title: KD3

city: NANJING

first: zhang

last: juan

address: CHANGLE ROAD 68#

institute: Nanjing First Hospital

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of sample NC1,NC2,NC3,KD1,KD2 and KD3 to the (ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gtf/triticum_aestivum/) Triticum aestivum L. reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: v36; (ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gtf/triticum_aestivum/) Triticum aestivum L. reference genome
Supplementary_files_format_and_content: xls include RPKM values for each Sample

growth_protocol: HT29 cells were cultured in RPMI-1640 medium containing 10% Fetal Bovine Serum in a 37℃ incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 6000 at the (lc-bio, China) following of the merchant's recommended protocol.
The paired-end libraries was 300 bp ( ± 50 bp)

treatment_protocol: The shKIAA1211 plasmids were generated using PLKO.1 (MiaoLingBio, China). The shRNAs plasmids were transfected into cells with lipofectamine 2000 (Invitrogen) according to the reagent instructions.

tag: tissue source

value: colon

value: Colorectal cancer cells


title: monthly_2_20H

status: Public on Feb 10 2022

type: genomic

city: Beijing

first: Jiesi

last: Lei

state: Beijing

address: School of Environment, Tsinghua

country: China

institute: Tsinghua University

description: collected in Feb, warming, replicate 3

hyb_protocol: The mixed solution was kept at 90 °C for 3 min for denaturation, and incubated at 37°C for 30 min before GeoChip hybridization was carried out at 67 °C for 24 hrs with a rotation at 20rpm in Agilent hybridization oven.

scan_protocol: After hybridization, Agilent Wash Buffers were applied to wash away unbounded DNA at ordinary temperature, and the arrays were scanned with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA) at 633 nm. Eventually the images data were extracted by Agilent Feature Extraction program.

data_processing:
Raw signals were uploaded to Microarray Data Manager (http://ieg.ou.edu/microarray) for data quality control and normalization. Samples from January to June and from July to December were hybridized in separate batches. The signal-to-noise ratio (SNR) was set to 7 for Jan to Jun samples or 3.5 for Jul to Dec samples to minimize the batch effect. Spots with minimum intensity < 100 or detected in < 50% replicate samples were removed before statistical analyses. Both the universal standard and functional gene spot intensities are used to normalize the signals among arrays. Data were logarithmically transformed after quality control and normalization.
Probe names and detailed info for PROBE_ID in raw data and proteinGI in the data matrix are provided seperately. One shall be able to easily process the raw data, get normalized data, and complete annotations using http://ieg.ou.edu/microarray/.
Processed data file includes: Normalized signal intensity

molecule: genomic DNA

organism: uncultured soil bacterium

source_name: soil DNA, Feb, warming, replicate 3

label_protocol: Purified DNA was first labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) using random priming as described previously (Cong et al., 2015), then purified by a QIAquick Purification kit (Qiagen, Valencia, CA, USA), and dried in a SpeedVac (Thermo Savant, NY, USA) at 45 °C for 45 min. The dried DNA was then resuspended into ??? μl of DNase/RNase-free distilled water and evenly mixed with ??? μl of hybridization solution, which contains 1 × Acgh blocking, 1 × HI-RPM hybridization buffer, 10 pM universal standard DNA, 0.05 μg/μl Cot-1 DNA, and 10% formamide (final concentrations).

extract_protocol: DNA was extracted by MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA). DNA concentrations were quantified with PicoGreen using a FLUOstar OPTIMA fluorescence plate reader (BMG LabTech, Jena, Germany), and DNA purity was determined by the ratios of O.D. 260/280 nm and O.D. 260/230 nm using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA).

tag: collection time

value: collected in Feb

tag: condition

value: warming

tag: replicate

value: replicate 3


title: WT-N2A-NT 1

type: SRA

first: Yunfei

last: Li

state: China

address: 38 Xueyuan Road, Haidian District, Beijing

department: Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China

institute: Peking University

description:
1-fpkm.xlsx
WT-N2A-NT-1-LDK0832_L1

library_source: transcriptomic

data_processing:
The raw fastq files were trimmed to clean data by trim-galore software.
The clean data were aligned to mm10 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differentially expressed genes.
Genome_build: UCSC mm10 genome was used as reference genome.
Supplementary_files_format_and_content: *-fpkm.xlsx: Excel spreadsheets include the FPKM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: N2a cells

growth_protocol: N2a cells were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co., Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: Transfecting plasmids encoding RfxCas13d and NT crRNA into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

tag: cell line

tag: genotype

value: WT

tag: transfection

value: RfxCas13d and NT cRNA


title: 1566 Mock 1 DPI replicate 3

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

country: USA

institute: Center for Regenerative Medicine, Boston University

molecule: polyA RNA

organism: Homo sapiens

source_name: 1566 Mock 1 DPI replicate 3

growth_protocol: Both BU3 NGPT and 1566 iPSC lines were differentiated into airway epithelium according to the methods described by Hawkins et al., Cell Stem Cell, 2021 (PMID: 33098807). The protocol involves the step-wise directed differentiation of iPSCs to airway as published previously.  In brief, it recapitulates the major stages of embryonic lung development as follows:   Stage 1) Definitive endoderm (D0-3) using STEMdiff™ Definitive Endoderm Kit;  Stage 2) Anterior foregut endoderm (D3-6) through TGFb and BMP inhibition; Stage 3) Lung specification (D6-15) using a combination of CHIR 99021 (to activate WNT signaling), BMP4, and retinoid acid and evidenced by the expression of NKX2-1. We then purify these NKX2-1+ lung epithelial progenitors at D15 through either sorting on GFP (BU3 NGPT) or for non-reporter line, utilizing a CD47hi/CD26neg sorting strategy;  Stage 4) Early airway organoids (D15-30), where  GFP+ (BU3 NGPT) or CD47hi/CD26neg sorted cells (1566) are plated in 3D Matrigel and cultured in media containing FGF2 and FGF10 for patterning toward proximal airway-like organoids composed of immature secretory and basal progenitors.  Stage 5) iBCs (D30-45), during which the iPSC-3D organoids are further expanded in dual-SMAD inhibition media with DMH-1 and A83-01 for ~12 days 74, 75.   iBCs were either serially passaged or cryopreserved, thawed and then serially passaged to generate cells for stage 6. Stage 6) Airway differentiation on ALI culture (>D45) iBCs are identified and purified by sorting on NGFR+ cells, and purified cells are expanded and differentiated on Transwells in dual-SMAD inhibition media then transitioned to ALI media when >80% confluent. Apical chamber media is removed to initiate ALI to recapitulate a physiologically-relevant environment and stimulate differentiation.  After 14 days, iBCs form a pseudostratified airway epithelium that displays morphologic, molecular, and functional similarities to primary human airway epithelial cells and is comprised of the major airway cell types of multi-ciliated, secretory, and basal cells40.

extract_protocol:
RNeasy Mini Kit (Qiagen)
poly(A) selection & reverse transcription

treatment_protocol: Prior to infection, the apical side of iPSC-airway plated in ALI culture was washed with 100 μL of PBS for 5-10 minutes at 37 C to remove the mucus.  Then, purified SARS-CoV-2 stock (100 μL of inoculum prepared in PBS) or PBS without virus (mock infection) was added at the apical chambers of each Transwell at a multiplicity of infection (MOI) of 4 and allowed to adsorb for 1 hour at 37oC and 5% CO2.  After adsorption, the inoculum was removed and cells were incubated at ALI at 37 C for 3 days.

tag: media

value: PneumaCult ALI

tag: culture format

value: Air liquid interface culture on Transwells

tag: cell type

value: iPSC-derived airway epithelium


title: 1566 SARS-CoV-2 1 DPI replicate 1

source_name: 1566 SARS-CoV-2 1 DPI replicate 1


title: monthly_2_1H

description: collected in Feb, warming, replicate 1

source_name: soil DNA, Feb, warming, replicate 1

value: replicate 1


title: NC2

tag: treatment

value: normal


title: WT-N2A-NT 2

description:
1-fpkm.xlsx
WT-N2A-NT-2-LDK0833_L1


title: monthly_2_23C

description: collected in Feb, control, replicate 4

source_name: soil DNA, Feb, control, replicate 4

value: control

value: replicate 4


title: 1566 Mock 1 DPI replicate 1

source_name: 1566 Mock 1 DPI replicate 1


title: Fc-02

city: Seattle

first: Mark

last: Maurer

state: WA

address: 188 E Blaine St. Suite 200

department: Translation Science

institute: Alpine Immune Sciences

data_processing:
Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads using Galaxy FASTQ Trimmer tool v1.0.0.
The FASTQs were aligned to the mouse reference genome, using TopHat aligner (v1.4.1) with the NCBIM37 reference genome and gene annotations from ensembl release 67.
Gene counts were generated using HTSeq-count (v0.4.1).
Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1).
Genome_build: NCBIM37
Supplementary_files_format_and_content: Processed_RNAseq_data_Maurer_etal.xlsx

source_name: MC38/hPD-L1 tumor - Fc control Rep 2

extract_protocol:
Tumors were snap frozen and then RNA isolated by sonication and standard mRNA isolation kit from Qiagen.
Total RNA (0.5 ng) was added to lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

treatment_protocol: Animals were dosed intraperitoneally with a single dose of test article and then tumors were collected and mRNA isolated 72 hours later

tag: tissue

value: MC38/hPD-L1 tumor

value: Fc Control

tag: mouse strain


title: monthly_2_19C

description: collected in Feb, control, replicate 3

source_name: soil DNA, Feb, control, replicate 3


title: KD1


title: HT29_3D3

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of sample HT29_2D1，HT29_2D2,HT29_2D3,HT29_3D1,HT29_3D2 and HT29_3D3 to the (ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gtf/triticum_aestivum/) Triticum aestivum L. reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: v36
Supplementary_files_format_and_content: Excel file includes counts and FPKM values for each Sample

source_name: colon

treatment_protocol: For 2D cell culture, the cells are cultured on rigid dishes. The 3D fibrin gel cell culture is carried out as follows. T7 buffer (50 mM Tris, 150 mM NaCl, pH 7.4) and fibrinogen were mixed at a ratio of 9:1 to obtain diluted fibrinogen of 2 mg/mL, corresponding to the final 90-Pa soft fibrin gel. 250 μL of cells and fibrin solution are mixed with 5μL Thrombin in the center of each well. After 30 minutes, 1mL medium was added, and then the cell culture plate was put back to the 5% CO2 incubator for culture. The medium on the soft fibrin gel was changed once every 2 to 3 days.

