title: 0_percent_d30_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d30


title: control_rat2

status: Public on Feb 15 2021

type: SRA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

library_source: transcriptomic

data_processing:
Trimming with preprocessReads from the systemPipeR package in R (Parameter: cutoff=20, low_quality_rate=0.4, batchsize=100000)
Aligment:tophat v2.1.1 bowtie v2.2.9 Parameter: -g 1 --segment-length 25 -i 30 -I  3000 Genome RN6
Read Counts: summarizeOverlaps from the GenomicsAlignments package in R Parameter: mode=Union, ignore.strand=TRUE, inter.feature=FALSE, singleEnd=TRUE
RPKM Normalization with the returnRPKM function from systemPipeR package in R
Genome_build: RN6
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: left kidney

growth_protocol: Male Sprague Dawley (SD) rats (250g) were purchased from Janvier Labs (Le Genest Saint Isle, France). Experiment started after 2 weeks of acclimatization. The animals had free access to pelleted standard rat chow (rat/mouse maintenance V1534-0001, Ssniff, Soest, Germany) and water in a temperature- and humidity- controlled facility (22°C, 55+/-5% rel. Hum.) with 12h light/12h dark cycle.

extract_protocol:
fresh left kidney was collected and snap frozen
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: Rats were treated with a single intraperioteneal dose of cisplatin (7mg/kgBW). 15 days after animals were sacrificed and the left kidney was collected from gene expression profiling

tag: strain

value: Sprague Dawley

tag: treatment

value: Cisplatin

tag: tissue

value: full kidney


title: control_rat3


title: 0_percent_d24.1_Hsap_Mmul_Chimera

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

country: USA

institute: Dana Farber Cancer Institute

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d24.1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped to chimera transcriptome using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: A joint hg19/mm10 transcriptome reference was built by appending hg19 or mm10 respectively to the chromosome sequences and gene symbols. Tagging the gene symbols with the ID of the reference genome ensured easy decomposition of the resulting expression estimates into mouse and human subsets.
Supplementary_files_format_and_content: collated rsem output into tab files, expected counts (ec), transcripts per million (tpm's), and fragments per kilobase million (fpkm)

organism: Mus musculus

source_name: Co-cultured human and mouse pluripotent stem cell-derived neural cells

growth_protocol: All cells were differentiated in vitro in DF3S (DMEM/F12, 64 mg/L L-ascorbic acid phosphate Mg salt, 0.014 mg/L sodium selenite, 1,743 mg/L sodium bicarbonate; Thermo Fisher Scientific, USA) + N2 and B27 Supplements (Thermo Fisher Scientific, USA) + 100ng/mL Noggin (R&D Systems, USA) on matrigel-coated multiwell culture plates.

extract_protocol:
Total RNA was then purified from 350 µL RLT-Plus Buffer using RNeasy Plus 96 and Micro Kits (Qiagen, Netherlands) and quantitated with the Quant-iT RNA Assay Kit (Thermo Fisher Scientific, USA).  RNA was diluted to one hundred nanograms for input.
The Ligation-Mediated Sequencing (LM-Seq) protocol was used to prepare and index all cDNA libraries (Hou et al 2015). Final cDNA libraries were quantitated with the Quant-iT PicoGreen Assay Kit (Thermofisher, Waltham, Massachusetts).
Twenty-five to forty-eight uniquely indexed samples were pooled per lane on an Illumina HiSeq 2500 with a single 51 base pair read and a 10 base pair index read.

treatment_protocol: For RNA sample collection, samples were washed with 1XPBS (Thermo Fisher Scientific, USA) and lysed in 700 µL RLT-PLUS buffer (Qiagen, USA), and stored at -80C until further processing.

tag: tissue composition

value: Mus musculus cells only

tag: cell type

tag: growth time (days)

tag: mixing day

tag: mixing percent human

tag: biological replicate number

value: Neural induction medium (see protocols section below)


title: 0_percent_d24_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d24

value: pluripotent stem cell-derived neural cells


title: control_rat1


title: 100_percent_d5.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d5.1

organism: Homo sapiens

value: Homo sapiens cells only


title: 100_percent_d5_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d5


title: 100_percent_d4.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d4.1


title: 0_percent_d26_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d26


title: COS_2_6

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
base calling and demultiplexed with bcl2fastq
Sequencing quality was assessed with FastQC (v0.11.8)
Trimming of adapters and low quality bases with Trimmomatic (v0.39)
Trimmed reads were aligned to the Ensembl rhesus macaque reference genome (Mmul_10) with STAR (v2.7.0) using default parameters
Gene counts were obtained via STAR with the "--quantMode GeneCounts" parameter and Ensembl annotation (Mmul_10.99)
Genome_build: Mmul_10
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample

organism: Macaca mulatta

source_name: Blastocysts

growth_protocol: After IVF for 14-16 hr, oocytes were stripped of excess sperm by pipetting and visually assessed for fertilization; i.e., the presence of two pronuclei and/or two polar bodies. The zygotes were cultured for 6-8 days till they reached the blastocyst stage of development in 100 μL of one-step commercial medium supplemented with 10% serum protein (LifeGlobal, Guildford, CT) under mineral oil (Sage™, Trumbull, CT) at 37°C with 6% CO2, 5% O2

extract_protocol:
RNA was extracted from the blastocysts and cDNA prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (TakaraBio, Shiga, Japan) and the amplified cDNA was purified using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA), both according to manufacturer’s instructions. cDNA was then sheared to approximately 250 base pairs in length using a Covaris M220 sonicator.
Sheared cDNA was resuspended in Tru-seq Resuspension Buffer and libraries prepared using a Tru-Seq Nano kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, except that 16 cycles of amplification were performed to account for the low input samples. Fragment size was measured using a Fragment Analyzer 5200 and samples quantified with qPCR and pooled at equimolar concentration. Multiplexed samples were sequenced across seven lanes of a single-read, 75 cycle run on an Illumina HiSeq 4000 sequencer.

treatment_protocol: Blastocysts were collected and incubated in EmbryoMax Acidic Tyrode’s Solution EMD Millipore, Burlington MA) for ~30 seconds for removal of the zona pellucida. These zona free blastocysts were then transferred to the extraction buffer of the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific KIT0204, Waltham, MA) and frozen at -80oC until RNA isolation.

tag: diet

value: Western Style Diet

tag: morphology durign development

value: Fragmented, non-multipolar


title: 0_percent_d22.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d22.1


title: 100_percent_d4_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d4


title: COS_2_3


title: COS_2_2


title: mouse E10.5 control embryo, replicate 5

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
scRNA.MetaData.105.csv
scRNA.integrated.scaled.assay105.csv
scRNA.normalized.assay105.csv

data_processing:
Demultiplexing was done with cellranger/3.1.0 mkfastq
Alignment and quantification of single cell features was done with cellranger counts
Aggregation of multiple GEM wells was done using-  cellranger aggr
Cells with under 200 expressing genes, over 4000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis
Genome_build: mm10
Supplementary_files_format_and_content: proccessed data is divided into three different matrices created using Seurat 3.0: Normalized - contains normalized counts of all genes across all cells. MetaData - contains  information of each of the cells, and Intagrated-  with anchors the two in-utero &ex-utero matrixes bases on the top 2000 most variable genes

source_name: E10.5 mouse embryo

extract_protocol:
Embryos were dissociated into single cells at a concentration of 1000 cells per microliter and processed in the 10X Chromium Single Cell 3ʹ v3 platform
RNA libraries were prepared with the Chromium Single Cell 3ʹ v3 by following the manufacturer instructions

tag: embryo growth conditions

value: in utero

tag: embryonic day


title: 0_percent_d20.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d20.1


title: mouse E10.5 control embryo, replicate 4


title: mouse E10.5 embryo, ex utero, replicate 7

value: ex utero


title: COS_2_1


title: 100_percent_d3_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d3


title: 0_percent_d22_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d22


title: 100_percent_d3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d3.1


title: mouse E10.5 control embryo, replicate 3


title: COS_2_5


title: 0_percent_d20_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d20


title: 100_percent_d6_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d6


title: 100_percent_d2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d2.1


title: COS_1_15

value: Standard Chow Diet

value: Non-fragmented, non-multipolar


title: 0_percent_d18.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d18.1


title: COS_2_4


title: 0_percent_d18_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d18


title: 100_percent_d1.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d1.1


title: mouse E10.5 embryo, ex utero, replicate 6


title: 100_percent_d2_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d2


title: COS_1_13


title: 0_percent_d16.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d16.1


title: COS_1_12


title: mouse E10.5 embryo, ex utero, replicate 5


title: COS_1_11


title: 0_percent_d16_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d16


title: day 5 after first of two fractions (d0, d3), rep 2

type: RNA

description: Gene expression of exponentially growing GS4 fibroblasts, day 5 after first of 2× 4 Gy

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human  U133 Plus 2.0 Array-type from Affymetrix. A Custom CDF Version 24 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: skin fibroblasts GS4, exp. growth

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: AmnioMax C-100 basal medium with 7.5% AmnioMax supplement and 7.5% fetal calf serum, 2 mM glutamine plus penicillin/streptomycin

extract_protocol: Total RNA was prepared using Trizol (Gibco) followed by additional purification using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Irradiation with 6 MV X-rays given asa  single dose of 4 Gy or fractions of 4 Gy/fraction.

tag: dosis[gy]

tag: post-ir[day]

value: day 5 after first IR, day 2 after  last IR


title: 100_percent_d1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d1


title: 0_percent_d14.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d14.1


title: mouse E10.5 control embryo, replicate 2 [InUt_E105_2]

description:
InUt_E105_2
processed data file:
scRNA.normalized.assay105.csv.gz
scRNA.MetaData.105.csv.gz
scRNA.integrated.scaled.assay105.csv.gz

data_processing:
Demultiplexing was done with cellranger/3.1.0 mkfastq
Alignment and quantification of single cell features was done with cellranger counts
Aggregation of multiple GEM wells was done using-  cellranger aggr
Cells with under 200 expressing genes, over 4000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis
Genome_build: mm10
Supplementary_files_format_and_content: proccessed data is divided into three different matrices created using Seurat 3.0: Normalized - contains normalized counts of all genes across all cells. MetaData - contains information of each of the cells, and Intagrated-  with anchors the two in-utero &ex-utero matrixes bases on the top 2000 most variable genes


title: 100_percent_d0_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d0


title: 100_percent_d0.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d0.1


title: COS_1_10


title: mouse E10.5 control embryo, replicate 1 [InUt_E105_1]

description:
InUt_E105_1
processed data file:
scRNA.normalized.assay105.csv.gz
scRNA.MetaData.105.csv.gz
scRNA.integrated.scaled.assay105.csv.gz


title: 0_percent_d14_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d14


title: COS_1_9


title: mouse E8.5 embryo, ex utero, replicate 2, 3 pooled embryos [ExUt_E85_pool-3emb]

description:
ExUt_E85_pool-3emb
processed data file:
scRNA.normalized.assay85.csv.gz
scRNA.MetaData.85.csv.gz
scRNA.integrated.scaled.assay85.csv.gz

source_name: E8.5 mouse embryo


title: COS_1_8


title: COS_1_14


title: SCM_PlusATC_Rep3

city: Heidelberg

first: Cosimo

last: Jann

address: Meyerhofstr. 1

department: Genome Biology

institute: EMBL Heidelberg

description: PCR-amplified DNA barcodes

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Sequencing data was demultiplexed with Jemultiplexer with standard parameters and base call quality controlled with FastQC. Reads were trimmed and aligned to the FASTA of DNA barcode sequences (FASTA available on series record) with the Burrows-Wheeler algorithm to compute read counts.
Fold changes for gRNA barcodes and for genes were computed in R code using the edgeR package, although other read-count based packages can be used alternatively, such as limma or DeSeq2. Read counts were normalized by library size. Fitness fold changes were calculated as contrasts between +ATc and -ATc condition (+ATc/-ATc) of populations that underwent competitive growth selection in any of the used media. Gene log2FCs were computed as mean log2FC of all gRNAs per gene. Alternatively, these can be computed without prior calculation of gRNA log2FCs by starting the edgeR analysis from the geometric mean of readcounts per gene. We further calculate rank-based gene score measures based on a subset of gRNAs with extreme effects and the median log2FC of gRNAs.
Supplementary_files_format_and_content: Raw read counts and Log2 fold changes of gRNAs and genes.

