Street

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

data_processing:
For scRNAseq, FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
For scRNAseq, downstream processing was conducted with Cellranger 3.0.2 with the default parameters.
For scRNAseq, cells were accepted with greater than 500 and fewer than 10000 unique mapped genes, and fewer than 100000 gene transcripts. Analysis was performed on cells with less than 5% mitochondrial mapping for P4PMEC, Engineered lung, Preseeded iPSC, and iPSC-ECFC lung samples and less than 20% for the P7native sample.
Genome_build: Reads were aligned to rat reference genome Ensembl Rnor6.0 release 95 an human reference genome GRCh38 release 31 (GRCh38.p12), respectively.
Supplementary_files_format_and_content: *.mtx: sparse matrix file of raw counts, *genes.tsv: genelist (rownames for .mtx file), *barcodes.tsv: barcodes (column names for .mtx file), *.idents.tsv: celltype idents (metadata)

organism: Rattus norvegicus

source_name: Lung Endothelium

growth_protocol: Rodent pulmonary microvascular endothelial cells were isolated from postnatal day 7 rat lungs. The isolated cells were cultured on fibronectin-coated 6 well-plate at a density of 5000 cells/cm2 in endothelial culture medium (Vasculife (VEGF) medium (Lifeline cell technology) supplemented with 10 % FBS and 1.5% antibiotic/antimycotic (A/A)) for 7 days with daily complete medium change.  Human iPSC-derived endothelial colony forming cells were cultured on collagen I-coated flasks (50 μg/mL) in endothelial culture medium.

extract_protocol:
Lungs were extracted from the animals and transferred into 60mm petri dish. A syringe fitted with 25G needle was injected into lung pieces with enzyme solution (DMEM (low glucose) + 1 mg/mL Collagenase/Dispase + 3 U/mL Elastase + 20 U/mL DNAse).  The tissue pieces were minces into small pieces and transfered to a 50 mL conical tube. Incubate the tissue pieces at 37C for 20 minutes at a agitation of ~75rpm. The tissue was dissociated through a wire mesh strainer and rinsed with medium, followed by centrifugation and filtration. The number of cells was counted and the cell solution was diluted to a final concentration of 1M cells/mL in 0.01% BSA in PBS.
scRNAseq libraries were generated with the Chromium Single Cell 3’ assay (10x Genomics). Samples were diluted for an expected cell recovery population of 10,000 cells per lane. Bulk RNAseq libraries were prepared using the Pair End Sequencing Prep Kit.
For scRNAseq, libraries sequenced on the HiSeq4000 platform to a depth of 180 to 500 million reads per library. Downstream processing was conducted with Cellranger 3.0.2 with the default parameters. For bulk RNAseq, libraries were sequenced through NovaSeq with sequencing read length of 100 base pairs (bp).

value: Lung Endothelium

value: Postnatal day 7


title: mg132_3h_1

description:
3K
total RNA (ribosomal RNA depleted)


title: Engineered_Lung

description: 10x Genomics

value: Passage 5


title: mg132+a-aman_3h_1

description:
4K
total RNA (ribosomal RNA depleted)


title: cyt-1: cyt DHFR - with CHX - Replicate 1

description: ribosome footprints


title: P4PMEC

description: 10x Genomics

value: Passage 4


title: PC9 cells-antagomir_1

description: tsRNA-5001a knockdown


title: Control Rep 2

status: Public on Dec 13 2021

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Sequencing data was demultiplexed using Cell Ranger mkfastq version 4.0.0
FASTQ files were aligned and counted to mm10 (10X Genomics transcript version 1.2.0) using Cell Ranger version 4.0.0
Matrix files were analyzed using the browser-based tool BIOMEX 1.0-5 (Taverna et al, 2020, Nucelic Acid Res)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered and compiled matrix output file following BIOMEX 1.0-5 analysis
Supplementary_files_format_and_content: tab-delimited matrix output files from Cell Ranger count
Supplementary_files_format_and_content: cloupe files from Cell Ranger output

source_name: distal jejunum

extract_protocol:
For single-cell RNA sequencing, mouse distal jejuna were collected 18.5h after small intestinal ischemia/reperfusion surgery. Two mice were used for each group: Control I/R-18.5h and EC-Foxc-DKO I/R-18.5h. Briefly, mice were anesthetized by isoflurane. Blood was removed by cardiac perfusion with cold PBS. The distal jejunum was then dissected from each individual, washed with cold PBS and cut into small pieces. The tissue was processed for scRNA-seq upon dissociating into single cell suspension in a digestion buffer (2 mg/mL Collagenase D, 0.2mg/mL DNAase I, 2 mg/mL Dispase II, 100 units/mL penicillin and 100 µg/mL streptomycin in HBSS) for 35 min at 37°C, followed by filtration through a 70μm and a 40μm cell strainer. Cells were washed with washing buffer (0.5% BSA, 2mM EDTA in PBS, pH 7.4) for three times, and resuspended in PBS with 0.04% BSA at a concentration of 1200 cells/μL (according to 10x Genomics Document #CG00053 Rev B) before being passed through a 30 μm MACS SmartStrainer. The cell viability was tested by using the Cellometer Auto 2000 Cell Viability Counter (Nexcelom Bioscience, USA). The cell sample was processed for scRNA-seq only when the cell viability was more than 70%.
Single cell 3’ gene expression libraries were constructed from samples by using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s manual CG000204 Rev D. The single cell libraries were then assessed for quality (TapeStation 4200, Agilent, Santa Clara, CA, USA) and then run by using paired-end 50 bp sequencing on the Illumina HiSeq 4000 platform (Illumina, San Diego, CA, USA). 10,000 cells were targeted for each sample with a sequencing depth of 20,000 read pairs per cell.

value: distal jejunum

tag: surgery (i/r)

value: small intestinal ischemia and reperfusion surgery

tag: time post i/r


title: EC-Foxc-DKO Rep 1


title: Control Rep 1


title: EC-Foxc-DKO Rep 2


title: placenta_healthy_288

type: RNA

city: Rotterdam

first: Michelle

last: Broekhuizen

address: Dr. Molewaterplein 40

institute: Erasmus MC

hyb_protocol: A total of 200 ng RNA was hybridized to the PanCancer Immune Profiling Panel for 17 hours at 67°C, following the manufacturing procedure (NanoString, Seattle, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver™ software (version 4.0, NanoString Technology).

source_name: placenta

extract_protocol: RNA was extracted from snap-frozen placenta samples using the Qiagen RNA easy mini kit.

tag: group

value: healthy

tag: mode of delivery

value: section

tag: gestational age (weeks)

tag: bmi

tag: birth weight (grams)

tag: fetal sex

value: male


title: placenta_loPE_130

value: loPE

value: female


title: placenta_loPE_152


title: placenta_loPE_135


title: placenta_loPE_180


title: placenta_healthy_289


title: placenta_loPE_210


title: Prrx1(R1A)_PCM1sort_Atria_2 (RNA-seq)

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

description: nuclear RNA

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Prrx1(R1A)_pcm1_atria_RNA_DEG.xlsx (Excel file with differential expression analysis (DESeq2) and NormCounts).

molecule: nuclear RNA

source_name: atrial cardiomyocyte nuclei

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines.

extract_protocol:
Isolated nuclei from both atria pooled together per individual were stained for PCM1 (pericentreolar material 1). Samples were FACS-sorted and gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. Nuclei were collected and successively washed with PBS, RNA was extracted using ReliaPrep RNA Miniprep System (Promega) and used as input for library preparation according to protocol. Libraries were sequenced on an Illumina Hiseq4000.
Ovation RNA-seq System V2 (M01206 v9, NuGen

tag: age

value: 8-12 week

tag: tissue

value: left and right atria

tag: genotype


title: Prrx1(R1A)_PCM1sort_Atria_1 (RNA-seq)

description: nuclear RNA


title: Prrx1(R1A)_PCM1sort_Atria_3 (RNA-seq)

description: nuclear RNA


title: placenta_healthy_168


title: Control_PCM1sort_Atria_2 (RNA-seq)

description: nuclear RNA

value: control


title: Control_PCM1sort_Atria_3 (RNA-seq)

description: nuclear RNA


title: Control_PCM1sort_Atria_1 (RNA-seq)

description: nuclear RNA


title: 651441WTDay1neuron

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling and fastq.gz conversion were performed using Illumina pipeline scripts.
Raw reads were mapped to mouse genome (mm10) .
RNA-Seq reads were counted using FeaturesCount.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_exonCounts.txt: Counts files

source_name: Hippocampal sorted neurons

extract_protocol:
Nuclei isolation from frozen mouse hippocampal tissues (n = 6 per group) were performed according to a previously published protocol (Sakib et al., 2021) with modifications. Isolated nuclei were stained with Anti-NeuN-Alexa488 conjugated antibody (Millipore, MAB377) for 1 hour at 4°C and Neuronal nuclei were sorted using BD FACS Aria III sorter based on NeuN signal. Sorted nuclei were collected and RNA was isolated using Trizol LS reagent (Invitrogen) and Zymo RNA clean & concentrator-5 kit (Zymo R1014).
RNAseq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara), followed by Nextera XT library preparation kit (Illumina) according to manufacturers’ guidelines. Libraries were sequenced in Illumina Hiseq 2000 to get single end 50 base pair reads.

