title: 01_31ET

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

description: bisulfite conversion

data_processing:
NextSeq550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings. Reads were filtered for full-length(70bp) reads.
Fastq header contains 8 nt index sequence and N6 Nugen RRBS duplicate information. Adaptors and low quality reads were trimmed with Trim_galore v0.4.5. and reads containing adapter were discarded.
Following adaptor and quality trimming, the fastq files were further trimmed with NuGEN custom python script trimRRBSdiversityAdaptCustomers.py. Potential PCR or optical duplicates were removed using NuGEN python script Nudup.py
Trimmed reads was aligned to the human genome, allowing for 1 mismatch and retaining only uniquely mapped reads. Bam files were generated using Bismark v0.16.334. CpG coverage reports were generated using MethylKit from bam files.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: CpG coverage report in text format

source_name: cerebellum from deceased patient

extract_protocol:
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
Nugen Ovation RRBS Methyl-Seq protocol with QIAGEN EpiTech Fast DNA Bisulfite Kit for bisulfite conversion

tag: disease state

value: essential tremor

value: cerebellum

value: male


title: AL3

status: Public on Feb 04 2020

type: SRA

city: Anyang

first: Jianyong

last: Wu

address: Huanghe Dadao 38#

country: China

institute: Institute of Cotton Research, CAAS

description: 1st true leaves fully expanded

library_source: transcriptomic

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Supplementary_files_format_and_content: xls include FPKM values for each Sample

molecule: total RNA

organism: Gossypium hirsutum

source_name: Leaf

growth_protocol: Standard Hydroponic solution in the Lab

extract_protocol:
T.RNA with Sigma Spectrum Plant Total RNA kit (Sigma-  448 Aldrich, USA)
Accordance with the protocol for the mRNA-Seq sample preparation kit   (Illumina, San Diego, USA)

tag: cultivar

tag: tissue

value: Leaf

tag: developmental stage

value: Seedling stage


title: Sample_I17_24h_5mG_E1

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

description: Exposed

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with 2PASS STAR v020201 against  GRCz11 zebrafish reference genome and Ensembl v95 exon-exon junctions
Quantification and normalization with Desq2 v1.22.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw reads in fastq
Supplementary_files_format_and_content: Read count files from RNAstar

organism: Danio rerio

source_name: entire embryos

growth_protocol: Zebrafish eggs were collected just after fertlization and grown in 9mm Petri dishes with embryo medium (60mg/L Instant Ocean, 0.01 % (w/v) of methylene blue). Eggs were grown in Panasonic incubator (MIRE) at 28°C.

extract_protocol:
Total RNA extraction with trizol no DNaseI treatment, followed by two rounds of mRNA extraction with illumina magnetic Beads
Stranded mRNAseq v2 Illumina with dual UDT indexes

treatment_protocol: External continuous irradiation to gamma radiation (137Cs) at 0.5mGy/h, 5mGy/h 50mGy/h or non-exposed controls

value: entire embryos

tag: genetic background

value: AB

tag: irradiation batch

tag: dose rate in mgy/h


title: Sample_I17_24h_50mG_E4

description: Exposed


title: uninjected_st41_repl1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Fluorescence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files using bcl2fastq 2.17.1.14
Assessment of quality control of sequences using FastQC 0.11.5
Alignment of sequences to Xenopus Laevis reference genome using STAR 2.5.2a
Counting unique reads within genes using featureCounts 1.5.0-p1
Data normalization and testing for differentially expressed genes using DESeq2 1.8.2
Genome_build: Xenla9.1 (http://www.xenbase.org)
Supplementary_files_format_and_content: gene counts

organism: Xenopus laevis

growth_protocol: Injected and uninjected Xenopus laevis embryos were cultivated in 0.1x MBS culture buffer.

extract_protocol:
Total RNA was extracted using Trizol reagent (peqGOLD TriFast reagent, peQlab) according to instructions.
TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes)

value: stage 41

value: whole embryo


title: AL2

description: 1st true leaves fully expanded


title: 06_19ET

country: USA

description: bisulfite conversion

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: age

tag: Sex


title: 20ng_ERFE_MO2_st37_38_repl1

value: stage 37/38

tag: injected morpholino

value: 20 ng ERFE-MO2


title: AL1

description: 1st true leaves fully expanded


title: Sample_I17_24h_50mG_E3

description: Exposed


title: 06_15

description: bisulfite conversion

value: control

value: female


title: uninjected_st35_36_repl2

value: stage 35/36


title: 20ng_cMO_st37_38_repl1

value: 20 ng cMO


title: 00_49

description: bisulfite conversion


title: 20ng_cMO_st41_repl1


title: 13_49ET

description: bisulfite conversion


title: Sample_I17_24h_50mG_E1

description: Exposed


title: Sample_I10_96h_C9

description: Control

value: Control


title: 10ng_ERFE_MO1_st37_38_repl1

value: 10 ng ERFE-MO1


title: 10ng_cMO_st41_repl1

value: 10 ng cMO


title: AR2

description: 1st true leaves fully expanded

source_name: Root

value: Root


title: AR3

description: 1st true leaves fully expanded


title: 01_44

description: bisulfite conversion

value: cerebellum


title: Sample_I10_96h_C12

description: Control


title: 10ng_cMO_st37_38_repl1


title: uninjected_st37_38_repl1


title: AR1

description: 1st true leaves fully expanded


title: 03_39

description: bisulfite conversion

value: male


title: Sample_I10_96h_C11

description: Control


title: RGT1_ALL_Kang2020

city: St. Louis

first: Yiming

last: Kang

state: MO

address: 1 Brookings Dr

department: Computer Science and Engineering

institute: Washington University in St. Louis

description: Calling Card Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor

data_processing:
Library strategy: "Calling Card" Assay
Paired-End sequence reads were filtered for presence of Read1 initial 5bp barcode followed by unique 17-mer sequence (AATTCACTACGTCAACA) and Read2 initial 8bp barcode.
The remaining sequence after the 17-mer sequence of Read1 was mapped to the 2008 S. cerevisiae reference genome (R-61-1-1) sequence using NovoAlign with default parameter settings.
Insertion position and number of reads mapping to each insertion are reported in gnashy file.
Genome_build: S288C-R61
Supplementary_files_format_and_content: gnashy: a table indicating genomic position of the retrotransposon insertion and number of reads aligning to that position

organism: Saccharomyces cerevisiae

growth_protocol: The indicated yeast strain was co-transformed with a plasmid carrying the indicated transcription factor fused at the C-terminus to Sir4p and a plasmid carrying a barcoded HIS3-carrying Ty5 retrotransposon under the control of the GAL1/10 promoter.  A single clone was then incubated for 3 days on selective media with galactose as the carbon source.  Plates were then sequentially replica-plated to YPD (2 days), followed by SC-HIS with 5'FOA agar plates (3 days).

extract_protocol:
Genomic DNA was extracted from all cells using standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol.
Genomc DNA was digested in three separate restriction enzyme digests (HinPI1, HpaII, and Taq-alphaI), self-ligated with T4 DNA ligase, and an inverse PCR reaction was performed to amplify genomic DNA downstream of each inserted Ty5 retrotransposon.
"Calling Card" Assay to identify in vivo genomic targets of DNA-binding factors

treatment_protocol: "Calling Card" Assay performed as previously described: 1. "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins." Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.  Genome Research, 2011, May 21(5):748-55. PMID 21471402. 2. "Calling Card Analysis in Budding Yeast." Mayhew D, Mitra RD.  Cold Spring Harbor Protocols, 2016, Feb 1, 2016(2). PMID 26832687.

tag: strain

tag: genotype

tag: transcription factor


title: 04_18

description: bisulfite conversion


title: Sample_I10_96h_C10

description: Control


title: 20ng_ERFE_MO2_st35_36_repl1


title: 00_15

description: bisulfite conversion


title: U2OS/MTX300 shCBX4_1 cells

city: Guang Zhou

first: Xin

state: State...

address: Dongfengdong road 651

institute: Sun Yat-sen University Cancer Center

description:
Gene expression of U2OS/MTX300 transfected with CBX4_1 shRNA
U2OS/MTX300-shCBX4_1
shCBX4_vs_shControl.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: .txt files include read counts, FPKM values, log2 fold change, p-value and padj for each Sample.

source_name: osteosarcoma cell U2OS/MTX300

growth_protocol: The base medium for this cell line is ATCC-formulated McCoy's 5a Medium Modified, Catalog No. 30-2007. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).. RNA was quantified using a NanoDrop ND-100 UV-VIS spectrophotometer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U2OS/MTX300 cell was transfected with Vector, CBX4, shControl, shCBX4_1 or shCBX4_2, then these sample were used for the global transcriptomes analysis.

tag: cell line

tag: cell type

value: osteosarcoma cell


title: Sample_I10_96h_05mG_E9

description: Exposed

value: entire embryos


title: U2OS/MTX300 shCBX4_2 cells

description:
Gene expression of U2OS/MTX300 transfected with CBX4_2 shRNA
U2OS/MTX300-shCBX4_2
shCBX4_vs_shControl.txt


title: 04_26ET

description: bisulfite conversion

value: essential tremor


title: 10ng_ERFE_MO1_st35_36_repl1


title: U2OS/MTX300 cells overexpressing CBX4

description:
Gene expression of U2OS/MTX300 transfected with pSIN-CBX4
U2OS/MTX300-WT
WT_vs_Vector.txt


title: 02_27ET

description: bisulfite conversion


title: 10ng_cMO_st35_36_repl1


title: Sample_I10_96h_05mG_E11

description: Exposed

value: AB


title: Sample_I32_24h_C4

description: Control


title: U2OS/MTX300 reference cells

description:
Gene expression of U2OS/MTX300 transfected with pSIN-Vector
U2OS/MTX300-Vector
WT_vs_Vector.txt


title: Sample_I10_48h_C8

description: Control


title: Sample_I10_48h_C7

description: Control


title: 02_24ET

description: bisulfite conversion


title: 04_38ET

description: bisulfite conversion


title: 99_58

description: bisulfite conversion


title: 20ng_ERFE_MO2_st41_repl3

value: stage 41

value: whole embryo


title: uninjected_st35_36_repl1


title: 20ng_cMO_st35_36_repl1


title: Sample_I10_48h_C6

description: Control


title: U2OS/MTX300 control shRNA cells

description:
Gene expression of U2OS/MTX300 transfected with control shRNA
U2OS/MTX300-shControl
shCBX4_vs_shControl.txt


title: Sample_I10_96h_05mG_E10

description: Exposed


title: 03_58

description: bisulfite conversion


title: Sample_I10_48h_05mG_E7

description: Exposed


title: Sample_I10_48h_05mG_E6

description: Exposed


title: 08_85ET

description: bisulfite conversion


title: 04_05ET

description: bisulfite conversion


title: EC-E2

type: RNA

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

hyb_protocol: sample was hybridized to the Affymetrix Clariom S Assay,human (Cat No 902926) for 16-18 h at 45°C. Following hybridization, the microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G.

data_processing:
The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method Values are presented according to log2 RMA signal intensity
We defined the genes with a fold-change of more than 1.5 or less than 1.5 and a p-value of less than 0.05 as different expression genes, which were selected to undergo basic analysis

label: biotin

label_protocol: sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT)

extract_protocol: Total RNA was extracted by Trizol (Invitrogen, Carlsbad, CA, USA), and a total of 500 ng RNA was used for cDNA synthesis

value: overexpression of the EN2

value: esophageal squamous cell carcinoma


title: EC-N2

value: control


title: matched non-tumor Tissue of Triple negative breast cancer 6

city: nanjing

first: tang

last: li

address: No. 42 Baiziting Road,

department: Laboratory department

institute: Jiangsu Cancer Hospital

description: lncRNA and mRNA expression data from matched non-tumor tissue of Triple negative breast cancer(TNBC)

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human LncRNA Microarray v4.0, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: non-tumor tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: TNBC and matched non-tumor tissues

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from TNBC surgury were immediately frozen with TRIzol reagent (Invitrogen) in liquid nitrogen as soon as cutting off at the time of surgery, and then stored at -80℃ until required

value: non-tumor tissue

value: Triple negative breast cancer

tag: gender

value: female


title: Triple negative breast cancer Tumor Tissue 6

description: lncRNA and mRNA expression data from  Triple negative breast cancer(TNBC) tumor tissue

source_name: tumor tissue

value: tumor tissue


title: Sample_I10_48h_05mG_E5

description: Exposed


title: matched non-tumor Tissue of Triple negative breast cancer 5


title: DKO_Ctrl_P15_4

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

hyb_protocol: Following fragmentation and labelling, 2.5 ug of cDNA were hybridized for 16 hr at 45°C onto Affymetrix Mouse ClariomS arrays. Then microarrays were  washed and stained using Affymetrix Fluidics FS450 machines.