value: 3D culture


title: WT-N2A-NT 4

description:
1-fpkm.xlsx
N-NT-2-LDL3819_L3


title: NC1

value: colon


title: BU3 NGPT SARS-CoV-2 3 DPI replicate 2

source_name: BU3 NGPT SARS-CoV-2 3 DPI replicate 2


title: monthly_2_6C

description: collected in Feb, control, replicate 2

source_name: soil DNA, Feb, control, replicate 2

value: replicate 2


title: BU3 NGPT SARS-CoV-2 3 DPI replicate 1

source_name: BU3 NGPT SARS-CoV-2 3 DPI replicate 1


title: monthly_2_3C

description: collected in Feb, control, replicate 1

source_name: soil DNA, Feb, control, replicate 1

value: collected in Feb


title: BU3 NGPT Mock 3 DPI replicate 3

source_name: BU3 NGPT Mock 3 DPI replicate 3


title: HT29_3D2

value: Colorectal cancer cells


title: HT29_3D1


title: monthly_1_16H

description: collected in Jan, warming, replicate 4

source_name: soil DNA, Jan, warming, replicate 4

value: collected in Jan

value: warming


title: monthly_1_20H

description: collected in Jan, warming, replicate 3

source_name: soil DNA, Jan, warming, replicate 3

value: replicate 3


title: HT29_2D3


title: 1566 Mock 1 DPI replicate 2

source_name: 1566 Mock 1 DPI replicate 2

value: PneumaCult ALI


title: monthly_1_10H

description: collected in Jan, warming, replicate 2

source_name: soil DNA, Jan, warming, replicate 2


title: HT29_2D2


title: KD2


title: EC109 shRBM6 #2

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description: strand-specific RNA-Seq

data_processing:
Differential alternative splicing (AS) events between RBM6 KD duplicates and scrambled control were identified by using rMATS 4.1.0 (http://rnaseq-mats.sourceforge.net/) with default parameters by using CSI NGS Portal (https://csibioinfo.nus.edu.sg/csingsportal).
The output included events for 5 major types as: A5SS, A3SS, MXE, RI, SE. The significant AS events were defined as:
1. sum(IJC_KD1, SJC_KD1) >= 20
2. sum(IJC_KD2, SJC_KD2) >= 20
3. sum(IJC_Scr, SJC_Scr) >= 20
4. abs(IncLevelDifference) >= 0.1
5. FDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Spreadsheet containing tables of significant AS events identified by rMATS in RBM6 KD duplicates vs Scr control.

growth_protocol: RPMI medium 10%FBS

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Directional mRNA library preparation (rRNA removal)

treatment_protocol: Human ESCC cells were treated with specific shRNAs for silencing RBM6.

value: human esophageal squamous carcinoma cells EC109

value: RBM6 knockdown


title: monthly_1_19C

description: collected in Jan, control, replicate 3

source_name: soil DNA, Jan, control, replicate 3


title: BU3 NGPT SARS-CoV-2 1 DPI replicate 3

source_name: BU3 NGPT SARS-CoV-2 1 DPI replicate 3

value: Air liquid interface culture on Transwells

value: iPSC-derived airway epithelium


title: BU3 NGPT SARS-CoV-2 1 DPI replicate 2

source_name: BU3 NGPT SARS-CoV-2 1 DPI replicate 2


title: HT29_2D1

value: normal


title: EC109 shRBM6 #1

description: strand-specific RNA-Seq

source_name: human esophageal squamous carcinoma cells


title: BU3 NGPT Mock 1 DPI replicate 3

source_name: BU3 NGPT Mock 1 DPI replicate 3


title: NC3


title: EC109 shScr (control for shRBM6)

description: strand-specific RNA-Seq

value: scramble shRNA treated


title: monthly_1_23C

description: collected in Jan, control, replicate 4

source_name: soil DNA, Jan, control, replicate 4

value: control

value: replicate 4


title: BU3 NGPT SARS-CoV-2 1 DPI replicate 1

source_name: BU3 NGPT SARS-CoV-2 1 DPI replicate 1


title: monthly_1_6C

description: collected in Jan, control, replicate 2

source_name: soil DNA, Jan, control, replicate 2


title: monthly_2_10H

description: collected in Feb, warming, replicate 2

source_name: soil DNA, Feb, warming, replicate 2


title: BU3 NGPT Mock 1 DPI replicate 1

source_name: BU3 NGPT Mock 1 DPI replicate 1


title: BU3 NGPT Mock 3 DPI replicate 2

source_name: BU3 NGPT Mock 3 DPI replicate 2


title: RSEM_PXR_3

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Raw sequence files were merged across lanes according to sample and subjected to a first round of quality control using the FastQC tool (www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina universal adapters were trimmed from all samples using Trim Galore ([www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and samples were then subjected to a second round of quality control
Reads were mapped to the human Hg38 reference genome using Bowtie2
The edgeR package with Limma/Voom was used for linear modeling, empirical Bayes smoothing, TMM normalization, generation of Log2(CPM), and statistical analysis
Genome_build: Hg38
Supplementary_files_format_and_content: Log2(Normalized Counts per Million)

growth_protocol: All cells were maintained according to respective ATCC recommended culture conditions

extract_protocol:
Total RNA was extracted from each cell line using the Maxwell 16 LEV automation system and simplyRNA purification kit (Promega, Cat. No. 1280) according to the manufacturer’s protocol. The extracted RNA was quantified by spectrophotometry using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA) to ensure a reading of OD260/OD280 between 1.8 and 2.0.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: Cells were not drug treated

value: HepaRG

value: hepatic stem cell line

tag: disease

value: cancer

value: Liver

tag: genotype/variation

value: functional knockout of PXR


title: RSEM_PXR_2


title: monthly_1_3C

description: collected in Jan, control, replicate 1

source_name: soil DNA, Jan, control, replicate 1

value: collected in Jan

value: replicate 1


title: RSEM_PXR_1


title: RSEM_WT_3

value: wild type


title: Jin-SN148-MMS-S1

city: Nantong

first: Jinrong

last: Feng

address: Qixiu Road

institute: Nantong University

data_processing:
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans SC5314 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

organism: Candida albicans

source_name: treated with MMS

extract_protocol: We used 0.015% MMS to treat the Candida albicans cells and explored the global transcription profile in response to MMS in C. albicans through RNAseq assay.

tag: strain

value: treated with MMS


title: Jin-SN148-S2

source_name: without treatment

value: without treatment


title: MCF10A cells, High-resolution phototagging rep 1

city: Rotterdam

first: Miao-Ping

last: Chien

address: Wytemaweg 80

department: Molecular Genetics

country: Netherlands

institute: Erasmus University Medical Center

data_processing:
scRNA-seq data was aligned and preprocessed by Single Cell Discoveries as described by Muraro et al. (2016).  They generally use the following pipeline:
For each lane in each plate, their script finds reads with a proper cell specific barcode and creates a new fastq file per lane (i.e., this "combines" information from the forward and reverse reads). Then the Illumina adaptors were trimmed from the FastQ files. These (trimmed) FastQ files were mapped against the reference genome (hg38) using STAR 2.7.3a. The final count tables thus contain information from all 4 lanes per plate.
Gene expression matrices were processed using Seurat v4 (Hao et al., 2021).
Genome_build: hg38 (Ensembl 99)
Supplementary_files_format_and_content: Matrix table (.tsv) with raw gene counts for every gene in each cell
Excel file with PlateLayout (Used to annotate the samples. In these files, the annotation shows how each cell was labelled during the phototagging process (inner/middle/outer), which later helps to identify variations in gene expression between the different regions. )
Demultiplexing_barcodes.txt (the cell barcodes that are used for demultiplexing the fastq files, they are in the same order as the columns appear in the processed tables).

source_name: Mammary gland

growth_protocol: MCF10A_H2B_GFP  were cultured DMEM/F12 medium without phenol red (Gibco), supplemented with 5% Donor Equine Serum, 1% penicillin/streptomycin, 20 ng/ml EGF, 500 ng/ml hydrocortisone, 100 ng/ml cholera toxin and 10 μg/ml insulin. Before conducting experiments, 10,000 cells were seeded in a circular patch on 20 mm glass bottom dishes, coated with 0.1 mg/ml fibronectin. The patch of cells was then cultured in MCF10A medium at 37°C and 5% CO2 for 6 days.

extract_protocol:
Cells were harvested using trypsin-EDTA without phenol red (Sigma), centrifuged and resuspended in HBSS buffer (Gibco). Live single cells (validated by Draq7 viability staining) were  sorted into 384-well plates using the BD FACSMelody Cell Sorter (BD Biosciences), spun-down and stored at −80°C.
Library preparation and single-cell RNA sequencing was performed by Single Cell Discoveries (Utrecht, Netherlands) using their custom SORT-seq protocol. cDNA libraries were sequenced at 150 k reads/cell on the Illumina NextSeq 500 platform.

treatment_protocol: Cell labeling was performed on the Ultrawide Field-of-view Optical (UFO) microscope. Cells were incubated with 40 μM photoactivatable Janelia Fluor 646 (JF646) dye (Tocris) for 20 min and washed with MCF10A culture medium. Bright-field images were used to localize the patch of cells, after which we identified the cells to be labeled using a low-resolution or high-resolution approach. In the low-resolution tagging approach, we fit three concentric rings with equal bandwidth (1,000–1,500 μm bandwidth) in the area of the patch. In the high-resolution approach, we divide the patch of cells in three layers: the outermost 250 μm of cells (~10 cell wide band), the next 250 μm, and the inside of the patch. In both approaches, the outer population of cells was then selectively illuminated for 2 min with 405 nm light using a digital micromirror device (DMD), thereby phototagging these cells with JF646. Next, cells were incubated with 40 μM photoactivatable Janelia Fluor 549 (JF549) dye29 (Tocris) for 20 min and washed with MCF10A culture medium. The imaging and labeling process was repeated, but now illuminating the middle population of cells. These cells are thus phototagged with JF549 and JF646, as both dyes are present in the cytoplasm and become activated upon illumination.