tag: cell type

value: Hippocampal neurons

value: Wildtype

tag: strain


title: 651440WTDay1neuron


title: 651439WTDay1neuron


title: placenta_loPE_221


title: placenta_healthy_165


title: placenta_healthy_157


title: placenta_healthy_163


title: placenta_healthy_155


title: placenta_healthy_159


title: placenta_healthy_174


title: placenta_healthy_154


title: placenta_healthy_160


title: 1499TBA83Day1neuron

description: C57BL/6J overexpressing human Aβ4-42

value: APP Transgenic

value: C57BL/6J overexpressing human Abeta4-42


title: 1260TBA83caffeineDay1neuron

description:
APP Transgenic+Caffeine treatment
C57BL/6J overexpressing human Aβ4-42

tag: treatment

value: Caffeine


title: 1500TBA83Day1neuron

description: C57BL/6J overexpressing human Aβ4-42


title: 1501TBA83Day1neuron

description: C57BL/6J overexpressing human Aβ4-42


title: 1259TBA83caffeineDay1neuron


title: 1261TBA83caffeineDay1neuron


title: Control_Atria_PCM1+_4 (ATAC-seq)

description: PCM1 sorted nuclei

data_processing:
Reads were mapped to mm10 build of the mouse genome using BWA (Li et al., 2009) using default settings.
The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into sliding window bins of 500bp. Differential peak calling was performed on bins using DESeq2 (Love et al., 2014)
BED files (peaks called differential or stable between G125R heterozygous and control mice).
Genome_build: mm10
Supplementary_files_format_and_content: diff_peaks_Prrx1(R1A)_ATAC-seq.xlsx (containing differential peaks)

extract_protocol:
Isolated nuclei from both atria pooled together per individual were stained for PCM1 (pericentreolar material 1). Samples were FACS sorted and gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. Nuclei were collected and successively washed with PBS and used as input for ATAC-seq using Illumina Tagment DNA enzyme and buffer (20034197) according to protocol. Libraries were sequenced paired end 150bp on an Illumina Hiseq4000.
Illumina Tagment DNA enzyme and buffer (20034197) according to protocol

value: left and right atrium


title: CMT64_TGFb

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

data_processing:
CLC Genomics workbench software (Qiagen) was used to generate RPKM data.
Adapter sequences were removed, and read mapping was carried out using the default settings of RNA-Seq analysis package (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and maximum number of hits for a read set to: 30).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

growth_protocol: CMT64 cells were cultured in Dulbecco's Modified Eagle Medium with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from CMT64 cells 24 h after stimulation.
The mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: TGF-β1 and TNF-α were used at the concentrations of 5 ng/ml and 10 ng/ml, respectively.

value: stimulates with TGFb


title: Control_Atria_PCM1+_3_rep2 (ATAC-seq)

description: PCM1 sorted nuclei


title: CMT64_TGFb_TNFa

value: stimulates with TGFb and TNFa


title: CMT64_TNFa

value: stimulates with TNFa


title: CMT64_NC

value: stimulates with negative control


title: placenta_healthy_144

value: healthy

value: section


title: placenta_healthy_150

value: male


title: Control_Atria_PCM1+_1_rep1 (ATAC-seq)

description: PCM1 sorted nuclei


title: placenta_eoPE_232

value: eoPE

value: female


title: Prrx1(R1A)_Atria_PCM1+_4 (ATAC-seq)

description: PCM1 sorted nuclei

value: 8-12 week


title: Prrx1(R1A)_Atria_PCM1+_3 (ATAC-seq)

description: PCM1 sorted nuclei


title: Control_Atria_PCM1+_3_rep1 (ATAC-seq)

description: PCM1 sorted nuclei

value: control


title: Control_Atria_PCM1+_2 (ATAC-seq)

description: PCM1 sorted nuclei


title: placenta_eoPE_220


title: placenta_eoPE_219


title: placenta_eoPE_237


title: Control_Atria_PCM1+_1_rep2 (ATAC-seq)

description: PCM1 sorted nuclei


title: Prrx1(R1A)_Atria_PCM1+_2 (ATAC-seq)

description: PCM1 sorted nuclei


title: placenta_eoPE_197


title: Prrx1(R1A)_Atria_PCM1+_1 (ATAC-seq)

description: PCM1 sorted nuclei


title: placenta_eoPE_176

value: unkown


title: placenta_eoPE_172


title: C60_b6_cast_lcmv_cd8_d07_cr_rvb1_r2

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

data_processing:
Library strategy: CUT&RUN
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align CUT&RUN reads: STAR v2.5.0c [disable splicing alignment]
Remove CUT&RUN duplicates: Picard v1.141
Call CUT&RUN peaks: MACS2 v2.1.1
Genome_build: GRCm38, CAST/EiJ and SPRET/EiJ
Supplementary_files_format_and_content: Alignment file: BAM format; Peak file: txt format

source_name: B6/Cast F1 Spleen activated CD8 T cell

extract_protocol:
Cells were washed and incubated in antibody buffer, and washed and resuspended to activate Mnase. 2 X stop solution was added and incubated to release cleaved chromatin fragments.
Kapa Hyper Prep Kit and Kapa UDI Adaptor Kit were used prepare the library. Libraries were amplified for an average of 15 cycles using a 10 s 60°C annealing/extension step to enrich for shorter library fragments.

value: B6/Cast F1

value: Spleen

value: activated CD8 T cell

tag: chip antibody


title: placenta_eoPE_175


title: H-SRS_fish2

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299) as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray was scanned at 5 µm resolution and 90% of laser power using a ScanArray Gx Plus scanner and ScanArray Express software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

organism: Salmo salar

source_name: Head kidney tissue, H-SRS, individual fish

label_protocol: Five individual fish per group (5 control, 5 L-SRS, 5 H-SRS; 15 samples in total) were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified head kidney total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quality and quantity of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

extract_protocol: RNAlater was removed prior to RNA extraction. All samples were homogenized in TRIzol reagent (Invitrogen/Life Technologies, Carlsbad, CA, USA), and subjected to RNA extraction according to the manufacturer's instructions. The resulting crude total RNA samples were treated with DNase I (Qiagen, Mississauga, ON, Canada) to degrade residual genomic DNA, and then purified using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocols. RNA integrity was verified by 1% agarose gel electrophoresis, and RNA purity was assessed by A260/280 and A260/230 ratios using NanoDrop spectrophotometry (Thermo Fisher, Mississauga, ON, Canada).

treatment_protocol: Atlantic salmon parr were anesthetized using Benzocaine (150 µl L-1 BZ-20®, Veterquímica S.A., Maipú, Santiago, Chile) and intraperitoneally (IP) injected with 0.1 mL of a low dose bacterial inoculum with a titer of 100.83 TCID50/mL (50% Tissue Culture Infective Dose) or 0.1 mL of a medium that was used to prepare the bacterial inoculum (i.e. minimum essential medium, MEM). Ten fish per tank [3 tanks from the challenge group (i.e. P. salmonis-injected) and 4 tanks from the control group (CON)] were euthanized using an overdose of Benzocaine (300 µl L-1 BZ-20®) and dissected on the day before injection (PRE) of the remaining fish, as well as 2, 7, 13, 21 and 42 days post-injection (DPI). Head kidney samples were collected and stored in RNAlater (Ambion/Life Technologies, Austin, TX, USA) for 48 h at 4°C and transferred to -80°C until RNA extraction. Two infection level phenotypes [low (L-SRS) and high (H-SRS) infection level] were revealed in infected individuals at 21 days post-injection (DPI) based on multivariate analyses of expression of four antibacterial biomarker transcripts (campb, hampa, il8a, tlr5a) and pathogen level measured by qPCR. Five fish from each group (Control, L-SRS, and H-SRS) were selected for transcriptome profiling with a common reference design.