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 7G system

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

organism: Mus musculus

source_name: P15_DKO_mammary cells

label_protocol: Biotinylated cDNA were prepared according to the Ovation® Pico WTA System V2 protocol and the Nugen Encore Biotin Module from 500pg total RNA

growth_protocol: Not applied (fresh tissue)

extract_protocol: Qiagen micro-columns

value: Mammary cells

tag: cell subtype

value: a3a6KO luminall cells


title: Triple negative breast cancer Tumor Tissue 5

tag: disease state


title: Sample_I10_24h_C3

description: Control

value: Control


title: matched non-tumor Tissue of Triple negative breast cancer 4


title: 97_45

description: bisulfite conversion

value: cerebellum

value: male


title: Sample_I10_48h_C5

description: Control

value: entire embryos


title: Sample_I10_24h_05mG_E4

description: Exposed


title: Sample_I10_24h_C2

description: Control


title: 03_26

description: bisulfite conversion


title: Sample_I10_24h_05mG_E2

description: Exposed


title: 05_36

description: bisulfite conversion


title: 04_52ET

description: bisulfite conversion

value: essential tremor


title: Triple negative breast cancer Tumor Tissue 4


title: matched non-tumor Tissue of Triple negative breast cancer 3


title: 10_63ET

description: bisulfite conversion


title: Sample_I10_24h_05mG_E1

description: Exposed

value: AB


title: German_shepherd_blood_WGBS

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

description: MethylC-seq

data_processing:
Adaptor sequences and low quality bases were removed using trimmomatic tool (Bolger et al, 2014)
Sequencing reads were aligned to in-silico bisulphite-converted reference genome Canis lupus familiaris (Nala.recalled.contigs.arrow2_racon_polished.fasta) using WALT mapping tool (Chen et al, 2016)
DNA methylation calling was performed using MethylDackel (https://github.com/dpryan79/MethylDackel)
Genome_build: Canis lupus familiaris (VSDE00000000)
Supplementary_files_format_and_content: bigtable.tsv / For bigtable.tsv" processed data files the column headers are as follows: column 1 - assembly (chromosome). column 2 - position: coordinate for the cytosine position on the chromosome. column 3 (.C) - number of reads depicting a methylated cytosine. column 4 (.cov) - total number of reads at that position.

organism: Canis lupus familiaris

source_name: Blood-derived DNA subject to WGBS

growth_protocol: German Shepherd's whole blood

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue kit (Qiagen, USA).
MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 300 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA).

treatment_protocol: no treatment

tag: breed

value: German Shepherd

value: blood


title: NK cells, 397_BM_I

status: Public on Feb 03 2020

city: Pittsburgh

first: Mark

middle: Jay

last: Shlomchik

state: PA

address: W1052 Biomedical Science Tower 200 Lothrop St

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
RNA-Seq reads were aligned to hg38 with STAR aligner v.2.5.2b with default parameters
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
DESeq2 was used to normalize the read counts for library size difference correction and ComBat (sva) package was used to correct to sequencing batch differences
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: BM

growth_protocol: Tissues were obtained from deceased organ donors as part of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement with LiveOnNY as described previously (Carpenter et al., 2018; Gordon et al., 2017; Granot et al., 2017; Kumar et al., 2017; Miron et al., 2018; Senda et al., 2019). Donors were previously healthy and free of cancer, chronic diseases, seronegative for hepatitis B, C, and HIV, and represented diverse ages (Table S1). This study does not qualify as “human subjects” research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals.

extract_protocol:
CD56brightCD16- and CD56dimCD16+ NK cell were sorted from blood, BM, spleen, lung and LN of four donors (D363,D368, D372, D397) using the BD-influx sorter. RNA was isolated from cell pellets using the RNeasy Mini Kit (Qiagen), and RNA concentration and quality was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies).
standard Truseq with poly-A pulldown

treatment_protocol: Tissue samples were maintained in cold saline and brought to the laboratory within 2-4hrs of organ procurement. Spleen, lung, and intestinal samples were processed using enzymatic and mechanical digestion resulting in high yields of live leukocytes, as described previously (Sathaliyawala et al., 2013; Thome et al., 2014). Lymphocytes were isolated from blood samples using centrifugation through lymphocyte separation medium (Corning) for recover of mononuclear cells.

tag: individual

tag: tissue

value: BM

value: NK

tag: subset


title: NK cells, 368_SP_M

source_name: Spleen

value: Spleen


title: NK cells, 397_LN_M

source_name: LN

value: LN


title: NK cells, 368_SP_I


title: Triple negative breast cancer Tumor Tissue 2

value: Triple negative breast cancer


title: NK cells, 397_LN_I


title: matched non-tumor Tissue of Triple negative breast cancer 1

value: non-tumor tissue

value: female


title: NK cells, 397_LU_M

source_name: Lung

value: Lung


title: NK cells, 368_BL_M

source_name: Blood

value: Blood


title: matched non-tumor Tissue of Triple negative breast cancer  2


title: Triple negative breast cancer Tumor Tissue 1

value: tumor tissue


title: NK cells, 368_BL_I


title: NK cells, 372_LN_M


title: NK cells, 372_SP_I


title: NK cells, 372_SP_M


title: NK cells, 372_BL_M


title: NK cells, 372_BL_I


title: NK cells, 363_LU_M


title: NK cells, 363_LN_M


title: NK cells, 372_LU_I


title: NK cells, 372_LU_M


title: NK cells, 397_LU_I


title: Triple negative breast cancer Tumor Tissue 3


title: NK cells, 397_BM_M


title: NK cells, 363_LN_I


title: NK cells, 363_LU_I


title: NK cells, 363_SP_M


title: NK cells, 372_LN_I


title: NK cells, 363_SP_I


title: NK cells, 372_BM_M


title: NK cells, 363_BM_I


title: NK cells, 363_BL_M


title: NK cells, 363_BL_I


title: NK cells, 372_BM_I


title: STAG2nullA_ATACRep2

city: Dunedin

first: Jisha

last: Antony

state: Otago

address: 58 Hanover Street

department: Pathology

country: New Zealand

institute: University of Otago

description: CRISPR-Cas9 edited

data_processing:
Reads were adaptor trimmed using cutadapt .version v1.15.
Reads were aligned hg19 human genome using bowtie2 (version 2.2.9) with the following options: --local -k 4 --maxins 2000
Reads falling into blackregions were excluded and duplicates were removed using (picard MarkDuplicates)
Peaks were called using MACS2 (version 2.1.0.) with the following parameters: -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all  --call-summits
Regions were defined as 500 nucleotides centered on peak summit.
Genome_build: Human GRCh37 (hg19)
Supplementary_files_format_and_content: Peak files are in tab separated format

source_name: K562 cell line

growth_protocol: K562 cells were obtained from ATCC and grown in Isocove’s Modified Dulbecco’s Media (IMDM) (Life Technologies) containing 10% fetal bovine serum. Adherent STAG2 R614* mutant homozyogus cells were detached for subculture using trypsin-EDTA at 0.005% final concentration (Life technologies).

extract_protocol: ATAC assays using bacterial Tn5 transposase were performed as described previously (PMID: 25559105 ;PMID: 28118844). Briefly 50,000 cells/sample/replicate were washed and lysed. Transposition reactions were set up with the Illumina Nextera DNA Preparation and indexing kits (Illumina #FC-121-1030). Genomic DNA was then purified, and libraries were PCR-amplified with indexing primers and sequenced on HiSeq 2500 as 100 bp single end reads at the Otago Genomics Facility (New Zealand)

tag: mutation

value: STAG2 R614*


title: STAG2heterozygous1_ATACRep3

description: CRISPR-Cas9 edited


title: STAG2nullA_ATACRep1

description: CRISPR-Cas9 edited


title: STAG2nullA_ATACRep3

description: CRISPR-Cas9 edited


title: Sonication_ChIPseq_Input_0h

city: Berkeley

first: Eugene

last: Oh

address: 330 Li Ka Shing

institute: UC Berkeley

data_processing:
For ChIPseq samples, reads were aligned with Bowtie2 (2.3.4.1) using the following parameters (bowtie2 --local -x hg19 -U filename.fastq.gz -S filename.sam). ChIP peaks were called with macs14 (1.4.2) using the following parameters (macs14 -t ChIP.bam -c Input.bam -n filename -g 2.7e9 -S -w). bigWig files were generated with deeptools (3.2.1) using the following parameters (bamCoverage -b file_sorted.bam -o file.bw --binSize 25 --normalizeUsing CPM --extendReads 100).
For RNAseq samples, reads were aligned to transcripts with kallisto (0.44.0) under the following parameters (kallisto quant -i hg19.idx -o filename R1.fastq.gz R2.fastq.gz -b 200). Processed RNAseq data include tab-delimited text files of TPM values.
Genome_build: hg19

growth_protocol: H1s were grown on hESC-qualified Matrigel (Corning) in mTeSR medium (Stemcell Technologies).

extract_protocol:
DNA was sheared by sonication and protein-DNA complexes were isolated with aK11 antibody (lab reagent).
Sheared DNA was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.

treatment_protocol: H1s were treated with 5 µM STLC for mitotic synchronization (14 h). Cells were then subjected to formaldehyde crosslinking (1% final) for 10 min at room temperature prior to harvesting.

value: human embryonic stem cells

tag: chip antibody


title: Sonication_ChIPseq_aK11_0h

value: aK11 (lab reagent)


title: MLL-r AML PDX treated with combination treatment replicate 1

city: Adelaide

first: Richard

last: D'Andrea

state: South Australia

address: Cancer Research Institute, Frome Road

department: Centre for Cancer Biology

institute: University of South Australia

data_processing:
Sequence mapping to human genome (UCSC hg19) and gene counts were computed using STAR (v2.5.3a). Differential gene expression (DGE) analysis compare to vehicle treated sample was performed in R with package edgeR (v3.22.5), with trimmed mean of M-values (TMM) normalization. A filter of false discorvery rate (FDR) < 0.05 and absolute log2 fold change (FC) > 1 in expression compare to vehicle treated cells was applied to filter for significantly differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files of raw gene counts for all samples computed by STAR

growth_protocol: Cryopreserved MLL-r AML (AML-18) PDX cells were thawed and allowed to equilibrate for 3 hours prior to in vitro drug treatment

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and purified using the RNeasy kit (Qiagen)
Whole transcriptome libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold rRNA depletion

treatment_protocol: Cells were treated in vitro with 250 nM CDKI-73, 1480 nM JQ1, the combination of both drugs or vehicle control (DMSO) for 4 hours

value: Patient Derived Xenograft

tag: aml subtype

value: MLL-r

tag: treatment

tag: time

value: 4 hour treatment period


title: STAG2heterozygous1_ATACRep1

description: CRISPR-Cas9 edited


title: K562WT_ATACRep1

description: original K562 cells

value: parental no mutation in STAG2

value: wild type


title: MLL-r AML PDX treated with CDKI-73 replicate 2

value: 250nM CDKI-73


title: MLL-r AML PDX treated with CDKI-73 replicate 3


title: MLL-r AML PDX treated with JQ1 replicate 3


title: K562WT_ATACRep2

description: original K562 cells


title: MLL-r AML PDX treated with combination treatment replicate 2


title: NK cells, 363_BM_M

value: BM

value: NK


title: MLL-r AML PDX treated with JQ1 replicate 2


title: K562WT_ATACRep3

description: original K562 cells


title: STAG2heterozygous1_ATACRep2

description: CRISPR-Cas9 edited


title: MLL-r AML PDX treated with DMSO replicate 3

value: DMSO


title: 1481 12hr Rep2

city: Cincinnati

first: Daniel

last: Starczynowski

state: Ohio

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
N2_12hr
1481_12hr-vs-DMSO_Voom_noFilter.xls.txt

data_processing:
Single-end reads (first-stranded dUTP-library prep) were aligned to human reference genome (GRCh37) using TopHat v2.0.13 and a GTF file from iGENOME.
Raw gene counts were calculated from each BAM file using featureCounts v1.5.2 and then all count files were merged into a single matrix.
Raw counts were normalized using edgeR's TMM normalization method
Voom/limma package was used to predict differentially expressed genes.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: (1) Matrix *.csv file of raw counts for each gene. (2) Tab-delimited text files include log fold change realtive to DMSO control samples
Supplementary_files_format_and_content: AC220_6hr-vs-DMSO_Voom_noFilter.txt: log fold change of AC220 (6hr) relative to DMSO control
Supplementary_files_format_and_content: AC220_12hr-vs-DMSO_Voom_noFilter.txt: log fold change of AC220 (12hr) relative to DMSO control
Supplementary_files_format_and_content: 1481_6hr-vs-DMSO_Voom_noFilter.xls.txt: log fold change of NCGC1481 (6hr) relative to DMSO control
Supplementary_files_format_and_content: 1481_12hr-vs-DMSO_Voom_noFilter.xls.txt: log fold change of NCGC1481 (12hr) relative to DMSO control

source_name: CD34+ umbilical cord blood

growth_protocol: Cells were grown in IMDM media with 20% FBS and 1% Pen/Strep

extract_protocol:
RNA was extracted using Quick-RNA MiniPrep (Zymo Research, Cat#R1055) following manufacturer's protocol
RNA libraries were prepared according to the Illumina TruSeq Stranded mRNA (polyA capture) library protocol