value: Untransformed mammary epithelial cells

value: Mammary gland

tag: disease state

value: 2D epithelial tumor model

tag: phototagging

value: High resolution

tag: phototagging details

value: Cells phototagged in 3 concentric rings with varying widths, profiling the invasive edge with a ~10 cell wide band


title: MCF10A cells, High-resolution phototagging rep 2


title: MCF10A cells, Low-resolution phototagging rep 2

value: Low resolution

value: Cells phototagged in 3 concentric rings of equal width


title: Dessau8_TMZ_Gy4_3

status: Public on Feb 09 2022

city: Leipzig

first: Susann

last: Haehnel

address: Liebigstrasse 13

department: Institute of Anatomy

country: Germany

institute: University of Leipzig

description:
Neuro_Organo_kallisto_gene_tpm
Neuro_Organo_kallisto_estimated_gene_counts

data_processing:
Illumina bcl2fastq v2.17.1 software was used for basecalling.
For adaptor trimming AdaptorRemoval v.2.3.1 was used with additional parameters as follows: --trimns –trimqualities –minquality 20, and –minlength 20 in order to trim terminating ambiguous bases or bases with a quality score less than 20 and to discard reads shorter than 20 bases.
Transcript abundancy estimation was conducted using Kallisto v.0.46.0 by specifying a reverse stranded library. Human transcriptome FASTA file was downloaded from GENCODE (release 31 GRCh38.p12) and used to create a Kallisto index.
Gene level quantifications were generated from the Kallisto estimated counts per transcript using tximport v.1.18.0.
Genome_build: hg38
Supplementary_files_format_and_content: text file containing estimated gene counts and Transcripts Per Million (TPM) for each sample with the corresponsing ensemble_id

source_name: glioblastoma tissue

growth_protocol: Glioblastoma tissue from 25 patients was surgically resected, processed in 350 µm tissue slices and cultivated on membrane inserts on a liquid-air-interface. Cultivation medium consisted of MEM (Gibco) with 25 % Hank's Balanced Salt Solution (HBSS, ThermoFisher Scientific), 10 % heat-inactivated horse serum (Gibco), 1 % L-glutamine (Gibco), 1 % Glucose (Mediatech Inc.), and 1 % penicillin/streptomycin (Gibco), was exchanged every 2 to 3 days. Tissue slices were cultivated in a humidified incubator at 37°C and 5 % CO2.

extract_protocol:
After radiochemotherapy, all 3 slices of each insert were pooled together, transferred to the QIAzol Lysis Reagent (Qiagen) and homogenized by a hollow needle attached to a syringe. The extraction of total RNA was performed using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Isolated RNA was diluted in 30 µl of RNAse-free water and stored at -80°C.
RNA concentration was determined using the Qubit 2.0 (Life Technologies). The quality of the isolated RNA was determined by the Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies). RNA was DNase-digested twice using the TURBO DNA free Kit (Ambion®, ThermoFisher Scientific). For library preparation with the Truseq-Stranded Total RNA Sample Prep Kit (Illumina) up to 200 ng RNA per sample were used. An rRNA depletion step was conducted according to the manufacturer’s protocol and – depending on the quality of each sample – a fragmentation was done. Every library was equipped with two barcodes to allow multiplexing of the samples. Concentrations were determined using the Qubit DNA Kit and the DNA quality was detected by the Bioanalyzer 2100 (DNA1000 Kit). According to the average size, which is determined by the Bioanalyzer, and the exact concentration of the samples, the molarity of each library was calculated. The samples were sequenced at the HiSeq2500 with 2 x 126 bp paired-end reads. 12 pM of DNA were put on the flowcell using one lane per sample.
Sequencing was performed with 2 x 126 bp paired-end reads at a HiSeq2500 (Illumina).

treatment_protocol: Tissue slices were randomly distributed to the membrane inserts with 3 individual slices per insert. 24 hours prior to x-irradiation, slices were pre-treated with 200 µM temozolomide or DMSO as vehicle control. Total x-irradiation dose was 4 Gy. 24 hours after x-irradiation, the slices received fresh temozolomide- or DMSO-supplemented medium. After a total incubation time of 72 hours, total RNA was isolated or slices were fixed with 4 % paraformaldehyde for histology.

value: glioblastoma

value: temozolomide + x-irradiation for 72 h

tag: concentration


title: RSEM_WT_1

value: HepaRG

value: hepatic stem cell line

value: cancer


title: Dessau8_TMZ_Gy4_2


title: MCF10A cells, Low-resolution phototagging rep 1


title: Dessau8_TMZ_Gy4_1


title: Dessau5_TMZ_4Gy_2


title: Dessau8_1

value: untreated

value: 0 uM


title: Dessau8_2


title: Dessau5_TMZ_4Gy_1


title: Dessau5_2


title: Dessau1_TMZ_Gy4_3


title: Dessau5_1


title: Dessau1_3


title: Dessau1_TMZ_Gy4_1


title: BU3 NGPT Mock 3 DPI replicate 1

source_name: BU3 NGPT Mock 3 DPI replicate 1

value: PneumaCult ALI

value: Air liquid interface culture on Transwells

value: iPSC-derived airway epithelium


title: Dessau1_TMZ_Gy4_2


title: Dessau1_1


title: monthly_1_1H

description: collected in Jan, warming, replicate 1

source_name: soil DNA, Jan, warming, replicate 1

tag: collection time

value: collected in Jan

tag: condition

value: warming

tag: replicate

value: replicate 1


title: RSEM_WT_2

tag: cell line

value: Liver

value: wild type


title: Dessau8_3


title: Jin-SN148-S1

value: without treatment


title: 6096055_TMZ_4Gy_2


title: 6096055_TMZ_4Gy_1


title: 6073997_1


title: 6096055_2


title: 6073997_TMZ_4Gy_2


title: 6073997_TMZ_4Gy_1


title: 6057638_TMZ_4Gy_1


title: 6096055_1


title: 6057638_2


title: 6045754_unbehandelt_2


title: 6045754_unbehandelt_1


title: 6045754_TMZ_4Gy_2


title: 6042791_unbehandelt_2


title: 6045754_TMZ_4Gy_1


title: 6057638_TMZ_4Gy_2


title: BU3 NGPT SARS-CoV-2 3 DPI replicate 3

source_name: BU3 NGPT SARS-CoV-2 3 DPI replicate 3

tag: media


title: Dessau1_2


title: 6042791_TMZ_4Gy_1


title: 6042240_unbehandelt_2


title: 6042240_unbehandelt_1


title: 6042791_TMZ_4Gy_2


title: 6042240_unbehandelt_3


title: 6042240_TMZ_4Gy_3


title: 6042240_TMZ_4Gy_2


title: 6042240_TMZ_4Gy_1


title: 6073997_2


title: 6032618_unbehandelt_2


title: 6057638_1


title: 6042791_unbehandelt_1


title: BU3 NGPT Mock 1 DPI replicate 2

source_name: BU3 NGPT Mock 1 DPI replicate 2

tag: culture format


title: Jin-SN148-MMS-S2

value: treated with MMS


title: 4703730_TMZ_4Gy_1

value: glioblastoma


title: 6032618_TMZ_4Gy_1

value: temozolomide + x-irradiation for 72 h


title: 4703730_TMZ_4Gy_2


title: 4872958_1


title: 4867112_TMZ_4Gy_1


title: 4703730_1


title: 6032618_unbehandelt_1


title: 4872958_TMZ_4Gy_2


title: 6022488_TMZ_4Gy_1


title: 4867112_1


title: 6022488_unbehandelt_1


title: 4896315_TMZ_4Gy_1


title: 4867112_TMZ_4Gy_2


title: 4896315_unbehandelt_1


title: 6032618_TMZ_4Gy_2


title: 4867112_2


title: 6022319_unbehandelt_1


title: 4872958_TMZ_4Gy_1


title: 4654857_unbehandelt_1


title: 4654857_unbehandelt_2


title: 4872958_TMZ_4Gy_3


title: 4872958_3


title: 4872958_2


title: 4703730_2


title: 4653324_2


title: 6022319_TMZ_4Gy_1


title: 6015889_unbehandelt_1


title: 6015889_TMZ_4Gy_1


title: 6008648_TMZ_4Gy_1


title: 4382548_TMZ_4Gy_1


title: 4405471_unbehandelt_1


title: 6008648_unbehandelt_1


title: 4405471_TMZ_4Gy_2


title: 4382548_1


title: 4580007_unbehandelt_2


title: 4580007_unbehandelt_3


title: 4382548_TMZ_4Gy_2


title: 4580007_TMZ_4Gy_3


title: 4453170_TMZ_4Gy_1


title: 4653324_1


title: 4382548_2


title: 4405471_unbehandelt_2


title: 4453170_TMZ_4Gy_2


title: 4340385_TMZ_4Gy_1


title: 4405471_TMZ_4Gy_1


title: 4453170_unbehandelt_1


title: 4340385_unbehandelt_1


title: 4580007_unbehandelt_1


title: 4653324_TMZ_4Gy_2


title: 4654857_TMZ_4Gy_1


title: 4653324_TMZ_4Gy_1


title: 4580007_TMZ_4Gy_1


title: 4654857_TMZ_4Gy_2


title: Patient 220

city: Toronto

first: Andrzej

last: Chruscinski

state: Ontario

address: 200 Elizabeth St.

country: Canada

institute: University Health Network

description:
Pre-immnosuppression withdrawal
T_220B

data_processing:
Adaptors were trimmed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) v. 0.5.0. Trim Galore is running Cutadapt (https://cutadapt.readthedocs.org/en/stable/) v. 1.10. Trim Galore is run with the following parameters: -q 25 – the reads are trimmed from the 3' end base by base, trimming stops if the quality of the base is greater than 25; --clip_R1 6, --clip_R2 6 – clip the first 6 nucleotides from the 5' ends of read 1 and read 2; --stringency 5 – at least 5 nucleotides overlap with the Illumina primer sequence are needed for trimming; --length 40 – any read that is shorter than 40 nucleotides as a result of trimming is discarded; --paired – only pairs of reads are retained (for paired-end reads only, not for single reads).
The raw trimmed reads are aligned to the reference genome (GRCh38, Gencode annotations, Release 36) using the STAR aligner, v.2.6.0c.
The filtered STAR alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2(HTSeq, http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Two-condition differential gene expression analysis was performed with DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html and http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html) v. 1.26.0s, using R v.3.6.1.  Initial minimal filtering of 10 read counts per gene for at least 3 samples was applied to the dataset.
Genome_build: GRCh38, Gencode annotations, Release 36.
Supplementary_files_format_and_content: tab-delimited text DESeq2 file including FPKM values for each sample

source_name: liver allograft

extract_protocol:
Liver biopsies were placed in RNA later (Qiagen) and RNA was isolated using the PureLink RNA minikit (Ambion). RNA library preparation was performed following the NEB NEBNext Ultra II Directional RNA Library Preparation protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: Non-Tolerant


title: Patient 203

description:
Pre-immnosuppression withdrawal
T_203B


title: 4453170_unbehandelt_2

tag: treatment


title: Patient 180

description:
Pre-immnosuppression withdrawal
B_T_180


title: Patient 181

description:
Pre-immnosuppression withdrawal
181B


title: Patient 210

description:
Pre-immnosuppression withdrawal
B_210T

value: Operatiionally Tolerant


title: Patient 208

description:
Pre-immnosuppression withdrawal
208T_B


title: Patient 266

description:
Pre-immnosuppression withdrawal
266T_B2


title: Patient 233

description:
Pre-immnosuppression withdrawal
233T_2B


title: Patient 184

description:
Pre-immnosuppression withdrawal
T_184B


title: Patient 243

description:
Pre-immnosuppression withdrawal
243T_B2


title: Patient 201

description:
Pre-immnosuppression withdrawal
B_201T


title: Patient 206

description:
Pre-immnosuppression withdrawal
T_206B


title: Patient 170

description:
Pre-immnosuppression withdrawal
B_T_170


title: Patient 229

description:
Pre-immnosuppression withdrawal
229B


title: 1092s_P1_S200_L002_

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
The Genome Analyzer Analysis Pipeline (Illumina, USA) was used to process the sequencing files of raw reads in the FASTQ format
Sequenced reads were trimmed for low-quality using Trimmomatic (default parameters)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 (default parameters)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq-count values for each Sample

extract_protocol:
Cells within chimeric heart slices were isolated by dissociation using 20 U/ml papain (Worthington Biochemical, USA). Single cells were collected using FACSAria III (Becton Dickinson)  into individual wells of 384-well plates containing Smart-Seq2 cell lysis buffer.
RNAseq libraries were prepared using compatible Tn5 and Nextera index primers (Illumina, USA) after complementary deoxyribonucleic acid (cDNA) synthesis using Smart-Seq2 protocol.