tag: phenotype

value: high (H-SRS) infection level

value: Head kidney

tag: life stage

value: parr

source_name: pool of RNAs from head kidney tissues invovled in the microarray experiment


title: placenta_eoPE_170


title: C58_b6_cast_lcmv_cd4_d07_cr_rvb1_r2

source_name: B6/Cast F1 Spleen activated CD4 T cell

value: activated CD4 T cell


title: H-SRS_fish3


title: Control_fish5

source_name: Head kidney tissue, Control, individual fish


title: H-SRS_fish1


title: placenta_eoPE_161


title: Control_fish4


title: C57_b6_cast_lcmv_cd4_d07_cr_rvb1_r1


title: H-SRS_fish5


title: L-SRS_fish4

source_name: Head kidney tissue, L-SRS, individual fish

value: low (L-SRS) infection level


title: placenta_eoPE_251


title: C56_b6_cast_lcmv_cd8_d07_cr_chd4_r2


title: H-SRS_fish4


title: L-SRS_fish1


title: L-SRS_fish5


title: L-SRS_fish3


title: L-SRS_fish2


title: C59_b6_cast_lcmv_cd8_d07_cr_rvb1_r1


title: placenta_eoPE_137


title: Control_fish3


title: placenta_eoPE_136

value: vaginally


title: SN9: Non-Trunking Sample 9

city: Kota Samarahan

first: Wei Jie

last: Yan

state: Sarawak

address: Jln Datuk Mohammad Musa

department: Molecular Biology

country: Malaysia

institute: Universiti Malaysia Sarawak

data_processing:
Base calling were performed according to BGISEQ500 internal standard
Raw reads were filtered by BGISEQ-500 internal software removing;  1) Remove reads with adaptors;  2) Remove reads in which unknown bases(N) are more than 5%;  3) Remove low quality reads (we define the low quality read as the percentage of base  which quality is lesser than 15 is greater than 20% in a read)  to produce clean reads
Clean reads were De novo assembled using Trinity (Version: v2.0.6; Parameters: --min_contig_length 150 --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr ') followed by cluster transcription using Tgicl (Version: v2.0.6; Parameters: -l 40 -c 10 -v 25 -O '-repeat_stringency 0.95 -minmatch 35 -minscore 35') to produce Unigenes
Clean reads were mapped to Unigenes using Bowtie2(Version: v2.2.5; Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-36/47 mixed --no-discordant -p 1 -k 200) and the genes expression level were calculated with RSEM (Version: v1.2.12; Parameters: default)
Annotation were performed using Blastn (Version: v2.2.23; Parameters : default), Blastx  (Version: v2.2.23; Parameters : default) or Diamond (Version: v0.8.31; Parameters : default) aligning Unigenes to NT, NR, KOG, KEGG and SwissProt database. NR annotation were processed with Blast2GO (Version: v2.5.0; Parameters : default) to perform GO annotation, and performed InterPro annotation using InterProScan5 (Version: v5.11-51.0; Parameters : default).
Genome_build: De novo
Supplementary_files_format_and_content: Fasta file (.fa) content the Unigenes sequence
Supplementary_files_format_and_content: Files (.txt) contain the annotated Unigenes expression in FPKM

organism: Metroxylon sagu

source_name: leaf tissue

growth_protocol: Peat soil plantation

extract_protocol:
CTAB RNA miniprep
RNA Library prepared according to standard BGISEQ-500 transcriptome sequencing

treatment_protocol: Trunking and Non-trunking selection from plantation

value: Non-trunking

value: leaf


title: C54_b6_cast_lcmv_cd4_d07_cr_chd4_r2


title: SN8: Non-Trunking Sample 8


title: C55_b6_cast_lcmv_cd8_d07_cr_chd4_r1


title: SN7: Non-Trunking Sample 7


title: C53_b6_cast_lcmv_cd4_d07_cr_chd4_r1


title: ST4: Trunking Sample 4

value: Trunking


title: C52_b6_cast_lcmv_cd8_d07_cr_snf2h_r2


title: C51_b6_cast_lcmv_cd8_d07_cr_snf2h_r1


title: ST5: Trunking Sample 5


title: C50_b6_cast_lcmv_cd4_d07_cr_snf2h_r2


title: Control_fish1


title: Control_fish2


title: ST1: Trunking Sample 1


title: C49_b6_cast_lcmv_cd4_d07_cr_snf2h_r1


title: C48_b6_cast_lcmv_cd8_d07_cr_brg1_r2


title: C47_b6_cast_lcmv_cd8_d07_cr_brg1_r1


title: 287-2019_S56

city: Canyon

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

description: Sex: S

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20 and a read length of less than 36 bases
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 8 --dta -x GCF_002263795.1_ARS-UCD1.2_genomic
Read assembly and quantification was performed with StringTie v2.1.2 with parameters -p 8 -G ref_ARS-UCD1.2, followed by ./stringtie --merge -p 8 -G ref_ARS-UCD1.2, and /stringtie -e -p 8 -G stringtie_merge.gtf -o. A read count matrix was generated with prepDE.py with parameters python2.7 ./prepDE.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.30.3.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text file of gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
RNA purification and extraction was performed with the Tempus Spin RNA Isolation kit (Applied Biosystems), per product instructions. RNA concentration and quality was measured with an Agilent 2100 (Agilent).
Library construction was performed with the TruSeq RNA Sample Library Kit (Illumina). 150bp paired-end sequencing was performed with an Illumina Novaseq 6000 (v1.7; S4 reagent kit v1.5) in one lane (~50M reads/sample).

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: arrival weight (lbs)

tag: times treated

tag: disease severity cohort

value: Treated Once

value: Whole blood


title: C46_b6_cast_lcmv_cd4_d07_cr_brg1_r2


title: 274-2019_S54

description: Sex: S

value: Treated Twice or Died


title: 295-2019_S57

description: Sex: S

value: Healthy


title: 285-2019_S55

description: Sex: S


title: C45_b6_cast_lcmv_cd4_d07_cr_brg1_r1


title: 272-2019_S53

description: Sex: S


title: C44_b6_cast_lcmv_cd8_d07_cr_nfatc1_r2


title: ML81SN

type: genomic

city: Lyon

first: Fazlur

middle: Rahman

last: Talukdar

state: Rhone Alps

address: 150 Cours Albert Thomas

department: Epigenetics

country: France

institute: International Agency for Research on Cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Processing and analysis was performed using standard protocol published online: https://github.com/IARCbioinfo/methylkey/find/master

label: Cy5 and Cy3

source_name: normal esophageal mucosa

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor and normal tissue samples using AllPrep DNA/RNA Mini Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: Fresh Frozen