treatment_protocol: Cells were treated with DMSO (1:1000), AC220 (0.3 nM), or NCGC1481 (0.1 nM) for 6 and 12 hours

tag: tumor type

value: Acute Myeloid Leukemia

tag: retroviral transgenes

value: MLL-AF9 fusion and FLT3-ITD

tag: agent

tag: time point


title: MLL-r AML PDX treated with DMSO replicate 1

tag: cell type


title: 1481 12hr Rep3

description:
N3_12hr
1481_12hr-vs-DMSO_Voom_noFilter.xls.txt


title: MLL-r AML PDX treated with DMSO replicate 2


title: 1481 6hr Rep3

description:
N3_6hr
1481_6hr-vs-DMSO_Voom_noFilter.xls.txt


title: 1481 6hr Rep2

description:
N2_6hr
1481_6hr-vs-DMSO_Voom_noFilter.xls.txt


title: 1481 12hr Rep1

description:
N1_12hr
1481_12hr-vs-DMSO_Voom_noFilter.xls.txt


title: MLL-r AML PDX treated with CDKI-73 replicate 1


title: AC220 12hr Rep2

description:
AC220_12hr_Rep2
AC220_12hr-vs-DMSO_Voom_noFilter.txt


title: AC220 12hr Rep3

description:
AC220_12hr_Rep3
AC220_12hr-vs-DMSO_Voom_noFilter.txt


title: MLL-r AML PDX treated with combination treatment replicate 3


title: AC220 6hr Rep1

description:
AC220_6hr_Rep1
AC220_6hr-vs-DMSO_Voom_noFilter.txt


title: AC220 12hr Rep1

description:
AC220_12hr_Rep1
AC220_12hr-vs-DMSO_Voom_noFilter.txt


title: 1481 6hr Rep1

description:
N1_6hr
1481_6hr-vs-DMSO_Voom_noFilter.xls.txt


title: DMSO Rep3

description:
Control3
AC220_6hr-vs-DMSO_Voom_noFilter.txt
AC220_12hr-vs-DMSO_Voom_noFilter.txt
1481_6hr-vs-DMSO_Voom_noFilter.xls.txt
1481_12hr-vs-DMSO_Voom_noFilter.xls.txt


title: DMSO Rep1

description:
Control1
AC220_6hr-vs-DMSO_Voom_noFilter.txt
AC220_12hr-vs-DMSO_Voom_noFilter.txt
1481_6hr-vs-DMSO_Voom_noFilter.xls.txt
1481_12hr-vs-DMSO_Voom_noFilter.xls.txt


title: MLL-r AML PDX treated with JQ1 replicate 1


title: DMSO Rep2

description:
Control2
AC220_6hr-vs-DMSO_Voom_noFilter.txt
AC220_12hr-vs-DMSO_Voom_noFilter.txt
1481_6hr-vs-DMSO_Voom_noFilter.xls.txt
1481_12hr-vs-DMSO_Voom_noFilter.xls.txt


title: AC220 6hr Rep3

description:
AC220_6hr_Rep3
AC220_6hr-vs-DMSO_Voom_noFilter.txt


title: AC220 6hr Rep2

description:
AC220_6hr_Rep2
AC220_6hr-vs-DMSO_Voom_noFilter.txt


title: revWL9

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

data_processing:
FastQC
BowTie2
Cufflinks

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plant were grown in continuous light conditions

extract_protocol:
RNA extraction using Sigma Spectrum Plant total RNA kit; library prep with Illumina TruSeq kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants were grown in either WL or WL+FR

value: white light

tag: genotype/variation

value: rev5 mutant


title: revFR12

value: white light + far red


title: woxFR7

value: wox4 mutant


title: revWL10


title: revFR11


title: woxFR8


title: woxWL5


title: ColWL1

value: Wild type


title: ColWL2


title: Riboseq.lizard.testis.wt.adult.rep1

city: Rochester

last: Li

state: NY

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

description: Ribosome footprints

data_processing:
Library strategy: Ribo-seq
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and green lizard genome release anoCar2 (GCA_000090745.1). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads; spike-in RNA was used to normalize the libraries with and without RNase treatment. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the uORF or UDR of a transcript.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis. Libraries from harringtonine treatment were further normalized to the sum of reads mapping to mitochondrial coding sequences. Libraries from puromycin treatment were further normalized to the sum of reads mapping to the 5´-UTR of mRNAs.
For Degradome data, reads were aligned to the genome using TopHat 2.0.12. Reads were mapped uniquely using the ‘-g 1’ flag. Uniquely mapping reads were selected for further analysis. Libraries were normalized to the sum of reads mapping to mRNA protein-coding regions, assuming that mRNA cleavage was largely unchanged during spermatogenesis.
Genome_build: Mouse: mm10 (GCA_000001635.7, GRCm38), Lizard: anoCar2 (GCA_000090745.1, AnoCar2.0).
Supplementary_files_format_and_content: For Small RNAseq, Ribo-seq and Degradome, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). RNAseq quantification results are .sf files output by Salmon software.

organism: Anolis carolinensis

source_name: testis

growth_protocol: Animals mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. Lizards were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA).
Ribo-seq: Testes samples were lysed, RNase T1 & A treated and loaded on sucrose gradients, and 80S monosomes were recovered for library construction. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and has been trimmed in the raw data.

treatment_protocol: The mice were anesthetized with Ketamine/Xylazine mixture (Ketamine 100 mg/kg; Xylazine 25 mg/kg) via intraperitoneal injection. After complete anesthesia, testes were exteriorized with a longitudinal incision around 1 cm at the center of abdomen. The tunica albuginea was penetrated using a sharp 26 G needle (BD, Franklin Lakes, NJ, USA, 30511) 1 mm from the vascular pedicle, and the needle was withdrawn to generate path for introducing a blunt end Hamilton needle (Hamilton, Reno, NV, USA, 7786-02). PBS containing 0.02% Fast Green FCF (Thermo Fisher Scientific, Waltham, MA, USA) with harringtonine (LKT labs, 0.5 μg/μl in a total volume of 10 μl) or puromycin dihydrochloride (Invitrogen, 2.5 μg/μl in a total volume of 10 μl) was slowly injected using a Hamilton microsyringe (1705RN) into one testis, and vehicle control without drug was injected into the other testis. The needle was held in place for 30 seconds before removal to prevent back flow of the solution. Successful completion of injection was indicated by testis filled with green solution. The testes were returned to the abdominal cavity after injection. The incisions were sutured. At the end point, the mice were euthanized by cervical dislocation, and the testes were collected.

value: whole testis

value: wt

tag: age

value: adult


title: ColFR3


title: MN_ChIPseq_H2B_t0_MM102

data_processing:
For ChIPseq samples, reads were aligned with Bowtie2 (2.3.4.1) using the following parameters (bowtie2 --local -x hg19 -U filename.fastq.gz -S filename.sam). ChIP peaks were called with macs14 (1.4.2) using the following parameters (macs14 -t ChIP.bam -c Input.bam -n filename -g 2.7e9 -S -w). bigWig files were generated with deeptools (3.2.1) using the following parameters (bamCoverage -b file_sorted.bam -o file.bw --binSize 25 --normalizeUsing CPM --extendReads 100).
Genome_build: hg19

extract_protocol:
DNA was digested by micrococcal nuclease protein-DNA complexes were isolated with aH2B antibody (CST, 12364).
Chromatin was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.

treatment_protocol: H1s were treated with 5 µM STLC for mitotic synchronization (14 h) and released into fresh medium containing indicated drugs and at indicated time points. Cells were then subjected to formaldehyde crosslinking (1% final) for 10 min at room temperature prior to harvesting.

value: human embryonic stem cells

value: aH2B (Cell Signaling, 12364)


title: MN_ChIPseq_H2B_t4_MM102


title: MN_ChIPseq_H2B_t4_DMSO


title: RNA-Seq of HS HEK293 LARP7 knockout cells (clone 1-11) replicates 1-2

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

institute: University of Regensburg

description: Alternative_splicing_events_HS_40_polyA-RNA.xlsx

data_processing:
Sequencing was performed using HiSeq Control Software HD 3.4.0.38 with read structure 76B + 8I + 98B.
Base calling was performed using Illumina RTA version 2.7.7 with IlluminaBasecallsToMultiplexSam version 2.18.11.
Bam to Sam conversion was performed with Samtools version 1.3.1.
Sam files were processed in R version 3.3.3 using the ShortRead 1.32.1 package and Fastq files were generated.
Differential splicing was analyzed using VAST-TOOLS version 2.0.2 with the additional "diff" module (Han et. al., 2017).
Genome_build: hg38
Supplementary_files_format_and_content: Excel file containing alternative splice sites.

molecule: polyA RNA

growth_protocol: HEK293 cells were cultivated in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 mg/mL streptomycin. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted with with the RNeasy Mini Kit (Qiagen) including the shredding step via QIAshredder columns (Qiagen) and the DNase digestion step. The RNA quality was assayed on a TapeStation 4200 device. For none of the samples the RINe value was below 9.0.
Libraries of polyA+ RNA were prepared with the Universal Plus mRNA-Seq Kit (NuGEN Technologies) according to the manufacturer’s instructions.

treatment_protocol: 24h prior treatment cells were seeded into 6-well plates. For the heat shocks, plates were sealed with parafilm and incubated in a pre-warmed water bath for 2 hours at 40°C.

tag: origin

value: human embryonic kidney

value: LARP7 knockout


title: RNA-Seq of HS HEK293 LARP7 knockout cells (clone 3-6) replicates 1-2


title: MN_ChIPseq_H2B_t0_DMSO


title: RNA-Seq of HS HEK293 cells replicates 1-2

value: wild type


title: B_LCL_AAAS14 replicates 1-2

description: Alternative_splicing_events_Alazami_polyA-RNA.xlsx

source_name: Blood lymphocytes

growth_protocol: B-LCLs cells were cultivated in RPMI-1640 with L-glutamine supplemented with 15% fetal bovine serum. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

value: human blood

tag: donor

value: male, 4 years, affected by Alazami syndrome

tag: genotype

value: homozygous for the LARP7 variant c.1669-1_1671del (NM_016648.3); dbSNP accession:rs778909076

tag: generation of cell line

value: B-LCL were established from Ficoll-isolated blood lymphocytes via transformation by Epstein-Barr virus.


title: B_LCL_AASD72 replicates 1-2

value: male, 46 years, healthy

value: heterozygous for the LARP7 variant c.1669-1_1671del (NM_016648.3); dbSNP accession:rs778909076


title: woxWL6

value: white light


title: MN_ChIPseq_K11_siCDC20

extract_protocol:
DNA was digested by micrococcal nuclease protein-DNA complexes were isolated with aK11 antibody (lab reagent).
Chromatin was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.

treatment_protocol: H1s were transfected with indicated siRNAs for 36 h and subsequently treated with 5 µM STLC for mitotic synchronization (14 h). Cells were then subjected to formaldehyde crosslinking (1% final) for 10 min at room temperature prior to harvesting.

value: aK11 (lab reagent)


title: MN_ChIPseq_Input_siWDR5

extract_protocol:
DNA was digested by micrococcal nuclease. Input DNA was purified following digestion.
Chromatin was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.


title: MN_ChIPseq_K11_siCTRL


title: MN_ChIPseq_K11_siWDR5


title: MN_ChIPseq_K11_t2_DMSO


title: MN_ChIPseq_K11_t0_DMSO


title: MN_ChIPseq_Input_t0_MM102


title: MN_ChIPseq_Input_t2_DMSO


title: MN_ChIPseq_K11_t0_MM102


title: MN_ChIPseq_Input_t2_NMS


title: ColFR4

value: white light + far red

value: Wild type


title: MN_ChIPseq_H3_10h

extract_protocol:
DNA was digested by micrococcal nuclease protein-DNA complexes were isolated with aH3 antibody (Abcam, 1791).
Chromatin was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.

treatment_protocol: H1s were treated with 5 µM STLC for mitotic synchronization (14 h) and released into fresh medium at indicated time points. Cells were then subjected to formaldehyde crosslinking (1% final) for 10 min at room temperature prior to harvesting.


title: MN_ChIPseq_Input_t0_DMSO


title: MN_ChIPseq_H3_8h


title: MN_ChIPseq_H3_2h


title: MN_ChIPseq_H3_0h


title: MN_ChIPseq_WDR5_10h

extract_protocol:
DNA was digested by micrococcal nuclease protein-DNA complexes were isolated with aWDR5 antibody (Diagenode, C15410027).
Chromatin was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.

value: aWDR5 (Diagenode, C15410027)


title: MN_ChIPseq_K11_10h_rep2


title: MN_ChIPseq_WDR5_2h


title: MN_ChIPseq_Input_siCDC20


title: MN_ChIPseq_K11_8h_rep2


title: MN_ChIPseq_Input_siCTRL


title: MN_ChIPseq_K11_2h_rep2


title: MN_ChIPseq_K11_0h_rep2


title: MN_ChIPseq_TBP_10h

extract_protocol:
DNA was digested by micrococcal nuclease protein-DNA complexes were isolated with aTBP (Cell Signaling, 44059).
Chromatin was end-repaired, poly-adenylated, Y adaptor-ligated, and PCR-amplified.

