title: Ventral_day3

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

institute: University of Miami Miller School of Medicine

data_processing:
CellRanger (3.0.2) “mkfastq” command was used to generate fastq files from Illumina bcl files
CellRanger (3.0.2) “count” command was used to generate bam files and raw gene-barcode matrices aligned to the mm10 Ensembl build 93 genome.
Genome_build: mm10 Ensembl build 93

source_name: mouse cardiac tissue

extract_protocol:
Single-cell preparations from 15 neonatal hearts (strain C57Bl6, male and female) were combined to generate two pools of dorsal and ventral cells, and cultured in vitro for 5 days as adherent cultures, in order to allow recovery from enzymatic and mechanical stress. On day 5, adherent cells from the dorsal and ventral cultures were collected by trypsinization, resuspended as single cells and processed for single-cell RNA sequencing on the 10X genomics Chromium instrument using the 3' single cell RNA-seq v3 kits.
10X genomics 3' single cell RNA-seq v3

tag: domain

value: Ventral


title: WT- rep1

status: Public on Oct 16 2020

type: SRA

city: Fredericton

first: Cheryl

middle: L.

last: Patten

state: New Brunswick

address: 10 Bailey Drive

department: Biology

country: Canada

institute: University of New Brunswick

library_source: transcriptomic

data_processing:
Sequence data was inspected for overall quality using FastQC v0.11.2 (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads and contaminating Illumina TruSeq adapter sequences were removed using Trimmomatic v0.3 with a sliding window size of 4 bp, cutting sequences when the average Phred score dropped below 15. Surviving paired reads were mapped to the E. cloacae UW5 reference genome (GenBank Accession number CP011798) using bwa (v0.7.9-r789) as single fragments with a maximum mismatch of 1%. Read alignments were sorted, indexed and converted to BAM format with SAMtools v0.1.19-44428cd. Sample read alignments were visualised using the Integrative Genomics Viewer v2.3.32 to ensure correct mapping of reads to genomic features. The number of reads that mapped to each genomic feature was calculated using the default parameters of HTSeq-count v 0.6.1.p1. Genes with significantly different levels of expression between wild-type and tyrR mutant strains were called using DESeq2 v1.12.4. Genes were considered to be differentially expressed when there was at least a four-fold change (i.e., |log2-fold change| > 2) in expression with a false discovery rate (FDR) threshold adjusted p-value (padj) of ≤ 0.001 as determined by the Benjamini-Hochberg correction method.
Genome_build: CP011798
Supplementary_files_format_and_content: Differential expression of all E. cloacae UW5 genes in the tyrR mutant vs. the wild-type provided in an Excel file

molecule: total RNA

organism: Enterobacter ludwigii

source_name: Rhizobacterium

growth_protocol: Overnight cultures from single colonies of wild-type and tyrR mutant E. cloacae were inoculated 1:100 into 3 ml fresh LB in quadruplicate and incubated at 30℃ and 250 rpm for ~2.5 hrs until reaching mid logarithmic phase of growth (OD600 = 0.6-0.9).

extract_protocol:
A total of 0.5 ml of cell culture were transferred to a 2 ml tube containing 1 ml RNAprotect Bacteria Reagent (Qiagen), incubated 5 minutes at room temperature, and then pelleted by centrifugation. Cell pellets were resuspended with 15 mg/ml lysozyme and 15 mg/ml Proteinase K in 200 µl TE buffer to lyse cells for 10 min at 4°C. Total RNA was extracted using the RNeasy Mini Kit (Qiagen). Contaminating genomic DNA was removed by treating 5 µg total RNA in a 50 µl reaction containing 5 units Amplification Grade DNase I (Invitrogen, CA, USA) and 5 µl 10x DNase I digestion buffer and incubating at 37°C for 60 minutes. The reaction was terminated with 1 mM EDTA and heating at 70°C for 10 minutes. The DNase-treated RNA was purified using the Qiagen MinElute Cleanup Kit (Qiagen, Hilden, Germany) and eluted into 30 µl RNase-free water. DNA removal was verified by PCR. The final quality and quantity of RNA samples were measured on an Agilent Bioanalyzer-RNA 6000 Pico chip (Agilent Technologies, CA, USA).
Construction of RNA-Seq libraries and sequencing were performed by the Genome Quebec Innovation Centre (McGill, Montreal, Quebec). Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Illumina, CA, USA). The resulting enriched mRNA was used to construct a 100 bp paired-end stranded Illumina library using the TruSeq RNA Library Prep Kit v2 (Illumina). The libraries were individually barcoded and sequenced together on a single Illumina HiSeq 2000 lane.

tag: genotype/variation

value: Wild-type

tag: strain

value: Strain UW5


title: WT_3

city: San Francisco

first: Zenghua

last: Fan

state: CA

address: 1550 4th Street

country: USA

institute: University of California, San Francisco

data_processing:
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 (v2.1.0).
Curated genes annotations from RefSeq were used to quantify gene expression as reads count by HTseq (v0.9.1)
Aggregation of raw reads count, preprocessing, normalization and differential expression analysis were performed by DESeq2 package in R environment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files for raw reads count for every gene by HTseq for each sample

organism: Mus musculus

source_name: Hippocampus

growth_protocol: Grm1b-R889W and Grm1-S458A knock-in mice were generated by CRISPR/Cas9. Male mice were used for all experiments.

extract_protocol:
Hippocampus tissues were isolated and flash frozen at ZT20, and then stored at -80 degree.
Paried-end RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All experimental animals were singly housed on a LD 12:12 cycle and given ad libitum access to food and water.

tag: age

value: 5 months

tag: genotype

value: wild type


title: Dorsal_day3

value: Dorsal


title: Stellate cells treated with PACO18 conditioned medium

status: Public on Oct 15 2020

type: RNA

city: Heidelberg

first: Elisa

last: Espinet

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

hyb_protocol: cRNA was hybridized to human whole-genome Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc.)

scan_protocol: BeadChips were scanned with an Illumina iScan system (Illumina Inc.) Scanning and feature extraction was performed using BeadScan and BeadStudio sofware (Illumina) with standard settings for the chips used.

data_processing: The analysis was done on the bead-level data using R following outlier removal (by taking only beads with an expression value > 20 before using the 2.5 MADs rule). The ProbeIDs expression values are the mean of the remaining beads. Finaly, quantile normalization was performed.

label: biotin

organism: Homo sapiens

source_name: Primary Cell line

label_protocol: RNA (500 ng per sample) were labelled using the Illumina® TotalPrep™ RNA Amplification Kit according to the manufacturers' instructions.

growth_protocol: Stellate cells were expanded in Stellate Cell Medium. Conditioned medium was CSC reduced.

extract_protocol: Cells were harvested directly by addition of Qiazol to the culture dishes. Total RNA was extracted using teh Qiagen RnEasy Mini Kit according to manufacturer's instructions.

treatment_protocol: Stellate cells were treated with conditioned medium (CM) from stellate cells or primary human PDAC cells (PACO) for 12 hours.

tag: tissue

value: Pancreas


title: 5395A

type: genomic

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

hyb_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

data_processing: Raw iDAT files were downloaded and pre-processed using ssNOOB. Outlying samples and any probes that failed detection p-value (p=0.01) were removed. Probes near SNPs at the CpG interrogation or extension were removed. Data was processed using the BMIQ function in the ChAMP R package. For analysis, probes on the X/Y chromosomes as well as probes mapping to CpG within the vicinity of SNPs with MAF > 1% in AA or EA populations, as according to 1000G were also removed.

molecule: genomic DNA

source_name: Colon Biopsy

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

extract_protocol: Standard Illumina Protocol

tag: pair

tag: location

value: R

tag: gender

value: F

tag: race

value: AA

tag: adenoma history

value: No

tag: sample plate


title: 4712A

scan_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

value: Yes


title: Stellate cells treated with PACO17 conditioned medium


title: Stellate cells treated with PACO14 conditioned medium


title: 5161D

value: L

value: EA


title: Stellate cells treated with PACO20 conditioned medium


title: 4048A


title: Stellate cells treated with stellate cell conditioned medium rep1


title: 4346A

value: M


title: Human PDAC primary cell line PACO14

description:
Human PDAC primary cell line
This sample has also been deposited in ArrayExpress E-MTAB-4029

growth_protocol: Cell lines were cultured in vitro in serum free medium containing growth factors EGF, bFGF and IGF-1. The cell lines were primary pancreatic adenocarcinoma (PACO) cells derived in our laboratory from patient-derived xenografts. Cells were cultured in Primaria plates under adherent conditions and 5%CO2 at 37°C.

value: PDAC


title: Stellate cells treated with stellate cell conditioned medium rep2


title: 4826D


title: 4125A


title: 2540004, CELIAC

city: Cincinnati

first: Yael

last: Haberman

state: OH

address: 3333 Burnet Ave

department: Gastroenterology

institute: Cincinnati Children's Hospital

description:
2540004-9
CELIAC_Male

data_processing:
Basecalling performed with bcl2fastq v2.20.0
Transcript quantification performed with kallisto v0.43.1, using the GenCode v24 gene reference and the --bias parameter
Gene quantification reported as sum of constituent transcript TPMs
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix file containing expression (in TPM) for protein-coding genes in all samples

source_name: duodenum

extract_protocol:
RNA/DNA were isolated from duodenal biopsies obtained during diagnostic esophagogastroduodenoscopy using the Qiagen AllPrep RNA/DNA Mini Kit (Qiagen, Valencia, CA)
Illumina TruSeq

tag: diagnosis

value: CELIAC

tag: Sex

value: Male

value: duodenal biopsy

tag: age at biopsy


title: M1048

city: Baltimore

first: Monika

last: Looney

state: MD

address: 1503 E Jefferson Street

institute: Johns Hopkins University

data_processing:
miRNA alignment performed using miRge2.0 in R
tRFs were called using -tRF function in miRge2.0 in R
Genome_build: Human NCBI genome build GRCh38
Supplementary_files_format_and_content: CSV files containing a matrix of either tRF or miRNA counts for each sample

source_name: Primary monocyte-derived macrophages

growth_protocol: Monocytes were isolated from platelet-depleted whole human blood by Ficoll density gradient centrifugation followed by passive plastic-adherence. Non-adherent cells were washed away, adherent monocytes were allowed to differentiate into macrophages over a periof of one week before infection. Primary human monocyte-derived macrophages were cultured in RPMI + 10% fetal bovine serum + 4mM L-glutamine.

extract_protocol:
Total RNA including small RNA was isolated using the Qiagen miRNeasy Mini Kit (Qiagen, Cat # 217004). Manufacturer instructions were followed exactly.
Small RNA sequencing libraries were constructed using the Qiagen QIAseq miRNA Library Kit (Qiagen, Cat # 331505). Manufacturer instructions were followed exactly.