molecule: genomic DNA

organism: synthetic construct

source_name: Saccharomyces cerevisiae transformed with Plasmid-encoded DNA barcodes

growth_protocol:
Design protocol: Guide RNA oligonucleotides were designed to target 161 TFs (De Boer and Hughes, 2012) and 129 PKs (Breitkreutz et al., 2010), consisting of 885 and 668 gRNAs, respectively (see Jann et al., 2020 for details to library generation). Each gene was covered by up to six different gRNAs. Guide RNA oligonucleotides were integrated into the NotI site of the pRS416 dCas9-Mxi1 plasmid via Gibson Assembly, amplified in E. coli, and transformed into the S. cerevisiae BY4743 SSA1pr-GFP reporter strain.
Transformed yeast populations were constantly grown in sythetic complete uracil dropout medium (URA3 selection gene on CRISPRi plasmids).

extract_protocol:
Before and after selection procedures, plasmid DNA was extracted using enzymatic yeast cell wall degradation in combination with standard extraction methods. The gRNA barcodes amplified from the one-copy-per-cell CEN-plasmids. Illumina sequencing was performed in paired-end and 75-100 base pairs read length on NextSeq500 machines with 15% PhiX spike-in.
DNA barcode libraries were generated by introducing standard Illumina P5 and P7 adapters and inline sample barcodes by PCR. Library preparation is otherwise performed according to standard Illumina protocols

treatment_protocol: Bulk yeast populations were treated with 250ng/µl anhydrotetracycline (ATc) to induce gRNA expression and CRISPR interference and without ATc as reference in 3 replicates. Yeast populations were grown in exponential phase and profiled for growth in oxygen-limited condition for 25 generations in SCM, SCM supplemented with 10% spruce hydrolysate and SCM supplemented with 45% Inhibitor Cocktail (a defined mixture of 8 growth-inhibiting lignocellulosic toxin compounds).

tag: yeast strain

value: SCM

tag: replicate

value: Replicate 3

value: With Atc

tag: sequenced molecule

value: plasmid DNA


title: mouse E8.5 embryo, ex utero, replicate 1 [ExUt_E85_1]

description:
ExUt_E85_1
processed data file:
scRNA.normalized.assay85.csv.gz
scRNA.MetaData.85.csv.gz
scRNA.integrated.scaled.assay85.csv.gz


title: 0_percent_d12.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d12.1

tag: treatment


title: SCM_PlusATC_Rep1

description: PCR-amplified DNA barcodes

value: Replicate 1


title: SCM_PlusATC_Rep2

description: PCR-amplified DNA barcodes

value: Replicate 2


title: 0_percent_d10.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d10.1

value: Mus musculus cells only


title: mouse E10.5 embryo, ex utero, replicate 3 [ExUt_E105_3]

description:
ExUt_E105_3
processed data file:
scRNA.normalized.assay105.csv.gz
scRNA.MetaData.105.csv.gz
scRNA.integrated.scaled.assay105.csv.gz


title: SCM_MinusATC_Rep3

description: PCR-amplified DNA barcodes

value: No Atc


title: 0_percent_d10_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d10

value: pluripotent stem cell-derived neural cells

value: Neural induction medium (see protocols section below)


title: mouse E10.5 embryo, ex utero, replicate 4 [ExUt_E105_4]

description:
ExUt_E105_4
processed data file:
scRNA.normalized.assay105.csv.gz
scRNA.MetaData.105.csv.gz
scRNA.integrated.scaled.assay105.csv.gz


title: COS_1_5


title: COS_1_6


title: COS_1_7


title: SCM_MinusATC_Rep2

description: PCR-amplified DNA barcodes


title: 0_percent_d8.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d8.1


title: COS_1_3


title: 0_percent_d8_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d8


title: mouse E10.5 embryo, ex utero, replicate 2 [ExUt_E105_2]

description:
ExUt_E105_2
processed data file:
scRNA.normalized.assay105.csv.gz
scRNA.MetaData.105.csv.gz
scRNA.integrated.scaled.assay105.csv.gz


title: UM047 cells FR treated

city: Saint Louis

first: Michael

middle: D

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

data_processing:
FastQ files aligned with STAR.
Biologic replicates analyzed by edgeR and Sailfish for gene-level features.
Normalized abundance measurements generated from edgeR.
Genome_build: ENSEMBL_R76
Supplementary_files_format_and_content: *.txt: Tab-delimited text files of gene-level moderated log2 CPM.

source_name: biopsy sample from primary eye tumor

growth_protocol: 5% CO2, 37˚C, RPMI 1640 with 10% FBS for cell lines; 5% CO2, 37˚C, MDMF for human samples.

extract_protocol:
Qiagen RNeasy mini kit.
RNA-polyA

treatment_protocol: 100 nM FR900359 in DMSO added to medium at start.

tag: tissue

value: biopsy sample from primary eye tumor

tag: genotype

tag: molecular class

value: class 1


title: COS_1_4

value: Fragmented, non-multipolar


title: InhibC45_PlusATC_Rep3

description: PCR-amplified DNA barcodes


title: InhibC45_PlusATC_Rep2

description: PCR-amplified DNA barcodes


title: 0_percent_d7.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d7.1

tag: tissue composition

tag: cell type

tag: growth time (days)


title: mouse E10.5 embryo, ex utero, replicate 1 [ExUt_E105_1]

description:
ExUt_E105_1
processed data file:
scRNA.normalized.assay105.csv.gz
scRNA.MetaData.105.csv.gz
scRNA.integrated.scaled.assay105.csv.gz

value: ex utero


title: 0_percent_d12_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d12

tag: mixing day

tag: mixing percent human

tag: biological replicate number


title: UM047 cells vehicle treated

value: DMSO


title: 0_percent_d7_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d7


title: COS_1_1

tag: diet

value: Standard Chow Diet

tag: morphology durign development


title: InhibC45_PlusATC_Rep1

description: PCR-amplified DNA barcodes


title: UM052E single-cell FR

data_processing:
FastQ files aligned with CellRanger
filter out low abundance features and cell clusters
generate cell/feature matrix file
Genome_build: hg38
Supplementary_files_format_and_content: .h5 CellRanger matrix files

source_name: biopsy sample from enucleated eye

growth_protocol: 5% CO2, 37˚C, MDMF (Melanoblast-Defined Medium with bFGF)

extract_protocol:
10X Genomics Chromium Single Cell 3' V3
3' V3

treatment_protocol: 100 nM FR900359 in DMSO added to medium at start

value: class 2


title: 0_percent_d6_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d6


title: InhibC45_MinusATC_Rep3

description: PCR-amplified DNA barcodes


title: UM052E single-cell vehicle


title: UM046 cells FR treated


title: InhibC45_MinusATC_Rep2

description: PCR-amplified DNA barcodes


title: UM051E single-cell vehicle


title: UM046 cells vehicle treated


title: 100_percent_d16.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d16.1

value: Homo sapiens cells only


title: UM051E single-cell FR


title: UM045 cells FR treated


title: 0_percent_d5.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d5.1


title: SCM_MinusATC_Rep1

description: PCR-amplified DNA barcodes

value: SCM


title: InhibC45_MinusATC_Rep1

description: PCR-amplified DNA barcodes


title: 0_percent_d5_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d5


title: UM045 cells vehicle treated


title: UM049E single-cell FR


title: UM044 cells FR treated


title: HydroL10_PlusATC_Rep2

description: PCR-amplified DNA barcodes

value: With Atc


title: UM044 cells vehicle treated


title: 0_percent_d4.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d4.1


title: EPT1248

city: Toronto

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

data_processing:
The fastq files were quality checked using FASTQC v0.72  and low quality sequences and adapter sequences were trimmed using Trim Galore v0.6.3
Reads were mapped against hg38 using HISAT2 v2.1.0
Raw counts were obtained using Featurecounts v1.6.3
The raw counts were normalized and log transformed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample
Matrix table of log transformed normalized CPM values for every gene and every sample

source_name: ependymoma tissue

extract_protocol:
RNA was extracted by Trizol Extraction
The RNA sequencing library was prepared using ribodeplete protocol as per manufacturer's instructions

value: ependymoma

tag: chr 6q status

value: 6q balanced


title: HydroL10_PlusATC_Rep3

description: PCR-amplified DNA barcodes

value: Replicate 3

value: plasmid DNA


title: UM043 cells FR treated


title: EPT0995


title: 0_percent_d6.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d6.1

value: Mus musculus cells only


title: EPT0988


title: 0_percent_d3_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d3

value: pluripotent stem cell-derived neural cells


title: 0_percent_d3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d3.1

value: Neural induction medium (see protocols section below)


title: HydroL10_PlusATC_Rep1

description: PCR-amplified DNA barcodes

value: Replicate 1


title: HydroL10_MinusATC_Rep2

description: PCR-amplified DNA barcodes

value: Replicate 2

value: No Atc


title: EPT0655


title: EPT0644


title: HydroL10_MinusATC_Rep3

description: PCR-amplified DNA barcodes


title: 0_percent_d2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d2.1


title: HydroL10_MinusATC_Rep1

description: PCR-amplified DNA barcodes


title: 0_percent_d1.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d1.1


title: AD24

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids), features.tsv (gene ids).

source_name: Skin Suction blister

extract_protocol:
Skin suction blisters were formed using a low pressure device from Electronic Diversities (Ridge Road, Finksburg, Md) by mounting 2 sterile 5-hole (5-mm diameter per hole) skin suction plates onto each antecubital fossa. Negative pressure (150-200 mm Hg) was applied over 1 to 2 hours, and blister fluid obtained was centrifuged to clear the fluid from cells and debris. The blister roof (constituting an epidermal sheet) was collected using standard surgical instruments and processed using 0.25% trypsin/EDTA (10 minutes at 37°C; Invitrogen, San Diego, Calif) to obtain a single-cell suspension. Cells from blister fluid and from the epidermis (blister roof) were enriched for CD45+ cells using fluorescence-activated cell sorting ([FACS]; FACSAria III, BD Biosciences, Franklin Lakes, NJ) and pooled within each donor sample. CD45− cells from the blister fluid and the epidermis were added to obtain a total number of 15,000 cells per scRNA-seq sample. Immediately after sorting, cells were subjected to scRNA-seq processing (10x Genomics, Pleasanton, Calif).
Single-cell libraries were generated using the Chromium Controller and Single Cell 3‘ Library & Gel Bead Kit version 3 (10x Genomics) according to the manufacturer’s protocol.