value: aTBP (Cell Signaling, 44059)


title: MN_ChIPseq_K11_t2_NMS

value: human embryonic stem cells


title: MN_ChIPseq_TBP_8h


title: MN_ChIPseq_K11_8h_rep1


title: MN_ChIPseq_K11_10h_rep1


title: MN_ChIPseq_TBP_2h


title: MN_ChIPseq_TBP_0h


title: MN_ChIPseq_K11_2h_rep1


title: RNAseq_8h

description: poly(A) selected RNA

extract_protocol:
Total RNA was purified from cells by TRIzol. Poly-adenylated mRNA was then purified from total RNA.
Libraries from poly(A)-selected RNA were made using the KAPA mRNA HyperPrep kit (KK8580).

treatment_protocol: H1s were treated with 5 µM STLC for 14 h and released into fresh mTeSR medium at indicated time points (in h).


title: MN_ChIPseq_Input_10h


title: MN_ChIPseq_Input_8h


title: RNAseq_0h

description: poly(A) selected RNA


title: RNAseq_siWDR5_rep2

description: poly(A) selected RNA

treatment_protocol: H1s were transfected with indicated siRNAs for 48 h with RNAiMAX.


title: MN_ChIPseq_K11_0h_rep1


title: RNA-Seq of HEK293 cells replicates 1-2

data_processing:
Sequencing was performed using HiSeq Control Software HD 3.4.0.38 with read structure 150B + 16I + 8I + 150B.
Base calling was performed using Picard Tools Illumina2bam version 1.17. The Nugen Ovation SoLo RNA-seq system provides an eight bases unique molecular identifier. The UMI starts at position 9 in SAM tag "BC", corresponding quality values can be found in SAM tag "QT".
Bam to Sam conversion was performed with Samtools version 1.3.1.
Sam files were processed in R version 3.3.3 using the ShortRead 1.32.1 package and Fastq files were generated.
Adapter clipping was performed using Cutadapt version 1.6.
Reads were mapped to ENSEMBL human genome (hg38) using STAR aligner version 2.5.3a.
Transcript expression levels were quantified with Salmon version 1.6.
Differential analysis was performed in R version 3.5.1 with the Bioconductor package edgeR version 3.24.3.
Differential splicing was analyzed using VAST-TOOLS version 2.0.2 with the additional "diff" module (Han et. al., 2017).
Genome_build: hg38
Supplementary_files_format_and_content: Salmon quantification output for each replicate.
Supplementary_files_format_and_content: Excel file containing alternative splice sites.

source_name: HEK293 wildtype

extract_protocol:
Total RNA was extracted with the TRIzol reagent (Invitrogen) and the quality was assayed on a TapeStation 4200 device. For none of the samples the RINe value was below 9.0.
Libraries were prepared with the Ovation SoLo RNA-seq system (NuGEN Technologies) according to the manufacturer’s instructions. Sequencing was performed using the Ovation SoLo Custom R1 primer included in the Ovation SoLo RNA-seq kit.

tag: cell line


title: MN_ChIPseq_Input_2h


title: MN_ChIPseq_WDR5_0h


title: MN_ChIPseq_WDR5_8h


title: FlagCDC20_Input_rep2

data_processing:
Reads were aligned using Bowtie2 under the following parameters (bowtie2 --local -x hg19 -1 R1.fastq.gz -2 R2.fastq.gz -S filename.sam).
ChIP peaks were called with macs14 (1.4.2) using the following parameters (macs14 -t ChIP.bam -c Input.bam -n filename -g 3.3e9 -S -w).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: WIG and peaks.bed files were generated using macs14 (1.4.2).

source_name: HEK 293T cells

growth_protocol: HEK 293T cells were grown in DMEM+10% FBS.

extract_protocol:
DNA was sheared by sonication and protein-DNA complexes were isolated with Flag M2 antibody (Sigma F1804).
Libraries were generated using the Wafergen DNA prep kit (Illumina PrepX). Indexing and fragment enrichment were performed by PCR (Kapa HiFi PCR kit). DNA fragments were further size selected using SAGE Pippin Prep (<600 bp).

treatment_protocol: HEK 293T cells were PEI-transfected with plasmids containing FlagCDC20 or FlagWDR5 for 48 h. Cells were then subjected to formaldehyde crosslinking (1% final) for 10 min at room temperature prior to harvesting.

value: HEK 293T

tag: overexpression


title: FlagWDR5-Input

tag: chip antibody


title: FlagCDC20_CHIP_rep1

value: Flag M2 (Sigma F1804)


title: RNAseq_siCTRL_rep2

description: poly(A) selected RNA


title: LungEC-Ribotag-168hr-rep4 (Sample 215)

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 840 S Wood St

institute: University of Illinois at Chicago

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequenced reads from all samples were aligned to the mouse (mm10) reference genome with STAR v. 2.4.2 44, and the aligned reads were used to quantify mRNA expression by using HTSeq-count v. 0.6.1 45.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

extract_protocol:
[RiboTag]  The tissue samples were extracted from Cdh5CreERT2/+; Rpl22HA/+ mice, flash-frozen in liquid nitrogen and then stored at −80 °C. The samples were then homogenized on ice in ice-cold homogenization buffer (50 mM Tris, pH7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:100 protease inhibitor (Sigma), 200 units/mL RNasin (Promega) 1 mg/mL heparin and 0.1 mg/mL cycloheximide (Sigma) in RNase free DDW) 10% w/v with a Dounce homogenizer (Sigma) until the suspension was homogeneous. To remove cell debris, 1 mL of the homogenate was transferred to an Eppendorf tube and was centrifuged at 10,000xg and 4°C for 15 min. Supernatants were subsequently transferred to a fresh Eppendorf tube on ice, then 100 μL was removed for “input” analysis and 3 μL (=3 µg) of anti-HA antibody (ab9110, Abcam) or 3 μL (=1µg) of mouse monoclonal IgG1 antibody (Sigma, Cat# M5284) or 6 μL anti-RPL22 (Invitrogen Cat# PA5-68320) was added to the supernatant, followed by 1h of incubation with slow rotation in a cold room at 4 °C. Meanwhile, Pierce™ Protein A/G Magnetic Beads (Thermo Fisher Scientific), 100 μL per sample, were equilibrated to homogenization buffer by washing three times. At the end of 1h of incubation with antibody, beads were added to each sample, followed by incubation 1 h in cold room at 4 °C. After that, samples were washed three times with high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:200 protease inhibitor, 100 units/mL RNasin and 0.1 mg/mL cycloheximide in RNase free DDW), 5 min per wash in a cold room on a rotator. At the end of the washes, beads were magnetized, and excess buffer was removed, 350 µL Lysis Buffer was added to the beads and RNA was extracted with RNeasy plus Mini kit (Qiagen). RNA was eluted in 30 μL H2O and taken for RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen treatment: 5mg of tamoxifen were administered to mice by gavage 4 times every other day at the age of 4-6 weeks. LPS treatment: LPS was injected intraperitonealy 10mg/kg, mice were sacrificed at 6h, 24hr, 48hr, 72hr, 168hr post injection

tag: strain

tag: tissue

value: Lung Endothelium

tag: developmental stage

value: adult

value: Cdh5CreERT2/+; Rpl22HA/+

value: LPS


title: RNAseq_siWDR5_rep1

description: poly(A) selected RNA


title: RNAseq_10h

description: poly(A) selected RNA


title: LungEC-Ribotag-168hr-rep3 (Sample 213)

tag: treatment

tag: time


title: LungEC-Ribotag-168hr-rep2 (Sample 212)


title: RNAseq_siCTRL_rep1

description: poly(A) selected RNA


title: RNA-Seq of HEK293 LARP7 knockout cells (clone 1-11) replicates 1-2

value: human embryonic kidney

value: LARP7 knockout


title: FlagCDC20_CHIP_rep2


title: LungEC-Ribotag-168hr-rep5 (Sample 217)


title: RNAseq_2h

description: poly(A) selected RNA


title: LungEC-Ribotag-72hr-rep3 (Sample 207)


title: LungEC-Ribotag-168hr-rep5 (Sample 216)


title: LungEC-Ribotag-168hr-rep1 (Sample 211)


title: LungEC-Ribotag-72hr-rep4 (Sample 208)


title: FlagCDC20_Input_rep1


title: LungEC-Ribotag-72hr-rep2 (Sample 206)


title: LungEC-Ribotag-72hr-rep5 (Sample 210)


title: LungEC-Ribotag-168hr-rep4 (Sample 214)


title: LungEC-Ribotag-72hr-rep2 (Sample 204)


title: 02_06ET

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

institute: Loma Linda University

description: bisulfite conversion

data_processing:
NextSeq550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings. Reads were filtered for full-length(70bp) reads.
Fastq header contains 8 nt index sequence and N6 Nugen RRBS duplicate information. Adaptors and low quality reads were trimmed with Trim_galore v0.4.5. and reads containing adapter were discarded.
Following adaptor and quality trimming, the fastq files were further trimmed with NuGEN custom python script trimRRBSdiversityAdaptCustomers.py. Potential PCR or optical duplicates were removed using NuGEN python script Nudup.py
Trimmed reads was aligned to the human genome, allowing for 1 mismatch and retaining only uniquely mapped reads. Bam files were generated using Bismark v0.16.334. CpG coverage reports were generated using MethylKit from bam files.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: CpG coverage report in text format

source_name: cerebellum from deceased patient

extract_protocol:
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
Nugen Ovation RRBS Methyl-Seq protocol with QIAGEN EpiTech Fast DNA Bisulfite Kit for bisulfite conversion

tag: disease state

value: essential tremor

value: cerebellum

tag: Sex

value: female


title: LungEC-Ribotag-72hr-rep1 (Sample 199)


title: LungEC-Ribotag-72hr-rep2 (Sample 203)


title: LungEC-Ribotag-72hr-rep1 (Sample 202)


title: LungEC-Ribotag-72hr-rep2 (Sample 205)


title: LungEC-Ribotag-72hr-rep1 (Sample 201)


title: LungEC-Ribotag-72hr-rep1 (Sample 200)


title: LungEC-Ribotag-48hr-rep7 (Sample 197)


title: FlagWDR5-ChIP


title: LungEC-Ribotag-72hr-rep5 (Sample 209)


title: LungEC-Ribotag-48hr-rep2 (Sample 189)


title: LungEC-Ribotag-48hr-rep3 (Sample 192)


title: LungEC-Ribotag-48hr-rep4 (Sample 193)


title: LungEC-Ribotag-48hr-rep6 (Sample 195)


title: LungEC-Ribotag-48hr-rep2 (Sample 190)


title: LungEC-Ribotag-48hr-rep2 (Sample 191)


title: LungEC-Ribotag-48hr-rep1 (Sample 187)


title: LungEC-Ribotag-48hr-rep6 (Sample 196)


title: LungEC-Ribotag-48hr-rep2 (Sample 188)


title: LungEC-Ribotag-48hr-rep1 (Sample 186)


title: LungEC-Ribotag-48hr-rep1 (Sample 185)


title: LungEC-Ribotag-24hr-rep2 (Sample 181)


title: LungEC-Ribotag-24hr-rep3 (Sample 183)


title: LungEC-Ribotag-24hr-rep1 (Sample 180)


title: LungEC-Ribotag-24hr-rep3 (Sample 182)


title: LungEC-Ribotag-48hr-rep1 (Sample 184)


title: LungEC-Ribotag-6hr-rep4 (Sample 178)


title: LungEC-Ribotag-6hr-rep5 (Sample 179)


title: LungEC-Ribotag-6hr-rep3 (Sample 177)


title: LungEC-Ribotag-6hr-rep3 (Sample 174)


title: LungEC-Ribotag-6hr-rep3 (Sample 175)


title: LungEC-Ribotag-48hr-rep7 (Sample 198)


title: LungEC-Ribotag-6hr-rep2 (Sample 173)


title: LungEC-Ribotag-6hr-rep3 (Sample 176)


title: LungEC-Ribotag-6hr-rep2 (Sample 171)


title: LungEC-Ribotag-6hr-rep2 (Sample 172)


title: LungEC-Ribotag-6hr-rep1 (Sample 168)


title: LungEC-Ribotag-6hr-rep1 (Sample 169)


title: LungEC-Ribotag-6hr-rep2 (Sample 170)


title: LungEC-Ribotag-6hr-rep1 (Sample 167)


title: LungEC-Ribotag-0hr-rep3 (Sample 163)

value: control


title: LungEC-Ribotag-0hr-rep3 (Sample 162)


title: LungEC-Ribotag-0hr-rep5 (Sample 165)


title: LungEC-Ribotag-0hr-rep2 (Sample 159)


title: LungEC-Ribotag-0hr-rep3 (Sample 161)


title: LungEC-Ribotag-0hr-rep3 (Sample 160)


title: LungEC-Ribotag-0hr-rep4 (Sample 164)