treatment_protocol: Macrophages were either left uninfected or infected with Mtb at a multiplicity of infection of 5 or 10 for 24 or 48 hours before RNA harvest.

tag: cell type

value: Primary monocyte-derived macrophages

tag: donor

tag: infected with

value: Mycobacterium tuberculosis (Mtb), strain H37Rv

tag: moi

tag: time post-infection

value: 48 hours


title: M1024

value: 24 hours


title: 4707D

tag: age


title: 5283D


title: 5334A


title: M548


title: 4171A


title: 4068D


title: MM24

value: uninfected


title: WT- rep3

tag: genotype/variation

value: Wild-type

tag: strain

value: Strain UW5


title: Human PDAC primary cell line PACO20

description: Human PDAC primary cell line

tag: tissue


title: 4171D

tag: pair

tag: location

value: F

value: AA


title: LM24


title: LM48


title: 4524A

value: R

tag: gender

tag: race

value: No


title: Experiment 2 Linezolid cycle 4 rep 2

city: Mainz

first: Tim

middle: X

last: Sparwasser

state: Mainz

address: Langenbeckstr. 1

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description: Expression Browser_mouse.txt

data_processing:
The platform used for sequensing is Hiseq2000 (Hiseq V4 75bp PE) and Basecalling is performed using built-in Illumina CASAVA software
Raw FASTQ files were quality controlled, trimmed, and mapped to the Mus musculus reference genome (GRCm38.p5) using the RNA-seq Analysis workflow of QIAGEN’s CLC Genomics Workbench 8
Expression levels were estimated as RPKM (Reads Per Kilobase of exon model per Million mapped reads) using RNA-seq Analysis workflow of QIAGEN’s CLC Genomics Workbench 8
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: The processed data is given in a tab-delemited file for RPKM expression values for each of the genes in the row and samples in the column.

source_name: T lymphocytes

growth_protocol: CD4+ CD25- T cells were isolated ex vivo from spleens and lymph nodes of mice by enrichment with EasyStepTM Mouse CD4+ Isolation Kit (Stemcell Technologies) in combination with a biotin-conjugated antibody against CD25, followed by immunomagnetic negative isolation. The purity of the isolated cells was ~90%. IMDM GlutaMAX medium (Life Technologies) was used for Th17 cultures, respectively. Medium was supplemented with 10% heat-inactivated FCS (Biochrom), 500 U penicillin-streptomycin (PAA laboratories), and 50 μM β-mercaptoethanol (Life Technologies). For Th17 induction, 1.5 to 3×10^5 naïve T cells were cultured for 4 days with plate-bound αCD3e (10 μg mL–1, clone 145-2C11; Bio X Cell), αCD28 (1 μg/mL, clone 37.51; Bio X Cell), αIFN-γ (5 μg/mL, clone XMG1.2; Bio X Cell), αIL-4 (5 μg mL–1, clone 11B11; Bio X Cell), rhTGF-β1 (2 ng mL–1; Peprotech), rmIL-6 (7.5 ng mL–1; Peprotech), and rmIL-1β (50 ng mL–1; Peprotech).

extract_protocol: On day 4, CD4+ live cells were sorted based on Celltrace violet intensity; individual peaks were sorted. Total RNA was isolated using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: Prior to culture, cells were labelled with the cell proliferation dye CellTraceTM Violet.

tag: technical replicates

value: in vitro differentiated Th17 cells

tag: treatment

value: 100uM Linezolid

tag: proliferation cycle

tag: sample id


title: Experiment 2 Linezolid cycle 3 rep 3

description: Expression Browser_mouse.txt

tag: cell type


title: Experiment 2 Linezolid cycle 4 rep 1

description: Expression Browser_mouse.txt


title: Experiment 2 Linezolid cycle 4 rep 3

description: Expression Browser_mouse.txt


title: Human PDAC primary cell line PACO18

value: PDAC


title: Human PDAC primary cell line PACO28

description: Human PDAC primary cell line


title: Human PDAC primary cell line PACO2


title: 4795A

value: M

value: EA

tag: adenoma history

tag: sample plate


title: 4369A


title: L1048

tag: donor

tag: infected with

tag: moi


title: 4459A

tag: age

value: Yes


title: Experiment 2 Linezolid cycle 3 rep 2

description: Expression Browser_mouse.txt

tag: strain


title: Experiment 2 Linezolid cycle 3 rep 1

description: Expression Browser_mouse.txt


title: L1024

value: Primary monocyte-derived macrophages

tag: time post-infection


title: 4900D

tag: pair

value: L


title: M524

value: Mycobacterium tuberculosis (Mtb), strain H37Rv


title: L524

value: 24 hours


title: Experiment 2 Linezolid cycle 2 rep 3

description: Expression Browser_mouse.txt


title: KM48

value: uninfected

value: 48 hours


title: Experiment 2 Linezolid cycle 2 rep 2

description: Expression Browser_mouse.txt


title: 4694D

tag: location


title: KM24


title: Experiment 2 Linezolid cycle 2 rep 1

description: Expression Browser_mouse.txt


title: 4208A

tag: gender


title: L548


title: Experiment 1 Linezolid cycle 4 rep 2

description: Expression Browser_mouse.txt


title: Experiment 1 Linezolid cycle 4 rep 1

description: Expression Browser_mouse.txt


title: Human PDAC primary cell line PACO17

tag: tissue


title: K1024


title: K548


title: K524


title: Experiment 1 Linezolid cycle 3 rep 1

description: Expression Browser_mouse.txt

tag: technical replicates


title: JM24


title: J1048


title: JM48


title: Experiment 1 Linezolid cycle 3 rep 2

description: Expression Browser_mouse.txt

tag: treatment


title: Experiment 1 Linezolid cycle 2 rep 1

description: Expression Browser_mouse.txt

tag: proliferation cycle


title: Experiment 1 Linezolid cycle 2 rep 3

description: Expression Browser_mouse.txt

tag: sample id


title: Experiment 1 Linezolid cycle 4 rep 3

description: Expression Browser_mouse.txt

tag: cell type


title: Experiment 2 Arg C cycle 4 rep 3

description: Expression Browser_mouse.txt

value: 60mM Arg C


title: Experiment 2 Arg C cycle 4 rep 2

description: Expression Browser_mouse.txt


title: J524


title: J548


title: K1048


title: Experiment 2 Arg C cycle 4 rep 1

description: Expression Browser_mouse.txt


title: Experiment 2 Arg C cycle 3 rep 3

description: Expression Browser_mouse.txt


title: pxpr rep3

city: Tampa

first: Mingxiang

last: Teng

address: 12902 Magnolia Dr

department: Department of Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center and Research Institute

description: processed data file: chaf1b.pxpr.diff.genes.csv

library_source: genomic

data_processing:
Gene expression was directly quantified from fastq files using Salmon for GENCODE annotated human genes and Akata genes.
Gene expression differential analysis was performed using DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: chaf1b.pxpr.diff.genes.csv: Comma-separated value file containing normalized gene expression signal and significance of differential analysis.

source_name: Akata cells

growth_protocol: Akata EBV+ cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc. Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: Akata EBV+ cells were transduced with lentiviruses expressing control or CHAF1B sgRNA. At day 6 post-transduction, cells were subjected to Dead cell removal kit (#130-090-101, Miltenyi Biotec). The live cells were then subjected to RNAseq analysis.

value: Akata EBV+ Burkitt Lymphoma cells

tag: genotype/variation

value: Control


title: chaf1b rep1

value: CHAF1B knock-out


title: chaf1b rep2


title: chaf1b rep3


title: pxpr rep2


title: Experiment 2 Arg C cycle 3 rep 2

description: Expression Browser_mouse.txt


title: Experiment 2 Arg C cycle 2 rep 3

description: Expression Browser_mouse.txt


title: Experiment 1 Linezolid cycle 3 rep 3

description: Expression Browser_mouse.txt


title: Experiment 2 Arg C cycle 3 rep 1

description: Expression Browser_mouse.txt


title: Experiment 1 Linezolid cycle 2 rep 2

description: Expression Browser_mouse.txt


title: pxpr rep1


title: Experiment 2 Arg C cycle 2 rep 2

description: Expression Browser_mouse.txt


title: Experiment 2 Arg C cycle 2 rep 1

description: Expression Browser_mouse.txt


title: 18_026D_1250-cmpd-6h_3h-Rem_r2_BRD4

city: Basel

first: Guglielmo

last: Roma

address: Fabrikstrasse 22

country: Switzerland

institute: Novartis Institutes for Biomedical Research

description: BRD4_CHIP_BETi_Cmpd1250_6m3h_rep1-rep2.IDR0.05.filt.narrowPeak.gz

data_processing:
All paired-end ChIP-seq datasets were processed with the AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline).
Reads were aligned using Bowtie2 (version 2.2.8) to build version NCBI37/HG19. Alignments were performed using all default parameters.
We used the MACS version 1.4.2 (Model based analysis of ChIP-seq) peak finding algorithm to identify regions of ChIP-seq enrichment over background.
Differential analysis was performed using Diffbind, and heatmaps were generated using the Enriched Heatmap package.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are provided for visualization of results in the UCSC genome browser.

source_name: keratinocytes

growth_protocol: Treated keratinocytes (9x106 per condition) were fixed with a final concentration of 1% formaldehyde in medium for 15min and quenched with 0.125M glycine. Frozen cross-linked pellets were shipped to Active Motif (La Hulpe, Belgium) for ChIP-seq analysis as a fee-for-service. Frozen cross-linked pellets were shipped to Active Motif (La Hulpe, Belgium) for ChIP-seq analysis as a fee-for-service.

extract_protocol:
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA regions of interest were isolated using (6 µg of) antibody against BRD4 (Bethyl, lot number: A301-985A100-6).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit and sequenced on a NextSeq 500 at 75-bp in paired end mode.

treatment_protocol: BRD4 chromatin binding was analyzed following two BETi treatments [125nM (low) versus 1250nM (high)] and three time points (30min, 6h and 6h treatment followed by compound removal for 3h (6m3h)).