value: Skin Suction blister

tag: diagnosis

value: Spontaneously healed atopic dermatitis

tag: atopic comorbidities

value: Allergic rhinoconjunctivitis, asthma

tag: chemistry

value: Single Cell 3' v3


title: UM049E single-cell vehicle

value: DMSO

value: class 2


title: 0_percent_d1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d1


title: EPT1244

value: 6q loss


title: E264_3

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

department: Department of Clinical Laboratory

country: China

institute: Third Military Medical University

data_processing:
The sequenced libraries were mapped against predicted transcripts from the  Burkholderia thailandensis E264 and Burkholderia thailandensis BPM respectively   using TopHat v2.0.4
The transcript abundance (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) and significant changes in transcript expression were estimated using Cufflinks v2.0.2
Transcripts with p-values less than 0.05, determined using CuffDiff
Genome_build: NZ_CP008785.1 and NZ_CP008786.1 were used as the reference genomes of Burkholderia thailandensis E264; CP050020.1 and CP050021.1 were used as the reference genomes of Burkholderia thailandensis BPM;
Supplementary_files_format_and_content: counts

organism: Burkholderia thailandensis

growth_protocol: Fresh bacterial colonies taken directly from sheep blood agar that were incubated at 37℃ for 16–20 h

extract_protocol:
Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions
Barcoded sequencing libraries
Pooled libraries were enriched for the exome using hybridization (TruSeq Exome Enrichment Kit, Illumina), quantified using quantitative PCR and pooled in 1:1 ratio for pairedend sequencing on a HiSeq2500 (Illumina)

treatment_protocol: were re-suspended in sterile Mueller–Hinton broth to obtain a suspension of 0.5 McFarland turbidity.

tag: strain

value: Burkholderia thailandensis E264

tag: sample type

value: Standard strain


title: AD20

tag: tissue


title: EPT0770

value: ependymoma


title: E264_2


title: E264_1


title: Pdk1-null Tfh cells 2

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
Read quality was checked for each sample using FastQC (v0.11.5).
Reads were mapped to the reference genome (mm9) using Bowtie2 (v2.1.0).
Raw alignment counts calculated with R/Bioconductor package GenomicRanges (v1.36.1) as described in the protocol from Michael Lawrence et al., PLoS Comput Biol, 2013.
Differential expression analysis was performed with DESeq2 (v1.24.0) from the counts.
Genome_build: mm9 (NCBIM37)
Supplementary_files_format_and_content: RPKM.txt: Tab-delimited text file includes RPKMs for each sample.

source_name: Tfh cell

extract_protocol:
Tfh cells were sorted, and RNA was harvested using Trizol reagent.
The cDNA libraries were generated from 1 μg of total RNA using the Smart-seq protocol following Illumina Sequencing manual of SMARTer Ultra Low RNA Kit (Clontech).

value: Spleen

tag: age

value: 8 week

tag: genotype/variation

value: KO


title: 0_percent_d0.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d0.1

tag: tissue composition

value: Mus musculus cells only

value: pluripotent stem cell-derived neural cells

tag: treatment

value: Neural induction medium (see protocols section below)


title: 0_percent_d2_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d2

tag: cell type

tag: growth time (days)


title: BPM_3

value: Burkholderia thailandensis BPM

value: Clinically isolated strain


title: 0_percent_d4_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d4

tag: mixing day

tag: mixing percent human


title: BPM_2


title: AD25

value: Skin Suction blister

value: Spontaneously healed atopic dermatitis

value: Allergic rhinoconjunctivitis


title: UM043 cells vehicle treated

value: biopsy sample from primary eye tumor

value: DMSO

tag: genotype

tag: molecular class

value: class 1


title: WT Tfh cells 1

value: WT


title: Pdk1-null Tfh cells 1


title: EPT0699

tag: chr 6q status

value: 6q loss


title: WT Tfh cells 2


title: EPT0067

value: ependymoma


title: EPT0718


title: 0_percent_d0_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d0

tag: biological replicate number


title: AD21

tag: diagnosis

tag: atopic comorbidities

value: Single Cell 3' v3


title: STAR-T cells - 72h-rep1

status: Public on Feb 14 2021

first: Xin

last: Lin

address: Shuangqing Street, Haidian District

department: School of Medicine

institute: Tsinghua University

description: Sample 34

data_processing:
base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
filtered fastq data with quality of bases higer than 20 were processed by Cutadapt (V1.9.1) to be high quality clean data.
clean data were aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and each gene

source_name: primary CD8 T cells

growth_protocol: T cells were culture in RPMI 1640 + 10% heat-inactivated FBS + GlutaMax + NEAA + P/S + 200IU/ml IL2

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel.1 μg total RNA with RIN value above 6.5 was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T cells were stimulated with target cells or target antigen protein in RPMI 1640 + 10% heat-inactivated FBS + GlutaMax + NEAA + P/S

value: primary CD8 T cells

tag: target antigen

value: EGFR

tag: stimulation

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:34

tag: stimulation time

value: 72 hours


title: EGFR-28zCAR-T cells

description: Sample 37

value: immobilized EGFR protein (2 ug/ml)


title: STAR-T cells - 72h-rep3

description: Sample 36

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:36


title: EGFR-BBzCAR-T cells

description: Sample 38


title: STAR-T cells - 72h-rep2

description: Sample 35

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:35


title: EGFR-mutSTAR-T cells

description: Sample 39


title: STAR-T cells - 24h-rep3

description: Sample 33

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:33

value: 24 hours


title: STAR-T cells - 24h-rep2

description: Sample 32

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:32


title: BPM_1

tag: strain

value: Burkholderia thailandensis BPM

tag: sample type

value: Clinically isolated strain


title: STAR-T cells - 24h-rep1

description: Sample 31

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:31


title: STAR-T cells - 0h-rep3

description: Sample 27

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:27

value: 0 hour


title: STAR-T cells - 0h-rep1

description: Sample 25

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:25


title: STAR-T cells - 6h-rep2

description: Sample 29

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:29

value: 6 hours


title: TCR-T cells - 72h-rep1

description: Sample 22

value: primary CD8 T cells

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:22


title: STAR-T cells - 0h-rep2

description: Sample 26

value: EGFR

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:26


title: STAR-T cells - 6h-rep1

description: Sample 28

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:28


title: TCR-T cells - 72h-rep2

description: Sample 23

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:23

value: 72 hours


title: TCR-T cells - 72h-rep3

description: Sample 24

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:24


title: TCR-T cells - 24h-rep3

description: Sample 21

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:21

value: 24 hours


title: TCR-T cells - 6h-rep3

description: Sample 18

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:18


title: Overexpression of SOX17, TFAP2C, GATA3, clone_1; day77

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C, GATA3 series, clone 1, harvested at day77, BTAG-sorted

data_processing:
All reads were processed with Trim_galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove 4 bases from 5’-ends, 1 base from 3’-ends, adaptor sequences, and low-quality reads (quality score < 20).
The processed reads were mapped onto human genome (GRCh38.p2) with bismark program from Bismark (v0.17.0) with “--pbat” option (Krueger and Andrews, 2011).
Mapped data (BAM format) were converted to methylation levels using bismark_methylation_extractor program from Bismark.
Samtools (v1.3) (Li et al, 2009) and IGVTools (v2.3.52) (James et al., 2011) were used to manipulate BAM files and create wig files. Only CpGs, whose read depth are between 4 and 200, are included in the bigWig files.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: bigWig. bismark_CpG_repor

source_name: day77, from 585B1 hiPSC BTAG reporter line

growth_protocol: 585B1 hiPSCs (XY) was cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015; Kojima et al., 2017).

extract_protocol:
The cells were pelleted down and snap frozen until use.  The cellular lysate were used for PBAT reaction.
Bisulfite conversion and library construction was performed by the post-bisulfite adaptor tagging (PBAT) method (Miura 2012). The protocol is freely available at the website of International Human Epigenome Consortium (IHEC) (http://www.crest-ihec.jp/english/epigenome/index.html)
Whole Genome Bisulfite Sequence (WGBS)

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), Y27632 (10µM) and BMP4 (200 ng/mL) or Dox (1.0 µg/mL) in GMEM containing 15% KSR, until the harvest day.
BTAG positive cells at day 6 were aggregated with mouse female E12.5 gonadal somatic cells and maintained at air-liquid interphase culture in MEMalpha with 10% FBS up to day 77 and BTAG positive cells were collected.

tag: cell line

value: 585B1 hiPSCs

tag: sampled time point

value: day 77

tag: reporter transgene

value: Blimp1-tdTomato, TFAP2C-EGFP

tag: other transgenes

value: rtTA; tetO-TFAP2C; tetO-BLIMP1


title: TCR-T cells - 24h-rep2

description: Sample 20

tag: cell type

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:20


title: STAR-T cells - 6h-rep3

description: Sample 30

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:30

value: 6 hours


title: TCR-T cells - 0h-rep2

description: Sample 14

value: primary CD8 T cells

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:14

value: 0 hour


title: TCR-T cells - 6h-rep1

description: Sample 16

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:16


title: TCR-T cells - 0h-rep1

description: Sample 13

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:13


title: TCR-T cells - 6h-rep2

description: Sample 17

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:17


title: TCR-T cells - 0h-rep3

description: Sample 15

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:15


title: CAR-T cells - 24h-rep2

description: Sample 8

value: EGFR

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:08


title: CAR-T cells - 72h-rep3

description: Sample 12

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:12

value: 72 hours


title: CAR-T cells - 72h-rep2

description: Sample 11

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:11


title: CAR-T cells - 6h-rep3

description: Sample 6

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:06


title: CAR-T cells - 24h-rep1

description: Sample 7

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:07

value: 24 hours


title: CAR-T cells - 24h-rep3

description: Sample 9

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:09


title: CAR-T cells - 72h-rep1

description: Sample 10

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:10


title: CAR-T cells - 6h-rep1

description: Sample 4

value: primary CD8 T cells

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:04

value: 6 hours


title: CAR-T cells - 0h-rep1

description: Sample 1

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:01

value: 0 hour


title: CAR-T cells - 0h-rep2

description: Sample 2

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:02


title: CAR-T cells - 0h-rep3

description: Sample 3

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:03


title: TCR-T cells - 24h-rep1

description: Sample 19

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:19


title: QKI KO rep3 B3_KO3_S12

city: HOUSTON

first: Jian

last: Hu

state: TEXAS

address: 1881 East Road

department: Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

description: QKI KO rep3

data_processing:
For the cell line data: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10/hg19 whole genome using STAR-2.6.1b with parameters --outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate. For the tissue data: mapping was done by applying hisat2 (2.0.4) with parameters -p 8 --rna-strandness RF --no-mixed --no-discordant --known-splicesite-infile mm10/gencode.vM8.basic.annotation.splicesites -x mm10_hisat2
For the cell line data: Counting reads in features with htseq-count (htseq/0.11.0) with parameters --stranded reverse --additional-attr gene_name gene_type (human annotation file: hg19/gencode.v29lift37.annotation.gtf, mouse annotation file: mm10/gencode.vM20.primary_assembly.annotation.gff3). For the tissue data: Counting reads in features with featureCounts with parameters -p -s 2 -g gene_name -a mm10/gencode.vM8.basic.annotation.gtf
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files include Read Counts for each Sample

source_name: human lens epithelial cell line (HLE-B3)