title: LungEC-Ribotag-6hr-rep1 (Sample 166)


title: LungEC-Ribotag-0hr-rep2 (Sample 158)


title: LungEC-Ribotag-0hr-rep2 (Sample 156)


title: HeartEC-Ribotag-168hr-rep5 (Sample 154)

source_name: Heart

value: Heart Endothelium


title: LungEC-Ribotag-0hr-rep1 (Sample 155)


title: LungEC-Ribotag-0hr-rep2 (Sample 157)


title: HeartEC-Ribotag-168hr-rep4 (Sample 152)


title: HeartEC-Ribotag-168hr-rep3 (Sample 150)


title: HeartEC-Ribotag-168hr-rep4 (Sample 151)


title: HeartEC-Ribotag-168hr-rep5 (Sample 153)


title: HeartEC-Ribotag-72hr-rep5 (Sample 147)


title: HeartEC-Ribotag-168hr-rep1 (Sample 148)


title: HeartEC-Ribotag-72hr-rep4 (Sample 145)


title: HeartEC-Ribotag-72hr-rep3 (Sample 144)


title: HeartEC-Ribotag-72hr-rep5 (Sample 146)


title: HeartEC-Ribotag-72hr-rep2 (Sample 143)


title: HeartEC-Ribotag-168hr-rep2 (Sample 149)


title: LungEC-Ribotag-48hr-rep5 (Sample 194)


title: HeartEC-Ribotag-72hr-rep2 (Sample 142)


title: HeartEC-Ribotag-72hr-rep2 (Sample 141)


title: HeartEC-Ribotag-72hr-rep2 (Sample 140)


title: HeartEC-Ribotag-72hr-rep1 (Sample 136)


title: HeartEC-Ribotag-72hr-rep1 (Sample 138)


title: HeartEC-Ribotag-48hr-rep2 (Sample 127)


title: HeartEC-Ribotag-48hr-rep7 (Sample 134)


title: HeartEC-Ribotag-48hr-rep3 (Sample 129)


title: HeartEC-Ribotag-48hr-rep1 (Sample 122)


title: HeartEC-Ribotag-72hr-rep1 (Sample 137)


title: HeartEC-Ribotag-48hr-rep1 (Sample 123)


title: HeartEC-Ribotag-48hr-rep5 (Sample 131)


title: HeartEC-Ribotag-48hr-rep2 (Sample 125)


title: HeartEC-Ribotag-48hr-rep6 (Sample 133)


title: HeartEC-Ribotag-48hr-rep1 (Sample 121)


title: HeartEC-Ribotag-48hr-rep6 (Sample 132)


title: HeartEC-Ribotag-24hr-rep4 (Sample 118)


title: HeartEC-Ribotag-24hr-rep2 (Sample 115)


title: HeartEC-Ribotag-24hr-rep5 (Sample 120)


title: HeartEC-Ribotag-24hr-rep5 (Sample 119)


title: HeartEC-Ribotag-24hr-rep3 (Sample 116)


title: HeartEC-Ribotag-48hr-rep1 (Sample 124)


title: HeartEC-Ribotag-48hr-rep4 (Sample 130)


title: HeartEC-Ribotag-24hr-rep4 (Sample 117)


title: HeartEC-Ribotag-24hr-rep2 (Sample 114)


title: HeartEC-Ribotag-48hr-rep7 (Sample 135)


title: HeartEC-Ribotag-72hr-rep1 (Sample 139)


title: HeartEC-Ribotag-24hr-rep2 (Sample 113)


title: HeartEC-Ribotag-48hr-rep2 (Sample 126)


title: HeartEC-Ribotag-24hr-rep1 (Sample 111)


title: HeartEC-Ribotag-48hr-rep2 (Sample 128)


title: HeartEC-Ribotag-24hr-rep2 (Sample 112)


title: HeartEC-Ribotag-6hr-rep6 (Sample 110)


title: HeartEC-Ribotag-6hr-rep5 (Sample 109)


title: HeartEC-Ribotag-6hr-rep4 (Sample 108)


title: HeartEC-Ribotag-6hr-rep3 (Sample 104)


title: HeartEC-Ribotag-6hr-rep4 (Sample 105)


title: HeartEC-Ribotag-6hr-rep4 (Sample 107)


title: HeartEC-Ribotag-6hr-rep3 (Sample 103)


title: HeartEC-Ribotag-6hr-rep4 (Sample 106)


title: HeartEC-Ribotag-6hr-rep3 (Sample 102)


title: HeartEC-Ribotag-6hr-rep2 (Sample 99)


title: HeartEC-Ribotag-6hr-rep1 (Sample 96)


title: HeartEC-Ribotag-6hr-rep2 (Sample 97)


title: HeartEC-Ribotag-6hr-rep2 (Sample 100)


title: HeartEC-Ribotag-6hr-rep3 (Sample 101)


title: HeartEC-Ribotag-6hr-rep2 (Sample 98)


title: HeartEC-Ribotag-6hr-rep1 (Sample 93)


title: HeartEC-Ribotag-6hr-rep1 (Sample 94)


title: HeartEC-Ribotag-6hr-rep1 (Sample 95)


title: HeartEC-Ribotag-0hr-rep5 (Sample 90)


title: HeartEC-Ribotag-0hr-rep6 (Sample 92)


title: HeartEC-Ribotag-0hr-rep5 (Sample 89)


title: HeartEC-Ribotag-0hr-rep5 (Sample 91)


title: HeartEC-Ribotag-0hr-rep4 (Sample 87)


title: HeartEC-Ribotag-0hr-rep5 (Sample 88)


title: HeartEC-Ribotag-0hr-rep4 (Sample 84)


title: HeartEC-Ribotag-0hr-rep4 (Sample 86)


title: HeartEC-Ribotag-0hr-rep3 (Sample 83)


title: HeartEC-Ribotag-0hr-rep4 (Sample 85)


title: HeartEC-Ribotag-0hr-rep3 (Sample 82)


title: HeartEC-Ribotag-0hr-rep3 (Sample 81)


title: BrainEC-Ribotag-168hr-rep5 (Sample 77)

source_name: Brain

value: Brain Endothelium


title: BrainEC-Ribotag-168hr-rep4 (Sample 74)


title: BrainEC-Ribotag-168hr-rep4 (Sample 75)


title: BrainEC-Ribotag-168hr-rep5 (Sample 76)


title: BrainEC-Ribotag-168hr-rep3 (Sample 73)


title: BrainEC-Ribotag-168hr-rep2 (Sample 72)


title: BrainEC-Ribotag-168hr-rep1 (Sample 71)


title: BrainEC-Ribotag-72hr-rep5 (Sample 69)


title: BrainEC-Ribotag-72hr-rep4 (Sample 68)


title: BrainEC-Ribotag-72hr-rep2 (Sample 66)


title: BrainEC-Ribotag-72hr-rep3 (Sample 67)


title: BrainEC-Ribotag-72hr-rep2 (Sample 64)


title: BrainEC-Ribotag-72hr-rep1 (Sample 62)


title: BrainEC-Ribotag-72hr-rep1 (Sample 61)


title: BrainEC-Ribotag-72hr-rep2 (Sample 65)


title: BrainEC-Ribotag-72hr-rep1 (Sample 60)


title: BrainEC-Ribotag-72hr-rep1 (Sample 59)


title: BrainEC-Ribotag-48hr-rep7 (Sample 58)


title: HeartEC-Ribotag-0hr-rep2 (Sample 79)


title: HeartEC-Ribotag-0hr-rep3 (Sample 80)


title: HeartEC-Ribotag-0hr-rep1 (Sample 78)


title: BrainEC-Ribotag-72hr-rep2 (Sample 63)


title: BrainEC-Ribotag-48hr-rep6 (Sample 55)


title: BrainEC-Ribotag-48hr-rep4 (Sample 53)


title: BrainEC-Ribotag-48hr-rep7 (Sample 57)


title: BrainEC-Ribotag-48hr-rep5 (Sample 54)


title: BrainEC-Ribotag-48hr-rep6 (Sample 56)


title: BrainEC-Ribotag-48hr-rep3 (Sample 52)


title: MN_ChIPseq_Input_0h

tag: cell type


title: BrainEC-Ribotag-72hr-rep5 (Sample 70)


title: BrainEC-Ribotag-48hr-rep2 (Sample 50)


title: BrainEC-Ribotag-48hr-rep2 (Sample 48)


title: BrainEC-Ribotag-48hr-rep1 (Sample 47)


title: BrainEC-Ribotag-48hr-rep1 (Sample 46)


title: BrainEC-Ribotag-48hr-rep1 (Sample 45)


title: BrainEC-Ribotag-24hr-rep5 (Sample 43)


title: BrainEC-Ribotag-24hr-rep3 (Sample 39)


title: BrainEC-Ribotag-24hr-rep4 (Sample 41)


title: BrainEC-Ribotag-48hr-rep1 (Sample 44)


title: BrainEC-Ribotag-24hr-rep5 (Sample 42)


title: BrainEC-Ribotag-24hr-rep4 (Sample 40)


title: BrainEC-Ribotag-24hr-rep2 (Sample 37)


title: BrainEC-Ribotag-24hr-rep2 (Sample 38)


title: BrainEC-Ribotag-6hr-rep4 (Sample 31)


title: BrainEC-Ribotag-24hr-rep2 (Sample 35)


title: BrainEC-Ribotag-6hr-rep4 (Sample 29)


title: BrainEC-Ribotag-6hr-rep4 (Sample 30)


title: BrainEC-Ribotag-24hr-rep1 (Sample 34)


title: BrainEC-Ribotag-6hr-rep6 (Sample 33)


title: BrainEC-Ribotag-6hr-rep3 (Sample 27)


title: BrainEC-Ribotag-6hr-rep5 (Sample 32)


title: BrainEC-Ribotag-6hr-rep4 (Sample 28)


title: BrainEC-Ribotag-6hr-rep3 (Sample 25)


title: BrainEC-Ribotag-6hr-rep3 (Sample 24)


title: BrainEC-Ribotag-48hr-rep2 (Sample 51)


title: BrainEC-Ribotag-48hr-rep2 (Sample 49)


title: BrainEC-Ribotag-6hr-rep3 (Sample 26)


title: BrainEC-Ribotag-6hr-rep2 (Sample 21)


title: BrainEC-Ribotag-6hr-rep2 (Sample 23)


title: BrainEC-Ribotag-6hr-rep2 (Sample 22)


title: BrainEC-Ribotag-6hr-rep1 (Sample 18)


title: BrainEC-Ribotag-6hr-rep1 (Sample 16)


title: BrainEC-Ribotag-6hr-rep1 (Sample 17)


title: BrainEC-Ribotag-24hr-rep2 (Sample 36)


title: BrainEC-Ribotag-0hr-rep5 (Sample 13)


title: BrainEC-Ribotag-0hr-rep5 (Sample 14)


title: BrainEC-Ribotag-0hr-rep6 (Sample 15)


title: BrainEC-Ribotag-0hr-rep4 (Sample 10)


title: BrainEC-Ribotag-0hr-rep5 (Sample 11)


title: BrainEC-Ribotag-0hr-rep4 (Sample 9)


title: BrainEC-Ribotag-0hr-rep4 (Sample 8)


title: BrainEC-Ribotag-0hr-rep4 (Sample 7)


title: BrainEC-Ribotag-0hr-rep3 (Sample 3)


title: BrainEC-Ribotag-0hr-rep2 (Sample 2)


title: BrainEC-Ribotag-0hr-rep1 (Sample 1)


title: BrainEC-Ribotag-6hr-rep1 (Sample 19)


title: BrainEC-Ribotag-0hr-rep3 (Sample 4)


title: BrainEC-Ribotag-6hr-rep2 (Sample 20)


title: BrainEC-Ribotag-0hr-rep3 (Sample 6)


title: RNAseq_Basal_organoids_TIP5KO_PtenKD_rep2

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

description: DESeq2_organoids_Basal_WT_PtenKD_vs_Basal_Tip5KO_PtenKD.csv

data_processing:
The quality of the 120 bp single end reads generated by the machine was check by FastQC, a quality control tool for high throughput sequence data (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter  ribosomal RNA; b) Trimmomatic (Bolger, 2014) (version 0.36) software package to trim the sorted (a) reads. The sorted (a), trimmed (b) reads were mapped against the mouse genome (mm10) using the default parameters of the STAR (Spliced Transcripts Alignment to a Reference, version 2.4.0.1) (Dobin et al., 2013). For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
The clustering and principal component analyses (PCA) based on the RPKM values were performed using R (version 2.14.0). EdgeR (Robinson et al., 2010) (version 3.12.0, common dispersion estimate) and DESeq2 (Love et al., 2014) (version 1.10.0, dispersion estimate based on the “fit only” model) packages were used to assess the differential expression between the samples. Only genes with more than one read per million in at least three samples were conserved for the analysis.
The functional annotation analysis of the differentially expressed genes was performed using DAVID (Database for Annotation, Visualization and Integrated Discovery) (Huang da et al., 2009).
Genome_build: mm8