tag: disease state

value: Adjacent normal


title: ML50T

source_name: tumor tissue

value: Tumor


title: ML55N

value: Female


title: ET39T


title: 266-2019_S52

description: Sex: S


title: ML89T


title: ML84SN


title: BR56N


title: C43_b6_cast_lcmv_cd8_d07_cr_nfatc1_r1

value: B6/Cast F1

value: Spleen

value: activated CD8 T cell


title: ML70T


title: 255-2019_S51

description: Sex: S


title: ML72T


title: ET6T


title: ML47N


title: C42_b6_cast_lcmv_cd4_d07_cr_nfatc1_r2

value: activated CD4 T cell


title: ML42T


title: ML88T


title: SD11T


title: ET22T


title: ML81T


title: ML25SN


title: ML84T


title: ML25T


title: ML44T


title: SD13T


title: 254-2019_S50

description: Sex: S


title: ML40N


title: ML3T


title: ML24T


title: C41_b6_cast_lcmv_cd4_d07_cr_nfatc1_r1


title: BR45T


title: C40_b6_cast_lcmv_cd8_d07_cr_bhlhe40_r2


title: C39_b6_cast_lcmv_cd8_d07_cr_bhlhe40_r1


title: 252-2019_S49

description: Sex: S


title: 248-2019_S48

description: Sex: S


title: 246-2019_S47

description: Sex: S


title: SD9N


title: C38_b6_cast_lcmv_cd4_d07_cr_bhlhe40_r2


title: C37_b6_cast_lcmv_cd4_d07_cr_bhlhe40_r1


title: 212-2019_S46

description: Sex: S


title: BR53N


title: 211-2019_S45

description: Sex: S


title: ML24SN


title: ML26T


title: C36_b6_cast_lcmv_cd8_d07_cr_irf4_r2


title: C35_b6_cast_lcmv_cd8_d07_cr_irf4_r1


title: 205-2019_S43

description: Sex: S


title: 210-2019_S44

description: Sex: S


title: C34_b6_cast_lcmv_cd4_d07_cr_irf4_r2


title: 199-2017_S33

description: Sex: B


title: C33_b6_cast_lcmv_cd4_d07_cr_irf4_r1


title: C32_b6_cast_lcmv_cd8_d07_cr_jun_r2

value: jun


title: ML23T


title: 197-2019_S42

description: Sex: S


title: ML80T


title: 195-2017_S32

description: Sex: B


title: C31_b6_cast_lcmv_cd8_d07_cr_jun_r1


title: ML79T


title: 194-2019_S41

description: Sex: S


title: 187-2017_S31

description: Sex: B


title: C30_b6_cast_lcmv_cd4_d07_cr_jun_r2


title: ML60T


title: 185-2017_S30

description: Sex: B


title: C29_b6_cast_lcmv_cd4_d07_cr_jun_r1


title: SD20T


title: C28_b6_cast_lcmv_cd8_d07_cr_tbet_r2

value: tbet


title: BR27T


title: 181-2017_S29

description: Sex: B


title: ML16T


title: BR27SN


title: ET7T


title: C27_b6_cast_lcmv_cd8_d07_cr_tbet_r1


title: SD12N


title: ML17N


title: ML74T


title: C26_b6_cast_lcmv_cd4_d07_cr_tbet_r2


title: ML16N


title: ML71T


title: ET11T


title: ML56T


title: ET35N


title: ML62T


title: ML46T


title: ET38N


title: C25_b6_cast_lcmv_cd4_d07_cr_tbet_r1


title: 169-2017_S27

description: Sex: B


title: C24_b6_cast_lcmv_cd8_nav_cr_ets1_r2

source_name: B6/Cast F1 Spleen naïve CD8 T cell

value: naive CD8 T cell


title: ML34T


title: ML14SN


title: SD8T


title: 168-2017_S26

description: Sex: S


title: 175-2019_S40

description: Sex: S


title: C23_b6_cast_lcmv_cd8_nav_cr_ets1_r1


title: BR19N


title: 167-2017_S25

description: Sex: B


title: 177-2017_S28

description: Sex: B


title: ML14T


title: BR20T


title: C22_b6_cast_lcmv_cd8_d07_cr_ets1_r2


title: ET30T


title: C21_b6_cast_lcmv_cd8_d07_cr_ets1_r1


title: 166-2019_S39

description: Sex: S


title: 162-2017_S24

description: Sex: S


title: 160-2017_S23

description: Sex: B


title: C20_b6_cast_lcmv_cd4_nav_cr_ets1_r2

source_name: B6/Cast F1 Spleen naïve CD4 T cell

value: naive CD4 T cell


title: C19_b6_cast_lcmv_cd4_nav_cr_ets1_r1


title: 158-2017_S22

description: Sex: B

value: Treated Once


title: C17_b6_cast_lcmv_cd4_d07_cr_ets1_r1


title: C18_b6_cast_lcmv_cd4_d07_cr_ets1_r2


title: 156-2017_S21

description: Sex: B

value: Whole blood


title: SD6T


title: ET33T


title: C16_b6_cast_lcmv_cd8_nav_cr_tcf1_r2


title: 155-2019_S38

description: Sex: S

value: Treated Twice or Died


title: ML83T


title: ML82T


title: ML82SN


title: ML85T


title: C15_b6_cast_lcmv_cd8_nav_cr_tcf1_r1


title: 139-2017_S19

description: Sex: S


title: 155-2017_S20

description: Sex: B

value: Healthy


title: ET21T

value: Male


title: C14_b6_cast_lcmv_cd8_d07_cr_tcf1_r2


title: ET32N

value: Fresh Frozen


title: ET36T


title: ML61T


title: ML32T


title: ML10T


title: SD4T


title: ML41T


title: ML41SN

value: Adjacent normal


title: SD18N


title: C12_b6_cast_lcmv_cd4_nav_cr_tcf1_r2


title: ML68T

value: Tumor


title: 134-2019_S37

description: Sex: S


title: SD1T

value: Female


title: BR4N


title: ML31T


title: C13_b6_cast_lcmv_cd8_d07_cr_tcf1_r1

value: B6/Cast F1


title: 130-2017_S17

description: Sex: B


title: C11_b6_cast_lcmv_cd4_nav_cr_tcf1_r1

value: Spleen


title: 125-2017_S16

description: Sex: B


title: SD17T


title: ET31T


title: C10_b6_cast_lcmv_cd4_d07_cr_tcf1_r2


title: ML19T


title: C9_b6_cast_lcmv_cd4_d07_cr_tcf1_r1


title: BR15T


title: BR3T


title: 121-2019_S36

description: Sex: S


title: ML6T


title: ML22T


title: ET20T


title: C8_b6_cast_lcmv_cd8_nav_cr_runx1_r2


title: 119-2017_S14

description: Sex: B


title: C7_b6_cast_lcmv_cd8_nav_cr_runx1_r1


title: ML35T


title: 118-2019_S35

description: Sex: S


title: 133-2017_S18

description: Sex: B


title: ML2T


title: 115-2017_S13

description: Sex: S


title: C6_b6_cast_lcmv_cd8_d07_cr_runx1_r2

value: activated CD8 T cell


title: C5_b6_cast_lcmv_cd8_d07_cr_runx1_r1


title: ML35SN


title: 113-2019_S34

description: Sex: S


title: C4_b6_cast_lcmv_cd4_nav_cr_runx1_r2


title: R122C IQ3neg-2020D-2

city: Singapore

first: Daisuke

last: Douchi

address: 14 Medical Drive

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Raw reads were aligned to mouse reference genome version GRCm38 gencode M23 (downloaded from https://www.gencodegenes.org/) using STAR aligner version 2.7.1a with default parameters (Dobin et al., Bioinformatics 2013)
Read counts per gene were generated using featureCounts function in the subread package version 2.0.0. (Liao et al., Nucleic Acids Res 2013)
Counts per million (cpm) values were calculated using cpm function of the edgeR R package (Robinson et al., Bioinformatics 2010)
xxxxxxxxxx Note xxxxxx
Genome_build: mm10

source_name: Stomach

extract_protocol:
Isolated mouse stomach was chopped into 2 mm2 pieces and incubated with chelating buffer (5 mM EDTA and 0.52 mM DTT in PBS) for 2 h at 4oC on a shaking platform, then gastric units were released by vigorous shaking in cold dissociation buffer (54.8 mM D-sorbitol and 44 mM Sucrose in PBS). Isolated mouse gastric units were incubated in TrypLE Express (Thermo Fisher Scientific) with Y-27632 (Merck) for 12 minutes at 37oC with repetitive pipetting for digestion into single cells. The cells were passed through a 30 μm cell strainer (Miltenyi Biotech) and labeled with antibodies in HBSS with 2% FBS. Antibodies for the flow cytometry are as follows: anti-EpCAM APC/Cy7-conjugated (BioLegend). Dead cells were excluded by DAPI staining, and labeled cells were sorted by using FACSAria II (BD Bioscience). RNA in FACS-sorted Iqgap3high (IQ3pos) and Iqgap3low/neg (IQ3neg) cells was extracted using NucleoSpin RNA XS (MACHEREY-NAGEL) by following the manufacturer’s manual.
RNA were sent to Beijing Genomics Institute (BGI) for PCR amplification, transcriptome library preparation and sequencing.

value: Stomach (corpus)

value: Runx3 R122C;Iqgap3-2A-tdTomato

value: 6-8 weeks

tag: numbers

value: 3 mice

tag: sorted cells

value: Iqgap3low/neg epithelial cell


title: R122C IQ3pos-2020C-2

tag: age

value: Iqgap3high epithelial cell


title: C3_b6_cast_lcmv_cd4_nav_cr_runx1_r1

tag: tissue

value: naive CD4 T cell


title: 109-2017_S12

description: Sex: B

value: Treated Once

value: Whole blood


title: ML63N

value: Male


title: 105-2017_S11

description: Sex: B


title: ET29T

value: Fresh Frozen


title: 123-2017_S15

description: Sex: B

value: Treated Twice or Died


title: 104-2017_S10

description: Sex: B

value: Healthy


title: SD15T

value: Female

value: Tumor


title: C1_b6_cast_lcmv_cd4_d07_cr_runx1_r1

value: B6/Cast F1

value: Spleen

value: activated CD4 T cell


title: B49T


title: WT IQ3neg-2003B

value: Stomach (corpus)

tag: genotype

value: Runx3 WT;Iqgap3-2A-tdTomato


title: BR2T


title: R122C IQ3pos-1910C-1

value: Runx3 R122C;Iqgap3-2A-tdTomato

value: 6-8 weeks

value: 3 mice


title: B116T


title: ML9T


title: ET15T


title: AE104(delta e4+zupT) with 50 µM EDTA replicate 3

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

hyb_protocol: Hybridisation was done by the service provider IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service provider IMGM Laboratories GmbH (Martinsried)

data_processing: The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength

organism: Cupriavidus metallidurans

source_name: AE104(delta e4+zupT) with 50 µM EDTA

label_protocol: Labeling was done by the service provider IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans strains were grown in Mineral salts medium + 0.2 % Na-gluconate to a cell turbidity of 100 Klett, 100 µM Zn or 50 µM EDTA was added and after 10 min  cells were harvest by centrifugation for 1' at RT in 2.0 ml tubes.

extract_protocol: RNeasy Plus Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: 100 µM ZnCl2 or 50 µM EDTA was added at a cell turbitity of 100 Klett for 10 min

tag: strain background

value: (delta e4 + zupT)

value: 50 µM EDTA


title: WT IQ3pos-2003A

tag: strain

value: Iqgap3high epithelial cell


title: R11_b6_cast_lcmv_cd8_nav_r1_RNAseq

data_processing:
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align CUT&RUN reads: STAR v2.5.0c [disable splicing alignment]
Remove CUT&RUN duplicates: Picard v1.141
Call CUT&RUN peaks: MACS2 v2.1.1
Genome_build: GRCm38, CAST/EiJ and SPRET/EiJ
Supplementary_files_format_and_content: Alignment file: BAM format; Peak file: txt format

extract_protocol:
Cells were sorted into Tizol reagent. Isopropanol and linear acrylamide were used to precipitate RNA.
RNA underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit. Amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit.