growth_protocol: Neural stem cell-derived lens progenitor-like cells (NLPCs) were differentiated from neural stem cells in DMEM/F-12 supplemented with 0.05% BSA, 1% nonessential amino acids, 50 units/mL penicillin G, and 50 μg/mL streptomycin, 1X N2 and 1X B27 with two-step growth factor treatment, 1st step with 100 ng/ml Noggin and 2nd step with 100 ng/ml bFGF, 20 ng/ml BMP4, and 20 ng/ml BMP7. HLE-B3 cells were cultured in EMEM containing 20% fetal bovine serum, 50 units/mL penicillin G, and 50 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated from all three systems (Mouse eye lens tissue, NLPCs, HLE-B3) using a RNeasy Mini Kit with the treatment of DNase (Qiagen) for library preparation.
Illumina Truseq stranded Library Prep

value: QKI KO

tag: tissue

value: cell line


title: QKI KO rep1 B3_KO1_S10

description: QKI KO rep1

tag: genotype


title: WT rep1 B3_WT1_S7

description: WT rep1

value: wild type


title: WT rep2 B3_WT2_S8

description: WT rep2


title: WT rep3 B3_WT3_S9

description: WT rep3


title: CAR-T cells - 6h-rep2

description: Sample 5

value: EGFR

value: EGFR+ A549 o/e NY-ESO-1 and HLA*02:05


title: Obese_20

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalls performed using Illumina’s OLB v1.9.
The transcript abundance quantification was conducted using the ultrafast quasi-alignment tool Kallisto, which pseudo-aligned the sequencing reads from each sample to the assembly based on the FANTOM-CAT.
The gene-level estimates were obtained by summing the corresponding transcript-level estimates using a biocondutor package, Tximport (Soneson et al., 2015).
Differential gene expression analysis was conducted at the gene level using EdgeR, selecting for genes with a false discovery rate of <0.05
Genome_build: hg19
Supplementary_files_format_and_content: .tsv files report counts and tpms

source_name: Obese, subcutaneous white adipose tissue

extract_protocol:
Total RNA was extracted from samples of cohort 1 using the RNeasy Lipid Tissue Mini Kit (74804, Qiagen, Hilden, Germany) as per manufacturer’s instructions. RNA concentration and purity was measured using a using Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Lafayette, USA).
RNA libraries for sequencing were prepared using TruSeq RNA kits (Illumina, CA, USA) according to the manufacturer's instructions with the following changes. The protocols were automated using an MBS 1200 pipetting station (Nordiag AB, Sweden). All purification steps and gel-cuts were replaced by the magnetic bead clean-up methods as previously described (Borgstrom et al., 2011). The samples were sequenced on an Illumina HiSeq 2000 as paired-end reads to 100 bp.

tag: disease state

value: Obese

tag: bmi

tag: gender

value: Female

tag: age

value: subcutaneous white adipose tissue


title: Obese_19


title: Obese_18


title: Obese_16


title: Obese_23


title: Obese_24


title: Obese_26


title: Obese_25


title: Obese_28


title: lean_12

source_name: lean, subcutaneous white adipose tissue

value: lean


title: Obese_17


title: lean_13


title: Obese_22


title: lean_14


title: QKI KO rep2 B3_KO2_S11

description: QKI KO rep2


title: Obese_21


title: lean_11


title: lean_10


title: Obese_27


title: lean_8


title: lean_7


title: lean_9


title: lean_6


title: lean_4


title: lean_3


title: lean_5


title: lean_2


title: DP_P_Chuong_296 posterior

city: Los Angeles

first: Wei-Ling

last: Chang

address: 2011 Zonal Ave HMR 313B

institute: Keck School of Medicine

data_processing:
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/QC were done in Partek Flow.
Partek's modified expectation-maximization (EM) algorithm was used for quantification
Reads Per Kilobase of exon per Megabase of library size (RPKM) wereused fornormalization
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Gallus gallus

source_name: dermal papilla, dorsal feather

extract_protocol:
Dissected tissue was extracted in Trizol reagent.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2.

treatment_protocol: untreated

tag: breed

value: White Leghorn

value: dermal papilla complex

tag: developmental stage

value: growing stage


title: DP_A_Chuong_294 anterior


title: DP_P_Chuong_295 posterior


title: UNC_P40_KO3_CTX_BS

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
BSmap (Xi et al., 2009) was used to map reads to the mm9 mouse genome assembly and only uniquely mapping reads were retained for analyses. Methylation levels were determined by calculating #C/(#C+#T) for all cytosines, where #C is the number of C reads and #T is the number of T reads.
Genome_build: mm9
Supplementary_files_format_and_content: txt
Supplementary_files_format_and_content: text files: column 1= Gene name; column 2= #C calls within gene;  column 3= #T+#C calls within gene

source_name: Cortex

growth_protocol: Brain tissue was taken from wild-type mice or transgenic mice maintained under standard housing conditions.

extract_protocol:
Mouse cortices were collected and DNA was extracted using Qiagen Blood and Tissue kit.
Genomic DNA was extracted from mice cortex with the DNeasy Blood & Tissue Kit (Qiagen) and sonicated with a Covaris S2 instrument to generate 200 bp fragments. Unmethylated lambda DNA (0.1%–0.5%; Promega D1521) was spiked in to assess conversion rates. Whole genome bisulfite-sequencing was performed  as described (Stroud et al., 2017).

value: Cortex

value: miR29 KO

tag: background


title: UNC_P40_WT4_CTX_BS

value: WT


title: UNC_P40_WT2_CTX_BS


title: UNC_P40_KO4_CTX_BS


title: UNC_P40_WT3_CTX_BS


title: UNC_P40_WT1_CTX_BS


title: UNC_P40_KO2_CTX_BS


title: lean_1


title: Wildtype left ventricle 129-SvEv

first: Joshua

middle: M

last: Gorham

address: 77 Ave Louis Pasteur, NRB 256

institute: Harvard Medical School

data_processing:
Illumina fastq short reads were aligned by STAR aligner to create BAM files.
BAM files were analyzed as described: McKean et al. Nat Commun 2016 Sep 27;7:12824. doi: 10.1038/ncomms12824.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 151204.mm10.rpm.expr.txt: Tab-delimited text file

source_name: Wildtype left ventricle

growth_protocol: Mice were 10 weeks old.

extract_protocol:
Christodoulou et al. J Clin Invest. 2014;124(3):1364-1370.
McKean et al. Nat Commun 2016 Sep 27;7:12824. doi: 10.1038/ncomms12824.

value: Wildtype

tag: Sex

value: Male

value: 10 weeks

value: Cardiac left ventricle


title: S-NSC-34_clone2

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

country: Spain

institute: CNIO

description: Clone2.RPM; Clone2.raw-counts

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to fastq file format was performed with the bcl2fastq software from Illumina.
RNA-seq reads were aligned to the mouse genome assembly, with transcript annotations from Gencode (Version M16 - Ensembl 91),  using STAR (2.5.3) with --quantMode GeneCounts option  (Dobin A et al. Bioinformatics 29:15, 2013).
Differential gene expression analysis was subsequently performed with DESeq2 (Love MI et al. Genome Biol 15:550, 2014)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: "Counts.txt" tab-delimited text file contains the read counts for the three samples as measured by STAR. Column "RPM" reflects Reads Per Million of mapped reads to facilitate comparisons between individual samples.
Supplementary_files_format_and_content: Differential gene expression DESeq2 analysis is presented in "resultTable_Clones-v-Ctrl.txt" tab-delimited text file. "Clone07" and "Clone16" have been treated as replicates and compared to the "Ctrl" sample.

source_name: Hybrid cell line, with properties of motor neurons

growth_protocol: NSC34 cells were grown on gelatin at 37°C, 5% CO2, in high glucose DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS), 1% glutamine and 1% Penicillin/Streptomycin

extract_protocol:
RNA was purified by using absolutely RNA kit from Agilent.
1 µg of total RNA samples with RIN above 9 were converted to sequencing libraries with the "TruSeq Stranded mRNA LT Sample Prep Kit" (Illumina) by following manufacturer instructions (TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E).

treatment_protocol: 10 µM of PR20 during 3 weeks

value: NSC-34 is produced by fusion of motor neuron enriched, embryonic mouse spinal cord cells with mouse neuroblastoma

value: WT-spontaneously resistant to PR20

tag: treatment

value: 10 µM of PR20 during 3 weeks


title: Lamp2 knockout LV 129-SvEV

source_name: Lamp2 knockout left ventricle

tag: strain

value: Lamp2 knockout


title: UNC_4mo_DNMT3AmiR29MUT2_CTX

value: Dnmt3a mi5

value: 4 months


title: UNC_4mo_DNMT3AmiR29MUT1_CTX


title: UNC_4mo_DNMT3AWT2_CTX


title: Normal human embryonic lung cells - high does of Diesel exhaust particles treated 2

city: Cheongju-si

first: Joong Won

last: Lee

state: Chungcheongbuk-do

address: 187, Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu

department: Division of Allergy and Respiratory Disease Research

country: South Korea

institute: Korea National Institute of Health

data_processing:
Illumina NextSeq 500 software used for basecalling.
Potentially existing sequencing adapters and raw quality bases in the raw reads were trimmed by Skewer ver 0.2.2. The cleaned high quality reads after trimming the low-quality bases and sequencing adapters were mapped to the reference genome by STAR ver 2.5 software.
Since the sequencing libraries were prepared strand-specifically by using Illumina’s strand-specific library preparation kit, the strand-specific library option, --library-type=fr-first-strand was applied in the mapping process. To quantify the mapped reads on the reference genome into the gene expression values, HTSeq ver 0.9.1 with the strand-specific library option, -s reverse and with the option for overlapping features, –m intersection-nonempty. Other default options were used.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

source_name: WI-38_high does of Diesel exhaust particles treated

growth_protocol: Normal human embryonic lung cells (WI-38) were were cultured in 24-well or 96-well plates and grown in minimum essential medium (MEM; Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS; Gibco Life Technologies) and penicillin/streptomycin (100 U, Gibco Life Technologies) in a hu-midified 5% CO2 atmosphere at 37℃.