source_name: prostate basal cell origin organoids

growth_protocol: Prostate cells were re-suspended in cold ADMEM/F12 5+ medium at density 5.000 cells per 40 μl for total organoid culture, and at 4.000 cells per 40 μl for basal and luminal organoid culture. Cell suspension was mixed with 60 μl of of pre-thawed growth factor reduced Matrigel (Corning) and plated in a form of drop into the middle of a well of 24-well plate (TPP). Mix for multiple wells of the same conditions was prepared together. Organoids were cultured in 500 μl of ADMEM/F12 supplemented with B27 (Gibco Life Technologies), Glutamax (Gibco Life Technologies), 10 mM HEPES (Gibco Life Technologies), 2% FBS, 100μg/ml Primocin  (ADMEM/F12 5+ medium) and contained following growth factors and components: mEGF (Gibco Life Technologies), TGF-β/Alk inhibitor A83-01 (Tocris), Dihydrotestosterone (DHT) (Sigma-Aldrich) with the addition of 10 μM ROCK inhibitor Y-27632 for the first week after seeding (organoid culture complete medium). Medium was changed every 2-4 days by aspiration of the old one and addition of fresh 500 μl of culture organoid medium. After 11 days in culture, organoids were split into single cells for the following experiments. Matrigel drops were dissolved by addition of 125ul Dispase at 5mg/ml to each well of the 24-well plate to make the final concentration of Dispase 1mg/ml and incubation at 37°C for 10 min. Matrigel drop was then disrupted by pipetting up and down several times and organoid suspension was transferred to conical tube. Samples were centrifuged at 350g for 5 min at room temperature. Supernatants were aspirated, pellets were washed with cold PBS to remove the rest of the medium, and centrifuged at 350 g for 5 min. 1ml of warm TrypLE was added and organoids were incubated at 37°C for 5 min. To dissociate them into single cells, organoids were pipetted up and down for 30s and transferred into conical tube prefilled with 2 ml cold HBSS + 2% FBS to quench the reaction. Samples were centrifuged at 350g for 5 min and supernatants were removed. Cell pellets were resuspended in ADMEM/F12 + 2% FBS and viable cells were counted using hemacytometer and trypan blue.

extract_protocol:
Total RNA for all downstream analyses was purified with TRIzol reagent (Life Technologies). The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed.
The TruSeq Stranded mRNA (Illumina, Inc, California, USA)protocol was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Fragment Analyzer (Agilent, Santa Clara, California, USA). The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. HiSeq4000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol.  Sequencing were paired end at 2 X150 bp or single end 100 bp.

treatment_protocol: For induction of Cre recombinase activity and Tip5 deletion, cells were cultured in medium supplemented with 1 μM 4-OH Tamoxifen (4-OH TAM) (Sigma-Aldrich) on the day of plating (day 0). Sequences encoding control shRNA (CACAAGCTGGAGTACAACTAC),  shRNA targeting Pten (CGACTTAGACTTGACCTATAT) were cloned into lentiviral vectors. Each lentivirus was generated using a one 10 cm plate of HEK293T cells. 10 ml of lentiviral supernatants were collected after 24 and 48 hours, centrifuged and frozen in -80°C over night. To enhance cell transduction, lentiviral supernatants were concentrated 100 times using Lenti-X Concentrator (Clontech) according to manufacturer's protocol. 40 μl of concentrated virus was mixed with 100.000 cells suspended in transduction medium (ADMEM/F12, B27 Glutamax, 10 mM HEPES, 100μg/ml Primocin, 2μg/ml Polybrene (Sigma-Aldrich), 10 μM ROCK inhibitor). Cells were incubated with virus for 20 min at RT, centrifuged for 40 min at 800 g at RT, and placed in incubator for 3.5 h to recover. Cells were plated in Matrigel at 5.000 cells/well density and after 3 days postseeding 1 μg/ml puromycin (Gibco) was applied to select organoids stably expressing shRNA-control or shRNA-Pten.

value: prostate

tag: type

value: organoids

tag: mouse line

value: CMV-Cre-ERT2, Tip5 lox/lox, ROSA26-mTmg-Tg+ (inducible Tip5-KO)

value: 4-OH Tam followed by lentiviral transduction with shRNA-Pten


title: RNAseq_Luminal_organoids_WT_PtenKD_rep1

description:
DESeq2_organoids_Luminal_WT_PtenKD_vs_Luminal_WT.csv
DESeq2_oragnoids_Luminal_WT_PtenKD_vs_Luminal_Tip5KO_PtenKD.csv
DESeq2_organoids_Luminal_WT_PtenKD_vs_Luminal_PtenKD_Tip5KO.csv

source_name: prostate luminal cell origin organoids

treatment_protocol: Sequences encoding control shRNA (CACAAGCTGGAGTACAACTAC),  shRNA targeting Pten (CGACTTAGACTTGACCTATAT) were cloned into lentiviral vectors. Each lentivirus was generated using a one 10 cm plate of HEK293T cells. 10 ml of lentiviral supernatants were collected after 24 and 48 hours, centrifuged and frozen in -80°C over night. To enhance cell transduction, lentiviral supernatants were concentrated 100 times using Lenti-X Concentrator (Clontech) according to manufacturer's protocol. 40 μl of concentrated virus was mixed with 100.000 cells suspended in transduction medium (ADMEM/F12, B27 Glutamax, 10 mM HEPES, 100μg/ml Primocin, 2μg/ml Polybrene (Sigma-Aldrich), 10 μM ROCK inhibitor). Cells were incubated with virus for 20 min at RT, centrifuged for 40 min at 800 g at RT, and placed in incubator for 3.5 h to recover. Cells were plated in Matrigel at 5.000 cells/well density and after 3 days postseeding 1 μg/ml puromycin (Gibco) was applied to select organoids stably expressing shRNA-control or shRNA-Pten

value: lentiviral transduction with shRNA-Pten

value: Pten-KD


title: RNAseq_Luminal_organoids_WT_PtenKD_rep2


title: RNAseq_Luminal_organoids_TIP5KO_PtenKD_rep1

description: DESeq2_oragnoids_Luminal_WT_PtenKD_vs_Luminal_Tip5KO_PtenKD.csv


title: RNAseq_Basal_organoids_TIP5KO_PtenKD_rep1


title: BrainEC-Ribotag-0hr-rep5 (Sample 12)

value: adult


title: RNAseq_Basal_organoids_WT_PtenKD_rep2

description:
DEseq2_organoids_Basal_WT_PtenKD_vs_Basal_WT.csv
DESeq2_organoids_Basal_WT_PtenKD_vs_Basal_Tip5KO_PtenKD.csv


title: RNAseq_Basal_organoids_WT_rep2

description: DEseq2_organoids_Basal_WT_PtenKD_vs_Basal_WT.csv

value: lentiviral transduction with shRNA-control

value: WT


title: RNAseq_Basal_organoids_WT_PtenKD_rep1


title: RNAseq_Luminal_organoids_PtenKD_TIP5KO_rep2

description: DESeq2_organoids_Luminal_WT_PtenKD_vs_Luminal_PtenKD_Tip5KO.csv

treatment_protocol: Sequences encoding control shRNA (CACAAGCTGGAGTACAACTAC),  shRNA targeting Pten (CGACTTAGACTTGACCTATAT) were cloned into lentiviral vectors. Each lentivirus was generated using a one 10 cm plate of HEK293T cells. 10 ml of lentiviral supernatants were collected after 24 and 48 hours, centrifuged and frozen in -80°C over night. To enhance cell transduction, lentiviral supernatants were concentrated 100 times using Lenti-X Concentrator (Clontech) according to manufacturer's protocol. 40 μl of concentrated virus was mixed with 100.000 cells suspended in transduction medium (ADMEM/F12, B27 Glutamax, 10 mM HEPES, 100μg/ml Primocin, 2μg/ml Polybrene (Sigma-Aldrich), 10 μM ROCK inhibitor). Cells were incubated with virus for 20 min at RT, centrifuged for 40 min at 800 g at RT, and placed in incubator for 3.5 h to recover. Cells were plated in Matrigel at 5.000 cells/well density and after 3 days postseeding 1 μg/ml puromycin (Gibco) was applied to select organoids stably expressing shRNA-control or shRNA-Pten. For induction of Cre recombinase activity and Tip5 deletion, cells were cultured in medium supplemented with 1 μM 4-OH Tamoxifen (4-OH TAM) (Sigma-Aldrich)

value: lentiviral transduction with shRNA-Pten followed by 4-OH tamoxifen


title: RNAseq_Luminal_organoids_WT_rep1

description: DESeq2_organoids_Luminal_WT_PtenKD_vs_Luminal_WT.csv


title: BrainEC-Ribotag-0hr-rep3 (Sample 5)

value: Cdh5CreERT2/+; Rpl22HA/+


title: RNAseq_Basal_organoids_WT_rep1


title: RNAseq_Lauminal_Cells_TIP5KO_rep2

description: DEseq2_cells_Luminal_WT_vs_Luminal_Tip5KO.csv

source_name: prostate luminal cells

growth_protocol: cells were isolated from 10 weeks old mice

value: primary cells

value: CMV-Cre, Tip5 lox/lox (constitutive Tip5-KO)


title: RNAseq_Luminal_organoids_TIP5KO_PtenKD_rep2


title: RNAseq_Luminal_Cells_WT_rep3

description:
DEseq2_cells_Luminal_WT_vs_Basal_WT.csv
DEseq2_cells_Luminal_WT_vs_Luminal_Tip5KO.csv


title: RNAseq_Basal_Cells_TIP5KO_rep1

description: DEseq2_cells_Basal_WT_vs_Basal_Tip5KO.csv

source_name: prostate basal cells


title: RNAseq_Basal_Cells_TIP5KO_rep2


title: RNAseq_Luminal_Cells_WT_rep1


title: RNAseq_Luminal_Cells_WT_rep2


title: RNAseq_Basal_Cells_WT_rep3

description:
DEseq2_cells_Luminal_WT_vs_Basal_WT.csv
DEseq2_cells_Basal_WT_vs_Basal_Tip5KO.csv


title: RNAseq_Basal_Cells_WT_rep1


title: [ATAC-seq] MEF flagMyod1 (rep1)

city: Singapore

first: Qian Yi

last: Lee

address: Biopolis Drive

department: R&D

country: Singapore

institute: Nuevocor

data_processing:
Adaptor trimming with in-house algorithm
Aligning reads to mm10 using Bowtie 2.1.0 with following parameter:  --very-sensitive
Removed mitochondria reads with awk '$3!="chrM"'
Removed duplicate reads with picard-tools v1.79 using the following parameters: -Xmx4G VALIDATION_S  TRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
RPKM values were calculated counting reads within ±100bp from merged FLAG ChIP peak summits
RPKM values were normalized using the normalize.quantiles function in the preprocessCore package in R
Genome_build: mm10
Supplementary_files_format_and_content: Processed tab-delimited file contains peak information (chr, start, stop) and normalized RPKM values for each replicate. Includes MEF only, MEF+rtTA and MEF+Ascl1 data from GSE101397.

source_name: Mouse embryonic fibroblasts

growth_protocol: Homozygous TauEGFP knock-in mice were bred with C57B/6 mice (Charles River) to generate heterozygous embryos. Heterozygous TauEGFP knock-in TauEGFP mouse embryonic fibroblasts (MEFs) were then isolated from E13.5 embryos.

extract_protocol:
At 48hr post-dox induction, ATAC-seq was performed as described in Buenrostro, et al., Nat. Methods (2016).
ATAC-seq libraries were sequenced on Illumina HiSeq 2000.

treatment_protocol: P3 MEFs were co-infected with reverse tetracycline transactivator (rtTA) and doxycycline (dox) inducible Myod1 overnight and then cultured in MEF media (DMEM; Invitrogen) containing 10% cosmic calf serum (CCS; Hyclone), beta-mercaptoethanol (Sigma), non-essential amino acids, sodium pyruvate and penicillin/streptomycin (all from Invitrogen) supplemented with 2 µg/ml dox (Sigma) for 48h.

value: Mouse embryonic fibroblasts

tag: transgenes

value: flagMyod1 + rtTA

tag: days post transgene induction

value: 2 days


title: RNAseq_Luminal_organoids_WT_rep2

tag: genotype


title: RNAseq_Luminal_organoids_PtenKD_TIP5KO_rep1


title: Ctrl_239_RBG22813

city: Shanghai

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

description: Ctrl_ICGScluster1_097_HSCs (CD31+kit+CD45-)

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.6.0) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: the Aorta surrounded by Gonads and Mesonephros tissues (AGM)

extract_protocol:
CD31+kit+CD45- cells were FACS-purified.
Cells were sorted in 2.3 µl of lysis buffer containing 0.2% Triton X-100 (Sigma-Aldrich) and 1U of Superase-In RNase Inhibitor (Ambion) and processed following the Smart-Seq2 protocol.
Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6. The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher) and size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer).
Libraries were prepared using the Illumina Nextera XT DNA preparation kit.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
Samples were used to construct Nextera XT libraries (Illumina) from 125 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems).