tag: cell type

value: naive CD8 T cell


title: AE104(delta e4+zupT) with 50 µM EDTA replicate 2

tag: treatment


title: R12_b6_cast_lcmv_cd8_nav_r2_RNAseq

tag: chip antibody


title: AE104(delta e4+zupT) with 50 µM EDTA replicate 1


title: K21T

value: Male

value: Paraffin Embedded


title: R10_b6_cast_lcmv_cd8_d60_r2_RNAseq

source_name: B6/Cast F1 Spleen memory CD8 T cell

value: memory CD8 T cell


title: R122C IQ3neg-1910D-1

value: Iqgap3low/neg epithelial cell


title: B14T

value: Fresh Frozen

value: Tumor


title: WT IQ3pos-1910A-2

value: 4 mice


title: C2_b6_cast_lcmv_cd4_d07_cr_runx1_r2

value: B6/Cast F1

value: Spleen

value: activated CD4 T cell


title: AE104(delta e4+zupT) with 100 µM Zn replicate 3

source_name: AE104(delta e4+zupT) with 100 µM Zn

value: 100 µM Zn


title: R9_b6_cast_lcmv_cd8_d60_r1_RNAseq


title: WT IQ3neg-1910B-2

value: Stomach (corpus)

value: Runx3 WT;Iqgap3-2A-tdTomato

value: 6-8 weeks


title: ML9SN

value: Adjacent normal


title: Finch_Male_S1

first: JAE

middle: YONG

last: HAN

department: Department of Agricultural Biotechnology

data_processing:
Cell Ranger v5.0.0 was used for demultiplexing
Seurat3.1.3 was used for quantification
Aggregate two samples for down-stream analysis
Genome_build: bTaeGut1_v1
Supplementary_files_format_and_content: h5 matrix, barcodes.tsv, features.tsv, and Matrix.mtx files

organism: Taeniopygia guttata

source_name: Gonadal cells

extract_protocol:
Gonads were collected from zebra finch embryos at Hamburger Hamilton stage 28. Seven male and seven female embryonic gonads were pooled in 100 ul trypsin 0.05% with same-sex and incubated at 37℃ for 5 min with gentle pipetting. The digestion was stopped with 100 ul of Dulbecco’s Modified Eagle Medium containing 10% fetal bovine serum and washed with 500 ul PBS. Cells were pelleted down and resuspended in PBS. Single cell libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol.
Libraries were prepared using Chromium Next GEM Single Cell 3p RNA library v3.1. Single Cell 3' GEX and feature barcode libraries are sequenced on the Illumina sequencing system.

tag: Sex

tag: Stage

value: Hamburger Hamilton Stage 28


title: AE104(delta e4+zupT) with 100 µM Zn replicate 1

value: (delta e4 + zupT)


title: R8_b6_cast_lcmv_cd8_d07_r2_RNAseq

source_name: B6/Cast F1 Spleen activated CD8 T cell

value: activated CD8 T cell


title: AE104(delta e4+zupT) untreated replicate 3

source_name: AE104(delta e4+zupT) untreated

value: none; untreated


title: K18T

value: Female

value: Paraffin Embedded


title: SA10T

value: Fresh Frozen


title: WT IQ3neg-1909B-1

value: 3 mice

value: Iqgap3low/neg epithelial cell


title: B10T

value: Male

value: Tumor


title: AE104(delta e4+zupT) untreated replicate 2


title: B6T


title: Finch-Female_S1


title: E11T


title: K22T


title: R5_b6_cast_lcmv_cd4_nav_r1_RNAseq

value: B6/Cast F1

value: Spleen

value: naive CD4 T cell


title: B65T


title: R7_b6_cast_lcmv_cd8_d07_r1_RNAseq


title: B15T


title: Ir21T


title: AE104(delta e4+zupT) untreated replicate 1


title: R3_b6_cast_lcmv_cd4_d60_r1_RNAseq

source_name: B6/Cast F1 Spleen memory CD4 T cell

value: memory CD4 T cell


title: AE104(delta e4) with 50 µM EDTA replicate 3

source_name: AE104(delta e4) with 50 µM EDTA

value: (delta e4)

value: 50 µM EDTA


title: WT IQ3pos-1909A-1

value: Stomach (corpus)

value: Runx3 WT;Iqgap3-2A-tdTomato

value: 6-8 weeks

value: Iqgap3high epithelial cell


title: BAL cells, 36056_necropsy-1

city: St Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St.Louis

data_processing:
10x pipeline bam (Cell Ranger Single-Cell Software Suite v3.0)
Demultiplexing, barcode processing, single-cell 3' counting was performed with Cell Ranger Single-Cell Software Suite v3.0
Alignment was performed using Cell Ranger
See detailed methods in Singh et al.
Genome_build: mmul8 (rheMac8)
Supplementary_files_format_and_content: Cell annotations, filtered matrixex of gene by cell expression, files with barcodes and files with expressed genes. Files are ready to be imported to Seurat package.
Supplementary_files_format_and_content: Annotation for all cells - cd45_cells_annotation.tsv
Supplementary_files_format_and_content: Annotation for myeloid cells subset - myeloid_cells_annotation.tsv
Supplementary_files_format_and_content: Annotation for lymphoid cells subset - lymphoid_cells_annotation.tsv

organism: Macaca mulatta

source_name: broncho-alveolar lavage (BAL)

extract_protocol:
Single-cell suspensions from BAL obtained at different time points were collected and cryopreserved in Cryostor-CS10 (Biolife Solutions, USA) at -70ºC and then used for single cell RNAlibrary preparation as per manufacturer's instructions (10x genomics).
Single-cell libraries were prepared using standard 10x Genomics protocols.
scRNA-seq

value: 3 years, 324 days

value: Female

tag: timepoint

value: Post-acute Covid-19 (12-17dpi)

value: broncho-alveolar lavage (BAL) cells


title: BAL cells, 36189_necropsy-1

value: 3 years, 269 days


title: B11T

value: Fresh Frozen


title: SA8T

value: Male

value: Tumor


title: R4_b6_cast_lcmv_cd4_d60_r2_RNAseq

value: B6/Cast F1

value: Spleen


title: B8T


title: R2_b6_cast_lcmv_cd4_d07_r2_RNAseq

source_name: B6/Cast F1 Spleen activated CD4 T cell

value: activated CD4 T cell


title: AE104(delta e4) with 50 µM EDTA replicate 2

value: (delta e4)


title: BAL cells, 36052_necropsy-1

value: 3 years, 323 days


title: B13T


title: R1_b6_cast_lcmv_cd4_d07_r1_RNAseq


title: A12_b6_cast_lcmv_cd8_nav_r2_ATACseq

extract_protocol:
Cells were lysed using ATAC-seq lysis buffer and incubated in transposition buffer.
Transposed DNA fragments were isolated, amplified and size selected.

value: naive CD8 T cell


title: BAL cells, 35969_necropsy-1

value: 3 years, 343 days


title: R6_b6_cast_lcmv_cd4_nav_r2_RNAseq

value: naive CD4 T cell


title: AE104(delta e4) with 100 µM Zn replicate 3

source_name: AE104(delta e4) with 100 µM Zn

value: 100 µM Zn


title: AE104(delta e4) with 100 µM Zn replicate 2


title: BAL cells, 36207_necropsy-1

value: 3 years, 258 days


title: A10_b6_cast_lcmv_cd8_d60_r2_ATACseq

value: memory CD8 T cell


title: AE104(delta e4) with 100 µM Zn replicate 1


title: AE104(delta e4) with 50 µM EDTA replicate 1

value: 50 µM EDTA


title: A9_b6_cast_lcmv_cd8_d60_r1_ATACseq


title: BAL cells, 36189_d3-1

value: Female

value: Acute Covid-19 (3dpi)

value: broncho-alveolar lavage (BAL) cells


title: AE104(delta e4) untreated replicate 3

source_name: AE104(delta e4) untreated

value: none; untreated


title: SA6T

value: Male

value: Fresh Frozen

value: Tumor


title: AE104(delta e4+zupT) with 100 µM Zn replicate 2

value: (delta e4 + zupT)


title: A8_b6_cast_lcmv_cd8_d07_r2_ATACseq

value: B6/Cast F1

value: Spleen

value: activated CD8 T cell


title: BAL cells, 36056_d3-1

value: 3 years, 324 days


title: B9T


title: A7_b6_cast_lcmv_cd8_d07_r1_ATACseq


title: AE104(delta e4) untreated replicate 2

value: (delta e4)


title: BAL cells, 36052_d3-1

value: 3 years, 323 days


title: BAL cells, 35969_d3-1

value: 3 years, 343 days


title: AE104 with 50 µM EDTA replicate 3

source_name: AE104 with 50 µM EDTA


title: A11_b6_cast_lcmv_cd8_nav_r1_ATACseq

value: naive CD8 T cell


title: B12T

source_name: tumor tissue


title: SA7T


title: A6_b6_cast_lcmv_cd4_nav_r2_ATACseq

value: naive CD4 T cell


title: BAL cells, 35951_d3-1

value: 3 years, 350 days


title: BAL cells, 35951_necropsy-1

value: Post-acute Covid-19 (12-17dpi)


title: B7T


title: AE104 with 50 µM EDTA replicate 2

value: 50 µM EDTA


title: A5_b6_cast_lcmv_cd4_nav_r1_ATACseq


title: BAL cells, 36207_d3-1

value: 3 years, 258 days

value: Acute Covid-19 (3dpi)