tag: chip antibody

value: BETi treatments 1250nM

tag: time point

value: 6h followed by 3h


title: Experiment 1 Arg C cycle 4 rep 3

description: Expression Browser_mouse.txt

value: in vitro differentiated Th17 cells


title: Experiment 1 Arg C cycle 4 rep 2

description: Expression Browser_mouse.txt


title: 16_026B_1250-cmpd-6h_r2_BRD4

description: BRD4_CHIP_BETi_Cmpd1250_6h_rep1-rep2.IDR0.05.filt.narrowPeak.gz


title: 17_026C_1250-cmpd-6h_3h-Rem_r1_BRD4


title: MM48

tag: donor

tag: infected with


title: 15_026A_1250-cmpd-6h_r1_BRD4


title: 12_0267_Cmpd-125-6h_3h-Rem_r2_BRD4

description: BRD4_CHIP_BETi_Cmpd125_6m3h_rep1-rep2.IDR0.05.filt.narrowPeak.gz

value: BETi treatments 125nM


title: Experiment 1 Arg C cycle 3 rep 2

description: Expression Browser_mouse.txt


title: Experiment 1 Arg C cycle 3 rep 3

description: Expression Browser_mouse.txt


title: 13_0268_1250-Cmpd-30m_r1_BRD4

description: BRD4_CHIP_BETi_Cmpd1250_30min_rep1-rep2.IDR0.05.filt.narrowPeak.gz


title: 14_0269_1250-Cmpd-30m_r2_BRD4


title: 11_0266_Cmpd-125-6h_3h-Rem_r1_BRD4


title: Experiment 1 Arg C cycle 3 rep 1

description: Expression Browser_mouse.txt


title: Experiment 1 Arg C cycle 2 rep 2

description: Expression Browser_mouse.txt


title: 10_0265_Cmpd-125-6h_r2_BRD4

description: BRD4_CHIP_BETi_Cmpd125_6h_rep1-rep2.IDR0.05.filt.narrowPeak.gz


title: Experiment 1 Arg C cycle 2 rep 1

description: Expression Browser_mouse.txt


title: Experiment 2 dmso cycle 4 rep 3

description: Expression Browser_mouse.txt

value: control


title: 08_0263_Cmpd-125-30m_r2_BRD4

description: BRD4_CHIP_BETi_Cmpd125_30min_new_rep1-rep2.IDR0.05.filt.narrowPeak.gz


title: Experiment 2 dmso cycle 4 rep 1

description: Expression Browser_mouse.txt


title: Experiment 1 Arg C cycle 2 rep 3

description: Expression Browser_mouse.txt


title: 06_0261_DMSO-6h_3h-Rem_r2_BRD4

description: BRD4_CHIP_BETi_DMSO_6m3h_rep1-rep2.IDR0.05.filt.narrowPeak.gz

value: DMSO


title: Experiment 1 Arg C cycle 4 rep 1

description: Expression Browser_mouse.txt


title: 04_025G_DMSO-6h_r2_BRD4

description: BRD4_CHIP_BETi_DMSO_6h_rep1-rep2.IDR0.05.filt.narrowPeak.gz


title: 03_025F_DMSO-6h_r1_BRD4


title: 09_0264_Cmpd-125-6h_r1_BRD4


title: 07_0262_Cmpd-125-30m_r1_BRD4


title: Experiment 2 dmso cycle 3 rep 3

description: Expression Browser_mouse.txt


title: 02_025E_DMSO-30m_r2_BRD4

description: BRD4_CHIP_BETi_DMSO_30min_rep1-rep2.IDR0.05.filt.narrowPeak.gz


title: Experiment 2 dmso cycle 3 rep 1

description: Expression Browser_mouse.txt


title: 01_025D_DMSO-30m_r1_BRD4


title: Experiment 2 dmso cycle 2 rep 3

description: Expression Browser_mouse.txt


title: 1540039, EED

description:
1540039-4-R
EED_Male

tag: diagnosis

value: EED

tag: Sex

value: Male

value: duodenal biopsy

tag: age at biopsy


title: Experiment 2 dmso cycle 2 rep 1

description: Expression Browser_mouse.txt

tag: strain


title: Experiment 2 dmso cycle 2 rep 2

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 4 rep 3

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 4 rep 2

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 4 rep 1

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 3 rep 2

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 2 rep 3

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 3 rep 3

description: Expression Browser_mouse.txt


title: 05_025H_DMSO-6h_3h-Rem_r1_BRD4


title: Experiment 1 dmso cycle 2 rep 1

description: Expression Browser_mouse.txt


title: Experiment 1 dmso cycle 2 rep 2

description: Expression Browser_mouse.txt


title: Experiment 2 dmso cycle 3 rep 2

description: Expression Browser_mouse.txt


title: BM3_liver_7d

city: Shanghai

first: hong

last: li

address: 320 Yueyang Road

country: China

institute: SIBS

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and removed low-quality bases, then were mapped to mouse genome mm10. Gene expression levels were estimated by the RSEM algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the expression values of UCSC known genes.

source_name: liver

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were challenged percutaneously with 40 ± 1 Schistosoma japonicum cercariae.

value: BLAB/c

value: liver


title: J1024

value: Primary monocyte-derived macrophages

value: Mycobacterium tuberculosis (Mtb), strain H37Rv

tag: moi

tag: time post-infection

value: 24 hours


title: Fibro_WT_Wnt_invitro_3

city: Frankfurt am Main

first: Mohammed

middle: Hossameldin

last: Mosa

state: Hessen

address: Paul-Ehrlich Str. 42-44

description:
mouse colonic fibroblasts cultured in 3D matrigel and treated with Wnt3a condition medium
For sample 19-24, mouse colonic fibroblasts cultures were established and maintained as reported before (Farin 2012). Fibroblasts were then stimulated for 3 days with either control medium or 20% Wnt3a condition medium before the cells were collected and RNA was extracted.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 24

data_processing:
FastQC Analysis
For human xenografts (samples 25-30), "Xenome" software (version 1.0.0) was used to deconvolute human and mouse reads from xenograft bulk RNA sequencing data and only host reads "mouse" were used for subsequent steps.
quality score filtering, poly-A trimming, artifact removal, removal of ‘N’ containing reads and clearing of rRNA contamination using a pipeline provided by the HUSAR platform, DKFZ.
Genomic mapping to mm10 was performed using TopHat2 (version 2.0.14)
The number of reads per gene was determined using HTSeq count and the gencode annotations (release 24)
differential analysis was performed using   ‘DESeq2’  (version 1.12.4) for samples 25-30, "Limma" package (version: 3.9)  was used for performing differntial analysis.
Genome_build: mm10
Supplementary_files_format_and_content: .txt. processed data files contain readcounts as well as DESeq analysis results

source_name: mouse colonic fibroblasts

extract_protocol:
RNA was extracted using the Macherey-Nagel NucleoSpin RNA kit.
2 ug of RNA was used for library synthesis using  HiSeq SBS Kit v5 50 cycle kit. For Sample 13-18, 25 ng of RNA was used for library synthesis using SMART-seq v4 ultra low input kit. All samples were sequenced by HiSeq 2000 instrument.

tag: condition

value: Wnt

value: fibroblasts

tag: status

value: in vitro


title: BM3_liver_42d

tag: tissue


title: Fibro_WT_Wnt_invitro_2

description:
mouse colonic fibroblasts cultured in 3D matrigel and treated with Wnt3a condition medium
For sample 19-24, mouse colonic fibroblasts cultures were established and maintained as reported before (Farin 2012). Fibroblasts were then stimulated for 3 days with either control medium or 20% Wnt3a condition medium before the cells were collected and RNA was extracted.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 23


title: Fibro_WT_control_invitro_2

description:
mouse colonic fibroblasts cultured in 3D matrigel and treated with control medium
For sample 19-24, mouse colonic fibroblasts cultures were established and maintained as reported before (Farin 2012). Fibroblasts were then stimulated for 3 days with either control medium or 20% Wnt3a condition medium before the cells were collected and RNA was extracted.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 20


title: CAF_Pdgfra_APN_control_invivo_2

description:
sorted Pdgfra+ CAFs from APN-control injected subcutaneously in rag1 mice
For sample 13-18, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Pdgfra+ fibroblasts were sorted before RNA was collected.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 14

source_name: sorted Pdgfra+ cells from mouse s.c.tumors

value: Pdgfra+ sorted fibroblasts

value: in vivo


title: Fibro_WT_control_invitro_1

description:
mouse colonic fibroblasts cultured in 3D matrigel and treated with control medium
For sample 19-24, mouse colonic fibroblasts cultures were established and maintained as reported before (Farin 2012). Fibroblasts were then stimulated for 3 days with either control medium or 20% Wnt3a condition medium before the cells were collected and RNA was extracted.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 19


title: CAF_Pdgfra_APN_control_invivo_3

description:
sorted Pdgfra+ CAFs from APN-control injected subcutaneously in rag1 mice
For sample 13-18, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Pdgfra+ fibroblasts were sorted before RNA was collected.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 15


title: BM3_liver_28d


title: Fibro_WT_Wnt_invitro_1

description:
mouse colonic fibroblasts cultured in 3D matrigel and treated with Wnt3a condition medium
For sample 19-24, mouse colonic fibroblasts cultures were established and maintained as reported before (Farin 2012). Fibroblasts were then stimulated for 3 days with either control medium or 20% Wnt3a condition medium before the cells were collected and RNA was extracted.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 22


title: CAF_Pdgfra_APN_Sfrp1_invivo_1

description:
sorted Pdgfra+ CAFs from APN-Sfrp1 injected subcutaneously in rag1 mice
For sample 13-18, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Pdgfra+ fibroblasts were sorted before RNA was collected.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 16


title: Fibro_WT_control_invitro_3

description:
mouse colonic fibroblasts cultured in 3D matrigel and treated with control medium
For sample 19-24, mouse colonic fibroblasts cultures were established and maintained as reported before (Farin 2012). Fibroblasts were then stimulated for 3 days with either control medium or 20% Wnt3a condition medium before the cells were collected and RNA was extracted.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 21


title: CAF_Pdgfra_APN_Sfrp1_invivo_2

description:
sorted Pdgfra+ CAFs from APN-Sfrp1 injected subcutaneously in rag1 mice
For sample 13-18, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Pdgfra+ fibroblasts were sorted before RNA was collected.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 17


title: Epcam_APN-Sfrp1_invivo_3

description:
sorted Epcam+ tumor cells from APN-Sfrp1 injected subcutaneously in rag1 mice
For sample 7-12, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Epcam+ tumor cells were sorted before RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 12

source_name: sorted Epcam+ cells from s.c.mouse tumors

value: Epcam+ sorted tumor cells


title: CAF_Pdgfra_APN_control_invivo_1

description:
sorted Pdgfra+ CAFs from APN-control injected subcutaneously in rag1 mice
For sample 13-18, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Pdgfra+ fibroblasts were sorted before RNA was collected.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 13


title: Experiment 1 dmso cycle 3 rep 1

description: Expression Browser_mouse.txt

tag: technical replicates

value: in vitro differentiated Th17 cells

tag: treatment

tag: proliferation cycle


title: Epcam_APN-Sfrp1_invivo_1

description:
sorted Epcam+ tumor cells from APN-Sfrp1 injected subcutaneously in rag1 mice
For sample 7-12, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Epcam+ tumor cells were sorted before RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 10

tag: cell type


title: Epcam_APN-Sfrp1_invivo_2

description:
sorted Epcam+ tumor cells from APN-Sfrp1 injected subcutaneously in rag1 mice
For sample 7-12, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Epcam+ tumor cells were sorted before RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 11