tag: cell type

value: hESC-derived cardiomyocytes

tag: time

value: D21 (without RFA)

tag: genotype

tag: age


title: 1092s_P8_S256_L002_


title: 1092s_P2_S208_L002_


title: 1092s_P13_S296_L002_


title: 1092s_P14_S304_L002_


title: 1092s_P6_S240_L002_


title: 1092s_P4_S224_L002_


title: 1092s_P18_S336_L002_


title: 1092s_P23_S376_L002_


title: 1092s_P7_S248_L002_


title: Patient 268

description:
Pre-immnosuppression withdrawal
268T_B2


title: Patient 178

description:
Pre-immnosuppression withdrawal
B_178T


title: 1092s_P11_S280_L002_


title: 1092s_P10_S272_L002_


title: 1092s_P12_S288_L002_


title: 1092s_O9_S72_L002_


title: 1092s_P24_S384_L002_


title: 1092s_P15_S312_L002_


title: 1092s_O6_S48_L002_


title: 1092s_O8_S64_L002_


title: 1092s_O5_S40_L002_


title: 1092s_O20_S160_L002_


title: 1092s_O22_S176_L002_


title: 1092s_O3_S24_L002_


title: 1092s_O21_S168_L002_


title: 1092s_O2_S16_L002_


title: Patient 224

description:
Pre-immnosuppression withdrawal
B_T_224


title: 1092s_O17_S136_L002_


title: 1092s_O18_S144_L002_


title: 1092s_O16_S128_L002_


title: 1092s_O15_S120_L002_


title: 1092s_O7_S56_L002_


title: 1092s_O14_S112_L002_


title: 1092s_N9_S263_L002_


title: 1092s_O11_S88_L002_


title: 1092s_O12_S96_L002_


title: 1092s_N7_S247_L002_


title: 1092s_O10_S80_L002_


title: 1092s_N6_S239_L002_


title: 1092s_N3_S215_L002_


title: 1092s_N4_S223_L002_


title: 1092s_O13_S104_L002_


title: 1092s_O19_S152_L002_


title: 1092s_O1_S8_L002_


title: 1092s_N5_S231_L002_


title: 1092s_N16_S319_L002_


title: 1092s_N15_S311_L002_


title: 1092s_N14_S303_L002_


title: 1092s_N20_S351_L002_


title: 1092s_N1_S199_L002_


title: 1092s_N19_S343_L002_


title: 1092s_N22_S367_L002_


title: 1092s_N23_S375_L002_


title: 1092s_N12_S287_L002_


title: 1092s_N13_S295_L002_


title: 1092s_N11_S279_L002_


title: 1092s_N10_S271_L002_


title: 1092s_N2_S207_L002_


title: 1092s_M8_S63_L002_


title: 1092s_N21_S359_L002_


title: 1092s_M2_S15_L002_


title: 1092s_M6_S47_L002_


title: 1092s_M24_S191_L002_


title: 1092s_M7_S55_L002_


title: 1092s_M3_S23_L002_


title: 1092s_N18_S335_L002_


title: 1092s_M5_S39_L002_


title: 1092s_M18_S143_L002_


title: 1092s_M19_S151_L002_


title: 1092s_M17_S135_L002_


title: 1092s_M1_S7_L002_


title: 1092s_N17_S327_L002_


title: 1092s_M16_S127_L002_


title: 1092s_M11_S87_L002_


title: 1092s_M12_S95_L002_


title: 1092s_M14_S111_L002_


title: 1092s_M10_S79_L002_


title: 1092s_L8_S254_L002_


title: 1092s_L7_S246_L002_


title: 1092s_L9_S262_L002_


title: 1092s_M13_S103_L002_


title: 1092s_L3_S214_L002_


title: 1092s_M20_S159_L002_


title: 1092s_M22_S175_L002_


title: 1092s_L2_S206_L002_


title: 1092s_L6_S238_L002_


title: 1092s_L19_S342_L002_


title: 1092s_L22_S366_L002_


title: 1092s_L23_S374_L002_


title: 1092s_L18_S334_L002_


title: 1092s_L15_S310_L002_


title: 1092s_L16_S318_L002_


title: 1092s_M15_S119_L002_


title: 1092s_L1_S198_L002_


title: 1092s_L11_S278_L002_


title: 1092s_L17_S326_L002_


title: 1092s_L14_S302_L002_


title: 1092s_L12_S286_L002_


title: 1092s_K4_S30_L002_


title: 1092s_K7_S54_L002_


title: 1092s_K3_S22_L002_


title: 1092s_K24_S190_L002_


title: 1092s_K6_S46_L002_


title: 1092s_K5_S38_L002_


title: 1092s_K21_S166_L002_


title: 1092s_K1_S6_L002_


title: 1092s_K19_S150_L002_


title: 1092s_K16_S126_L002_


title: 1092s_K12_S94_L002_


title: 1092s_L21_S358_L002_


title: 1092s_K18_S142_L002_


title: 1092s_K23_S182_L002_


title: 1092s_K10_S78_L002_


title: 1092s_L13_S294_L002_


title: 1092s_J9_S261_L002_


title: 1092s_J8_S253_L002_


title: 1092s_K20_S158_L002_


title: 1092s_K9_S70_L002_


title: 1092s_K22_S174_L002_


title: 1092s_K17_S134_L002_


title: 1092s_J6_S237_L002_


title: 1092s_J5_S229_L002_


title: 1092s_J7_S245_L002_


title: 1092s_K2_S14_L002_


title: 1092s_J3_S213_L002_


title: 1092s_J22_S365_L002_


title: 1092s_J1_S197_L002_


title: 1092s_J19_S341_L002_


title: 1092s_J24_S381_L002_


title: 1092s_J21_S357_L002_


title: 1092s_J18_S333_L002_


title: 1092s_J15_S309_L002_


title: 1092s_J16_S317_L002_


title: 1092s_J14_S301_L002_


title: 1092s_J10_S269_L002_


title: 1092s_J17_S325_L002_


title: 1092s_I9_S69_L002_


title: 1092s_I5_S37_L002_


title: 1092s_I3_S21_L002_


title: 1092s_I4_S29_L002_


title: 1092s_I6_S45_L002_


title: 1092s_I8_S61_L002_


title: 1092s_I2_S13_L002_


title: 1092s_I24_S189_L002_


title: 1092s_I23_S181_L002_


title: 1092s_I20_S157_L002_


title: 1092s_I1_S5_L002_


title: 1092s_I19_S149_L002_


title: 1092s_I17_S133_L002_


title: 1092s_I18_S141_L002_


title: 1092s_I14_S109_L002_


title: 1092s_I21_S165_L002_


title: 1092s_I13_S101_L002_


title: 1092s_I11_S85_L002_


title: 1092s_J11_S277_L002_


title: 1092s_I16_S125_L002_


title: 1092s_I10_S77_L002_


title: 1092s_H9_S260_L002_


title: 1092s_I7_S53_L002_


title: 1092s_H24_S380_L002_


title: 1092s_H8_S252_L002_


title: 1092s_H2_S204_L002_


title: 1092s_H21_S356_L002_


title: 1092s_H1_S196_L002_


title: 1092s_H22_S364_L002_


title: 1092s_H17_S324_L002_


title: 1092s_H19_S340_L002_


title: 1092s_H18_S332_L002_


title: 1092s_H16_S316_L002_


title: 1092s_H15_S308_L002_


title: 1092s_H13_S292_L002_


title: 1092s_I15_S117_L002_


title: 1092s_H11_S276_L002_


title: 1092s_H10_S268_L002_


title: 1092s_G8_S60_L002_


title: 1092s_G9_S68_L002_


title: 1092s_G7_S52_L002_


title: 1092s_G6_S44_L002_


title: 1092s_H12_S284_L002_


title: 1092s_G5_S36_L002_


title: 1092s_G23_S180_L002_


title: 1092s_G4_S28_L002_


title: 1092s_H4_S220_L002_


title: 1092s_G21_S164_L002_


title: 1092s_G1_S4_L002_


title: 1092s_G2_S12_L002_


title: 1092s_G13_S100_L002_


title: 1092s_G19_S148_L002_


title: 1092s_G14_S108_L002_


title: 1092s_G10_S76_L002_


title: 1092s_G12_S92_L002_


title: 1092s_F6_S235_L002_


title: 1092s_F9_S259_L002_


title: 1092s_F7_S243_L002_


title: 1092s_F8_S251_L002_


title: 1092s_F5_S227_L002_


title: 1092s_F4_S219_L002_


title: 1092s_F3_S211_L002_


title: 1092s_F1_S195_L002_


title: 1092s_F21_S355_L002_


title: 1092s_F20_S347_L002_


title: 1092s_F18_S331_L002_


title: 1092s_F19_S339_L002_


title: 1092s_F2_S203_L002_


title: 1092s_F17_S323_L002_


title: 1092s_F14_S299_L002_


title: 1092s_F12_S283_L002_


title: 1092s_F11_S275_L002_


title: 1092s_F15_S307_L002_


title: 1092s_E7_S51_L002_


title: 1092s_E3_S19_L002_


title: 1092s_E4_S27_L002_


title: 1092s_F10_S267_L002_


title: 1092s_E5_S35_L002_


title: 1092s_E2_S11_L002_


title: 1092s_E6_S43_L002_


title: 1092s_E20_S155_L002_


title: 1092s_E21_S163_L002_


title: 1092s_E24_S187_L002_


title: 1092s_F22_S363_L002_


title: 1092s_F13_S291_L002_


title: 1092s_E19_S147_L002_


title: 1092s_E1_S3_L002_


title: 1092s_E23_S179_L002_


title: 1092s_E16_S123_L002_


title: 1092s_E14_S107_L002_


title: 1092s_E18_S139_L002_


title: 1092s_E12_S91_L002_


title: 1092s_E13_S99_L002_


title: 1092s_E11_S83_L002_


title: 1092s_D9_S258_L002_


title: 1092s_D7_S242_L002_


title: 1092s_M4_S31_L002_


title: 1092s_D6_S234_L002_


title: 1092s_D3_S210_L002_


title: 1092s_E22_S171_L002_


title: 1092s_D5_S226_L002_


title: 1092s_D2_S202_L002_


title: 1092s_D23_S370_L002_


title: 1092s_D22_S362_L002_


title: 1092s_D4_S218_L002_


title: 1092s_D1_S194_L002_


title: 1092s_D19_S338_L002_


title: 1092s_D18_S330_L002_


title: 1092s_D15_S306_L002_


title: 1092s_D12_S282_L002_


title: 1092s_D10_S266_L002_


title: 1092s_D14_S298_L002_


title: 1092s_D17_S322_L002_


title: 1092s_E17_S131_L002_


title: 1092s_C9_S66_L002_


title: 1092s_C6_S42_L002_


title: 1092s_C5_S34_L002_


title: 1092s_C7_S50_L002_


title: 1092s_C2_S10_L002_


title: 1092s_D24_S378_L002_


title: 1092s_C3_S18_L002_


title: 1092s_C21_S162_L002_


title: 1092s_C24_S186_L002_


title: 1092s_C1_S2_L002_


title: 1092s_C22_S170_L002_


title: 1092s_C16_S122_L002_


title: 1092s_D16_S314_L002_


title: 1092s_C12_S90_L002_


title: 1092s_C20_S154_L002_


title: 1092s_C19_S146_L002_


title: 1092s_C18_S138_L002_


title: 1092s_C10_S74_L002_


title: 1092s_B9_S257_L002_


title: 1092s_C15_S114_L002_


title: 1092s_C23_S178_L002_


title: 1092s_C13_S98_L002_


title: 1092s_B7_S241_L002_


title: 1092s_C11_S82_L002_


title: 1092s_B8_S249_L002_


title: 1092s_B5_S225_L002_


title: 1092s_B24_S377_L002_


title: 1092s_B3_S209_L002_


title: 1092s_B4_S217_L002_


title: 1092s_B2_S201_L002_


title: 1092s_C4_S26_L002_


title: 1092s_B16_S313_L002_


title: 1092s_B10_S265_L002_


title: 1092s_B19_S337_L002_


title: 1092s_B18_S329_L002_


title: 1092s_B13_S289_L002_


title: 1092s_B1_S193_L002_


title: 1092s_B17_S321_L002_


title: 1092s_B14_S297_L002_


title: 1092s_A4_S25_L002_


title: 1092s_B23_S369_L002_


title: 1092s_B11_S273_L002_


title: 1092s_A8_S57_L002_


title: 1092s_A7_S49_L002_


title: 1092s_A20_S153_L002_


title: 1092s_B12_S281_L002_


title: 1092s_B15_S305_L002_


title: 1092s_A6_S41_L002_


title: 1092s_A5_S33_L002_


title: 1092s_A14_S105_L002_


title: 1092s_A13_S97_L002_


title: 1092s_A17_S129_L002_


title: 1092s_A3_S17_L002_


title: 1092s_A19_S145_L002_


title: 1092s_A15_S113_L002_


title: 822s_P9_S264_L005_

value: hESC-derived ventricular progenitors

value: D0 (without RFA)