value: broncho-alveolar lavage (BAL) cells


title: BAL cells, 36207_w-1-1

value: Male

value: pre-infection (-7dpi)

value: control


title: SA3T

value: Female

value: Fresh Frozen

value: Tumor


title: E9T

value: Paraffin Embedded


title: A4_b6_cast_lcmv_cd4_d60_r2_ATACseq

value: B6/Cast F1

value: Spleen

value: memory CD4 T cell


title: AE104 with 50 µM EDTA replicate 1


title: SA9T


title: BAL cells, 36189_w-1-1

value: 3 years, 269 days


title: B5T


title: K16T


title: A3_b6_cast_lcmv_cd4_d60_r1_ATACseq


title: K23T


title: A1_b6_cast_lcmv_cd4_d07_r1_ATACseq

value: activated CD4 T cell


title: BAL cells, 36052_w-1-1

value: 3 years, 323 days


title: BAL cells, 36056_w-1-1

value: 3 years, 324 days


title: AE104 with 100 µM Zn replicate 3

source_name: AE104 with 100 µM Zn

value: 100 µM Zn


title: BAL cells, 35969_w-1-1

value: 3 years, 343 days


title: AE104 with 100 µM Zn replicate 2


title: CMT64_Ascl1

data_processing:
CLC Genomics workbench software (Qiagen) was used to generate RPKM data.
Adapter sequences were removed, and read mapping was carried out using the default settings of RNA-Seq analysis package (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and maximum number of hits for a read set to: 30).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel

growth_protocol: CMT64 cells were cultured in Dulbecco modified essential medium with 10% fetal bovine serum and 1% penicillin-streptomycin and 1% L-glutamine.

extract_protocol:
Total RNA was extracted from CMT64 cells 24 h after siRNA transfection using the RNeasy Mini Kit (Qiagen).
The mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Mouse Ascl1 cDNA was inserted into MSCV-IRES-neo retrovirus vector. Retroviral infection in CMT64 cells was performed. G418 (Sigma-Aldrich, St. Louis, MO) was used for drug selection.

tag: cell line

tag: genotype/variation

value: transduced with Ascl1


title: AE104 with 100 µM Zn replicate 1


title: AE104 untreated replicate 3

source_name: AE104 untreated

value: none; untreated


title: CMT64_GFP

value: transduced with GFP


title: AE104(delta e4) untreated replicate 1

value: (delta e4)


title: AE104 untreated replicate 2


title: BAL cells, 35951_w-1-1

value: 3 years, 350 days

value: Male

value: pre-infection (-7dpi)

value: control

value: broncho-alveolar lavage (BAL) cells


title: A2_b6_cast_lcmv_cd4_d07_r2_ATACseq

value: B6/Cast F1

value: Spleen


title: SKBR3-Tuca-DTP-4_S8

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
scRNA-Seq Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
RNA-Seq Basecalls performed using CASAVA
RNA-Seq reads were mapped using STAR guided by GTF
RNA-Seq Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files, Count Tables, BAM files, gene names and genes-barcodes (tsv files) matrices (matrix file)

extract_protocol:
Samples were prepared by the Princess Margaret Genomic Centre following the 10X Genomics Single Cell 3‚Äô Reagent Kits v2 user guide. Briefly, samples were washed two times in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. The cell suspension was loaded onto a 10X single cell A chip. After droplet generation, samples were transferred onto pre-chilled 96-well plates (Eppendorf), heat-sealed, and incubated overnight in a Veriti 96-well thermal cycler (Thermo Fisher) for reverse transcription (RT).
Following RT, cDNA was recovered using the Recovery Agent provided by 10X, and subsequently purified by using Silane DynaBead (Thermo Fisher) mix, as outlined by the user guide. Purified cDNA was amplified for 13 cycles before purification on SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA), and cDNA concentration was determined with a  Bioanalyzer (Agilent Technologies). cDNA libraries were prepared as outlined by the Single Cell 3‚Äô Reagent Kits v2 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.

value: 14 day tucatinib

value: HER2 positive breast cancer cells


title: SA4T

tag: gender

value: Female

tag: sample type

value: Fresh Frozen

value: Tumor


title: Human spinal cord organoids

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

data_processing:
The raw sequence data were processed using the Cell Ranger pipeline (version 3.1.0, 10x Genomics).
Gene expression matrices were generated using the Seurat package (version 3.1.5) in R. Unless otherwise stated, we used functions of the Seurat package for downstream analysis. Several quality-control steps were performed to filter out unreliable cells and genes as follows: (i) removal of cells with >10 % of counts that were mapped to mitochondrial genes, (ii) removal of cells with more than 7,000 or fewer than 200 unique expressed genes, (iii) removal of genes detected in <10 cells.
After the quality control procedure, we obtained 18,365 genes across 11,038 cells for further analyses. For downstream analysis, the UMI count data were normalized and variance-stabilized using the R package SCTransform56. The effect of mitochondrial gene expression was removed during the normalization process. Highly variable genes were selected based on the variance of Pearson residuals from normalized negative binomial regression.
A graph-based clustering algorithm (FindClusters function of Seurat) was used for single-cell clustering. The t Stochastic Neighbor Embedding (tSNE) visualization was achieved using the top 20 principal components obtained from principal component analysis based on the elbow plot and jack Straw score. To identify the neuronal cell types, each cluster was annotated with the average expression value of known marker genes for each cell type from previous atudies.
Genome_build: Reads were aligned to the GRCh38 human genome reference using the STAR aligner (version 2.5.1b).
Supplementary_files_format_and_content: Cell Ranger output files, h5 file, dfferentially expressed genes in all clusters (each cluster was annotated with the average expression value of known marker genes for each cell type from previous studies)

source_name: hPSCs

growth_protocol: iPSCs-derived spinal cord brain organoids were routinely generated using neuromesodermal progenitors derived from iPSCs. Organoids were maintained in differentiation media (see method in mansucript), media were changed every other day throughout the in vitro culture.

extract_protocol:
The hSCOs were collected in a petri dish on day 100 and chopped into small pieces. After dissection, the hSCOs were dissociated by using papain containing L-cysteine by incubation at 37℃ with gentle shaking. Papain was removed after 30 min, and the dissociated cells were washed twice with ice-cold HBSS. Libraries were prepared using the Chromium controller according to the 10x Single Cell 3’ v3 protocol (10x Genomics)
The dissociated cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. The cell suspension was mixed with a master mix and loaded with Single-Cell 3′ Gel Beads and Partitioning Oil into a Single Cell 3′ Chip. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled. The cDNA pool was subjected to an end repair process, followed by the addition of a single ‘A’ base and ligation of the adapters. The products are then purified and enriched with PCR to develop the final cDNA library. The purified libraries were quantified using qPCR based on the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). The libraries were subsequently sequenced using the HiSeq platform (Illumina) with a read length of 28 bp for read 1 (cell barcode and unique molecular identifier, UMI), 8 bp index read (sample barcode), and 91 bp for read 2 (RNA read).
single cell RNA-seq

treatment_protocol: Not available

value: iPSCs

value: iPSCs-derived brain organoids

value: organoids at 3 months old


title: AE104 untreated replicate 1

value: none; untreated


title: IL33_R 2

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed
RNA-seq reads mapping were using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung group 2 innate lymphoid cell

extract_protocol:
Five hundred ILC2s from each condition were lysed in 5 mL 10 ´ lysis buffer. SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells
Amplify sscDNA by LD PCR and get enough dscDNA for library construction. cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA
paired-end sequencing on an Illumina Novaseq™ 6000

treatment_protocol: Purified lung ILC2 stimulated with IL-33 and IL-33 plus Ang II for 6 hour.

value: lung

value: Lung group 2 innate lymphoid cell

value: IL-33 for 6 hours


title: IL33+Ang II_R 1

value: IL-33 plus Ang II for 6 hours


title: B2T

value: Male

tag: disease state


title: ny_2

city: Hainan

first: Zengshu

last: Xing

address: No.43, Renmin Road, Meilan District, Haikou 570208, Hainan Prov., P.R. China.

institute: Affiliated Haikou Hospital of Xiangya Medical College, Central South University

data_processing:
Base identification (Base Calling) of the raw image files from Illumina high-throughput sequencing and conversion into raw sequenced sequences (Sequenced Reads) for subsequent analysis, i.e. a collection consisting of raw sequenced sequences, called Raw Data. Analysis software: bcl2fastq software; Analysis results: FASTQ files (abbreviated as fq).
Analysis of the base quality of sequenced sequences 5' to 3' and assessment of the content of A, T, C and G bases in the sequencing data, assessing the ratio of base types at each site at an overall level. Analysis software: FastQC software.
Filter the raw data to remove reads that do not meet the analysis criteria and obtain clean reads that can be used for subsequent comparisons, statistics and subsequent analysis. Analysis software: fastp software.
After quality control of the raw data, clean data is obtained, and the clean data is evaluated to see the effect of quality control. Analysis software: FastQC software.
Sequence alignment statistics: The clean reads are compared with the reference genome sequence. This step is the basis for all subsequent analyses. Analysis software: HISAT2/tophat2.
Classification of reads to the reference genome, reflecting the transcriptional profile of the sample in the genome. Analysis software: RSeQC.
Sequence assembly, gene and transcript reconstruction based on reads matching results, i.e. assembly. Analysis software: StringTie software.
Expression readcount calculation using featureCounts or Stringtie software. The FPKM of the gene and transcript were then calculated. In this process we performed a simple filtering of the expression. Analysis software: featureCounts, Stringtie software.
Analysis instructions: Use the limma package for comparison of differences with biological duplicates or pairs, and the DESeq package for comparison of differences without biological duplicates. Analysis software: limma/DESeq.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values of mRNAs and lncRNAs for each Sample.
Supplementary_files_format_and_content: *.fpkm.anno.xlsx: Excel files include FPKM values of genes and transcripts for each Sample.