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen) according to the manufacturer's protocol.
The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeq Stranded mRNA Sample preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: The diesel exhaust particle was dispersed in a serum-free cell medium, and cells were incubated with DEP at 6 concentrations (0, 25, 50, 100, 200, or 400 µg/ml) for 24.

tag: cell line

value: Normal human embryonic lung cells

value: 200 ug/ml of Diesel exhaust particles


title: NSC-34_Ctrl

description: Ctrl.RPM; Ctrl.raw-counts


title: UNC_4mo_DNMT3AWT1_CTX


title: Control replicate 2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Control

data_processing:
Raw reads are trimmed by Trimmomatics to filter out adapters and low-quality reads
FASTQ files were aligned to BAM by STAR aligner
BAM files were quantified by HTSEQ
Genome_build: mm10
Supplementary_files_format_and_content: HTSEQ raw count

source_name: LIVER

extract_protocol:
Liver were pelleted and lysed with RLT Buffer (Qiagen). RNA was isolated from the lysate using RNEasy kits (Qiagen).  Library preparation, sequencing, and bioinformatics analysis were performed by Medgenome (CA, USA).
Qubit Fluorometric Quantitation and TapeStation BioAnalyzer

value: liver

value: 3 months

value: Control


title: DKO replicate 1

description: DKO

value: DKO


title: Control replicate 3

description: Control


title: Control replicate 1

description: Control


title: DKO replicate 3

description: DKO


title: DKO replicate 2

description: DKO


title: UNC_P40_KO1_CTX_BS

value: Cortex

value: miR29 KO


title: Normal human embryonic lung cells - high does of Diesel exhaust particles treated 1


title: DP_A_Chuong_293 anterior

value: White Leghorn

value: dermal papilla complex

value: growing stage


title: S-NSC-34_clone1

description: Clone1.RPM; Clone1.raw-counts

value: NSC-34 is produced by fusion of motor neuron enriched, embryonic mouse spinal cord cells with mouse neuroblastoma


title: Normal human embryonic lung cells - control 2

value: untreated


title: Normal human embryonic lung cells - control 1


title: Normal human embryonic lung cells - low does of Diesel exhaust particles treated 2

source_name: WI-38_low does of Diesel exhaust particles treated

value: 100 ug/ml of Diesel exhaust particles


title: HDiPSC_bulk1

city: Jerusalem

first: Matan

last: Sorek

address: Edmond J. Safra Campus

department: Genetics

institute: The Hebrew University of Jerusalem

description:
all_raw_expected_counts.txt
all_normalized_counts.txt

data_processing:
Raw reads that passed the quality controls were aligned to human genome assembly hg38 using Bowtie2 (Langmead and Salzberg, 2012)
RSEM (Li and Dewey, 2011) version 1.2.31 was used to count number of reads aligned to each gene
Transcripts Per Million (TPM) were taken from RSEM output and were further normalized according qunatile normalization (Bolstad et al., 2003)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized TPM values for each sample

source_name: neural progenitor cells

growth_protocol: hESCs (Bradley et al., 2011), and hiPSCs were cultured as described (Takahashi et al., 2007). For neuronal induction, hiPSC colonies were induced for neuronal lineage differentiation using dual SMAD inhibition by blocking BMP and TGFb. hiPSC colonies were separated and seeded on Matrigel as single cells and incubated with human induction media [DMEM/F12, Neurobasal, N2, B27] supplemented with 2 SMADi (20 M SB, 100 nM LDN) and 1 μM XAV-939 for 10 days. From day 10 to 20 of differentiation, cells were incubated with neural induction media supplemented with 50 nM SAG and 1 μM XAV-939, inducing the cells to become neural progenitor cells (NPCs).

extract_protocol:
RNA was extracted from neurons using TCL-buffer (Qiagene, cat. 1031576) with 1% 2-Mercaptoethanol for sc-experiments. For bulk samples, DNA/RNA shield (Zymo Research, cat. R1100-50) was used.
library construction was carried out as published (Ding et al., 2019; Picelli et al., 2013)

value: human embryonic stem cells- and induced pluripotenet stem cells-derived neural progenitor cells

tag: derived from hesc/ipsc

value: iPSC

tag: wt/mut

value: MUT

tag: hd/asd

value: HD


title: HDiPSC_bulk2

tag: cell type


title: C116_bulk1

value: WT


title: C116_bulk2


title: H66_H11

value: ESC

value: ASD


title: H66_G11


title: H66_G2


title: H66_G3


title: H66_G10


title: H66_H8


title: H66_F7


title: H66_F8


title: H66_F2


title: H66_F11


title: H66_E10


title: H66_E1


title: H66_D9


title: H66_D6


title: Normal human embryonic lung cells - low does of Diesel exhaust particles treated 1

value: Normal human embryonic lung cells


title: H66_D4


title: H66_E3


title: H66_D8


title: H66_C11


title: H66_C2


title: H66_C10


title: H66_B6


title: H66_D5


title: H66_D12


title: H66_D11


title: H66_C8


title: H66_B4


title: H66_C5


title: H66_F5


title: H66_B3


title: H66_B12


title: H66_E11


title: H66_B10


title: lean_15

value: lean

value: Female

tag: tissue

value: subcutaneous white adipose tissue


title: H66_A5


title: H66_A6


title: H66_A3


title: H66_D10


title: AC2_H9


title: AC2_H8


title: AC2_H7


title: AC2_H5


title: H66_A11


title: H66_B5


title: H66_A8


title: AC2_H11


title: AC2_H3


title: AC2_G9


title: AC2_G6


title: AC2_G8


title: AC2_G5


title: AC2_G7


title: AC2_F9


title: AC2_G10


title: AC2_G11


title: AC2_G1


title: AC2_H6


title: AC2_H4


title: H66_E9


title: AC2_F5


title: AC2_F3


title: AC2_H2


title: AC2_F4


title: AC2_F2


title: AC2_F12


title: AC2_F7


title: AC2_F10


title: AC2_G4


title: AC2_F1


title: AC2_F11


title: AC2_E9


title: AC2_E8


title: AC2_E6


title: AC2_E5


title: AC2_E4


title: AC2_E10


title: AC2_E2


title: AC2_E3


title: AC2_E1


title: AC2_E11


title: AC2_E12


title: AC2_D9


title: AC2_D7


title: AC2_D8


title: AC2_D5


title: AC2_D4


title: AC2_D3


title: AC2_D6


title: AC2_D2


title: AC2_D11


title: AC2_D12


title: AC2_D10


title: AC2_C9


title: AC2_C5


title: AC2_C7


title: AC2_D1


title: AC2_C3


title: AC2_C8


title: AC2_C12


title: AC2_C1


title: AC2_C10


title: AC2_B9


title: AC2_C11


title: AC2_B6


title: AC2_B8


title: AC2_C2


title: AC2_B5


title: AC2_B4


title: AC2_B2


title: AC2_B10


title: AC2_B12


title: AC2_A7


title: AC2_B11


title: AC2_A9


title: AC2_B1


title: AC2_C6


title: AC2_A6


title: AC2_H10


title: AC2_A3


title: AC2_C4


title: AC2_A2


title: AC2_A4


title: AC2_A12


title: AC2_B7


title: AC2_A10


title: AC2_A11


title: HDiPSC_H9


title: HDiPSC_H8


title: AC2_A1


title: HDiPSC_H7


title: HDiPSC_H3


title: HDiPSC_H4


title: HDiPSC_H11


title: HDiPSC_H1


title: HDiPSC_H6


title: HDiPSC_H10


title: HDiPSC_H2


title: HDiPSC_H5


title: HDiPSC_G9


title: AC2_A8


title: HDiPSC_G6


title: HDiPSC_G3


title: HDiPSC_G11


title: HDiPSC_G8


title: HDiPSC_G5


title: HDiPSC_G7


title: HDiPSC_G4


title: HDiPSC_G10


title: HDiPSC_G1


title: HDiPSC_G2


title: HDiPSC_F6


title: HDiPSC_F8


title: HDiPSC_F5


title: HDiPSC_F7


title: HDiPSC_F1


title: HDiPSC_F11


title: HDiPSC_F12


title: HDiPSC_F2


title: HDiPSC_F4


title: HDiPSC_F3


title: HDiPSC_E9


title: HDiPSC_E5


title: HDiPSC_E11


title: HDiPSC_E3


title: HDiPSC_E12


title: HDiPSC_E1


title: HDiPSC_D7


title: HDiPSC_D9


title: HDiPSC_E10


title: HDiPSC_E2


title: HDiPSC_E4


title: HDiPSC_F9


title: HDiPSC_D4


title: HDiPSC_D3


title: HDiPSC_D8


title: HDiPSC_D12


title: HDiPSC_D5


title: HDiPSC_D2


title: HDiPSC_E8


title: HDiPSC_E6


title: HDiPSC_D1


title: HDiPSC_C6


title: HDiPSC_C9


title: HDiPSC_C7


title: HDiPSC_D11


title: HDiPSC_C3


title: HDiPSC_D10


title: HDiPSC_C2


title: HDiPSC_C10


title: HDiPSC_C1


title: HDiPSC_C8


title: HDiPSC_B8


title: HDiPSC_C4


title: HDiPSC_B7


title: HDiPSC_B11


title: HDiPSC_B6


title: HDiPSC_B5


title: HDiPSC_B12


title: HDiPSC_B4


title: HDiPSC_B10


title: HDiPSC_C5


title: HDiPSC_A9


title: HDiPSC_A7


title: HDiPSC_A8


title: HDiPSC_B1


title: HDiPSC_A6


title: HDiPSC_A5


title: HDiPSC_A2


title: HDiPSC_C12


title: HDiPSC_A11


title: HDiPSC_A12


title: AC2_F8


title: HDiPSC_C11


title: C116_H7


title: C116_H6


title: C116_H8


title: HDiPSC_A10


title: HDiPSC_B9


title: C116_H4


title: C116_H3


title: C116_H11


title: C116_H10


title: C116_H1


title: C116_G7


title: C116_G8


title: C116_G6


title: C116_G5


title: C116_G4


title: C116_G3


title: C116_G11


title: C116_G1


title: C116_F8


title: C116_F9


title: HDiPSC_A1


title: C116_F7


title: C116_F5


title: C116_H5


title: C116_F6


title: C116_H2


title: C116_F11


title: C116_F12


title: C116_F3


title: C116_F2


title: C116_G9


title: C116_F4


title: C116_F10


title: C116_E5


title: C116_E6


title: C116_E7


title: C116_E9


title: C116_F1


title: C116_E8


title: C116_G2


title: C116_E4


title: C116_E10


title: C116_E3


title: C116_E2


title: C116_E12


title: C116_E1


title: C116_D9


title: C116_D8


title: C116_D5


title: C116_D4


title: C116_D3


title: C116_D2


title: C116_D11


title: C116_D6


title: C116_C7


title: C116_C8


title: C116_D1


title: C116_D10


title: C116_C9


title: C116_C1


title: C116_C12


title: C116_C3


title: C116_C10


title: C116_C11


title: C116_C6


title: C116_C2


title: C116_B9


title: C116_D12


title: C116_B8


title: C116_D7


title: C116_B7


title: C116_B2


title: C116_B5


title: C116_B3


title: C116_B11


title: C116_C5


title: C116_A5


title: C116_A6


title: C116_B1


title: C116_A9


title: C116_B10


title: C116_A7


title: C116_A3


title: C116_A12


title: 96ex_H7


title: C116_A11


title: 96ex_H6


title: 96ex_H9


title: C116_A1


title: 96ex_F8


title: 96ex_H1


title: 96ex_H3


title: 96ex_G6


title: 96ex_G4


title: 96ex_G10


title: 96ex_F9


title: 96ex_F6


title: 96ex_F3


title: 96ex_F11


title: 96ex_F12


title: 96ex_F2


title: 96ex_E9


title: 96ex_E7


title: 96ex_E6


title: 96ex_E12


title: 96ex_E11


title: 96ex_D8


title: 96ex_G7


title: 96ex_D3


title: 96ex_F7


title: 96ex_D5


title: 96ex_D6


title: 96ex_D7


title: 96ex_D2


title: 96ex_D12


title: 96ex_F10


title: 96ex_C12


title: 96ex_C3


title: 96ex_C2


title: 96ex_C5


title: 96ex_B9


title: 96ex_B8


title: 96ex_C1


title: 96ex_B6


title: 96ex_B12


title: 96ex_B4


title: 96ex_E5


title: 96ex_B7


title: 96ex_B1


title: 96ex_D9


title: 96ex_B10


title: 96ex_C9


title: 96ex_A6


title: 96ex_B11


title: 96ex_A4


title: 96ex_A5


title: 96ex_A3


title: 96ex_A1


title: 96ex_A8


title: 180CAG_H9


title: 96ex_A12


title: 180CAG_H7


title: 96ex_C10


title: 180CAG_H8


title: 180CAG_H3


title: 180CAG_H2


title: 180CAG_H4


title: 180CAG_H11


title: 180CAG_H1


title: 180CAG_G8


title: 180CAG_G9


title: 180CAG_G5


title: 180CAG_G3


title: 180CAG_G2


title: 180CAG_G1


title: 96ex_A2


title: Qk KO rep3 KO3_S6

description: Qk KO rep3

source_name: NSC-derived lens progenitor-like cells (NLPCs)