title: 1092s_A2_S9_L002_


title: 822s_P8_S256_L005_


title: 822s_P7_S248_L005_


title: 1092s_A12_S89_L002_


title: 1092s_A23_S177_L002_


title: 1092s_A18_S137_L002_


title: 1092s_A11_S81_L002_


title: 1092s_A10_S73_L002_


title: 1092s_A22_S169_L002_


title: 822s_P6_S240_L005_


title: 1092s_L4_S222_L002_


title: 1092s_E10_S75_L002_


title: 822s_P3_S216_L005_


title: 822s_P5_S232_L005_


title: 822s_P19_S344_L005_


title: 822s_P20_S352_L005_


title: 822s_P2_S208_L005_


title: 822s_P16_S320_L005_


title: 822s_P24_S384_L005_


title: 822s_P18_S336_L005_


title: 822s_P1_S200_L005_


title: 822s_P23_S376_L005_


title: 822s_P10_S272_L005_


title: 822s_P12_S288_L005_


title: 822s_P15_S312_L005_


title: 822s_P11_S280_L005_


title: 822s_O6_S48_L005_


title: 822s_O9_S72_L005_


title: 822s_O8_S64_L005_


title: 822s_P13_S296_L005_


title: 822s_P22_S368_L005_


title: 822s_P21_S360_L005_


title: 822s_O4_S32_L005_


title: 822s_O2_S16_L005_


title: 822s_O3_S24_L005_


title: 822s_P17_S328_L005_


title: 822s_O7_S56_L005_


title: 822s_O23_S184_L005_


title: 822s_O18_S144_L005_


title: 822s_O17_S136_L005_


title: 822s_O16_S128_L005_


title: 822s_O24_S192_L005_


title: 822s_O21_S168_L005_


title: 822s_O19_S152_L005_


title: 822s_O15_S120_L005_


title: 822s_O1_S8_L005_


title: 822s_O12_S96_L005_


title: 822s_O10_S80_L005_


title: 822s_N9_S263_L005_


title: 822s_O11_S88_L005_


title: 822s_N5_S231_L005_


title: 822s_N4_S223_L005_


title: 822s_N3_S215_L005_


title: 822s_N23_S375_L005_


title: 822s_N24_S383_L005_


title: 822s_N22_S367_L005_


title: 822s_N7_S247_L005_


title: 822s_N2_S207_L005_


title: 822s_O14_S112_L005_


title: 822s_N1_S199_L005_


title: 822s_N20_S351_L005_


title: 822s_N21_S359_L005_


title: 822s_O13_S104_L005_


title: 822s_N19_S343_L005_


title: 822s_N17_S327_L005_


title: 822s_N14_S303_L005_


title: 822s_N12_S287_L005_


title: 822s_N8_S255_L005_


title: 822s_N16_S319_L005_


title: 822s_N13_S295_L005_


title: 822s_N10_S271_L005_


title: 822s_M21_S167_L005_


title: 822s_M4_S31_L005_


title: 822s_M3_S23_L005_


title: 822s_M8_S63_L005_


title: 822s_N18_S335_L005_


title: 822s_M2_S15_L005_


title: 822s_M23_S183_L005_


title: 822s_M1_S7_L005_


title: 822s_M19_S151_L005_


title: 822s_M14_S111_L005_


title: 822s_M15_S119_L005_


title: 822s_M18_S143_L005_


title: 822s_M16_S127_L005_


title: 822s_M13_S103_L005_


title: 822s_M17_S135_L005_


title: 822s_M12_S95_L005_


title: 822s_N15_S311_L005_


title: 822s_N11_S279_L005_


title: 822s_L7_S246_L005_


title: 822s_M11_S87_L005_


title: 822s_M10_S79_L005_


title: 822s_M6_S47_L005_


title: 822s_M22_S175_L005_


title: 822s_M7_S55_L005_


title: 822s_L6_S238_L005_


title: 822s_L4_S222_L005_


title: 822s_L5_S230_L005_


title: 822s_L18_S334_L005_


title: 822s_L20_S350_L005_


title: 822s_L24_S382_L005_


title: 822s_L9_S262_L005_


title: 822s_L22_S366_L005_


title: 822s_L15_S310_L005_


title: 822s_L2_S206_L005_


title: 822s_L16_S318_L005_


title: 822s_L21_S358_L005_


title: 822s_L19_S342_L005_


title: 1092s_B20_S345_L002_


title: 822s_L14_S302_L005_


title: 822s_L12_S286_L005_


title: 822s_L3_S214_L005_


title: 822s_K8_S62_L005_


title: 822s_K4_S30_L005_


title: 822s_K5_S38_L005_


title: 822s_K7_S54_L005_


title: 822s_K24_S190_L005_


title: 822s_K2_S14_L005_


title: 1092s_B21_S353_L002_


title: 822s_K22_S174_L005_


title: 822s_L23_S374_L005_


title: 822s_K21_S166_L005_


title: 1092s_C14_S106_L002_


title: 822s_K1_S6_L005_


title: 822s_K9_S70_L005_


title: 822s_K16_S126_L005_


title: 822s_K12_S94_L005_


title: 822s_K14_S110_L005_


title: 822s_K19_S150_L005_


title: 822s_J9_S261_L005_


title: 822s_K15_S118_L005_


title: 822s_J7_S245_L005_


title: 822s_K11_S86_L005_


title: 822s_K18_S142_L005_


title: 822s_K17_S134_L005_


title: 822s_K10_S78_L005_


title: 822s_J5_S229_L005_


title: 822s_K20_S158_L005_


title: 822s_J6_S237_L005_


title: 822s_J23_S373_L005_


title: 822s_J21_S357_L005_


title: 822s_J22_S365_L005_


title: 822s_J18_S333_L005_


title: 822s_J19_S341_L005_


title: 822s_J4_S221_L005_


title: 822s_J16_S317_L005_


title: 822s_J20_S349_L005_


title: 822s_J3_S213_L005_


title: 822s_J2_S205_L005_


title: 822s_J1_S197_L005_


title: 822s_J17_S325_L005_


title: 822s_J14_S301_L005_


title: 822s_J15_S309_L005_


title: 822s_J8_S253_L005_


title: 822s_I22_S173_L005_


title: 822s_I9_S69_L005_


title: 822s_I6_S45_L005_


title: 822s_I8_S61_L005_


title: 822s_I2_S13_L005_


title: 822s_J12_S285_L005_


title: 822s_J13_S293_L005_


title: 822s_I20_S157_L005_


title: 822s_J11_S277_L005_


title: 822s_I23_S181_L005_


title: 822s_I21_S165_L005_


title: 822s_I15_S117_L005_


title: 822s_I4_S29_L005_


title: 822s_I17_S133_L005_


title: 822s_I14_S109_L005_


title: 822s_I3_S21_L005_


title: 822s_I18_S141_L005_


title: 822s_I5_S37_L005_


title: 822s_I19_S149_L005_


title: 822s_I13_S101_L005_


title: 822s_H9_S260_L005_


title: 822s_H6_S236_L005_


title: 822s_I12_S93_L005_


title: 822s_I10_S77_L005_


title: 822s_H24_S380_L005_


title: 822s_I11_S85_L005_


title: 822s_H8_S252_L005_


title: 822s_H3_S212_L005_


title: 822s_H2_S204_L005_


title: 822s_H23_S372_L005_


title: 822s_H1_S196_L005_


title: 822s_G8_S60_L005_


title: 822s_H22_S364_L005_


title: 822s_H10_S268_L005_


title: 822s_H12_S284_L005_


title: 822s_H21_S356_L005_


title: 822s_H11_S276_L005_


title: 822s_G7_S52_L005_


title: 822s_H20_S348_L005_


title: 822s_G4_S28_L005_


title: 822s_H17_S324_L005_


title: 822s_H18_S332_L005_


title: 822s_G23_S180_L005_


title: 822s_H15_S308_L005_


title: 822s_H13_S292_L005_


title: 822s_G6_S44_L005_


title: 822s_G5_S36_L005_


title: 822s_G3_S20_L005_


title: 822s_G16_S124_L005_


title: 822s_G24_S188_L005_


title: 822s_G15_S116_L005_


title: 822s_G22_S172_L005_


title: 822s_G21_S164_L005_


title: 822s_G20_S156_L005_


title: 822s_F9_S259_L005_


title: 822s_G19_S148_L005_


title: 822s_G12_S92_L005_


title: 822s_F7_S243_L005_


title: 822s_G1_S4_L005_


title: 822s_G13_S100_L005_


title: 822s_F6_S235_L005_


title: 822s_F2_S203_L005_


title: 822s_F5_S227_L005_


title: 822s_G17_S132_L005_


title: 822s_F3_S211_L005_


title: 822s_F23_S371_L005_


title: 822s_F17_S323_L005_


title: 822s_G11_S84_L005_


title: 822s_F18_S331_L005_


title: 822s_F8_S251_L005_


title: 822s_G2_S12_L005_


title: 822s_G14_S108_L005_


title: 822s_F12_S283_L005_


title: 822s_F4_S219_L005_


title: 822s_F21_S355_L005_


title: 822s_F1_S195_L005_


title: 822s_F10_S267_L005_


title: 822s_E6_S43_L005_


title: 822s_E8_S59_L005_


title: 822s_E3_S19_L005_


title: 822s_E24_S187_L005_


title: 822s_F11_S275_L005_


title: 822s_E23_S179_L005_


title: 822s_E22_S171_L005_


title: 822s_F15_S307_L005_


title: 822s_E20_S155_L005_


title: 822s_F13_S291_L005_


title: 822s_E4_S27_L005_


title: 822s_E18_S139_L005_


title: 822s_E19_S147_L005_


title: 822s_E7_S51_L005_


title: 822s_E1_S3_L005_


title: 822s_E17_S131_L005_


title: 822s_E21_S163_L005_


title: 822s_E14_S107_L005_


title: 822s_E2_S11_L005_


title: 822s_D7_S242_L005_


title: 822s_E16_S123_L005_


title: 822s_E12_S91_L005_


title: 822s_D9_S258_L005_


title: 822s_D4_S218_L005_


title: 822s_D3_S210_L005_


title: 822s_D2_S202_L005_


title: 822s_D8_S250_L005_


title: 822s_D6_S234_L005_


title: 822s_D24_S378_L005_


title: 822s_D18_S330_L005_


title: 822s_D19_S338_L005_


title: 822s_D5_S226_L005_


title: 822s_D23_S370_L005_


title: 822s_D21_S354_L005_


title: 822s_D14_S298_L005_


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title: 822s_D13_S290_L005_


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title: 822s_C7_S50_L005_


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title: 822s_C2_S10_L005_


title: 822s_C4_S26_L005_


title: 822s_C5_S34_L005_


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title: 1092s_G22_S172_L002_


title: 822s_C1_S2_L005_


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title: 822s_B24_S377_L005_