title: BM2_liver_42d


title: BM2_liver_28d


title: CAF_Pdgfra_APN_Sfrp1_invivo_3

description:
sorted Pdgfra+ CAFs from APN-Sfrp1 injected subcutaneously in rag1 mice
For sample 13-18, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Pdgfra+ fibroblasts were sorted before RNA was collected.
20200715_Sfrp1_fibroblasts_invitro_invivo.txt
Sample 18


title: Epcam_APN-control_invivo_3

description:
sorted Epcam+ tumor cells from APN-control injected subcutaneously in rag1 mice
For sample 7-12, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Epcam+ tumor cells were sorted before RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 9

value: control


title: Human PDAC primary cell line PACO3

description: Human PDAC primary cell line

value: PDAC


title: BM3_liver_14d


title: BM2_liver_7d


title: Epcam_APN-control_invivo_1

description:
sorted Epcam+ tumor cells from APN-control injected subcutaneously in rag1 mice
For sample 7-12, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Epcam+ tumor cells were sorted before RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 7


title: BM2_liver_14d


title: APN-Sfrp1_invitro_3

description:
APN organoids overexpresses Sfrp1 in vitro
For sample 1-6, mouse tumor organoids that carry loss of function mutations in Apc, p53 and overexpression in Notch1 together with control or Sfrp1 Wnt antagonists were cultured in EN medium as described before(Farin 2012) for 3 days before total RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 6

source_name: mouse small intestinal tumor organoids

value: tumor organoids


title: APN-control_invitro_3

description:
control APN organoids in vitro
For sample 1-6, mouse tumor organoids that carry loss of function mutations in Apc, p53 and overexpression in Notch1 together with control or Sfrp1 Wnt antagonists were cultured in EN medium as described before(Farin 2012) for 3 days before total RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 3


title: BM3_liver_0d


title: BM1_liver_42d


title: APN-Sfrp1_invitro_2

description:
APN organoids overexpresses Sfrp1 in vitro
For sample 1-6, mouse tumor organoids that carry loss of function mutations in Apc, p53 and overexpression in Notch1 together with control or Sfrp1 Wnt antagonists were cultured in EN medium as described before(Farin 2012) for 3 days before total RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 5


title: BM1_liver_10d


title: APN-Sfrp1_invitro_1

description:
APN organoids overexpresses Sfrp1 in vitro
For sample 1-6, mouse tumor organoids that carry loss of function mutations in Apc, p53 and overexpression in Notch1 together with control or Sfrp1 Wnt antagonists were cultured in EN medium as described before(Farin 2012) for 3 days before total RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 4


title: BM2_liver_10d


title: BM1_liver_28d


title: BM2_liver_0d


title: APN-control_invitro_1

description:
control APN organoids in vitro
For sample 1-6, mouse tumor organoids that carry loss of function mutations in Apc, p53 and overexpression in Notch1 together with control or Sfrp1 Wnt antagonists were cultured in EN medium as described before(Farin 2012) for 3 days before total RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 1


title: Epcam_APN-control_invivo_2

description:
sorted Epcam+ tumor cells from APN-control injected subcutaneously in rag1 mice
For sample 7-12, mouse tumor organoids (APN-control or APN-Sfrp1) were subcutanoueously injected into the flank of Rag1 mice and the tumors were left to grow for about 8 weeks. The tumors were then dissected and the Epcam+ tumor cells were sorted before RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 8


title: APN-control_invitro_2

description:
control APN organoids in vitro
For sample 1-6, mouse tumor organoids that carry loss of function mutations in Apc, p53 and overexpression in Notch1 together with control or Sfrp1 Wnt antagonists were cultured in EN medium as described before(Farin 2012) for 3 days before total RNA was collected.
20200715_Sfrp1_tumor_cells_invitro_invivo.txt
Sample 2


title: IL33_5

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
Fastq file quality control was performed using FastQC v0.11.6 and MultiQC v1.6
Fastq files were aligned to the Mus musculus genome using STAR v2.5.4b
BAM files were sorted as part of read alignment with STAR
Read count tables were generated using htseq-count v0.9.1
Genome_build: Mus musculus GRCm38 v91 (GCA_000001635.8)
Supplementary_files_format_and_content: Tab delimited files containing uniquely mapped reads per gene for each sample

source_name: Lung tissue

growth_protocol: The protocol used was based on previous studies (Piyadasa et al., 2018; Salmond et al., 2012) and was approved by the University of Manitoba Animal Care Ethics Board

extract_protocol:
Lung tissues were collected 24 hours after last IL-33 challenge in RNALater, and RNA was extracted from the samples using RNeasy Plus Mini kit (Qiagen USA). RNA quality was checked with the Agilent Bioanalyzer (Santa Clara, CA, USA).
After polyA enrichment, cDNA libraries were constructed using the KAPA Stranded Total RNA Kit (KAPA Biosystems).

treatment_protocol: Mice were challenged once a day with 1μg of intranasal IL-33 for five consecutive days

value: BALB/c mice

tag: concentration


title: BM1_liver_14d


title: IL33_3


title: IL33_4


title: IL33_2


title: IL33_1


title: Control_5

value: Control


title: Control_4


title: BM1_liver_7d

value: BLAB/c


title: Control_3


title: BM1_liver_0d

value: liver


title: Control_2


title: ATAC-Seq LIver40_CD49a_pos_stim

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

description: Bulk ATAC-seq

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
For ATAC-seq low quality peaks such as blacklisted peaks were eliminated.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Supplementary_files_format_and_content: ATAC-seq peaks were identified by using the HOMER tool

source_name: NK cells

growth_protocol: freshly isolated cells from human Liver tissue

extract_protocol:
Human liver tissue was passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Leukocytes were isolated using Ficoll gradients.
Illumina
SMART-seq

treatment_protocol: protocol below every subset section

value: Liver

value: Liver CD49a+ NK cells

value: Stimulated by IL2


title: MF301_Liver_CD45_P_L17_RNA_transcriptome

description: 10x Genomics single cell RNA-seq

data_processing:
Cell Ranger (v3.0.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
Cell Ranger (v3.0.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Cell Ranger (v3.0.2) aggr method was used to aggregate the outputs from three runs of cellranger count.
Downstream analysis were perfored using R package Seurat v3.02 and 10x Genomics Loupe Browser.
Genome_build: hg38
Supplementary_files_format_and_content: Gene matrix and barcode files for each donor were created by Cell Ranger (v3.0.2)

source_name: CD45+ cells

extract_protocol:
Cells were resuspended in PBS with 0.04% BSA. 20K CD45+ cells were loaded on the chromium single cell controller of 10X Genomics  as described in the manufacturers protocol and processed using the 3' scRNA-seq workflow.
We followed the protocol according to the manufacturers instructions with no adaptations.

value: CD45+ cells

value: Unstimulated


title: ATAC-Seq LIver40_CD49a_neg_stim

description: Bulk ATAC-seq


title: ATAC-Seq LIver39_CD49a_neg_stim

description: Bulk ATAC-seq


title: MF301_Liver_CD45_P_L44_RNA_transcriptome

description: 10x Genomics single cell RNA-seq


title: MF301_Liver_CD45_P_L16_RNA_transcriptome

description: 10x Genomics single cell RNA-seq


title: ATAC-Seq LIver41_CD49a_neg_stim

description: Bulk ATAC-seq


title: ATAC-Seq LIver41_CD49a_pos_stim

description: Bulk ATAC-seq


title: 2540056, CONTROL

description:
2540056-9
CONTROL_Male

value: CONTROL

value: Male

value: duodenal biopsy


title: Control_1


title: ATAC-Seq LIver39_CD49a_pos_stim

description: Bulk ATAC-seq


title: 2540053, CELIAC

description:
2540053-9
CELIAC_Female

value: CELIAC

value: Female


title: ATAC-Seq LIver39_CD49a_pos_unstim

description: Bulk ATAC-seq


title: ATAC-Seq LIver40_CD49a_pos_unstim

description: Bulk ATAC-seq


title: ATAC-Seq LIver40_CD49a_neg_unstim

description: Bulk ATAC-seq


title: ATAC-Seq LIver41_CD49a_neg_unstim

description: Bulk ATAC-seq


title: 2540055, CONTROL

description:
2540055-9
CONTROL_Female


title: 2540052, CONTROL

description:
2540052-9
CONTROL_Male

value: 62 months


title: ATAC-Seq LIver41_CD49a_pos_unstim

description: Bulk ATAC-seq


title: ATAC-Seq LIver39_CD49a_neg_unstim

description: Bulk ATAC-seq


title: RNA-Seq LIver41_CD49a_pos_stim

description: Bulk RNA-seq


title: RNA-Seq LIver41_CD49a_neg_stim

description: Bulk RNA-seq


title: 2540050, CONTROL

description:
2540050-9
CONTROL_Female

value: 81.9 months


title: RNA-Seq LIver40_CD49a_pos_stim

description: Bulk RNA-seq


title: 2540048, CELIAC

description:
2540048-9
CELIAC_Female


title: 2540049, CELIAC

description:
2540049-9
CELIAC_Female


title: RNA-Seq LIver40_CD49a_neg_stim

description: Bulk RNA-seq


title: RNA-Seq LIver39_CD49a_pos_stim

description: Bulk RNA-seq


title: RNA-Seq LIver41_CD49a_neg_unstim

description: Bulk RNA-seq


title: 2540046, CELIAC

description:
2540046-9
CELIAC_Male


title: 2540044, CELIAC

description:
2540044-9
CELIAC_Female


title: RNA-Seq LIver40_CD49a_neg_unstim

description: Bulk RNA-seq


title: 2540047, CELIAC

description:
2540047-9
CELIAC_Female


title: RNA-Seq LIver39_CD49a_neg_unstim

description: Bulk RNA-seq


title: 2540039, CELIAC

description:
2540039-9
CELIAC_Male


title: RNA-Seq LIver39_CD49a_pos_unstim

description: Bulk RNA-seq


title: donor1_Sfrp1_xeno_invivo-3

description:
donor#1 Sfrp1-human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 30

organism:
Homo sapiens
Mus musculus

source_name: human xenograft

value: bulk tumor

value: in vivo


title: CD107a_plus_Liver_CD49a_plus_NK_cells_7

description: Single cell RNA-seq

value: CD107a+ Liver CD49a+ NK cells


title: 2540042, CELIAC

description:
2540042-9
CELIAC_Female


title: RNA-Seq LIver39_CD49a_neg_stim

description: Bulk RNA-seq


title: CD107a_plus_Liver_CD49a_plus_NK_cells_8

description: Single cell RNA-seq


title: 2540038, CELIAC

description:
2540038-9
CELIAC_Male


title: CD107a_plus_Liver_CD49a_plus_NK_cells_6

description: Single cell RNA-seq


title: 2540043, CONTROL

description:
2540043-9
CONTROL_Female


title: 2540045, CELIAC

description:
2540045-9
CELIAC_Male


title: RNA-Seq LIver40_CD49a_pos_unstim

description: Bulk RNA-seq


title: RNA-Seq LIver41_CD49a_pos_unstim

description: Bulk RNA-seq


title: 2540040, CONTROL

description:
2540040-9
CONTROL_Female


title: 2540041, CONTROL

description:
2540041-9
CONTROL_Male


title: donor1_Sfrp1_xeno_invivo-2

description:
donor#1 Sfrp1-human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 29