tag: genotype

value: primary cell line


title: 180CAG_F3


title: 180CAG_F6


title: 180CAG_F7


title: 180CAG_F5


title: Qk KO rep2 KO2_S5

description: Qk KO rep2


title: WT rep3 WT3_S3

description: WT rep3

value: wild type


title: 180CAG_H5


title: WT rep2 WT2_S2

description: WT rep2


title: 180CAG_F11


title: 180CAG_H6


title: 180CAG_F10


title: 180CAG_F2


title: Qk KO rep1 KO1_S4

description: Qk KO rep1


title: 180CAG_F1


title: WT rep1 WT1_S1

description: WT rep1


title: 180CAG_H10


title: 180CAG_E8


title: Qk KO rep3 Sample_20

description: Qk KO rep3

source_name: mouse eye lens tissue

value: Qk-iCKO

value: eye lens tissue

tag: condition

value: Nestin-CreERT2; QkL/L


title: WT rep3 Sample_18

description: WT rep3

value: Control

value: Nestin-CreERT2; QkL/+


title: Qk KO rep2 Sample_17

description: Qk KO rep2


title: 180CAG_E6

value: human embryonic stem cells- and induced pluripotenet stem cells-derived neural progenitor cells

value: iPSC


title: 180CAG_E4

value: MUT

value: HD


title: WT rep2 Sample_16

description: WT rep2


title: Qk KO rep1 Sample_13

description: Qk KO rep1


title: 180CAG_E5


title: WT rep1 Sample_11

description: WT rep1


title: 180CAG_E3


title: 180CAG_E11


title: 180CAG_E1


title: 180CAG_D9


title: 180CAG_E10


title: 180CAG_D6


title: 180CAG_D5


title: 180CAG_D8


title: 180CAG_D4


title: CAST-seq centromeric VEGFA CRISPR/Cas9 treated CD34+ cells, Day4 non-treated control

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Library strategy: CAST-Seq
Mate paired reads were merged using FLASH (v1.2.11) software. BBmap (v38.76) was used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Genome_build: hg38
Supplementary_files_format_and_content: matrix table of translocation sites detected with CAST-Seq pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

source_name: Hematopoietic stem and progenitor cells

growth_protocol: Cryopreserved human CD34+ HSPCs derived from cord blood (AllCells, Cat.# CB008F; StemCell-Technologies, Cat.# 70008.3) were thawed and cultivated in a density range of 0.5–1 x 106/ml at 37°C, 5% CO2 in GMP-grade CellGro media (CellGenix, Cat.# 20802-0500) complemented with TPO (100 ng/ml; Peprotech Cat.# 300-18), Flt-3 (300 ng/ml; Immunotools, Cat.# 60100864), SCF (300 ng/ml; Immunotools Cat.# 11343327), IL-3 (60 ng/ml; Immunotools Cat.# 11340035), 20 mg/ml streptomycin and 20 U/ml penicillin (Sigma Cat.# P0781)

extract_protocol:
Genomic DNA of at least 5 x 105 cells was isolated at the indicated time points using QIAamp® DNA Blood Mini Kit (Qiagen, Cat.# 51306)
DNA fragment by sonication (M220 Focused Ultrasonicator) or enzymatic digestion (NEBNext® Ultra™ II FS DNA Library Prep Cat.# E7805S) to obtain average fragment lengths of 350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions (NEBNext® Ultra™ II FS DNA Library Prep Cat.# E7805S) in order to enable the ligation of a linker sequence with a protruding 3’-T. After DNA purification (Qiagen, PCR purification kit, Cat.# 28104), two rounds of PCR utilizing Q5 polymerase (NEB, Cat.# M0493S) were performed using the following conditions: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). One or two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments
Third PCR introduced the barcoded Illumina adapter for sequencing (NEB, NEBNext Multiplex Oligos for Illumina, Cat.# E7335). Denatured amplicons at 6-10 pM were loaded into the Illumina MiSeq Reagent Kit V2-500 cycle (Illumina, Cat.# MS-102-2003) according to the manufacturer’s instructions.

treatment_protocol: For nucleofection, 5–7 x 105 CD34+ cells were resuspended in 20 μL of P3 solution (Lonza, Cat.# V4XP-3032) and mixed with previously assembled RNPs or TALEN mRNAs. For RNP assembly, 6 μg of Cas9 protein (PNA Bio, Cat.# CP02; IDT Alt-R® S.p. HiFi Cas9 Nuclease V3, 1081060) were complexed for five minutes with 225 pmol of gRNA (three 2'-O-methyl phosphorothioate linked nucleotides at either 5’ and 3’-end; Synthego, USA). TALEN encoding mRNA was generated as previously described (Patsali et al., 2019). All target sequences (gRNA and TALEN) are reported in Table S4. Nucleofection was performed with a 4D-Nucleofector (Lonza, Germany), program CA137 in a 16-well cuvette format.

value: CD34 positive HSPC

tag: sample

value: CAST-seq derived amplicons from gDNA

value: non-treated


title: CAST-seq centromeric VEGFA CRISPR/Cas9 treated CD34+ cells, duplicate Day4 non-treated control


title: 180CAG_D3


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, Day4 non-treated control


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, Day1 non-treated control


title: CAST-seq centromeric RAG1 CRISPR/Cas9 treated CD34+ cells, Day4 non-treated control


title: CAST-seq centromeric FANCF CRISPR/Cas9 treated CD34+ cells, duplicate Day4 non-treated control


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, Day14 non-treated control


title: 180CAG_D12


title: CAST-seq telomeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 non-treated control


title: CAST-seq telomeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day4 non-treated control


title: CAST-seq centromeric RAG1 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 non-treated control


title: CAST-seq centromeric FANCF CRISPR/Cas9 treated CD34+ cells, Day4 non-treated control


title: 180CAG_D2


title: 180CAG_C7


title: 180CAG_C9


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, duplicate Day4 non-treated control


title: 180CAG_C5


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day4 non-treated control


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 non-treated control


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day1 non-treated control


title: 180CAG_C3


title: 180CAG_C4


title: CAST-seq centromeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day14 non-treated control


title: 180CAG_C2


title: 180CAG_C12


title: CAST-seq centromeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day1 non-treated control


title: 180CAG_C11


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day14 non-treated control


title: 180CAG_C10


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day14 non-treated control


title: CAST-seq centromeric VEGFA CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment

value: CRISPR/CAS9 RNP


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 non-treated control


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day1 non-treated control


title: 180CAG_C6


title: CAST-seq centromeric VEGFA CRISPR/Cas9 treated CD34+ cells, Day4 post treatment


title: 180CAG_B8


title: 180CAG_C1


title: CAST-seq centromeric RAG1 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment


title: M4: Pygo2 mutant

city: Zurich

first: Claudio

last: Cantù

address: Winterthurerstrasse 190

department: IMLS

country: Switzerland

institute: University of Zurich

data_processing:
reads were mapped to the UCSC Mus musculus mm10 genome with the TopHat v.2.0.11 software
the gene features were counted with HTSeq v.0.6.1 (htseq-count) on the UCSC mm10 gene annotation
normalization and differential expression analysis were performed with R/Bioconductor package EdgeR v. 3.14
Genome_build: mm10

source_name: branchial arches

extract_protocol:
branchyal arches, along with looping hearts, were manually dissected from 10.5 days post coitum mouse embryos. Samples were snap frozen in liquid nitrogen, and RNA was extracted with TRIzol reagent
Illumina TruSeq stranded Total RNA library Prep kit with RiboZero was used for the library preparation with 300 ng of total RNA as input

value: branchial arches

value: Pygo2 mutant


title: CAST-seq centromeric RAG1 CRISPR/Cas9 treated CD34+ cells, Day4 post treatment


title: 180CAG_B7


title: M3: Pygo2 mutant


title: 180CAG_B5


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, Day14 post treatment

value: TALEN mRNA


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, duplicate Day4 post treatment


title: M2: Pygo2 mutant


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, Day1 post treatment


title: 180CAG_B2


title: M1: Pygo2 mutant


title: CAST-seq centromeric CCR5#2 TALEN treated CD34+ cells, Day4 post treatment


title: 180CAG_B12


title: CAST-seq centromeric FANCF CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day4 non-treated control


title: 180CAG_B9


title: C4: Pygo2 wild-type

value: Pygo2 wild-type


title: 180CAG_B11


title: CAST-seq centromeric FANCF CRISPR/Cas9 treated CD34+ cells, Day4 post treatment


title: CAST-seq telomeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment


title: CAST-seq centromeric CCR5#2 CRISPR/HiFiCas9 treated CD34+ cells, Day14 post treatment


title: C3: Pygo2 wild-type


title: CAST-seq telomeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day4 post treatment


title: CAST-seq centromeric CCR5#2 CRISPR/HiFiCas9 treated CD34+ cells, duplicate Day4 post treatment


title: C2: Pygo2 wild-type


title: C1: Pygo2 wild-type


title: 180CAG_B10


title: 180CAG_B1


title: 96ex_C4

value: WT


title: CAST-seq centromeric CCR5#2 CRISPR/HiFiCas9 treated CD34+ cells, Day1 post treatment


title: CAST-seq centromeric CCR5#2 CRISPR/HiFiCas9 treated CD34+ cells, Day4 post treatment