title: 822s_B2_S201_L005_


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title: 822s_B19_S337_L005_


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title: 820s_E6_S43_L003_


title: 820s_E7_S51_L003_


title: 820s_E4_S27_L003_


title: 820s_E8_S59_L003_


title: 820s_E5_S35_L003_


title: 820s_E2_S11_L003_


title: 820s_F11_S275_L003_


title: 820s_E22_S171_L003_


title: 820s_E24_S187_L003_


title: 820s_F19_S339_L003_


title: 820s_E9_S67_L003_


title: 820s_E21_S163_L003_


title: 820s_E23_S179_L003_


title: 820s_E3_S19_L003_


title: 820s_E15_S115_L003_


title: 820s_E19_S147_L003_


title: 820s_E18_S139_L003_


title: 820s_E16_S123_L003_


title: 820s_E1_S3_L003_


title: 820s_E20_S155_L003_


title: 820s_E14_S107_L003_


title: 820s_E13_S99_L003_


title: 820s_E12_S91_L003_


title: 820s_E11_S83_L003_


title: 820s_D9_S258_L003_


title: 820s_E10_S75_L003_


title: 820s_D7_S242_L003_


title: 820s_D4_S218_L003_


title: 820s_D5_S226_L003_


title: 820s_D1_S194_L003_


title: 820s_D21_S354_L003_


title: 820s_D17_S322_L003_


title: 820s_D23_S370_L003_


title: 820s_D24_S378_L003_


title: 820s_D18_S330_L003_


title: 820s_D2_S202_L003_


title: 820s_E17_S131_L003_


title: 820s_D14_S298_L003_


title: 820s_D20_S346_L003_


title: 820s_D11_S274_L003_


title: 820s_C5_S34_L003_


title: 820s_C7_S50_L003_


title: 820s_D16_S314_L003_


title: 820s_D10_S266_L003_


title: 820s_D13_S290_L003_


title: 820s_C9_S66_L003_


title: 820s_D12_S282_L003_


title: 820s_C8_S58_L003_


title: 820s_C6_S42_L003_


title: 820s_C22_S170_L003_


title: 820s_C23_S178_L003_


title: 820s_C21_S162_L003_


title: 820s_C2_S10_L003_


title: 820s_C1_S2_L003_


title: 820s_C4_S26_L003_


title: 820s_D3_S210_L003_


title: 820s_C19_S146_L003_


title: 820s_C18_S138_L003_


title: 820s_C15_S114_L003_


title: 820s_C17_S130_L003_


title: 820s_C16_S122_L003_


title: 820s_C13_S98_L003_


title: 820s_C12_S90_L003_


title: 820s_B6_S233_L003_


title: 820s_B8_S249_L003_


title: 820s_B3_S209_L003_


title: 820s_B4_S217_L003_


title: 820s_B5_S225_L003_


title: 820s_C10_S74_L003_


title: 820s_C11_S82_L003_


title: 820s_B23_S369_L003_


title: 820s_C3_S18_L003_


title: 820s_B22_S361_L003_


title: 820s_B7_S241_L003_


title: 820s_B2_S201_L003_


title: 820s_B21_S353_L003_


title: 820s_B20_S345_L003_


title: 820s_B19_S337_L003_


title: 820s_B1_S193_L003_


title: 820s_B17_S321_L003_


title: 820s_B15_S305_L003_


title: 820s_B14_S297_L003_


title: 820s_B13_S289_L003_


title: 820s_B11_S273_L003_


title: 820s_B12_S281_L003_


title: 820s_C14_S106_L003_


title: 820s_A8_S57_L003_


title: 820s_B24_S377_L003_


title: 820s_A6_S41_L003_


title: 820s_A4_S25_L003_


title: 820s_A20_S153_L003_


title: 820s_A23_S177_L003_


title: 820s_A3_S17_L003_


title: 820s_A19_S145_L003_


title: 820s_A21_S161_L003_


title: 820s_A1_S1_L003_


title: 820s_A22_S169_L003_


title: 820s_A17_S129_L003_


title: 820s_A16_S121_L003_


title: 820s_B16_S313_L003_


title: 820s_A15_S113_L003_


title: 820s_A12_S89_L003_


title: 820s_A11_S81_L003_


title: 820s_A10_S73_L003_


title: 820s_B10_S265_L003_


title: 461s_G7_S151_L008_

value: 24h after RFA injury


title: 820s_A13_S97_L003_


title: 461s_G8_S152_L008_


title: 820s_A9_S65_L003_


title: 461s_G6_S150_L008_


title: 461s_G5_S149_L008_


title: 820s_A7_S49_L003_


title: 820s_A5_S33_L003_


title: 820s_A2_S9_L003_


title: 461s_G4_S148_L008_


title: 820s_A24_S185_L003_


title: 461s_G9_S153_L008_


title: 820s_A18_S137_L003_


title: 461s_G2_S146_L008_


title: 820s_A14_S105_L003_


title: 461s_G23_S167_L008_


title: 461s_G20_S164_L008_


title: 461s_G18_S162_L008_


title: 461s_G24_S168_L008_


title: 461s_G1_S145_L008_


title: 461s_G17_S161_L008_


title: 461s_G22_S166_L008_


title: 461s_G15_S159_L008_


title: 461s_G12_S156_L008_


title: 461s_G13_S157_L008_


title: 461s_G11_S155_L008_


title: 461s_F7_S127_L008_


title: 461s_F6_S126_L008_


title: 461s_F23_S143_L008_


title: 461s_F22_S142_L008_


title: 461s_F4_S124_L008_


title: 461s_F8_S128_L008_


title: 461s_G3_S147_L008_


title: 461s_F20_S140_L008_


title: 461s_F5_S125_L008_


title: 461s_F9_S129_L008_


title: 461s_F3_S123_L008_


title: 461s_F2_S122_L008_


title: 461s_G19_S163_L008_


title: 461s_G21_S165_L008_


title: 461s_F1_S121_L008_


title: 461s_F21_S141_L008_


title: 461s_F16_S136_L008_


title: 461s_F12_S132_L008_


title: 461s_F14_S134_L008_


title: 461s_F11_S131_L008_


title: 461s_F15_S135_L008_


title: 461s_F10_S130_L008_


title: 461s_F19_S139_L008_


title: 461s_E8_S104_L008_


title: 461s_E6_S102_L008_


title: 461s_E9_S105_L008_


title: 461s_E3_S99_L008_


title: 461s_E2_S98_L008_


title: 461s_E4_S100_L008_


title: 461s_E15_S111_L008_


title: 461s_E23_S119_L008_


title: 461s_E20_S116_L008_


title: 461s_E18_S114_L008_


title: 461s_E14_S110_L008_


title: 461s_E21_S117_L008_


title: 461s_E11_S107_L008_


title: 461s_E24_S120_L008_


title: 461s_E16_S112_L008_


title: 461s_D9_S81_L008_


title: 461s_E12_S108_L008_


title: 461s_E17_S113_L008_


title: 461s_E10_S106_L008_


title: 461s_D8_S80_L008_


title: 461s_F13_S133_L008_


title: 461s_D22_S94_L008_


title: 461s_D23_S95_L008_


title: 461s_D20_S92_L008_


title: 461s_D3_S75_L008_


title: 461s_D2_S74_L008_


title: 461s_D19_S91_L008_


title: 461s_D1_S73_L008_


title: 461s_D18_S90_L008_


title: 461s_E1_S97_L008_


title: 461s_D14_S86_L008_


title: 461s_D16_S88_L008_


title: 461s_D13_S85_L008_


title: 461s_D6_S78_L008_


title: 461s_D12_S84_L008_


title: 461s_D11_S83_L008_


title: 461s_D10_S82_L008_


title: 461s_C9_S57_L008_


title: 461s_C7_S55_L008_


title: 461s_C6_S54_L008_


title: 461s_C8_S56_L008_


title: 461s_C4_S52_L008_


title: 461s_C5_S53_L008_


title: 461s_C2_S50_L008_


title: 461s_C3_S51_L008_


title: 461s_C23_S71_L008_


title: 461s_D21_S93_L008_


title: 461s_C24_S72_L008_


title: 461s_C22_S70_L008_


title: 461s_C18_S66_L008_


title: 461s_C21_S69_L008_


title: 461s_C17_S65_L008_


title: 461s_C13_S61_L008_


title: 461s_C16_S64_L008_


title: 461s_C12_S60_L008_


title: 461s_C1_S49_L008_


title: 461s_C14_S62_L008_


title: 461s_C10_S58_L008_


title: 461s_C11_S59_L008_


title: 461s_B9_S33_L008_


title: 461s_B8_S32_L008_


title: 461s_B7_S31_L008_


title: 461s_B6_S30_L008_


title: 461s_B5_S29_L008_


title: 461s_B23_S47_L008_


title: 461s_B24_S48_L008_


title: 461s_B21_S45_L008_


title: 461s_B20_S44_L008_


title: 461s_B16_S40_L008_


title: 461s_B17_S41_L008_


title: 461s_B18_S42_L008_


title: 461s_B19_S43_L008_


title: 461s_B15_S39_L008_


title: 461s_B12_S36_L008_


title: 461s_B11_S35_L008_


title: 461s_B13_S37_L008_


title: 461s_A5_S5_L008_


title: 461s_A9_S9_L008_


title: 461s_A8_S8_L008_


title: 461s_B10_S34_L008_


title: 461s_A2_S2_L008_


title: 461s_A24_S24_L008_


title: 461s_A7_S7_L008_


title: 461s_B4_S28_L008_


title: 461s_A20_S20_L008_


title: 461s_A1_S1_L008_


title: 461s_A21_S21_L008_


title: 461s_A19_S19_L008_


title: 461s_A18_S18_L008_


title: 461s_A13_S13_L008_


title: Sample_721_AR31_palm_dermis

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
data processing including quality control, read alignment and gene quantification were conducted using the 10X Cell Ranger software
Seurat was then used for normalization, data integration, and clustering analysis
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: 10X readcount

source_name: skin biopsy

extract_protocol:
Skin was harvested via punch biopsy
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. scRNA-seq was performed by the University of Michigan Advanced Genomics Core on the 10 Chromium system. Libraries were sequencing on the Illumina NextSeq sequencer.

tag: tissue type

value: Dermis

tag: tissue

value: Palm


title: Sample_721_AR31_palm_epi

value: Epidermis


title: 461s_A10_S10_L008_


title: 461s_A14_S14_L008_


title: 461s_A17_S17_L008_


title: Sample_721_AR31_hip_epi

value: Hip