title: 2540037, CONTROL

description:
2540037-9
CONTROL_Male


title: donor1_Sfrp1_xeno_invivo-1

description:
donor#1 Sfrp1-human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 28


title: 2540036, CONTROL

description:
2540036-9
CONTROL_Male

value: 45.7 months


title: CD107a_plus_Liver_CD49a_plus_NK_cells_5

description: Single cell RNA-seq


title: donor1_control_xeno_invivo-3

description:
donor#1 control human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 27

value: control


title: CD107a_plus_Liver_CD49a_plus_NK_cells_4

description: Single cell RNA-seq

value: Liver


title: donor1_control_xeno_invivo-2

description:
donor#1 control human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 26


title: CD107a_plus_Liver_CD49a_plus_NK_cells_3

description: Single cell RNA-seq


title: 2540035, CELIAC

description:
2540035-9
CELIAC_Male

value: 84.6 months


title: donor1_control_xeno_invivo-1

description:
donor#1 control human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 25


title: 2540034, CELIAC

description:
2540034-9
CELIAC_Female


title: CD107a_plus_Liver_CD49a_plus_NK_cells_2

description: Single cell RNA-seq


title: 2540033, CELIAC

description:
2540033-9
CELIAC_Male


title: 1540032, EED

description:
1540032-4-R
EED_Male

value: EED


title: CD107a_plus_Liver_CD49a_plus_NK_cells_1

description: Single cell RNA-seq


title: 2540026, CONTROL

description:
2540026-9
CONTROL_Female


title: 2540024, CONTROL

description:
2540024-9
CONTROL_Male


title: Experiment 2 dmso cycle 4 rep 2

description: Expression Browser_mouse.txt

value: in vitro differentiated Th17 cells

tag: sample id


title: 2540031, CELIAC

description:
2540031-9
CELIAC_Male


title: 2540025, CONTROL

description:
2540025-9
CONTROL_Male


title: CD107a_Liver_CD49a_plus_NK_cells_9

description: Single cell RNA-seq

value: CD107a- Liver CD49a+ NK cells

value: Unstimulated


title: CD107a_Liver_CD49a_plus_NK_cells_7

description: Single cell RNA-seq


title: CD107a_Liver_CD49a_plus_NK_cells_4

description: Single cell RNA-seq


title: CD107a_Liver_CD49a_plus_NK_cells_5

description: Single cell RNA-seq


title: CD107a_Liver_CD49a_plus_NK_cells_6

description: Single cell RNA-seq


title: CD107a_Liver_CD49a_plus_NK_cells_8

description: Single cell RNA-seq


title: 2540019, CONTROL

description:
2540019-9
CONTROL_Male

value: CONTROL

value: Male


title: 2540020, CONTROL

description:
2540020-9
CONTROL_Male

value: duodenal biopsy


title: 1540018, EED

description:
1540018-4-R
EED_Female

value: Female


title: CD107a_Liver_CD49a_plus_NK_cells_3

description: Single cell RNA-seq


title: 2540018, CONTROL

description:
2540018-9
CONTROL_Male


title: CD107a_Liver_CD49a_plus_NK_cells_2

description: Single cell RNA-seq


title: 2540032, CELIAC

description:
2540032-9
CELIAC_Female

value: CELIAC


title: 2540017, CONTROL

description:
2540017-9
CONTROL_Female


title: 2540022, CONTROL

description:
2540022-9
CONTROL_Male


title: 2540027, CONTROL

description:
2540027-9
CONTROL_Male

value: 74.7 months


title: 2540016, CONTROL

description:
2540016-9
CONTROL_Female

value: 84 months


title: CD107a_Liver_CD49a_plus_NK_cells_12

description: Single cell RNA-seq


title: 33131598

city: Madrid

first: Orlando

last: Domínguez

address: Melchor F. Almagro 3

country: Spain

institute: CNIO

description: extracted from FFPE samples

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina HiSeq Control Software. Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
Sequencing read alignment and quantification and differential gene expression analysis was performed in the Bluebee Genomics Platform, a cloud-based service provider (www.bluebee.com.)
Reads were first trimmed with bbduk from BBTools (Bushnell B., BBMap, https://sourceforge.net/projects/bbmap/) to remove adapter sequences and polyA tails.  Trimmed reads were aligned with STAR v 2.5 (Dobin A et al. Bioinformatics 29:15, 2013.) Read counting was performed with HTSeq (Anders S et al. Bioinformatics 31:166, 2015.)
Differential gene expression analysis was performed with DESeq2 (Love MI et al. Genome Biol 15:550, 2014)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Normalized counts and results table, both from DESeq2.

source_name: breast tissue biopsy

extract_protocol:
RNA from formalin-fixed paraffin-embedded tissue samples was isolated using the Maxwell RSC RNA FFPE kit (#AS1440, Promega) with the Maxwell RSC Instrument (Promega) according to manufacturer´s protocol.
Total RNA samples were used as provided by the user (6ng for B16-09806, 18-93ng for the rest). Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
3'-end RNA-seq

value: breast tumor

tag: tumor stage

value: advanced breast cancer

value: durvalumab (10mg/kg iv q2w) and bevacizumab (10mg/kg iv q2w)

tag: behavior

value: non-Responder


title: CD107a_Liver_CD49a_plus_NK_cells_10

description: Single cell RNA-seq

value: Liver


title: CD107a_Liver_CD49a_plus_NK_cells_11

description: Single cell RNA-seq


title: 33137518

description: extracted from FFPE samples

value: Responder


title: CD107a_Liver_CD49a_plus_NK_cells_1

description: Single cell RNA-seq


title: BM3_liver_10d

value: BLAB/c

value: liver


title: 2540011, CONTROL

description:
2540011-9
CONTROL_Male

tag: diagnosis

value: 123.8 months


title: 2540015, CONTROL

description:
2540015-9
CONTROL_Female

tag: Sex


title: 2540013, CONTROL

description:
2540013-9
CONTROL_Female

tag: age at biopsy


title: 2540009, CONTROL

description:
2540009-9
CONTROL_Female


title: 33131615

description: extracted from FFPE samples


title: 33133522

description: extracted from FFPE samples


title: 2540002, CELIAC

description:
2540002-9
CELIAC_Female


title: 33138749

description: extracted from FFPE samples


title: 1540064, EED

description:
1540064-4-R
EED_Male

value: EED


title: 33131808

description: extracted from FFPE samples


title: 2540001, CONTROL

description:
2540001-9
CONTROL_Female

value: CONTROL


title: WM164 MDK 2

first: David

last: Olmeda

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

data_processing:
RNA-seq processing:
RNA-seq data was analyzed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Table with gene FPKM values

molecule: polyA RNA

source_name: WM-164 MDK

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Lonza, cat. no. BE12-604F/U1) supplemented with 10% fetal bovine serum (FBS, Lonza, cat. no. DE14-801F) and 100 μg/mL Penicillin/Streptomycin (Invitrogen, cat. no. 15070-063).

extract_protocol:
Total RNA was extracted and purified from cell pellets using RNeasy Mini-Kit (QIAGEN) following the manufacturer’s instructions. RNA concentration was determined by NanoDrop Spectrophotometer ND-100 (NanoDrop Biotechnologies).
1 µg of total RNA samples, containing ERCC ExFold RNA Spike-In Mixes (Ambion 4456739), was used as provided by the user. Average sample RNA Integrity Number was 9.75 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
Stranded RNA-seq

treatment_protocol: Viral supernatants were generated on 293T cells transfected via standard calcium phosphate precipitation with 4 μg of vector plasmid, and 4 μg of each of the lentiviral packaging constructs. Media was changed 8–16 h after transfection and the viral supernatants were collected 36–40 h later. Melanoma cell infection were perfomed using a dilution of 1:4 of viral supernatants for 8 h. Infected cells were selected by incubation with puromycin (1µg/mL).

value: WM-164 melanoma cells

value: ORF lentiviral expression vector pReceiver-Lv105-A0792 (MDK)


title: WM164 MDK 3


title: 10 shM5 3

source_name: SK-Mel-147 ShMDK

value: SK-Mel-147 melanoma cells

value: Midkine depletion using MDK-sh5 (NM_010784.4-734s1c1)


title: 1540061, EED

description:
1540061-4-R
EED_Female

source_name: duodenum

value: Female

value: duodenal biopsy


title: 1540062, EED

description:
1540062-4-R
EED_Male

value: Male


title: WM164 MDK 1


title: 1540060, EED

description:
1540060-4-R
EED_Male


title: WM164 NEG 3

source_name: WM-164 Empty

value: ORF lentiviral expression vector pReceiver-Empty


title: WM164 NEG 2


title: 1540058, EED

description:
1540058-4-R
EED_Male


title: WM164 NEG 1


title: 1540057, EED

description:
1540057-4-R
EED_Male


title: 1540059, EED

description:
1540059-4-R
EED_Male


title: 10 shM5 2


title: 10 shCTRL 3

source_name: SK-Mel-147 ShControl

value: Non-Target shRNA Control (CAACAAGATGAAGAGCACCAA)


title: 1540056, EED

description:
1540056-4-R
EED_Female


title: 1540053, EED

description:
1540053-4-R
EED_Female


title: 1540052, EED

description:
1540052-4-R
EED_Male


title: 10 shM5 1


title: NTTSA-2E_ChIP

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

institute: Tongji University

data_processing:
(ChIP-seq) Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC mm10) using Bowtie2 (v2.3.4.3) with the parameters: -t --no-mixed --no-discordant --no-unal.(RNA-seq) Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC mm10) using Hisat2 (v2.1.0) with the parameters: --dta-cufflinks --no-unal.
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20.
(ChIP-seq)Duplicated reads were removed using sambamba (v0.6.8).
(RNA-seq)Selected reads were subsequently assembled into transcripts guided by the UCSC gtf annotation files using Stringtie (v1.3.4). The expression level of each gene was quantified with FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Genome-wide histone modification signals were calculated using a 50-bp window and normalized to the uniquely mapped fragments using ‘bam Coverage’ from deepTools (v2.5.7)

source_name: SCNT embryo

growth_protocol: MII oocytes were obtained from or C57BL/6n female mice (5–7-weeks old) were super-ovulated by injection with 6 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 6 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later.  For in vitro fertilization, sperm collected from the cauda epididymis of adult PWK/PhJ male mice (for zygote stage embryo samples) or DBA2 male mice (for early 2-cell, late 2-cell and morula stage embryo samples) was incubated in G-IVF PLUS medium (Vitrolife, 110128) for 20-30 min at 37°C under 5% CO2 to induce sperm swim-up. The zona pellucida of each MII oocyte was punched to make a small hole using a Piezo-drill micromanipulator. Oocytes were then placed in the prepared sperm suspension in G-IVF PLUS medium.  At 4h post-fertilization (h.p.f.), these embryos were washed and cultured in G1 PLUS medium (Vitrolife, 10136).  The fertilized oocytes that had developed to the two-cell stage by the next day were isolated for further culture and collection.