source_name: prostate cancer cell line

growth_protocol: PC3 was cultured in Dulbecco's modified Eagle’s medium (DMEM; Gibco, Grand Island, NY, USA) with 10% fetal bovine serum (FBS) and maintained in an incubator containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA from PC3 and PC3-DR cells with three parallel samples from each group was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA). The purity, concentration, and integrity of the total RNA were evaluated using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: PC3 cells were treated with DTX at 4 and 8 nmol/L for 48 h for 5 cycles. After treatment, the surviving cells were reseeded into new DMEM for 2–3 weeks. PC3 cells were treated with DTX at 8 and 12 nmol/L for 48 h for 12 cycles. The surviving cells were then reseeded into DMEM for 2–3 weeks. Cells were continuously maintained in DTX, with treatments beginning at 10 nmol/L and gradually increasing by 5 nmol/L increments to a final dose of 50 nmol/L. DMEM containing DTX was changed every 2–3 days. PC3-DR cells were maintained for 1 month with 40 nM DTX.

value: Prostate cancer cell line

tag: phenotype

value: Docetaxel resistant


title: ny_1


title: SKBR3-Tuca-DTP-3_S7


title: B3T

tag: age


title: B4T


title: IL33_R 1

tag: tissue


title: SKBR3-Tuca-DTP-2_S6


title: ny_3


title: SA1T


title: SKBR3-Tuca-DTP-1_S5


title: pc3_2

value: Docetaxel sensitive


title: SKBR3-P2_S6

value: untreated


title: day4sample4

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Fastqs files were used to quantify both spliced andunspliced counts by Alevin (Salmon v1.3.0) with default settings as described by Soneson (2020)
Abundances matrices were read in by R package tximeta(v1.8.1). The spliced counts were treated as the ex-pression counts.
We removed cells with less than 200 expressed genes and cells flagged as outliers (deviating more than triple median absolute deviations (MAD) from the median of log2(TotalUMIs),log2(number of expressed genes), percentage of mitochondrial gene counts, or log10(doublet scores)). Doublet scores were computed using doubletCells  function  in  R  package  scran  (v1.18.1). All mitochondrial  genes  and  any  genes  which  were expressed  in  less  than  20  cells  were  further excluded from all subsequent analyses.
Expression abundances were then library size normalized and log2 transformed by the `normalizeCounts` function in the R package scuttle (v1.0.2).
Biological samples were  integrated by  Seurat (v3.2.2).
Genome_build: GRCm38; GENCODE vM25
Supplementary_files_format_and_content: Hipp_colData.tsv is a tab-delimited file containing the phenotype data for each cell in the gene expression matrix; Hipp_rowData.tsv is a tab-delimited file containing the feature (row) information and annotation for the gene expression matrix; Hipp_logcount.mtx is a compressed Matrix Market Exchange file format containing the sparse raw gene count matrix.

source_name: Cultured mouse primary hippocampal NPCs (4-day differentiation;C57BL/6J)

growth_protocol: Female C57BL/6J mice (Jackson Laboratories) were mated to Kmt2d+/βgeo males and sacrificed for embryo harvest at embryonic day 18. Microdissected DG from Kmt2d+/βgeo and Kmt2d+/+ littermate embryos was processed for NSPC isolation and in vitro differentiation as described in Bernas et al 2017 (doi:10.21769/BioProtoc.2603). Briefly, cells were maintained in an undifferentiated state via supplementation with growth factors (EGF, FGF2) in Neurobasal media. Cultures from each genotypes were collected at the undifferentiated state (day 0) and then 2, 4, and 8 days after growth factor removal to induce neuronal differentiation. Cells were collected via trypsinization and pellets were washed and resuspended in Neurobasal media. scRNA-seq libraries were created with a Chromium Single-Cell 3' library & Gel Bead Kit v3 (10x Genomics) according to manufacturer protocol. Approximately 10,000 cells were targeted for each library.

extract_protocol:
Cultured primary hippocampal NPCs and their differentiated progeny were subjected to scRNA-Seq library construction on the 10x Genomics Chromium platform using Chromium Single Cell 3' v3 reagent kits according to manufacturer's protocol.
scRNA-Seq libraries were prepared using the 10x Chromium v3 3' kit using manufacturer recommendations.

tag: allele

value: wildtype


title: day8sample2

source_name: Cultured mouse primary hippocampal NPCs (8-day differentiation;Kmt2d+/βgeo)


title: day8sample4

source_name: Cultured mouse primary hippocampal NPCs (8-day differentiation;C57BL/6J)


title: pc3_1


title: SKBR3-P1_S5

value: HER2 positive breast cancer cells


title: day4sample2

source_name: Cultured mouse primary hippocampal NPCs (4-day differentiation;Kmt2d+/βgeo)


title: SA2T

value: Fresh Frozen


title: Bronchial_Spike_Protein_S1_rep6

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 21.0.1 was used to demultiplex the raw sequencing reads according to the sample indices.
The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. In short, the reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2). They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen). The reads were then mapped to the Human genome GRCh38
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.1 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 (Small-sample estimation of negative binomial dispersion, with applications to SAGE data) and incorporated in the EdgeR Bioconductor package (Robinson et al., 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data).
Genome_build: Human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

source_name: Primary bronchial epithelial cells from donor_1

growth_protocol: As described in the paper. Briefly, the bro-ALI model was developed using PBEC. The PBEC were harvested from healthy bronchial tissues obtained from donors in connection with lobectomy following written and informed consent, and approval by the Swedish Ethical Review Authority (Institutional ethic committee reference number 99-357, approved on 10th January 2000 ). The detailed protocol and details of cellular differentiation (club cells, goblet cells, basal cells, ciliated cells, etc.) of the bro-ALI model have been described previously (PMID: 28107509) and have been used in several studies (PMID: 28107509, PMID: 31462114, PMID: 31381966). All experiments and methods were carried out in accordance with relevant guidelines and regulations.   The alveolar model was developed using NCI-H441 (ATCC HTB-174) cell line, known to express constitutively the mRNA and protein of the major surfactant apo-protein. NCI-H441 cells were co-cultured with HULEC-5a (ATCC CRL-3244) representative of human lung microvascular endothelial cells for this purpose. Details of the development of alv-ALI model and its characteristics have been described recently (PMID: 33235237).

extract_protocol:
RNeasy Micro (QIAGEN)
UPX 3’ RNA sequencing technology using Qiagen Genomic Services, Germany

treatment_protocol: As described in the paper. Briefly, S1 protein, 10nM (mixed in a small volume of cell culture media; 80µl) was added on the apical surface of both bro-ALI and alv-ALI and incubated for 24 hours (h). The exposure dose was determined following a dose gradient study using 5nM, 10nM, and 20nM S1 protein and corresponding assessment of cytotoxicity, surface expression of ACE2, TLR2 and TLR4 by flow cytometry.

value: Primary bronchial epithelial cells

value: Spike Protein S1


title: K28T

value: Female

value: Paraffin Embedded

value: Tumor


title: Bronchial_Spike_Protein_S1_rep5


title: SKBR3-LAP-DTP2_S8

value: 14 day lapatinib


title: day2sample4

source_name: Cultured mouse primary hippocampal NPCs (2-day differentiation;C57BL/6J)


title: SKBR3-LAP-DTP1_S7


title: day2sample2

source_name: Cultured mouse primary hippocampal NPCs (2-day differentiation;Kmt2d+/βgeo)


title: Bronchial_Spike_Protein_S1_rep4


title: IL33+Ang II_R 2

value: lung

value: Lung group 2 innate lymphoid cell


title: Bronchial_Spike_Protein_S1_rep3


title: HCC1419-Tuca-DTP-4_S16

value: 14 day tucatinib


title: day0sample4

source_name: Cultured mouse primary hippocampal NPCs (undifferentiated;C57BL/6J)


title: K27T


title: Bronchial_Spike_Protein_S1_rep2


title: K6T

value: Male


title: SA5T


title: day0sample2

source_name: Cultured mouse primary hippocampal NPCs (undifferentiated;Kmt2d+/βgeo)


title: HCC1419-Tuca-DTP-3_S15


title: Bronchial_Spike_Protein_S1_rep1


title: HCC1419-Tuca-DTP-2_S14


title: HCC1419-Tuca-DTP-1_S13


title: pc3_3

value: Prostate cancer cell line


title: RNAseq_diff_mESC_T_Sox17_Rep2

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description:
T_Sox17_Rep2
Bulk RNA-sequencing of SOX17+/T+ sorted population after differentiation rep 2

data_processing:
RNAseq reads were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the reference genome mm10 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for transcript quantification, e.g. calculation of strand-specific coverage and TPMs (reference: mm10 gencode gene annotation gtf).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all_TPMs.txt: Tab-delimited text file containing gene names and abundances for all replicates (TPM).