title: 461s_A12_S12_L008_


title: 459s_L8_S272_L006_


title: 459s_L6_S270_L006_


title: 461s_A23_S23_L008_


title: 461s_A22_S22_L008_


title: HEK293T-FH-Ago2 siTRMT6/61A a-FLAG TGIRT small RNA rep3

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

description: size fractionation

data_processing: Adaptor is removed by cutadapt v1.15 (--nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 15). Reads are mapped to human sequence of miRBase Release 22, then to other small RNA sequences including genomic tRNA database, Ensembl Release 97 and SILVA rRNA database Release 132 by unitas v1.7.3 (–species_miR_only –species homo_sapiens).

source_name: HEK293T-FH-Ago2 siTRMT6/61A a-FLAG RNA

growth_protocol: Cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles medium with L-glutamine (GE #SH30081.01) plus 10% fetal bovine serum (Gibco #10437028) and 1% penicillin/streptomycin (Gibco #15140122).

extract_protocol:
Ago2 RIP was performed in stable FH-Ago2 HEK293T cells. Briefly, 1E7 cells were collected by scraping and washed with DPBS, before lysis in RIP buffer (50 mM Tris-HCl, pH 7.4, 150 mM KCl, 0.5% NP-40 substitute, 0.5 mM DTT, 100X proteinase inhibitor, RNase inhibitor). Cleared lysates were incubated at 4°C for 1 hr with M2 FLAG affinity gel (Sigma #A2220) or anti-MYC mouse antibody 9E10 conjugated on beads as a negative control. After washes, bound RNAs are eluted by Trizol extraction and ethanol precipitation.
Small RNA-seq library preparation was performed using NEBNext Small RNA Library Prep Set for Illumina (NEB #7330) with modification to use TGIRT-III RT enzyme (InGex). The resulting amplified libraries were size selected on 8% TBE polyacrylamide gel to enrich for insert of 15-50 nucleotides long RNA.

treatment_protocol: 10 nM final total concentration of siRNA (Dharmacon ON-TARGETplus, TRMT6: #L-017324-02-0005, TRMT61A: #L-015870-01-0005) was transfected twice with Lipofectamine RNAiMax (Thermo Fisher #13778150) and collected 96 hrs post first transfection (48 hrs post second transfection). Non-targeting control siRNA (Dharmacon #D-001810-10-20) was used as negative control.

value: siTRMT6/61A a-FLAG


title: Sample_721_AR31_hip_dermis


title: 459s_L9_S273_L006_


title: 459s_L24_S288_L006_


title: HEK293T-FH-Ago2 siCtrl a-FLAG TGIRT small RNA rep3

description: size fractionation

source_name: HEK293T-FH-Ago2 siCtrl a-FLAG RNA

value: siCtrl a-FLAG


title: HEK293T-FH-Ago2 siTRMT6/61A Input TGIRT small RNA rep3

description: size fractionation

source_name: HEK293T-FH-Ago2 siTRMT6/61A Input RNA

value: siTRMT6/61A Input


title: 459s_L21_S285_L006_


title: HEK293T-FH-Ago2 siTRMT6/61A a-FLAG TGIRT small RNA rep2

description: size fractionation


title: 459s_L22_S286_L006_


title: 459s_L23_S287_L006_


title: HEK293T-FH-Ago2 siCtrl Input TGIRT small RNA rep3

description: size fractionation

source_name: HEK293T-FH-Ago2 siCtrl Input RNA

value: siCtrl Input


title: HEK293T-FH-Ago2 siCtrl a-FLAG TGIRT small RNA rep2

description: size fractionation


title: 459s_L7_S271_L006_


title: HEK293T-FH-Ago2 siCtrl Input TGIRT small RNA rep2

description: size fractionation


title: HEK293T-FH-Ago2 siTRMT6/61A Input TGIRT small RNA rep2

description: size fractionation


title: HEK293T-FH-Ago2 siCtrl a-FLAG TGIRT small RNA rep1

description: size fractionation


title: 459s_L19_S283_L006_


title: 459s_L18_S282_L006_


title: 459s_L16_S280_L006_


title: 459s_L15_S279_L006_


title: HEK293T-FH-Ago2 siTRMT6/61A a-FLAG TGIRT small RNA rep1

description: size fractionation


title: 459s_L14_S278_L006_


title: HEK293T-FH-Ago2 siTRMT6/61A Input TGIRT small RNA rep1

description: size fractionation


title: 461s_B3_S27_L008_


title: 459s_L17_S281_L006_


title: U251 siTRMT6/61A ProtoScriptII small RNA

description:
size fractionation
HeLa_U251_siTRMT661A.xlsx

source_name: U251 siTRMT6/61A

extract_protocol:
Total RNAs was extracted from cell lines by TRIzol Reagent (Invitrogen #15596018) and Direct-zol RNA Miniprep Plus Kit with on-column DNase treatment (ZYMO #R2071).
Small RNA-seq library preparation was performed using NEBNext Small RNA Library Prep Set for Illumina (NEB #7330). The resulting amplified libraries were size selected on 8% TBE polyacrylamide gel to enrich for insert of 15-50 nucleotides long RNA.

value: U251 siTRMT6/61A


title: U251 siCtrl ProtoScriptII small RNA

source_name: U251 siCtrl

value: U251 siCtrl


title: 459s_L12_S276_L006_


title: 459s_L11_S275_L006_


title: HeLa siTRMT6/61A ProtoScriptII small RNA

source_name: HeLa siTRMT6/61A

value: HeLa

value: HeLa siTRMT6/61A


title: 459s_K9_S249_L006_


title: 459s_L10_S274_L006_


title: HeLa siCtrl ProtoScriptII small RNA

source_name: HeLa siCtrl

value: HeLa siCtrl


title: U251 siTRMT6/61A TGIRT small RNA

extract_protocol:
Total RNAs was extracted from cell lines by TRIzol Reagent (Invitrogen #15596018) and Direct-zol RNA Miniprep Plus Kit with on-column DNase treatment (ZYMO #R2071).
Small RNA-seq library preparation was performed using NEBNext Small RNA Library Prep Set for Illumina (NEB #7330) with modification to use TGIRT-III RT enzyme (InGex). The resulting amplified libraries were size selected on 8% TBE polyacrylamide gel to enrich for insert of 15-50 nucleotides long RNA.


title: 459s_K8_S248_L006_


title: 459s_L13_S277_L006_


title: HEK293T-FH-Ago2 siCtrl Input TGIRT small RNA rep1

description: size fractionation


title: 459s_K7_S247_L006_


title: HeLa siCtrl TGIRT small RNA


title: HEK293T siTRMT6/61A ProtoScriptII small RNA rep2

description:
size fractionation
HEK293T_siTRMT661A.xlsx

source_name: HEK293T siTRMT6/61A RNA


title: 459s_K5_S245_L006_


title: HEK293T siCtrl ProtoScriptII small RNA rep1

source_name: HEK293T siCtrl RNA

value: siCtrl


title: HEK293T siTRMT6/61A ProtoScriptII small RNA rep1


title: 459s_K3_S243_L006_

value: hESC-derived ventricular progenitors


title: 459s_K2_S242_L006_


title: 459s_K4_S244_L006_


title: 459s_K24_S264_L006_


title: 459s_K23_S263_L006_


title: HEK293T siTRMT6/61A TGIRT small RNA rep2


title: HeLa siTRMT6/61A TGIRT small RNA


title: U251 siCtrl TGIRT small RNA


title: 459s_K21_S261_L006_


title: 459s_K20_S260_L006_


title: HEK293T siTRMT6/61A TGIRT small RNA rep1


title: HEK293T siCtrl ProtoScriptII small RNA rep2


title: HEK293T siCtrl TGIRT small RNA rep1


title: 459s_K1_S241_L006_


title: HEK293T m1A RIP (abcam) ProtoScriptII small RNA rep2

description:
size fractionation
Normalized_read_count_HEK293T_m1ARIP_ProtoscriptII.csv

source_name: HEK293T m1A RIP (abcam) RNA

extract_protocol:
To purify <200nt small RNAs, PureLink miR isolation kit (Invitrogen #K157001) was used with 1E7 starting cells or 50-100 μg total RNAs.Briefly, 1-5 μg purified small RNAs were immunoprecipitated with 5 μg anti-m1A antibody (MBL #D3453, or Abcam #ab208196) or corresponding IgG controls (mouse normal IgG – Millipore #12-371, or rabbit normal IgG – Millipore #12-370) conjugated on Protein G Plus Agarose (Pierce #22851) in the presence of SUPERaseIn RNase Inhibitor (Invitrogen #AM2694) at 4°C for 3 hours. Post binding, resin was washed with 1X IPP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40) twice, low salt buffer (10 mM Tris-HCl, pH 7.4, 75 mM NaCl, 0.1% NP-40) once, high salt buffer (10 mM Tris-HCl, pH 7.4, 200 mM NaCl, 0.1% NP-40) once and TEN buffer (10 mM Tris-HCl, pH 7.4, 1 mM EDTA, 0.05% NP-40) twice. To elute bound RNAs, 3 mg/ml free 1-methyladenosine (Cayman Chemical #16937) in 1X IPP buffer was used to compete and displace m1A-containing RNAs at room temperature under rotation for 1 hour with a total number of two elutions. The eluted RNAs were further purified by acidic phenol-chloroform method and dissolved in water.
Small RNA-seq library preparation was performed using NEBNext Small RNA Library Prep Set for Illumina (NEB #7330). The resulting amplified libraries were size selected on 8% TBE polyacrylamide gel to enrich for insert of 15-50 nucleotides long RNA.