extract_protocol:
The zona pellucidae of the embryos were removed with 0.5% pronase E (Sigma) and the embryos were then incubated in Ca2+-free CZB medium for 10 -20 min. Polar bodies were removed by gentle pipetting using a fire-polished glass needle.  The zygote, 2-cell early, 2-cell late and morula stage wild- type embryos were collected at 13-14, 20-21, 33-34, 67-68 h.p.f. respectively. The 1-cell, 2-cell early, 2-cell late and morula stage SCNT and TSA treated SCNT embryos were collected at 13-14 h, 20-21 h, 33-34h, 67-68 h after activation, respectively.
The zygote, 2-cell early, 2-cell late and morula stage wild- type embryos were collected at 13-14, 20-21, 33-34, 67-68 h.p.f. respectively. The 1-cellzygote, 2-cell early, 2-cell late and morula stage SCNT and TSA treated SCNT embryos were collected at 13-14 h, 20-21 h, 33-3 4h, 67-68 h after activation, respectively.

tag: strain background

tag: developmental stage

value: early 2-cell

value: Trichostatin A

tag: chip antibody

value: H3K9ac (ab4441, Abcam)


title: 1540055, EED

description:
1540055-4-R
EED_Male


title: NT-morula-K9me3-rep1_ChIP

value: Morula

value: WT

value: H3K9me3 (39161, Active Motif)


title: NT-morula-K9me3-rep2_ChIP

description: processed data file:K9me3-NT-morula-merged.bw


title: NT+TSA-2L-5_MRNA

data_processing:
(ChIP-seq)Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC mm10) using Bowtie2 (v2.3.4.3) with the parameters: -t --no-mixed --no-discordant --no-unal.(RNA-seq) Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC mm10) using Hisat2 (v2.1.0) with the parameters: --dta-cufflinks --no-unal.
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20.
(ChIP-seq)Duplicated reads were removed using sambamba (v0.6.8).
(RNA-seq)Selected reads were subsequently assembled into transcripts guided by the UCSC gtf annotation files using Stringtie (v1.3.4). The expression level of each gene was quantified with FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Genome-wide histone modification signals were calculated using a 50-bp window and normalized to the uniquely mapped fragments using ‘bam Coverage’ from deepTools (v2.5.7)

tag: strain

value: late 2-cell


title: 10 shCTRL 2


title: NT+TSA-2L-3_MRNA


title: NT+TSA-2L-2_MRNA


title: 1540046, EED

description:
1540046-4-R
EED_Male

value: EED


title: NT+TSA-2L-1_MRNA


title: 1540043, EED

description:
1540043-4-R
EED_Male


title: 1540042, EED

description:
1540042-4-R
EED_Male


title: NT-2L-4_MRNA


title: NT-2L-3_MRNA


title: 1540040, EED

description:
1540040-4-R
EED_Female


title: NT-2E-5_MRNA


title: NT-2L-1_MRNA


title: NT-2L-2_MRNA


title: NT-2E-4_MRNA


title: 1540049, EED

description:
1540049-4-R
EED_Male


title: 1540038, EED

description:
1540038-4-R
EED_Male


title: NT+TSA-2L-4_MRNA


title: 1540051, EED

description:
1540051-4-R
EED_Female


title: NT-2E-2_MRNA


title: 1540035, EED

description:
1540035-4-R
EED_Female


title: 1540048, EED

description:
1540048-4-R
EED_Female


title: 1540045, EED

description:
1540045-4-R
EED_Female


title: NT-2E-3_MRNA


title: 1540047, EED

description:
1540047-4-R
EED_Female


title: NT-2L-5_MRNA


title: 10 shCTRL 1


title: 1540033, EED

description:
1540033-4-R
EED_Male


title: 1540030, EED

description:
1540030-4-R
EED_Female


title: NT-1C-5_MRNA


title: 1540031, EED

description:
1540031-4-R
EED_Male


title: 1540036, EED

description:
1540036-4-R
EED_Female


title: 1540041, EED

description:
1540041-4-R
EED_Male


title: NT-1C-4_MRNA


title: 1540029, EED

description:
1540029-4-R
EED_Male


title: Biosimilar treated mRNA sample, replicate 9

city: Waterloo

first: Karsten

last: Rinas

state: ON

address: 200 University Ave W

institute: University of Waterloo

description: Biosimilar 9

data_processing:
The quality of the sequence data was controlled with FastQC v3 before and after adapter trimming.
Trimming was performed with the BBDuk method from the BBTools suite. A k-mer size of 23 was used for trimming the 3’ ends of the reads.
Bowtie v1.2.1.1 was used to align the reads allowing a maximum of two mismatches in the first 25 bases of each read. The reads were aligned to the human transcriptome (version: GRCh38.p7) of the consensus coding sequence (CCDS) project.
RSEM v1.3.0 was used to estimate the accurate abundance of genes with default parameters
Genome_build: CCDS transcriptome (GRCh38.p7) with 32,524 CCDS IDs and 18,892 Gene IDs
Supplementary_files_format_and_content: RSEM pseudo counts, TPM and FPKM values for genes

source_name: Biosimilar treated mRNA

growth_protocol: The HER2-positive human breast cancer cell line, BT474 (HTB-20; ATCC, American Type Culture Collection, Manassas, USA), was cultured in Dulbecco’s modified Eagle’s medium (DMEM; Thermo Fisher Scientific, San Jose, USA) containing 10% (v/v) fetal bovine serum (FBS; Gibco, Mississauga, Canada) and 1% (v/v) penicillin/streptomycin [10,000 U/ml penicillin, 10,000 µg/ml streptomycin] (Gibco, Mississauga, Canada) at 37°C and 5% CO2. The cell line was confirmed to be free of mycoplasma contamination with the PCR Mycoplasma Test Kit (PromoKine, Heidelberg, Germany) according to the manufacturer’s protocol.

extract_protocol:
Total RNA was isolated from BT474 cells with Quick-RNA™ MiniPrep kit (Zymo Research, Irvine, USA) following the manufacturer’s instructions.
The cDNA library was constructed with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA).

treatment_protocol: The experimental design included ten biological replicates per condition. On Day 0, approximately 1.2 x 10e6 cells were plated into 10 cm petri dishes for the control and treatment groups. From Days 1 - 6 cells were incubated with either Herceptin (Genentech, San Francisco, USA) or the trastuzumab biosimilar, ApoTras (Apobiologix, Toronto, Canada) at a concentration of 4 µg/ml, or with no treatment (control). The culture media was replaced on Day 1 and Day 4. Total RNA extraction took place on Day 7.

tag: cell line

value: breast cancer cell line

tag: cell line origin

value: female caucasian with ductal carcinoma

value: treated with Biosimilar for 6 days


title: Biosimilar treated mRNA sample, replicate 10

description: Biosimilar 10


title: NT-1C-3_MRNA


title: 1540034, EED

description:
1540034-4-R
EED_Male

tag: tissue


title: NT-2E-1_MRNA

tag: treatment


title: Biosimilar treated mRNA sample, replicate 8

description: Biosimilar 8


title: 1540028, EED

description:
1540028-4-R
EED_Male


title: 1540027, EED

description:
1540027-4-R
EED_Female


title: 1540026, EED

description:
1540026-4-R
EED_Male


title: NT-1C-1_MRNA


title: Biosimilar treated mRNA sample, replicate 5

description: Biosimilar 5


title: NT+Dux-2l-4_MRNA

value: Dux microinjection


title: NT+Dux-2l-3_MRNA


title: Biosimilar treated mRNA sample, replicate 4

description: Biosimilar 4


title: NT+Dux-2l-2_MRNA


title: 1540025, EED

description:
1540025-4-R
EED_Male


title: 1540023, EED

description:
1540023-4-R
EED_Female

value: Female


title: 1540022, EED

description:
1540022-4-R
EED_Male

value: duodenal biopsy


title: CC-rep2_ChIP

source_name: cumulus cell (donor cell of SCNT)

value: somatic cell


title: Biosimilar treated mRNA sample, replicate 3

description: Biosimilar 3


title: RNA-seq_oschz1_repeat3

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Initial quality-control analysis for sequencing reads was performed using FastQC (Andrews S et al, 2013) . Raw sequencing reads were trimmed to remove the adapters and bases with low quality score (< 20) using Cutadapt (Martin 2011) . The trimmed reads were aligned to the Oryza sativa genome (MSU7) with HISAT2 (Kim, Langmead et al. 2015) with parameter "--rna-strandness RF". SAMtools (Li, Handsaker et al. 2009) was used to gain high quality mapped reads (samtools view -q 20), sort reads (samtools sort), add index (samtools index) and estimate the number of uniquely mapped reads (samtools view -F 4 -c). FeatureCounts (Liao, Smyth et al. 2014) was empolyed to assign aligned reads to genes with parameters "-p -s 2 -t exon -g gene_id ". Differentially expressed genes (DEGs) were called with DESeq2 (Love, Huber et al. 2014) filtering the genes without expression in all samples. Genes were considered to be significantly differentially expressed between mutant and wild-type when |log2foldchange| ≥ log2(1.5) and the P value ≤ 0.05.
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files generated using DeepTools with binsize of 10. The matrix including log2Foldchange and pvalue gernerated by DESeq2

organism: Oryza sativa

source_name: 30-day-old seedlings grown up under long-day condition (14 h light at 30°C and 10 h dark at 28°C)

growth_protocol: The husked rice seeds were surface-sterilized by treatment with 0.1% HgCl2 for 20 min and washed with sterilized water. After sterilization, seeds were then cultured on half-strength MS medium in artificial growth chambers under LD conditions (14 h 30 °C : 10 h 28°C, light : dark) for 10 days. Then, seedlings were transferred to MS medium and cultured under LD conditions for 20 days.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen).  PolyA+ RNA was enriched by selection with two rounds of oligo(dT) Dynabeads (Invitrogen).
Stranded RNA-seq library was constructed according to KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17; www.kapabiosystems.com).