value: Hematopoietic stem cells (CD31+kit+CD45-)

value: Ctrl

tag: icgs cluster


title: Ctrl_236_RBG22765

description: Ctrl_ICGScluster2_073_HSCs (CD31+kit+CD45-)


title: Ctrl_237_RBG22777

description: Ctrl_ICGScluster3_030_HSCs (CD31+kit+CD45-)


title: RNAseq_Basal_Cells_WT_rep2

value: prostate


title: Ctrl_234_RBG22836

description: Ctrl_ICGScluster3_029_HSCs (CD31+kit+CD45-)


title: Ctrl_232_RBG22764

description: Ctrl_ICGScluster6_014_HSCs (CD31+kit+CD45-)


title: Ctrl_238_RBG22789

description: Ctrl_ICGScluster3_031_HSCs (CD31+kit+CD45-)


title: Ctrl_227_RBG22751

description: Ctrl_ICGScluster3_027_HSCs (CD31+kit+CD45-)


title: Ctrl_235_RBG22753

description: Ctrl_ICGScluster7_008_HSCs (CD31+kit+CD45-)


title: Ctrl_230_RBG22835

description: Ctrl_ICGScluster2_072_HSCs (CD31+kit+CD45-)


title: Ctrl_226_RBG22834

description: Ctrl_ICGScluster2_071_HSCs (CD31+kit+CD45-)


title: Ctrl_231_RBG22752

description: Ctrl_ICGScluster3_028_HSCs (CD31+kit+CD45-)


title: Ctrl_224_RBG22774

description: Ctrl_ICGScluster3_025_HSCs (CD31+kit+CD45-)


title: Ctrl_229_RBG22775

description: Ctrl_ICGScluster6_013_HSCs (CD31+kit+CD45-)


title: Ctrl_233_RBG22824

description: Ctrl_ICGScluster1_096_HSCs (CD31+kit+CD45-)


title: Ctrl_223_RBG22833

description: Ctrl_ICGScluster1_094_HSCs (CD31+kit+CD45-)


title: Ctrl_225_RBG22822

description: Ctrl_ICGScluster3_026_HSCs (CD31+kit+CD45-)


title: Ctrl_222_RBG22821

description: Ctrl_ICGScluster6_012_HSCs (CD31+kit+CD45-)


title: Ctrl_220_RBG22785

description: Ctrl_ICGScluster4_009_HSCs (CD31+kit+CD45-)


title: Ctrl_217_RBG22832

description: Ctrl_ICGScluster1_093_HSCs (CD31+kit+CD45-)


title: Ctrl_219_RBG22773

description: Ctrl_ICGScluster3_024_HSCs (CD31+kit+CD45-)


title: Ctrl_221_RBG22797

description: Ctrl_ICGScluster4_010_HSCs (CD31+kit+CD45-)


title: Ctrl_216_RBG22820

description: Ctrl_ICGScluster2_070_HSCs (CD31+kit+CD45-)


title: Ctrl_215_RBG22796

description: Ctrl_ICGScluster2_069_HSCs (CD31+kit+CD45-)


title: Ctrl_214_RBG22760

description: Ctrl_ICGScluster3_023_HSCs (CD31+kit+CD45-)


title: Treat_244_RBG22831

description: Treated_ICGScluster2_072_HSCs (CD31+kit+CD45-)


title: Ctrl_228_RBG22763

description: Ctrl_ICGScluster1_095_HSCs (CD31+kit+CD45-)


title: Treat_242_RBG22807

description: Treated_ICGScluster5_007_HSCs (CD31+kit+CD45-)


title: Treat_235_RBG22806

description: Treated_ICGScluster3_033_HSCs (CD31+kit+CD45-)


title: Ctrl_218_RBG22761

description: Ctrl_ICGScluster6_011_HSCs (CD31+kit+CD45-)


title: Treat_239_RBG22759

description: Treated_ICGScluster2_070_HSCs (CD31+kit+CD45-)


title: Treat_237_RBG22830

description: Treated_ICGScluster5_006_HSCs (CD31+kit+CD45-)


title: Treat_238_RBG22747

description: Treated_ICGScluster3_034_HSCs (CD31+kit+CD45-)


title: Treat_236_RBG22818

description: Treated_ICGScluster1_086_HSCs (CD31+kit+CD45-)


title: Treat_240_RBG22771

description: Treated_ICGScluster3_035_HSCs (CD31+kit+CD45-)


title: Treat_241_RBG22783

description: Treated_ICGScluster2_071_HSCs (CD31+kit+CD45-)


title: Treat_226_RBG22828

description: Treated_ICGScluster2_068_HSCs (CD31+kit+CD45-)


title: Treat_230_RBG22805

description: Treated_ICGScluster3_030_HSCs (CD31+kit+CD45-)


title: Treat_233_RBG22746

description: Treated_ICGScluster4_012_HSCs (CD31+kit+CD45-)


title: Treat_232_RBG22829

description: Treated_ICGScluster2_069_HSCs (CD31+kit+CD45-)


title: Treat_228_RBG22757

description: Treated_ICGScluster3_029_HSCs (CD31+kit+CD45-)


title: Treat_231_RBG22817

description: Treated_ICGScluster3_031_HSCs (CD31+kit+CD45-)


title: Treat_222_RBG22756

description: Treated_ICGScluster1_083_HSCs (CD31+kit+CD45-)


title: Treat_234_RBG22782

description: Treated_ICGScluster3_032_HSCs (CD31+kit+CD45-)


title: Treat_229_RBG22793

description: Treated_ICGScluster6_019_HSCs (CD31+kit+CD45-)


title: Treat_224_RBG22780

description: Treated_ICGScluster1_085_HSCs (CD31+kit+CD45-)


title: Treat_220_RBG22827

description: Treated_ICGScluster3_027_HSCs (CD31+kit+CD45-)


title: Treat_219_RBG22791

description: Treated_ICGScluster6_018_HSCs (CD31+kit+CD45-)


title: Treat_218_RBG22779

description: Treated_ICGScluster6_017_HSCs (CD31+kit+CD45-)


title: Treat_243_RBG22819

description: Treated_ICGScluster3_036_HSCs (CD31+kit+CD45-)


title: Treat_217_RBG22767

description: Treated_ICGScluster2_065_HSCs (CD31+kit+CD45-)


title: Treat_216_RBG22755

description: Treated_ICGScluster2_064_HSCs (CD31+kit+CD45-)


title: RNAseq_Lauminal_Cells_TIP5KO_rep1

description: DEseq2_cells_Luminal_WT_vs_Luminal_Tip5KO.csv


title: Treat_227_RBG22745

description: Treated_ICGScluster3_028_HSCs (CD31+kit+CD45-)


title: Treat_215_RBG22743

description: Treated_ICGScluster2_063_HSCs (CD31+kit+CD45-)


title: Treat_225_RBG22792

description: Treated_ICGScluster2_067_HSCs (CD31+kit+CD45-)


title: Treat_211_RBG22778

description: Treated_ICGScluster5_005_HSCs (CD31+kit+CD45-)


title: Treat_212_RBG22802

description: Treated_ICGScluster4_011_HSCs (CD31+kit+CD45-)


title: Treat_223_RBG22768

description: Treated_ICGScluster1_084_HSCs (CD31+kit+CD45-)


title: Treat_221_RBG22744

description: Treated_ICGScluster2_066_HSCs (CD31+kit+CD45-)


title: Treat_209_RBG22742

description: Treated_ICGScluster2_062_HSCs (CD31+kit+CD45-)


title: Treat_210_RBG22754

description: Treated_ICGScluster7_011_HSCs (CD31+kit+CD45-)


title: Treat_207_RBG22729

description: Treated_ICGScluster2_061_HSCs (CD31+kit+CD45-)


title: Treat_214_RBG22826

description: Treated_ICGScluster1_082_HSCs (CD31+kit+CD45-)


title: Treat_201_RBG22692

description: Treated_ICGScluster3_025_HSCs (CD31+kit+CD45-)


title: Treat_213_RBG22814

description: Treated_ICGScluster7_012_HSCs (CD31+kit+CD45-)


title: Treat_202_RBG22716

description: Treated_ICGScluster2_058_HSCs (CD31+kit+CD45-)


title: Treat_199_RBG22727

description: Treated_ICGScluster3_024_HSCs (CD31+kit+CD45-)


title: Treat_208_RBG22741

description: Treated_ICGScluster1_081_HSCs (CD31+kit+CD45-)


title: Treat_203_RBG22728

description: Treated_ICGScluster2_059_HSCs (CD31+kit+CD45-)


title: Treat_194_RBG22726

description: Treated_ICGScluster4_009_HSCs (CD31+kit+CD45-)


title: Treat_197_RBG22703

description: Treated_ICGScluster1_079_HSCs (CD31+kit+CD45-)


title: Treat_206_RBG22717

description: Treated_ICGScluster7_010_HSCs (CD31+kit+CD45-)


title: Treat_195_RBG22738

description: Treated_ICGScluster1_078_HSCs (CD31+kit+CD45-)


title: Treat_196_RBG22691

description: Treated_ICGScluster2_057_HSCs (CD31+kit+CD45-)


title: Treat_198_RBG22715

description: Treated_ICGScluster4_010_HSCs (CD31+kit+CD45-)


title: Treat_193_RBG22714

description: Treated_ICGScluster1_077_HSCs (CD31+kit+CD45-)


title: Treat_200_RBG22739

description: Treated_ICGScluster1_080_HSCs (CD31+kit+CD45-)


title: Treat_191_RBG22666

description: Treated_ICGScluster1_076_HSCs (CD31+kit+CD45-)


title: Treat_189_RBG22725

description: Treated_ICGScluster6_016_HSCs (CD31+kit+CD45-)


title: Treat_188_RBG22713

description: Treated_ICGScluster4_008_HSCs (CD31+kit+CD45-)


title: Treat_184_RBG22736

description: Treated_ICGScluster2_055_HSCs (CD31+kit+CD45-)


title: Treat_204_RBG22740

description: Treated_ICGScluster2_060_HSCs (CD31+kit+CD45-)


title: Treat_187_RBG22701

description: Treated_ICGScluster3_023_HSCs (CD31+kit+CD45-)


title: Treat_205_RBG22657

description: Treated_ICGScluster3_026_HSCs (CD31+kit+CD45-)


title: Treat_183_RBG22724

description: Treated_ICGScluster4_007_HSCs (CD31+kit+CD45-)


title: Treat_182_RBG22712

description: Treated_ICGScluster2_054_HSCs (CD31+kit+CD45-)


title: Treat_181_RBG22700

description: Treated_ICGScluster6_015_HSCs (CD31+kit+CD45-)


title: Ctrl_212_RBG22723

description: Ctrl_ICGScluster3_022_HSCs (CD31+kit+CD45-)


title: Ctrl_213_RBG22735

description: Ctrl_ICGScluster1_092_HSCs (CD31+kit+CD45-)


title: Ctrl_210_RBG22699

description: Ctrl_ICGScluster2_068_HSCs (CD31+kit+CD45-)


title: Treat_180_RBG22676

description: Treated_ICGScluster1_074_HSCs (CD31+kit+CD45-)


title: Ctrl_211_RBG22711

description: Ctrl_ICGScluster1_091_HSCs (CD31+kit+CD45-)


title: Ctrl_205_RBG22698

description: Ctrl_ICGScluster3_020_HSCs (CD31+kit+CD45-)


title: Treat_192_RBG22702

description: Treated_ICGScluster2_056_HSCs (CD31+kit+CD45-)


title: Ctrl_202_RBG22733

description: Ctrl_ICGScluster3_019_HSCs (CD31+kit+CD45-)


title: Ctrl_208_RBG22663

description: Ctrl_ICGScluster2_067_HSCs (CD31+kit+CD45-)


title: Ctrl_207_RBG22734

description: Ctrl_ICGScluster1_090_HSCs (CD31+kit+CD45-)


title: Ctrl_204_RBG22686

description: Ctrl_ICGScluster4_008_HSCs (CD31+kit+CD45-)


title: Ctrl_209_RBG22687

description: Ctrl_ICGScluster3_021_HSCs (CD31+kit+CD45-)


title: Ctrl_201_RBG22721

description: Ctrl_ICGScluster1_087_HSCs (CD31+kit+CD45-)


title: Ctrl_200_RBG22709

description: Ctrl_ICGScluster1_086_HSCs (CD31+kit+CD45-)


title: Ctrl_203_RBG22674

description: Ctrl_ICGScluster1_088_HSCs (CD31+kit+CD45-)


title: Ctrl_206_RBG22722

description: Ctrl_ICGScluster1_089_HSCs (CD31+kit+CD45-)


title: Ctrl_199_RBG22697

description: Ctrl_ICGScluster2_066_HSCs (CD31+kit+CD45-)


title: Treat_190_RBG22737

description: Treated_ICGScluster1_075_HSCs (CD31+kit+CD45-)


title: Treat_185_RBG22653

description: Treated_ICGScluster3_022_HSCs (CD31+kit+CD45-)