value: m1A RIP (abcam)


title: 459s_K19_S259_L006_

value: 24h after RFA injury


title: 459s_K6_S246_L006_


title: 461s_B22_S46_L008_


title: 459s_K18_S258_L006_


title: HEK293T rabbit IgG RIP ProtoScriptII small RNA rep2

source_name: HEK293T rabbit IgG RIP RNA

value: rabbit IgG RIP


title: 461s_D4_S76_L008_


title: 459s_K17_S257_L006_


title: HEK293T m1A RIP (MBL) ProtoScriptII small RNA rep2

source_name: HEK293T m1A RIP (MBL) RNA

value: m1A RIP (MBL)


title: HEK293T mouse IgG RIP ProtoScriptII small RNA rep2

source_name: HEK293T mouse IgG RIP RNA

value: mouse IgG RIP


title: 459s_K16_S256_L006_


title: HEK293T m1A RIP (abcam) ProtoScriptII small RNA rep1


title: 461s_A3_S3_L008_


title: 459s_K15_S255_L006_


title: 459s_K14_S254_L006_


title: HEK293T Input ProtoScriptII small RNA rep2

source_name: HEK293T Input RNA

value: Input


title: 459s_K13_S253_L006_


title: HEK293T siCtrl TGIRT small RNA rep2


title: 459s_K12_S252_L006_


title: 459s_J9_S225_L006_


title: 459s_K11_S251_L006_


title: HEK293T rabbit IgG RIP ProtoScriptII small RNA rep1


title: HEK293T mouse IgG RIP ProtoScriptII small RNA rep1


title: HEK293T Input ProtoScriptII small RNA rep1

extract_protocol:
To purify <200nt small RNAs, PureLink miR isolation kit (Invitrogen #K157001) was used with 1E7 starting cells or 50-100 μg total RNAs.Briefly, 1-5 μg purified small RNAs were immunoprecipitated with 5 μg anti-m1A antibody (MBL #D3453, or Abcam #ab208196) or corresponding IgG controls (mouse normal IgG – Millipore #12-371, or rabbit normal IgG – Millipore #12-370) conjugated on Protein G Plus Agarose (Pierce #22851) in the presence of SUPERaseIn RNase Inhibitor (Invitrogen #AM2694) at 4°C for 3 hours. Post binding, resin was washed with 1X IPP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40) twice, low salt buffer (10 mM Tris-HCl, pH 7.4, 75 mM NaCl, 0.1% NP-40) once, high salt buffer (10 mM Tris-HCl, pH 7.4, 200 mM NaCl, 0.1% NP-40) once and TEN buffer (10 mM Tris-HCl, pH 7.4, 1 mM EDTA, 0.05% NP-40) twice. To elute bound RNAs, 3 mg/ml free 1-methyladenosine (Cayman Chemical #16937) in 1X IPP buffer was used to compete and displace m1A-containing RNAs at room temperature under rotation for 1 hour with a total number of two elutions. The eluted RNAs were further purified by acidic phenol-chloroform method and dissolved in water.
Small RNA-seq library preparation was performed using NEBNext Small RNA Library Prep Set for Illumina (NEB #7330) with modification to use TGIRT-III RT enzyme (InGex). The resulting amplified libraries were size selected on 8% TBE polyacrylamide gel to enrich for insert of 15-50 nucleotides long RNA.


title: HEK293T Input TGIRT small RNA rep2

description:
size fractionation
DESeq2_miRgene_m1ARIP_TGIRT.csv


title: 459s_J8_S224_L006_


title: 459s_J6_S222_L006_


title: 459s_K10_S250_L006_


title: 459s_J5_S221_L006_


title: HEK293T m1A RIP (MBL) TGIRT small RNA rep1


title: HEK293T Input TGIRT small RNA rep1


title: Pancreatic ductal adenocarcinoma tissue P-22T

city: Chiba city Chuo-ku

first: Yosuke

last: Iwatate

state: Chiba

address: Nitona-cho 666-2

department: Division of Hepato-Biliary-Pancreatic Surgery

country: Japan

institute: Chiba Cancer Center

description: Pancreatic ductal adenocarcinoma tissue

data_processing:
The library for sequence was built with the Ion Proton ™ equipment (Thermo Fisher Scientific) using a 2 × 75 base pair (bp) pair-end protocol for BAM file.
Reads Counts Per Million of library size (CPM) were calculated using a protocol from Subread package (http://subread.sourceforge.net/) from BAM file.
Genome_build: hg19
Supplementary_files_format_and_content: CPM values for every gene and every sample

source_name: Pancreatic ductal adenocarcinoma tissue

extract_protocol:
pancretic tissues were removed, flash frozen on Liquid nitrogen, and RNA was harvested using QIAzol Lysis reagent.miRNeasy Mini Kit (Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Proton ™ protocols

value: pancreas


title: 459s_J4_S220_L006_


title: Pancreatic ductal adenocarcinoma tissue P-17T

description: Pancreatic ductal adenocarcinoma tissue


title: Adjacent normal pancreatic tissue P-22N

description: Adjacent normal pancreatic tissue

source_name: Adjacent normal pancreatic tissue


title: Pancreatic ductal adenocarcinoma tissue P-12T

description: Pancreatic ductal adenocarcinoma tissue


title: 459s_J2_S218_L006_


title: 459s_J24_S240_L006_


title: HEK293T m1A RIP (MBL) ProtoScriptII small RNA rep1


title: 459s_J3_S219_L006_


title: 459s_J23_S239_L006_


title: Adjacent normal pancreatic tissue P-12N

description: Adjacent normal pancreatic tissue


title: Pancreatic ductal adenocarcinoma tissue P-1T

description: Pancreatic ductal adenocarcinoma tissue


title: Pancreatic ductal adenocarcinoma tissue P-8T

description: Pancreatic ductal adenocarcinoma tissue


title: HEK293T m1A RIP (MBL) TGIRT small RNA rep2


title: Adjacent normal pancreatic tissue P-1N

description: Adjacent normal pancreatic tissue


title: 459s_J22_S238_L006_


title: 459s_J21_S237_L006_


title: 459s_J20_S236_L006_


title: 459s_J1_S217_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-13T

description: Pancreatic ductal adenocarcinoma tissue


title: Pancreatic ductal adenocarcinoma tissue Bi-8T

description: Pancreatic ductal adenocarcinoma tissue


title: 459s_J19_S235_L006_


title: 459s_J17_S233_L006_


title: 459s_J16_S232_L006_


title: 461s_B1_S25_L008_


title: Adjacent normal pancreatic tissue Bi-8N

description: Adjacent normal pancreatic tissue


title: 459s_J15_S231_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-6T

description: Pancreatic ductal adenocarcinoma tissue


title: 461s_B14_S38_L008_


title: Adjacent normal pancreatic tissue Bi-3N

description: Adjacent normal pancreatic tissue


title: 459s_J11_S227_L006_


title: 459s_I8_S200_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-5T

description: Pancreatic ductal adenocarcinoma tissue


title: 459s_I7_S199_L006_


title: Adjacent normal pancreatic tissue Bi-13N

description: Adjacent normal pancreatic tissue


title: 459s_J14_S230_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-3T

description: Pancreatic ductal adenocarcinoma tissue


title: 459s_J13_S229_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-4T

description: Pancreatic ductal adenocarcinoma tissue


title: 459s_J12_S228_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-2T

description: Pancreatic ductal adenocarcinoma tissue


title: 459s_I9_S201_L006_


title: Pancreatic ductal adenocarcinoma tissue Bi-1T

description: Pancreatic ductal adenocarcinoma tissue


title: AHR KO_Stem cells_5nMFICZ-1

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description:
GEO_RSEM_normalised_data.txt.gz
KO1-5nMFICZ

data_processing:
The RSEM package (version 1.2.31) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm38 release 89  transcriptome
Normalization of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.16.1)  within the R programming environment (version 3.4.1)
Genome_build: GRCm38 release 89
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Organoids

growth_protocol: Cultured in WENR medium

extract_protocol:
Colon crypts were isloated with 2mM EDTA wash. Crypts embedded in matrigel were cultured in stem cell enrichment media containing Wnt-3A, Noggin, Rspondin-1 and EGF. RNA was extracted from organoids and quantified with Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO for 4hours or 5nM FICZ for 4 hours

value: AHR KO

value: 5nM FICZ for 4 hours

value: Colon

tag: sample type

value: Organoids


title: AHR KO_Stem cells_5nMFICZ-2

description:
GEO_RSEM_normalised_data.txt.gz
KO3-5nMFICZ


title: 459s_I5_S197_L006_


title: Wild type_Stem cells_5nMFICZ-1

description:
GEO_RSEM_normalised_data.txt.gz
WT1-5nMFICZ

value: Wild type


title: AHR KO_Stem cells_DMSO-2

description:
GEO_RSEM_normalised_data.txt.gz
KO3-DMSO

value: DMSO for 4 hours


title: Wild type_Stem cells_5nMFICZ-2

description:
GEO_RSEM_normalised_data.txt.gz
WT2-5nMFICZ


title: 459s_I3_S195_L006_


title: AHR KO_Stem cells_DMSO-1

description:
GEO_RSEM_normalised_data.txt.gz
KO1-DMSO


title: Wild type_Stem cells_DMSO-1

description:
GEO_RSEM_normalised_data.txt.gz
WT2-DMSO


title: 459s_I23_S215_L006_