value: seedling

tag: development stage

tag: genotype


title: Biosimilar treated mRNA sample, replicate 1

description: Biosimilar 1

tag: cell type


title: RNA-seq_oschz1_repeat2


title: CC-rep1_ChIP


title: 1540021, EED

description:
1540021-4-R
EED_Male

value: Male


title: 1540020, EED

description:
1540020-4-R
EED_Female


title: Herceptin treated mRNA sample, replicate 10

description: Herceptin 10

source_name: Herceptin treated mRNA

value: treated with Herceptin for 6 days


title: NT-1C-2_MRNA


title: Biosimilar treated mRNA sample, replicate 6

description: Biosimilar 6


title: CC-input_ChIP


title: Biosimilar treated mRNA sample, replicate 7

description: Biosimilar 7


title: Herceptin treated mRNA sample, replicate 9

description: Herceptin 9


title: RNA-seq_oschz1_repeat1


title: 1540019, EED

description:
1540019-4-R
EED_Male


title: 1540024, EED

description:
1540024-4-R
EED_Male


title: RNA-seq_NIP_repeat3

value: wild-type


title: 1540016, EED

description:
1540016-4-R
EED_Male


title: TSA-2l_ChIP

value: H3K9ac (ab4441, Abcam)

value: Trichostatin A


title: Herceptin treated mRNA sample, replicate 8

description: Herceptin 8


title: Biosimilar treated mRNA sample, replicate 2

description: Biosimilar 2


title: NT+Dux-2l-1_MRNA


title: TSA-2l-input_ChIP


title: 1540015, EED

description:
1540015-4-R
EED_Male


title: RNA-seq_NIP_repeat2


title: NT-morula-input_ChIP

value: WT

value: morula


title: Herceptin treated mRNA sample, replicate 7

description: Herceptin 7


title: RNA-seq_NIP_repeat1


title: Herceptin treated mRNA sample, replicate 6

description: Herceptin 6


title: 1540011, EED

description:
1540011-4
EED_Male


title: Mnase_oschz1_repeat2

data_processing:
Cleaned paired reads and single reads were mapped to the reference genome by Bowtie2 v2.3.4.1. Samtools v1.979 was used to remove reads with low mapping quality (Q< 20) and potential PCR duplicates. DANPOS (Chen et al., 2013) was used to extract nucleosome position and perform statistical test for significantly changed nucleosome.
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files were generated using DeepTools with binsize of 10. The excel combining the occupancy peaks and differential peaks and wig files contains smooth nucleosome occupancy  were gernerated by Danpos software.

extract_protocol:
nucleus was digested with micrococcal nuclease and mononucleosome-sized DNA fragments were gel purified
purifed mononucleosome-sized DNA fragments were used to construct a MNase-seq library as previously described (Muñoz-Viana et al, 2017).


title: NT-morula-rep2_ChIP


title: Herceptin treated mRNA sample, replicate 5

description: Herceptin 5


title: Mnase_oschz1_repeat1


title: 1540008, EED

description:
1540008-4
EED_Male

data_processing:
Basecalling performed with bcl2fastq v2.20.0
Transcript quantification performed with kallisto v0.43.1, using the GenCode v24 gene reference and the --bias parameter
Gene quantification reported as sum of constituent transcript TPMs
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix file containing expression (in TPM) for protein-coding genes in all samples


title: Herceptin treated mRNA sample, replicate 4

description: Herceptin 4


title: NT-morula-rep1_ChIP


title: Mnase_NIP_repeat2


title: NT-2l-rep1_ChIP

value: late 2-cell


title: 1540006, EED

description:
1540006-4
EED_Female

value: EED


title: 1540007, EED

description:
1540007-4
EED_Female


title: 1540005, EED

description:
1540005-4
EED_Male


title: Herceptin treated mRNA sample, replicate 2

description: Herceptin 2

value: breast cancer cell line


title: NT-2l-rep2_ChIP


title: Herceptin treated mRNA sample, replicate 1

description: Herceptin 1

value: female caucasian with ductal carcinoma


title: Herceptin treated mRNA sample, replicate 3

description: Herceptin 3


title: Untreated Control mRNA sample, replicate 10

description: Control 10

source_name: Untreated Control mRNA

value: untreated


title: 1540004, EED

description:
1540004-5
EED_Male


title: NT-2l-input_ChIP


title: 1540003, EED

description:
1540003-5
EED_Male


title: NT-2e-rep2_ChIP

value: early 2-cell


title: Untreated Control mRNA sample, replicate 9

description: Control 9


title: NT-2e-input_ChIP


title: Untreated Control mRNA sample, replicate 8

description: Control 8


title: BS-seq_NIP_repeat2

data_processing:
Bismark was used to map trimmed paired end reads to rice reference genome MSU7 and extract methylation regions (DMRs).
Genome_build: MSU7
Supplementary_files_format_and_content: Bismark coverage files containing DNA methylation calls for every cytosines measured

extract_protocol:
the total genomic DNA of wild-type and mutant plants was extracted from 30-day-old seedlings using the DNeasy plant maxi kit (QIAGEN) following manufacturer instructions.
the genomic DNA was sent to Genergy Biological Technology Company of Limited Liability (Shanghai, China) to treate with sodium bisulfite and construct library.


title: BS-seq_oschz1_repeat2


title: BS-seq_oschz1_repeat1


title: NT-2e-rep1_ChIP


title: DuxOE-2e-input_ChIP

value: Dux microinjection


title: Untreated Control mRNA sample, replicate 7

description: Control 7


title: DuxOE-2e_ChIP


title: MF3_liver_21d

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and removed low-quality bases, then were mapped to the genome of Microtus fortis. Gene expression levels were estimated by the RSEM algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the expression values of UCSC known genes.

organism: Alexandromys fortis

source_name: liver

treatment_protocol: The Microtus fortis were challenged percutaneously with 40 ± 1 Schistosoma japonicum cercariae.

value: liver


title: Mnase_NIP_repeat1


title: MF3_liver_28d


title: MF3_liver_7d


title: Untreated Control mRNA sample, replicate 6

description: Control 6


title: Untreated Control mRNA sample, replicate 5

description: Control 5


title: BS-seq_NIP_repeat1


title: DuxDeltaC_OE-2e_ChIP

value: Dux(C-term KO) microinjection


title: atac_hpek_NVS-BET2_48h_1

data_processing:
All paired-end ATAC-seq datasets were processed with the Encode pipeline ATAC v1.7.1 (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Reads were aligned using Bowtie2 (version 2.3.4.3) to homo sapiens genome version NCBI37/hg19. Alignments were performed using all default parameters.
We used the MACS2 peak finding algorithm (version 2.2.4) with default parameters to identify regions of enrichment over background.
Differential peaks were calculated using abs(log2FC) > 1 & p.value < 0.00001
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are provided for visualization of results in the UCSC genome browser.

source_name: keratinocytes

growth_protocol: Assay for Transposase-Accessible Chromatin (ATAC) was performed according to Omni-ATAC Supplementary Protocol 1 (Corces et al, Nature methods, 2017) using 3 × 10^5 HPEKs per treatment condition that were seeded in 6-well plates, washed once with 500 μl of PBS (on plate) and detached using Accutase (CELLnTEC).

extract_protocol:
Enriched nuclei were tagmented using Tn5 transposase (Illumina Tagment DNA Enzyme and Buffer Kit) at 37 °C for 30 min. Tagmented DNA was isolated using DNA Clean and Concentrator Kit  (Zymo).
ATAC-seq libraries were generated using NEBNext High Fidelity 2x PCR Mix (NEB) with IDT for Illumina Nextera DNA Unique Dual Indexes (UDI) using 10 cycles of amplification. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) and their concentration was measured using Qubit dsDNA HS Assay Kit (Invitrogen). Library integrity and size distribution was checked by Agilent TapeStation.
ATAC libraries were sequenced dual-indexed paired-end (2 x 76) using a NovaSeq 6000 instrument (Illumina) according to manufacturer’s instructions.

treatment_protocol: HPEKs were treated in culture for 6h and 48h (6h+42h wash-out) with either 125nM NVS-BET1, 125nM NVS-BET2, or 0.0125% DMSO as control in triplicate per condition.

value: keratinocytes

tag: time

value: 48h (6h + 42h wash-out)


title: MF3_liver_14d


title: atac_hpek_NVS-BET1_48h_3


title: atac_hpek_NVS-BET1_48h_2


title: atac_hpek_NVS-BET1_48h_1


title: 1540001, EED

description:
1540001-5
EED_Male

extract_protocol:
RNA/DNA were isolated from duodenal biopsies obtained during diagnostic esophagogastroduodenoscopy using the Qiagen AllPrep RNA/DNA Mini Kit (Qiagen, Valencia, CA)
Illumina TruSeq

value: Male

value: duodenal biopsy


title: MF3_liver_0d


title: DuxDeltaC_OE-2e-input_ChIP

value: H3K9ac (ab4441, Abcam)


title: Untreated Control mRNA sample, replicate 4

description: Control 4


title: NT-1C_ChIP


title: Untreated Control mRNA sample, replicate 1

description: Control 1


title: Untreated Control mRNA sample, replicate 3

description: Control 3


title: atac_hpek_DMSO_48h_3

value: DMSO


title: NT-1C-input_ChIP

value: WT


title: atac_hpek_NVS-BET2_48h_2


title: Untreated Control mRNA sample, replicate 2

description: Control 2


title: NF-morula-input_ChIP

source_name: natural fertilized embryo

value: C57BL/6 x DBA/2J

value: morula


title: MF2_liver_28d


title: atac_hpek_DMSO_48h_2


title: MF2_liver_21d


title: NF-morula-rep2_ChIP


title: F1_M3C-3

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

description: polyA RNA

data_processing:
sequencing: HISeq2000: 75 cycle flow cell (catalog#: FC-404-2005) with approximately 4-8 million reads per sample
Base-calling : Illumina-base caller (Base space)
Trim, quality filter: Trimmomatic software (v0.32)
Alignment: STAR (v2.5.2b) and the Gencode (gencode.vM20.annotation.gtf) annotation as the reference for splice junctions.
Samples were then quantified with HT_seq  and DGE was obtained using paired samples with DESeq2 - Here are the versions of the computational tools used A number of open source code was used to analyze this data as well as custom code.   open source code includes:   FastQC 0.11.5  samtools 1.8   Rstudio and R (both versions 3.2, 3.4 and 3.5 used - since some packages are specific to a certain version)   on R, we have used: Diffbind (3.9), Deseq2 (1.18.0 and 1.2.0), ggplot2 (3.1.0).  HT-seq 0.6  UCSC toolkit (no version available)
Genome_build: mm10
Supplementary_files_format_and_content: Differential gene expression by DeSeq2 between uninduced islets and islets expressing Pdx1, MAfA and Ngn3. Text format (n=5 for each group).

source_name: mouse pancreatic islet

growth_protocol: Male mice (8-12 weeks old) were euthanized by cervical dislocation before inflation of the pancreas via injection of collagenase solution (1mg/ml; Serva NB8) into the bile duct. Pancreata were then digested for 12 mins at 37°C in a water bath before purification of islets using a Histopaque gradient. Islets were hand-picked and cultured (5% CO2, 37°C) in RPMI medium containing 10% FCS, 100 units/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
RNA was extracted using 1mL Trizol (Thermo Fisher Scientific) per 100 islets as per the manufacturer's instructions.
Library prep using 2x Lexogen QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD), 24 preps (catalog#: 015.24.)