source_name: SOX17+/T+ sorted differentiated cells

growth_protocol: Mouse ESCs were cultured on gelatin surface using standard conditions on irradiated primary mouse embryonic fibroblasts and knockout DMEM containing 15% fetal bovine serum, 50 μg/ml penicillin/streptomycin, 2 mM L Glutamine, 100 μM non-essential amino acids, 80 μM ß-mercaptoethanol and 10^3 U/mL LIF.

extract_protocol: mESCs and their differentiated progenies were treated with TrypLE (Gibco, cat. no.12604013) for 10 min at 37°C, 5% CO2 to obtain a single cell suspension. Cells were then collected, washed with ice cold DPBS and centrifuged at 4°C, 300 x g for 5 min. Subsequently, cell pellets were resuspended in 1 ml FACS Buffer (PBS, 2%FBS, 0.5mM EDTA) and SOX17+, T+ and SOX17+/T+ populations were sorted based on the reporter expression in a 1.5 ml tube containing 350 µl RLT Plus buffer containing 1% β-mercaptoethanol (Thermo). After dissociation by trituration and vortexing, RNA was extracted using RNeasy Plus Micro Kit (Qiagen) and RNA concentration and quality was measured using the Agilent RNA 6000 Pico Kit (Agilent Technologies, 5067-1513) on an Agilent 2100 Bioanalyzer. All samples analyzed had a RINe value higher than 8,0, and were subsequently used for library preparation. mRNA libraries were prepared using KAPA Stranded RNA-Seq Kit (KapaBiosystem) according to the manufacturer’s instructions. 500 ng of total RNA was used for each sample to enter the library preparation protocol. For adapter ligation dual indexes were used (NEXTFLEX® Unique Dual Index Barcodes NOVA-514150) at a working concentration of 71nM (5 µl of 1 uM stock in each 70 µl ligation reaction). Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape (Agilent-Technologies, 5067- 5592) on an Agilent 4150 TapeStation. All libraries were sequenced using 100 bp paired-end sequencing (200 cycles kit) on a NovaSeq platform at a minimum of 50 million fragments /sample.


title: B14SN

source_name: normal esophageal mucosa

value: Adjacent normal


title: B11SN


title: HCC1419-P2_S14


title: RNAseq_diff_mESC_T_Rep3

description:
T_Rep3
Bulk RNA-sequencing of T+ sorted population after differentiation rep 3

source_name: T+ sorted differentiated cells


title: HCC1419-P1_S13


title: Bronchial_Control_rep4

value: control


title: HCC1419-LAP-DTP2_S16


title: B1T

source_name: tumor tissue


title: B5SN


title: RNAseq_diff_mESC_T_Sox17_Rep3

description:
T_Sox17_Rep3
Bulk RNA-sequencing of SOX17+/T+ sorted population after differentiation rep 3


title: RNAseq_diff_mESC_T_Sox17_Rep1

description:
T_Sox17_Rep1
Bulk RNA-sequencing of SOX17+/T+ sorted population after differentiation rep 1


title: Bronchial_Control_rep5


title: RNAseq_diff_mESC_T_Rep2

description:
T_Rep2
Bulk RNA-sequencing of T+ sorted population after differentiation rep 2


title: B15SN


title: HCC1419-LAP-DTP1_S15


title: Bronchial_Control_rep6


title: Bronchial_Control_rep2


title: EFM192A-Tuca-DTP-4_S12


title: SA9SN


title: B10SN


title: B6SN


title: B13SN


title: Bronchial_Control_rep3


title: B8SN


title: RNAseq_diff_mESC_Sox17_Rep1

description:
Sox17_Rep1
Bulk RNA-sequencing of SOX17+ sorted population after differentiation rep 1

source_name: SOX17+ sorted differentiated cells


title: RNAseq_diff_mESC_T_Rep1

description:
T_Rep1
Bulk RNA-sequencing of T+ sorted population after differentiation rep 1


title: EFM192A-Tuca-DTP-2_S10


title: RNAseq_diff_mESC_Sox17_Rep2

description:
Sox17_Rep2
Bulk RNA-sequencing of SOX17+ sorted population after differentiation rep 2


title: Alveolar_Spike_Protein_S1_rep5

source_name: NCI-H441 (ATCC HTB-174) cell line


title: SA10SN


title: RNAseq_diff_mESC_Sox17_Rep3

description:
Sox17_Rep3
Bulk RNA-sequencing of SOX17+ sorted population after differentiation rep 3


title: Alveolar_Spike_Protein_S1_rep4


title: RNAseq_undiff_mESC_Rep3

description:
mESC_Rep3
Bulk RNA-sequencing of undifferentiated mESCs rep3

source_name: undifferentiated mESC

value: undifferentiated mESCs


title: EFM192A-Tuca-DTP-3_S11


title: RNAseq_undiff_mESC_Rep2

description:
mESC_Rep2
Bulk RNA-sequencing of undifferentiated mESCs rep2


title: EFM192A-P2_S10

value: untreated


title: Alveolar_Spike_Protein_S1_rep3


title: EFM192A-P1_S9

value: HER2 positive breast cancer cells


title: EFM192A-Tuca-DTP-1_S9


title: Alveolar_Spike_Protein_S1_rep2


title: RNAseq_undiff_mESC_Rep1

description:
mESC_Rep1
Bulk RNA-sequencing of undifferentiated mESCs rep1


title: Cre1

city: Vari

first: Maria

last: Tsoumakidou

state: Attica

address: 34 Fleming Street

country: Greece

institute: B.S.R.C. "Alexander Fleming"

data_processing:
Quality of FASTQ files was assessed using FastQC(version 0.11.8)
Alignment of sequencing reads to the reference genome was performed using the software  HISAT2 (version 2.1.0 and parameters : --score-min L,0,-0.36 -k 2 --max-seeds 20 --rna-strandness F -p 6) with the  mm10 version of reference genome.
Bam files of uniquely aligned reads were summarized to to read counts table using the GenomicRanges  package through metaseqR2 pipeline(version 1.2.0), with the recommended settings for 3'UTR data.
The resulting gene counts table was subjected to differential expression analysis (DEA) with metaseqr2 function from metaseqR2 package(version 1.2.0), using DESeq2 algorithm for the normalization and statistical testing.
Genes with less than 5 raw counts in 75% of the samples were excluded from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab separated file containing the results from metaseqR2 analysis including fold change compared to control, p-value and FDR

source_name: solid tumor

extract_protocol:
Intratumoral CD45+CD3+CD4+ T cells were FACS sorted in RL buffer. Total RNA was isolated by using NucleoSpin RNA (Macherey-Nagel).
RNA libraries were prepared for sequencing using NEB Next Ultra RNA Library Prep Kit. 3′-UTR RNA-Seq

value: lung tumor

value: Intratumoral CD45+CD3+CD4+ T cells

value: over 8-week-old

tag: genotype

value: tamoxifen induction


title: EFM192A-LAP-DTP2_S12


title: B9SN

value: Female

value: Fresh Frozen


title: SA8SN


title: Cre2

tag: strain


title: WT_RO-IP for meRIP-seq

city: nantong

first: hong

last: shihao

address: 19 Qixiu Road

institute: Nantong university

data_processing:
Library strategy: MeRIP-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For  MeRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Genome_build: mm10

source_name: spermatogenic cells

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For MeRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).

value: testes

value: wild type

value: spermatogenic cells


title: Control5

tag: cell type

value: I-AbF/F


title: Bronchial_Control_rep1

value: Primary bronchial epithelial cells

tag: treatment


title: B7SN

extract_protocol: genomic DNA was extracted and purified from tumor and normal tissue samples using AllPrep DNA/RNA Mini Kit according to standard instructions

value: Male


title: Alveolar_Spike_Protein_S1_rep6

value: Spike Protein S1


title: Alveolar_Spike_Protein_S1_rep1


title: Alveolar_Control_rep6

value: control


title: SA7SN

value: Adjacent normal


title: WT_PA-IP for meRIP-seq


title: B12SN


title: SA6SN


title: Control3


title: BT474-Tuca-DTP-3_S3

value: 14 day tucatinib


title: Control4


title: SA3SN


title: BT474-Tuca-DTP-2_S2

value: HER2 positive breast cancer cells


title: WT_PA-input for meRIP-seq


title: Control2

value: lung tumor


title: Alveolar_Control_rep5


title: WT_RO-input for meRIP-seq


title: BT474-Tuca-DTP-1_S1


title: Control1

value: Intratumoral CD45+CD3+CD4+ T cells


title: KO_RO-input for meRIP-seq


title: BT474-P2_S2

value: untreated


title: Alveolar_Control_rep1


title: KO_PA-IP for meRIP-seq