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day4 post treatment


title: 180CAG_A7


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day1 post treatment


title: 180CAG_A5


title: CAST-seq centromeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day14 post treatment


title: CAST-seq centromeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day1 post treatment


title: 180CAG_A4


title: Pygo2-BA1

data_processing:
Data analysis – peak calling: All sequenced reads were mapped using the tool for fast and sensitive reads alignment, Bowtie 2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), onto the UCSC mm10 reference mouse genome.
The command "findPeaks" from the HOMER tool package (http://homer.salk.edu/homer/) was used to identify enriched regions in the beta-catenin immunoprecipitation samples using the "-style = factor" option (routinely used for transcription factors with the aim of identifying the precise location of DNA-protein contact). Input and IgG samples were used as enrichment-normalization controls. Peak calling parameters were adjusted as following: L = 4 (filtering based on local signal), F = 4 (fold-change in target experiment over input control).
Annotation of peaks' position (i.e. the association of individual peaks to nearby annotated genes) was obtained by the all-in-one program called "annotatePeaks.pl". Finally, the HOMER command "makeUCSCfile" was used to produce bedGraph formatted files that can be uploaded as custom tracks and visualized in the UCSC genome browser (http://genome.ucsc.edu/).
Genome_build: mm10
Supplementary_files_format_and_content: bed and bedGraph files: peaks visualization on genome browsers (i.e. UCSC genome growser, IGV)

source_name: anti-Pygo2 against wildtype protein

growth_protocol: tissue from mouse embryos

extract_protocol:
Ca. 200 branchial arches of E10.5 embryos were dissected and dissociated to a single cell suspension. Cells were cross-linked in 20 ml PBS for 40 min with the addition of 1.5 mM ethylene glycol-bis(succinimidyl succinate) (Thermo Scientific, Waltham, MA, USA), for protein-protein cross-linking, and 1% formaldehyde for the last 20 min of incubation, to preserve DNA-protein interactions. The reaction was blocked with glycine and the cells were subsequently lysed in 1 ml hepes buffer (0.3% SDS, 1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES). Chromatin was sheared using Covaris S2 (Covaris, Woburn, MA, USA) for 8 min with the following set up: duty cycle: max, intensity: max, cycles/burst: max, mode: Power Tracking. The sonicated chromatin was diluted to 0.15% SDS and incubated overnight at 4°C with anti IgG (Santa Cruz), anti-Pygo2 (Novus Biological, NBP1-46171) and anti-b-catenin (Santacruz, sc-7199). The beads were washed at 4°C with wash buffer 1 (0.1% SDS, 0.1% deoxycholate, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES), wash buffer 2 (0.1% SDS, 0.1% sodium deoxycho- late, 1% Triton X-100, 0.5 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES), wash buffer 3 (0.25 M LiCl, 0.5% sodium deoxycholate, 0.5% NP-40, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES), and finally twice with Tris EDTA buffer. The chromatin was eluted with 1% SDS, 0.1 M NaHCO3, de-crosslinked by incubation at 65°C for 5 h with 200 mM NaCl, extracted with phenol-chloroform, and ethanol precipitated. The immunoprecipitated DNA was used as input material for DNA deep sequencing.
Illumina TruSeq ChIP library Preparation kit was used for the library preparation with 5 to 10 ng of total immunoprecipitated DNA per sample


title: b-cat-BA2

source_name: anti-beta-catenin against wildtype protein


title: b-cat-BA1


title: CAST-seq telomeric CCR5#1 CRISPR/HiFiCas9 treated CD34+ cells, Day14 post treatment


title: CAST-seq telomeric CCR5#1 CRISPR/HiFiCas9 treated CD34+ cells, duplicate Day4 post treatment


title: CAST-seq telomeric CCR5#1 CRISPR/HiFiCas9 treated CD34+ cells, Day4 post treatment


title: CAST-seq centromeric CCR5#2 CRISPR/Cas9 treated CD34+ cells, Day14 post treatment


title: 180CAG_A3


title: IgG-BA1

source_name: pre-immune serum


title: CAST-seq telomeric CCR5#1 CRISPR/HiFiCas9 treated CD34+ cells, Day1 post treatment


title: 180CAG_A8


title: Pygo2-BA2


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day14 post treatment


title: 180CAG_A12


title: Input-BA2

source_name: wild-type tissue


title: Input-BA1


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day1 post treatment.


title: 180CAG_A10


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment


title: CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day4 post treatment


title: scATAC for Thymus cells, T-5442

status: Public on Feb 13 2021

city: Hefei

first: Kun

last: Qu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

description:
scATAC for Thymus cells
scATAC_Accesson.txt

data_processing:
Sequences were aligned using Cell Ranger version 1.3.1 from 10x Genomics with default parameters.
The GRCm38.p5 assembly was used as the reference genome, and ribosomal RNA, mitochondrial RNA (Mt-RNA) and pseudogenes were removed.
Cells with fewer than 500 detected genes and more than 4500 detected genes for which total mitochondrial gene expression exceeded 40% were removed. Genes that were expressed in fewer than three cells were also removed.
Quantile normalization was performed using qnorm in R.
Genome_build: hg38
Supplementary_files_format_and_content: 10x_log2_q_norm.txt - tab-delimited text file includes quantile normalized gene expression values for each cell
Supplementary_files_format_and_content: scATAC_Accesson.txt - tab delimited text file includes normalized accesson count values predicted by APEC for each cell

source_name: Thymocytes

extract_protocol:
Thymus tissues were harvested from mice aged 6 - 8 weeks and gently ground in 1 mL of RPMI-1640.
Single cells were captured in droplet emulsions using a GemCode Single-Cell Instrument (10x Genomics), and scRNA-seq libraries were constructed with the 10x Genomics protocol using a GemCode Single-Cell 3′ Gel Bead and Library V2 Kit. The libraries were sequenced using a HiSeq X-10 Sequencing System (Illumina). scATAC-seq experiments were performed as previously described by Li B et al, Genome Biology, 2020.