treatment_protocol: These islets were cultured over night before being treated with 100 μM doxycycline for 48hr prior to extraction.

value: male

value: pancreatic islet

tag: condition

tag: isolation (experiment/litter)

tag: background strain


title: NF-morula-rep1_ChIP


title: MF2_liver_7d


title: MF3_liver_10d


title: F1_M3C-1

description: polyA RNA

tag: Sex


title: atac_hpek_DMSO_48h_1


title: atac_hpek_NVS-BET2_6h_3


title: MF2_liver_14d


title: atac_hpek_NVS-BET2_6h_2


title: E1_WT-3

description: polyA RNA


title: MF2_liver_10d


title: IVF-2l-rep2_ChIP

source_name: IVF embryo

value: late 2-cell


title: D1_WT-5

description: polyA RNA


title: C2_M3C-6

description: polyA RNA


title: MF2_liver_0d


title: IVF-2l-rep1_ChIP


title: IVF-2l-input_ChIP


title: atac_hpek_NVS-BET1_6h_3


title: MF1_liver_28d


title: C1_M3C-5

description: polyA RNA


title: atac_hpek_NVS-BET1_6h_2


title: C1_WT-3

description: polyA RNA


title: MF1_liver_21d


title: MF1_liver_7d


title: IVF-2e-rep1_ChIP


title: atac_hpek_DMSO_6h_3


title: B2_WT-6

description: polyA RNA


title: B2_WT-1

description: polyA RNA


title: atac_hpek_NVS-BET2_6h_1


title: IVF-1C-rep1_ChIP

value: C57BL/6 x PWK/PhJ


title: MF1_liver_10d


title: A1_M3C-3

description: polyA RNA


title: atac_hpek_DMSO_6h_2


title: MF1_liver_0d


title: IVF-1C-input_ChIP


title: miR-210 mutant 3

status: Public on Oct 14 2020

city: Hangzhou

first: Wanzhong

last: Ge

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Basic reads quality check was performed with FastQC
Reads were mapped to the Drosophila melanogaster reference genome assembly (version dm6.09, 2016) using Hisat2 and gene quantification was carried out using FeatureCounts.
Differential expression analysis was performed using DEseq.

organism: Drosophila melanogaster

source_name: adult fly heads

extract_protocol:
RNA extractions was performed using Trizol.
Libraries were prepared according to the Illumina protocol and sequenced on an Illumina novaseq6000 platform

value: miR-210 mutant

value: adult heads


title: IVF-2e-rep2_ChIP

value: early 2-cell


title: IVF-2e-input_ChIP


title: miR-210 mutant 2


title: atac_hpek_NVS-BET1_6h_1


title: MDCK,transcriptome 01

city: Bethesda

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a
Transcript abundances in TPM were caculated by  rsem 1.3.0
Genome_build: Ensembl Release 94
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Canis lupus familiaris

source_name: MDCK,transcriptome 01

growth_protocol: Cell lines were grown on transwell (see manuscript) to confluence before RNA isolation.

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney Cells


title: MDCK,transcriptome 03

source_name: MDCK,transcriptome 03


title: miR-210 mutant 1


title: w1118 control 2

value: w1118 control


title: IVF-1C-rep2_ChIP


title: w1118 control 1


title: w1118 control 3


title: MF1_liver_14d

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: MDCK,transcriptome 02

source_name: MDCK,transcriptome 02


title: HEK293T cells, sp918

city: shanghai

first: Tian-Lin

last: Cheng

state: I am not in the U.S. or Canada

address: Dong An Road, No. 131

description: All.counts.exp.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
RNA sequencing data was aligned to the human reference genome (GRCh38) using STAR
Variants were called using the GATK best practices pipeline using Picard  and GATK 3.8
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contains counts for each sample

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM (Gibco/Life Technologies) with 10%  FBS (Gibco/Life Technologies) at 37 °C in a 5% CO2 incubator (Thermo Scientific  Heraeus)

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

treatment_protocol: HEK293T cells were plated into 6-well plates (Thermo Scientific) for transfection. About 20 h later, cells were transfected using 4 μL Lipofectamine 3000 (Thermo Scientific) with 3μg plasmid expressing specific base editor and/or 1ug plasmid expressing specific sgRNA according to the manufacturer’s manuals. After 48 h culture, positive cells were sorted using FACS for RNA purification.

value: human embryonic kidney epithelial cell line HEK293T

tag: transfection


title: HEK293T cells, SP894-2m

description: All.counts.exp.txt


title: HEK293T cells, sp793

description: All.counts.exp.txt


title: HEK293T cells, sp582

description: All.counts.exp.txt


title: HEK293T cells, SA850-2M2

description: All.counts.exp.txt


title: HEK293T cells, SA850-2M-3

description: All.counts.exp.txt


title: HEK293T cells, SA693-2M

description: All.counts.exp.txt


title: HEK293T cells, SA693-2M-2

description: All.counts.exp.txt


title: HEK293T cells, SA850282

description: All.counts.exp.txt


title: HEK293T cells, SA615-2M-2

description: All.counts.exp.txt


title: HEK293T cells, SA8502822

description: All.counts.exp.txt


title: HEK293T cells, SA615-2822

description: All.counts.exp.txt


title: HEK293T cells, SA615282

description: All.counts.exp.txt


title: HEK293T cells, NSA2822

description: All.counts.exp.txt


title: HEK293T cells, SA2M3

description: All.counts.exp.txt


title: HEK293T cells, SA693282

description: All.counts.exp.txt


title: HEK293T cells, NSA282

description: All.counts.exp.txt


title: HEK293T cells, NC201912

description: All.counts.exp.txt


title: HEK293T cells, MS-MU823

description: All.counts.exp.txt


title: HEK293T cells, MS-MU822

description: All.counts.exp.txt


title: HEK293T cells, MS-M82WTMU2

description: All.counts.exp.txt


title: HEK293T cells, MS-MU82

description: All.counts.exp.txt


title: HEK293T cells, MS-M82WTMU1

description: All.counts.exp.txt


title: HEK293T cells, MS-MOWTMU

description: All.counts.exp.txt

value: MS-MOWTMU


title: HEK293T cells, MS-3M3

description: All.counts.exp.txt


title: HEK293T cells, MS-3M

description: All.counts.exp.txt


title: HEK293T cells, SA850-2M

description: All.counts.exp.txt


title: HEK293T cells, MS-2M3

description: All.counts.exp.txt


title: HEK293T cells, MS-3M2

description: All.counts.exp.txt


title: HEK293T cells, MS-2M2

description: All.counts.exp.txt


title: HEK293T cells, GFP

description: All.counts.exp.txt

value: GFP


title: HEK293T cells, UBH14591249MU820619

description: all.counts.txt

treatment_protocol: HEK293T cells were plated into 6-well plates  (Thermo Scientific) for transfection. About 20 h later, cells were transfected using  4 μL Lipofectamine 3000 (Thermo Scientific) with 3μg plasmid expressing specific  base editor and/or 1ug plasmid expressing specific sgRNA according to the manufacturer’s  manuals. After 48 h culture, positive cells were sorted using FACS for RNA purification.


title: HEK293T cells, UBH1457800MU82

description: all.counts.txt

value: ABE-800-MU82, sgRNA-1


title: HEK293T cells, UBH1456769MU82

description: all.counts.txt

value: ABE-769-MU82, sgRNA-1


title: HEK293T cells, UBH1454NMU82

description: all.counts.txt


title: HEK293T cells, UBH1455535MU82

description: all.counts.txt

value: ABE-535-MU82, sgRNA-1


title: HEK293T cells, UBH14581029MU82

description: all.counts.txt


title: HEK293T cells, UBH1417N2M-1

description: all.counts.txt


title: HEK293T cells, UBH1434GFP

description: all.counts.txt


title: HEK293T cells, UBH1433GFP

description: all.counts.txt


title: HEK293T cells, Sa-n-2m-2-0729

description: all.counts.txt


title: HEK293T cells, Sa-n-2m-1-0729

description: all.counts.txt


title: HEK293T cells, Sa-615-2m-0729

description: all.counts.txt


title: HEK293T cells, NC

description: all.counts.txt

value: Negative control


title: HEK293T cells, NC0729

description: all.counts.txt


title: HEK293T cells, NC-PA-1

description: all.counts.txt


title: HEK293T cells, NC-PA-2

description: all.counts.txt


title: HEK293T cells, nc-0729

description: all.counts.txt


title: HEK293T cells, NBE-pa

description: all.counts.txt


title: HEK293T cells, N12-274

description: all.counts.txt


title: HEK293T cells, N7pa1

description: all.counts.txt


title: HEK293T cells, N7-pa2

description: all.counts.txt


title: HEK293T cells, N11-306

description: all.counts.txt


title: HEK293T cells, N10-pa2

description: all.counts.txt


title: HEK293T cells, N12-196-6

description: all.counts.txt


title: HEK293T cells, N10-PA1

description: all.counts.txt


title: HEK293T cells, N11-pa

description: all.counts.txt


title: HEK293T cells, N1-268

description: all.counts.txt


title: HEK293T cells, N-MU106-2

description: all.counts.txt


title: HEK293T cells, N-MU106-1

description: all.counts.txt


title: HEK293T cells, N-MU82-0619-1

description: all.counts.txt


title: HEK293T cells, N-2mpa

description: all.counts.txt


title: HEK293T cells, N-2mpa-904

description: all.counts.txt


title: HEK293T cells, N-MU82-0619-2

description: all.counts.txt


title: HEK293T cells, ms-282-2-0729

description: all.counts.txt


title: HEK293T cells, N-2mpa-769

description: all.counts.txt


title: HEK293T cells, Lenti-Sp36-sp1

description: all.counts.txt


title: HEK293T cells, ms-2m-2-0729

description: all.counts.txt


title: HEK293T cells, Lenti-SP36-pa2

description: all.counts.txt


title: HEK293T cells, N-MU106-3

description: all.counts.txt


title: HEK293T cells, NBE-254

description: all.counts.txt


title: HEK293T cells, ms-282-1-0729

description: all.counts.txt


title: HEK293T cells, ms-3m-2-0729

description: all.counts.txt


title: HEK293T cells, L8-164

description: all.counts.txt


title: HEK293T cells, GFP-pa

description: all.counts.txt


title: HEK293T cells, D10APA1-2

description: all.counts.txt


title: HEK293T cells, GFP-210

description: all.counts.txt


title: HEK293T cells, N1-261

description: all.counts.txt


title: HEK293T cells, D10APA1-1

description: all.counts.txt