title: Treat_186_RBG22689

description: Treated_ICGScluster7_009_HSCs (CD31+kit+CD45-)


title: Ctrl_198_RBG22685

description: Ctrl_ICGScluster3_018_HSCs (CD31+kit+CD45-)


title: Ctrl_197_RBG22661

description: Ctrl_ICGScluster4_007_HSCs (CD31+kit+CD45-)


title: Ctrl_196_RBG22732

description: Ctrl_ICGScluster1_085_HSCs (CD31+kit+CD45-)


title: Treat_179_RBG22664

description: Treated_ICGScluster3_021_HSCs (CD31+kit+CD45-)


title: Ctrl_193_RBG22684

description: Ctrl_ICGScluster1_084_HSCs (CD31+kit+CD45-)


title: Ctrl_194_RBG22696

description: Ctrl_ICGScluster7_007_HSCs (CD31+kit+CD45-)


title: Ctrl_195_RBG22708

description: Ctrl_ICGScluster2_065_HSCs (CD31+kit+CD45-)


title: Ctrl_192_RBG22672

description: Ctrl_ICGScluster1_083_HSCs (CD31+kit+CD45-)


title: Ctrl_190_RBG22731

description: Ctrl_ICGScluster2_064_HSCs (CD31+kit+CD45-)


title: Ctrl_191_RBG22660

description: Ctrl_ICGScluster3_017_HSCs (CD31+kit+CD45-)


title: Ctrl_188_RBG22695

description: Ctrl_ICGScluster3_015_HSCs (CD31+kit+CD45-)


title: Ctrl_189_RBG22707

description: Ctrl_ICGScluster3_016_HSCs (CD31+kit+CD45-)


title: Ctrl_186_RBG22671

description: Ctrl_ICGScluster2_062_HSCs (CD31+kit+CD45-)


title: Ctrl_185_RBG22647

description: Ctrl_ICGScluster4_006_HSCs (CD31+kit+CD45-)


title: Ctrl_183_RBG22718

description: Ctrl_ICGScluster2_061_HSCs (CD31+kit+CD45-)


title: Ctrl_184_RBG22730

description: Ctrl_ICGScluster3_014_HSCs (CD31+kit+CD45-)


title: Ctrl_181_RBG22694

description: Ctrl_ICGScluster1_082_HSCs (CD31+kit+CD45-)


title: Ctrl_187_RBG22683

description: Ctrl_ICGScluster2_063_HSCs (CD31+kit+CD45-)


title: Ctrl_176_RBG19309

description: Ctrl_ICGScluster1_081_HSCs (CD31+kit+CD45-)


title: Ctrl_182_RBG22706

description: Ctrl_ICGScluster4_005_HSCs (CD31+kit+CD45-)


title: Ctrl_178_RBG22658

description: Ctrl_ICGScluster6_010_HSCs (CD31+kit+CD45-)


title: Ctrl_180_RBG22682

description: Ctrl_ICGScluster7_006_HSCs (CD31+kit+CD45-)


title: Ctrl_177_RBG22646

description: Ctrl_ICGScluster6_009_HSCs (CD31+kit+CD45-)


title: Ctrl_174_RBG19285

description: Ctrl_ICGScluster2_060_HSCs (CD31+kit+CD45-)


title: Ctrl_179_RBG22670

description: Ctrl_ICGScluster4_004_HSCs (CD31+kit+CD45-)


title: Ctrl_172_RBG19237

description: Ctrl_ICGScluster1_079_HSCs (CD31+kit+CD45-)


title: Ctrl_175_RBG19297

description: Ctrl_ICGScluster1_080_HSCs (CD31+kit+CD45-)


title: Ctrl_173_RBG19249

description: Ctrl_ICGScluster2_059_HSCs (CD31+kit+CD45-)


title: Ctrl_169_RBG19093

description: Ctrl_ICGScluster1_077_HSCs (CD31+kit+CD45-)


title: Ctrl_166_RBG19057

description: Ctrl_ICGScluster6_008_HSCs (CD31+kit+CD45-)


title: Ctrl_170_RBG19105

description: Ctrl_ICGScluster7_005_HSCs (CD31+kit+CD45-)


title: Ctrl_167_RBG19069

description: Ctrl_ICGScluster1_075_HSCs (CD31+kit+CD45-)


title: Ctrl_168_RBG19081

description: Ctrl_ICGScluster1_076_HSCs (CD31+kit+CD45-)


title: Ctrl_171_RBG19117

description: Ctrl_ICGScluster1_078_HSCs (CD31+kit+CD45-)


title: Ctrl_165_RBG19045

description: Ctrl_ICGScluster1_074_HSCs (CD31+kit+CD45-)


title: Ctrl_164_RBG19308

description: Ctrl_ICGScluster1_073_HSCs (CD31+kit+CD45-)


title: Ctrl_163_RBG19296

description: Ctrl_ICGScluster1_072_HSCs (CD31+kit+CD45-)


title: Ctrl_161_RBG19248

description: Ctrl_ICGScluster2_058_HSCs (CD31+kit+CD45-)


title: Ctrl_160_RBG19236

description: Ctrl_ICGScluster1_070_HSCs (CD31+kit+CD45-)


title: Ctrl_162_RBG19284

description: Ctrl_ICGScluster1_071_HSCs (CD31+kit+CD45-)


title: Ctrl_155_RBG19080

description: Ctrl_ICGScluster1_068_HSCs (CD31+kit+CD45-)


title: Ctrl_156_RBG19092

description: Ctrl_ICGScluster2_056_HSCs (CD31+kit+CD45-)


title: Ctrl_154_RBG19068

description: Ctrl_ICGScluster2_055_HSCs (CD31+kit+CD45-)


title: Ctrl_157_RBG19104

description: Ctrl_ICGScluster2_057_HSCs (CD31+kit+CD45-)


title: Ctrl_153_RBG19056

description: Ctrl_ICGScluster5_006_HSCs (CD31+kit+CD45-)


title: Ctrl_158_RBG19116

description: Ctrl_ICGScluster1_069_HSCs (CD31+kit+CD45-)


title: Ctrl_147_RBG19271

description: Ctrl_ICGScluster1_065_HSCs (CD31+kit+CD45-)


title: Ctrl_148_RBG19283

description: Ctrl_ICGScluster2_053_HSCs (CD31+kit+CD45-)


title: Ctrl_149_RBG19295

description: Ctrl_ICGScluster1_066_HSCs (CD31+kit+CD45-)


title: Ctrl_152_RBG19044

description: Ctrl_ICGScluster1_067_HSCs (CD31+kit+CD45-)


title: Ctrl_145_RBG19235

description: Ctrl_ICGScluster2_051_HSCs (CD31+kit+CD45-)


title: Ctrl_159_RBG19224

description: Ctrl_ICGScluster3_013_HSCs (CD31+kit+CD45-)


title: Ctrl_150_RBG19307

description: Ctrl_ICGScluster2_054_HSCs (CD31+kit+CD45-)


title: Ctrl_144_RBG19223

description: Ctrl_ICGScluster6_007_HSCs (CD31+kit+CD45-)


title: Ctrl_143_RBG19115

description: Ctrl_ICGScluster1_064_HSCs (CD31+kit+CD45-)


title: Ctrl_151_RBG19032

description: Ctrl_ICGScluster4_003_HSCs (CD31+kit+CD45-)


title: Ctrl_142_RBG19103

description: Ctrl_ICGScluster3_012_HSCs (CD31+kit+CD45-)


title: Ctrl_140_RBG19079

description: Ctrl_ICGScluster6_006_HSCs (CD31+kit+CD45-)


title: Ctrl_139_RBG19067

description: Ctrl_ICGScluster1_062_HSCs (CD31+kit+CD45-)


title: Ctrl_138_RBG19055

description: Ctrl_ICGScluster1_061_HSCs (CD31+kit+CD45-)


title: Ctrl_141_RBG19091

description: Ctrl_ICGScluster1_063_HSCs (CD31+kit+CD45-)


title: Treat_177_RBG19282

description: Treated_ICGScluster1_073_HSCs (CD31+kit+CD45-)


title: Ctrl_136_RBG19031

description: Ctrl_ICGScluster1_059_HSCs (CD31+kit+CD45-)


title: Treat_178_RBG19294

description: Treated_ICGScluster7_008_HSCs (CD31+kit+CD45-)


title: Treat_176_RBG19270

description: Treated_ICGScluster2_053_HSCs (CD31+kit+CD45-)


title: Treat_175_RBG19258

description: Treated_ICGScluster1_072_HSCs (CD31+kit+CD45-)


title: Treat_174_RBG19246

description: Treated_ICGScluster1_071_HSCs (CD31+kit+CD45-)


title: Ctrl_146_RBG19247

description: Ctrl_ICGScluster2_052_HSCs (CD31+kit+CD45-)


title: Treat_172_RBG19222

description: Treated_ICGScluster1_069_HSCs (CD31+kit+CD45-)


title: Treat_173_RBG19234

description: Treated_ICGScluster1_070_HSCs (CD31+kit+CD45-)


title: Ctrl_134_RBG19102

description: Ctrl_ICGScluster1_057_HSCs (CD31+kit+CD45-)


title: Ctrl_133_RBG19090

description: Ctrl_ICGScluster2_050_HSCs (CD31+kit+CD45-)


title: Ctrl_135_RBG19114

description: Ctrl_ICGScluster1_058_HSCs (CD31+kit+CD45-)


title: Ctrl_132_RBG19078

description: Ctrl_ICGScluster1_056_HSCs (CD31+kit+CD45-)


title: Ctrl_130_RBG19054

description: Ctrl_ICGScluster2_048_HSCs (CD31+kit+CD45-)


title: Ctrl_131_RBG19066

description: Ctrl_ICGScluster2_049_HSCs (CD31+kit+CD45-)


title: Treat_170_RBG19293

description: Treated_ICGScluster1_067_HSCs (CD31+kit+CD45-)


title: Ctrl_129_RBG19042

description: Ctrl_ICGScluster5_005_HSCs (CD31+kit+CD45-)


title: Treat_166_RBG19245

description: Treated_ICGScluster2_051_HSCs (CD31+kit+CD45-)


title: Treat_167_RBG19257

description: Treated_ICGScluster6_014_HSCs (CD31+kit+CD45-)


title: Ctrl_137_RBG19043

description: Ctrl_ICGScluster1_060_HSCs (CD31+kit+CD45-)


title: Ctrl_126_RBG19101

description: Ctrl_ICGScluster2_046_HSCs (CD31+kit+CD45-)


title: Treat_168_RBG19269

description: Treated_ICGScluster2_052_HSCs (CD31+kit+CD45-)


title: Ctrl_127_RBG19113

description: Ctrl_ICGScluster2_047_HSCs (CD31+kit+CD45-)


title: Treat_165_RBG19233

description: Treated_ICGScluster2_050_HSCs (CD31+kit+CD45-)


title: Ctrl_125_RBG19089

description: Ctrl_ICGScluster3_010_HSCs (CD31+kit+CD45-)


title: Treat_164_RBG19221

description: Treated_ICGScluster6_013_HSCs (CD31+kit+CD45-)


title: Ctrl_124_RBG19077

description: Ctrl_ICGScluster1_055_HSCs (CD31+kit+CD45-)


title: Ctrl_123_RBG19065

description: Ctrl_ICGScluster2_045_HSCs (CD31+kit+CD45-)


title: Treat_163_RBG19304

description: Treated_ICGScluster5_004_HSCs (CD31+kit+CD45-)


title: Ctrl_120_RBG19029

description: Ctrl_ICGScluster2_044_HSCs (CD31+kit+CD45-)


title: Ctrl_122_RBG19053

description: Ctrl_ICGScluster3_009_HSCs (CD31+kit+CD45-)


title: Ctrl_121_RBG19041

description: Ctrl_ICGScluster1_054_HSCs (CD31+kit+CD45-)


title: Treat_162_RBG19292

description: Treated_ICGScluster3_020_HSCs (CD31+kit+CD45-)


title: Treat_171_RBG19305

description: Treated_ICGScluster1_068_HSCs (CD31+kit+CD45-)


title: Treat_161_RBG19280

description: Treated_ICGScluster7_007_HSCs (CD31+kit+CD45-)


title: Ctrl_128_RBG19030

description: Ctrl_ICGScluster3_011_HSCs (CD31+kit+CD45-)


title: Treat_159_RBG19256

description: Treated_ICGScluster1_065_HSCs (CD31+kit+CD45-)


title: Treat_158_RBG19244

description: Treated_ICGScluster1_064_HSCs (CD31+kit+CD45-)


title: Treat_160_RBG19268

description: Treated_ICGScluster2_049_HSCs (CD31+kit+CD45-)


title: Ctrl_119_RBG19100

description: Ctrl_ICGScluster3_008_HSCs (CD31+kit+CD45-)


title: Treat_156_RBG19220

description: Treated_ICGScluster3_019_HSCs (CD31+kit+CD45-)


title: Ctrl_118_RBG19088

description: Ctrl_ICGScluster2_043_HSCs (CD31+kit+CD45-)