value: 7 weeks

value: male

value: Thymus


title: scATAC for Thymus cells, T-5435

institute: University of Science and Technology of China


title: scATAC for Thymus cells, T-5420


title: scATAC for Thymus cells, T-5424


title: scATAC for Thymus cells, T-5411


title: scATAC for Thymus cells, T-5482


title: scATAC for Thymus cells, T-5450


title: scATAC for Thymus cells, T-5477


title: scATAC for Thymus cells, T-5453


title: scATAC for Thymus cells, T-5448


title: scATAC for Thymus cells, T-5473


title: scATAC for Thymus cells, T-5491


title: scATAC for Thymus cells, T-5479


title: scATAC for Thymus cells, T-5432


title: scATAC for Thymus cells, T-5466


title: scATAC for Thymus cells, T-5484


title: scATAC for Thymus cells, T-5425


title: scATAC for Thymus cells, T-5440


title: scATAC for Thymus cells, T-5474


title: scATAC for Thymus cells, T-5414


title: scATAC for Thymus cells, T-5445


title: scATAC for Thymus cells, T-5443


title: scATAC for Thymus cells, T-5494


title: scATAC for Thymus cells, T-5458


title: scATAC for Thymus cells, T-5486


title: scATAC for Thymus cells, T-5495


title: scATAC for Thymus cells, T-5475


title: scATAC for Thymus cells, T-5417


title: scATAC for Thymus cells, T-5427


title: scATAC for Thymus cells, T-5254


title: scATAC for Thymus cells, T-5256


title: scATAC for Thymus cells, T-5255


title: scATAC for Thymus cells, T-5250


title: scATAC for Thymus cells, T-5253


title: scATAC for Thymus cells, T-5251


title: scATAC for Thymus cells, T-5249


title: scATAC for Thymus cells, T-5434


title: scATAC for Thymus cells, T-5438


title: scATAC for Thymus cells, T-5248


title: scATAC for Thymus cells, T-5245


title: scATAC for Thymus cells, T-5244


title: scATAC for Thymus cells, T-5246


title: scATAC for Thymus cells, T-5243


title: scATAC for Thymus cells, T-5240


title: scATAC for Thymus cells, T-5237


title: scATAC for Thymus cells, T-5239


title: scATAC for Thymus cells, T-5238


title: scATAC for Thymus cells, T-5242


title: scATAC for Thymus cells, T-5235


title: scATAC for Thymus cells, T-5231


title: scATAC for Thymus cells, T-5232


title: scATAC for Thymus cells, T-5236


title: scATAC for Thymus cells, T-5233


title: scATAC for Thymus cells, T-5234


title: scATAC for Thymus cells, T-5430


title: scATAC for Thymus cells, T-5252


title: scATAC for Thymus cells, T-5230


title: scATAC for Thymus cells, T-5227


title: scATAC for Thymus cells, T-5229


title: scATAC for Thymus cells, T-5247


title: scATAC for Thymus cells, T-5228


title: scATAC for Thymus cells, T-5226


title: scATAC for Thymus cells, T-5225


title: scATAC for Thymus cells, T-5223


title: scATAC for Thymus cells, T-5222


title: scATAC for Thymus cells, T-5221


title: scATAC for Thymus cells, T-5241


title: scATAC for Thymus cells, T-5220


title: scATAC for Thymus cells, T-5219


title: scATAC for Thymus cells, T-5218


title: scATAC for Thymus cells, T-5215


title: scATAC for Thymus cells, T-5216


title: scATAC for Thymus cells, T-5211


title: scATAC for Thymus cells, T-5212


title: scATAC for Thymus cells, T-5217


title: scATAC for Thymus cells, T-5214


title: scATAC for Thymus cells, T-5213


title: scATAC for Thymus cells, T-5209


title: scATAC for Thymus cells, T-5208


title: scATAC for Thymus cells, T-5206


title: scATAC for Thymus cells, T-5207


title: scATAC for Thymus cells, T-5205


title: scATAC for Thymus cells, T-5204


title: scATAC for Thymus cells, T-5210


title: scATAC for Thymus cells, T-5202


title: scATAC for Thymus cells, T-5224


title: scATAC for Thymus cells, T-5200


title: scATAC for Thymus cells, T-5203


title: scATAC for Thymus cells, T-5201


title: scATAC for Thymus cells, T-5195


title: scATAC for Thymus cells, T-5199


title: scATAC for Thymus cells, T-5198


title: scATAC for Thymus cells, T-5196


title: scATAC for Thymus cells, T-5197


title: scATAC for Thymus cells, T-5447


title: scATAC for Thymus cells, T-5193


title: scATAC for Thymus cells, T-5406


title: scATAC for Thymus cells, T-5446


title: scATAC for Thymus cells, T-5485


title: scATAC for Thymus cells, T-5478


title: scATAC for Thymus cells, T-5407


title: scATAC for Thymus cells, T-5457


title: scATAC for Thymus cells, T-5452


title: scATAC for Thymus cells, T-5439


title: scATAC for Thymus cells, T-5413


title: scATAC for Thymus cells, T-5429


title: scATAC for Thymus cells, T-5418


title: scATAC for Thymus cells, T-5402


title: scATAC for Thymus cells, T-5469


title: scATAC for Thymus cells, T-5468


title: scATAC for Thymus cells, T-5422


title: scATAC for Thymus cells, T-5444


title: scATAC for Thymus cells, T-5412


title: scATAC for Thymus cells, T-5456


title: scATAC for Thymus cells, T-5194


title: scATAC for Thymus cells, T-5426


title: scATAC for Thymus cells, T-5483


title: scATAC for Thymus cells, T-5416


title: scATAC for Thymus cells, T-5470


title: scATAC for Thymus cells, T-5489


title: scATAC for Thymus cells, T-5405


title: scATAC for Thymus cells, T-5459


title: scATAC for Thymus cells, T-5460


title: scATAC for Thymus cells, T-5419


title: scATAC for Thymus cells, T-5192


title: scATAC for Thymus cells, T-5191


title: scATAC for Thymus cells, T-5190


title: scATAC for Thymus cells, T-5189


title: scATAC for Thymus cells, T-5449


title: scATAC for Thymus cells, T-5188


title: scATAC for Thymus cells, T-5186


title: scATAC for Thymus cells, T-5184


title: scATAC for Thymus cells, T-5187


title: scATAC for Thymus cells, T-5185


title: scATAC for Thymus cells, T-5183


title: scATAC for Thymus cells, T-5181


title: scATAC for Thymus cells, T-5180


title: scATAC for Thymus cells, T-5428


title: scATAC for Thymus cells, T-5465


title: scATAC for Thymus cells, T-5431


title: scATAC for Thymus cells, T-5179


title: scATAC for Thymus cells, T-5176


title: scATAC for Thymus cells, T-5175


title: scATAC for Thymus cells, T-5173


title: scATAC for Thymus cells, T-5178


title: scATAC for Thymus cells, T-5177


title: scATAC for Thymus cells, T-5174


title: scATAC for Thymus cells, T-5172


title: scATAC for Thymus cells, T-5171


title: scATAC for Thymus cells, T-5169


title: scATAC for Thymus cells, T-5165


title: scATAC for Thymus cells, T-5166


title: scATAC for Thymus cells, T-5170


title: scATAC for Thymus cells, T-5163


title: scATAC for Thymus cells, T-5164


title: scATAC for Thymus cells, T-5167


title: scATAC for Thymus cells, T-5162


title: scATAC for Thymus cells, T-5464


title: scATAC for Thymus cells, T-5476


title: scATAC for Thymus cells, T-5423


title: scATAC for Thymus cells, T-5182


title: scATAC for Thymus cells, T-5161


title: scATAC for Thymus cells, T-5461


title: scATAC for Thymus cells, T-5467


title: scATAC for Thymus cells, T-5433


title: scATAC for Thymus cells, T-5436


title: scATAC for Thymus cells, T-5463


title: scATAC for Thymus cells, T-5421


title: scATAC for Thymus cells, T-5410


title: scATAC for Thymus cells, T-5472


title: scATAC for Thymus cells, T-5451


title: scATAC for Thymus cells, T-5415


title: scATAC for Thymus cells, T-5404


title: scATAC for Thymus cells, T-5492


title: scATAC for Thymus cells, T-5168


title: scATAC for Thymus cells, T-5403


title: scATAC for Thymus cells, T-5496


title: scATAC for Thymus cells, T-5481


title: scATAC for Thymus cells, T-5401


title: scATAC for Thymus cells, T-5493


title: scATAC for Thymus cells, T-5455


title: scATAC for Thymus cells, T-5462


title: scATAC for Thymus cells, T-5454


title: scATAC for Thymus cells, T-5471


title: scATAC for Thymus cells, T-5409


title: scATAC for Thymus cells, T-5488


title: scATAC for Thymus cells, T-5437


title: scATAC for Thymus cells, T-5158


title: scATAC for Thymus cells, T-5159


title: scATAC for Thymus cells, T-5490


title: scATAC for Thymus cells, T-5487


title: scATAC for Thymus cells, T-5441


title: scATAC for Thymus cells, T-5157


title: scATAC for Thymus cells, T-5408


title: scATAC for Thymus cells, T-5154


title: scATAC for Thymus cells, T-5151


title: scATAC for Thymus cells, T-5150


title: scATAC for Thymus cells, T-5149


title: scATAC for Thymus cells, T-5156


title: scATAC for Thymus cells, T-5153


title: scATAC for Thymus cells, T-5155


title: scATAC for Thymus cells, T-5148


title: scATAC for Thymus cells, T-5480


title: scATAC for Thymus cells, T-5147


title: scATAC for Thymus cells, T-5145


title: scATAC for Thymus cells, T-5146


title: scATAC for Thymus cells, T-5142


title: scATAC for Thymus cells, T-5144


title: scATAC for Thymus cells, T-5143


title: scATAC for Thymus cells, T-5139


title: scATAC for Thymus cells, T-5140


title: scATAC for Thymus cells, T-5138


title: scATAC for Thymus cells, T-5141


title: scATAC for Thymus cells, T-5137


title: scATAC for Thymus cells, T-5160


title: scATAC for Thymus cells, T-5134


title: scATAC for Thymus cells, T-5133


title: scATAC for Thymus cells, T-5135


title: scATAC for Thymus cells, T-5132


title: scATAC for Thymus cells, T-5152


title: scATAC for Thymus cells, T-5130


title: scATAC for Thymus cells, T-5129


title: scATAC for Thymus cells, T-5032


title: scATAC for Thymus cells, T-5028


title: scATAC for Thymus cells, T-5131


title: scATAC for Thymus cells, T-5136


title: scATAC for Thymus cells, T-5029


title: scATAC for Thymus cells, T-5031


title: scATAC for Thymus cells, T-5027


title: scATAC for Thymus cells, T-5030


title: scATAC for Thymus cells, T-5025


title: scATAC for Thymus cells, T-5024


title: scATAC for Thymus cells, T-5026


title: scATAC for Thymus cells, T-5020


title: scATAC for Thymus cells, T-5022


title: scATAC for Thymus cells, T-5018


title: scATAC for Thymus cells, T-5021


title: scATAC for Thymus cells, T-5023


title: scATAC for Thymus cells, T-5017


title: scATAC for Thymus cells, T-5016


title: scATAC for Thymus cells, T-5015


title: scATAC for Thymus cells, T-5014


title: scATAC for Thymus cells, T-5012


title: scATAC for Thymus cells, T-5013


title: scATAC for Thymus cells, T-5011


title: scATAC for Thymus cells, T-5010


title: scATAC for Thymus cells, T-5008


title: scATAC for Thymus cells, T-5006


title: scATAC for Thymus cells, T-5007


title: scATAC for Thymus cells, T-5003


title: scATAC for Thymus cells, T-5005


title: scATAC for Thymus cells, T-5002


title: scATAC for Thymus cells, T-5128


title: scATAC for Thymus cells, T-5001


title: scATAC for Thymus cells, T-5004


title: scATAC for Thymus cells, T-5126


title: scATAC for Thymus cells, T-5127


title: scATAC for Thymus cells, T-5124


title: scATAC for Thymus cells, T-5122


title: scATAC for Thymus cells, T-5019


title: scATAC for Thymus cells, T-5123


title: scATAC for Thymus cells, T-5119


title: scATAC for Thymus cells, T-5120


title: scATAC for Thymus cells, T-5118


title: scATAC for Thymus cells, T-5121


title: scATAC for Thymus cells, T-5115


title: scATAC for Thymus cells, T-5114


title: scATAC for Thymus cells, T-5113


title: scATAC for Thymus cells, T-5112


title: scATAC for Thymus cells, T-5009


title: scATAC for Thymus cells, T-5111


title: scATAC for Thymus cells, T-5110


title: scATAC for Thymus cells, T-5109


title: scATAC for Thymus cells, T-5106


title: scATAC for Thymus cells, T-5107


title: scATAC for Thymus cells, T-5125


title: scATAC for Thymus cells, T-5105


title: scATAC for Thymus cells, T-5102


title: scATAC for Thymus cells, T-5103


title: scATAC for Thymus cells, T-5104


title: scATAC for Thymus cells, T-5099


title: scATAC for Thymus cells, T-5101


title: scATAC for Thymus cells, T-5098


title: scATAC for Thymus cells, T-5100


title: scATAC for Thymus cells, T-5096


title: scATAC for Thymus cells, T-5097


title: scATAC for Thymus cells, T-5117


title: scATAC for Thymus cells, T-5094


title: scATAC for Thymus cells, T-5095


title: scATAC for Thymus cells, T-5108


title: scATAC for Thymus cells, T-5116


title: scATAC for Thymus cells, T-5093


title: scATAC for Thymus cells, T-5091


title: scATAC for Thymus cells, T-5087


title: scATAC for Thymus cells, T-5086


title: scATAC for Thymus cells, T-5089


title: scATAC for Thymus cells, T-5085


title: scATAC for Thymus cells, T-5084


title: scATAC for Thymus cells, T-5088


title: scATAC for Thymus cells, T-5083


title: scATAC for Thymus cells, T-5082


title: scATAC for Thymus cells, T-5081


title: scATAC for Thymus cells, T-5079


title: scATAC for Thymus cells, T-5077


title: scATAC for Thymus cells, T-5076


title: scATAC for Thymus cells, T-5075


title: scATAC for Thymus cells, T-5074


title: scATAC for Thymus cells, T-5080


title: scATAC for Thymus cells, T-5073


title: scATAC for Thymus cells, T-5071


title: scATAC for Thymus cells, T-5092


title: scATAC for Thymus cells, T-5068


title: scATAC for Thymus cells, T-5070


title: scATAC for Thymus cells, T-5090


title: scATAC for Thymus cells, T-5066


title: scATAC for Thymus cells, T-5072


title: scATAC for Thymus cells, T-5067


title: scATAC for Thymus cells, T-5065


title: scATAC for Thymus cells, T-5062


title: scATAC for Thymus cells, T-5069


title: scATAC for Thymus cells, T-5063


title: scATAC for Thymus cells, T-5061


title: scATAC for Thymus cells, T-5064


title: scATAC for Thymus cells, T-5059


title: scATAC for Thymus cells, T-5056


title: scATAC for Thymus cells, T-5055


title: scATAC for Thymus cells, T-5060


title: scATAC for Thymus cells, T-5058


title: scATAC for Thymus cells, T-5054


title: scATAC for Thymus cells, T-5078


title: scATAC for Thymus cells, T-5053


title: scATAC for Thymus cells, T-5052


title: scATAC for Thymus cells, T-5051


title: scATAC for Thymus cells, T-5047


title: scATAC for Thymus cells, T-5050


title: scATAC for Thymus cells, T-5049


title: scATAC for Thymus cells, T-5045


title: scATAC for Thymus cells, T-5042


title: scATAC for Thymus cells, T-5041


title: scATAC for Thymus cells, T-5039


title: scATAC for Thymus cells, T-5043


title: scATAC for Thymus cells, T-5044


title: scATAC for Thymus cells, T-5040


title: scATAC for Thymus cells, T-5057


title: scATAC for Thymus cells, T-5038


title: scATAC for Thymus cells, T-5035


title: scATAC for Thymus cells, T-5036


title: scATAC for Thymus cells, DP-4288

source_name: Double positive T cells


title: scATAC for Thymus cells, T-5037


title: scATAC for Thymus cells, T-5034


title: scATAC for Thymus cells, DP-4287


title: scATAC for Thymus cells, DP-4286


title: scATAC for Thymus cells, T-5048


title: scATAC for Thymus cells, T-5046


title: scATAC for Thymus cells, DP-4274


title: scATAC for Thymus cells, DP-4280


title: scATAC for Thymus cells, DP-4276


title: scATAC for Thymus cells, DP-4281


title: scATAC for Thymus cells, DP-4275


title: scATAC for Thymus cells, DP-4282


title: scATAC for Thymus cells, DP-4283


title: scATAC for Thymus cells, DP-4278


title: scATAC for Thymus cells, T-5033


title: scATAC for Thymus cells, DP-4284


title: scATAC for Thymus cells, DP-4277


title: scATAC for Thymus cells, DP-4270


title: scATAC for Thymus cells, DP-4267


title: scATAC for Thymus cells, DP-4271


title: scATAC for Thymus cells, DP-4269


title: scATAC for Thymus cells, DP-4265


title: scATAC for Thymus cells, DP-4263


title: scATAC for Thymus cells, DP-4272


title: scATAC for Thymus cells, DP-4268


title: scATAC for Thymus cells, DP-4261


title: scATAC for Thymus cells, DP-4285


title: scATAC for Thymus cells, DP-4259


title: scATAC for Thymus cells, DP-4262


title: scATAC for Thymus cells, DP-4266


title: scATAC for Thymus cells, DP-4257


title: scATAC for Thymus cells, DP-4258


title: scATAC for Thymus cells, DP-4273


title: scATAC for Thymus cells, DP-4254


title: scATAC for Thymus cells, DP-4251


title: scATAC for Thymus cells, DP-4250


title: scATAC for Thymus cells, DP-4264


title: scATAC for Thymus cells, DP-4253


title: scATAC for Thymus cells, DP-4252


title: scATAC for Thymus cells, DP-4255


title: scATAC for Thymus cells, DP-4256


title: scATAC for Thymus cells, DP-4260


title: scATAC for Thymus cells, DP-4248