title: UM-Chor5_RNA_parental_Rep1

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: The parental samples were used in some of the wet bench experiments/figures, but none of the RNA-seq data using them made the final manuscript

data_processing:
Reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 to remove any sequencing adapters.
After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. Cell lines JHC7, MUG-Chor1, U-CH1, U-CH2, and UM-Chor1 were run with option -Q 64 instead.
Reads were aligned to the hg19 genome using STAR (v2.5.4b) with options --quantMode TranscriptomeSAM, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, and --outFilterMultimapNmax 1.
To calculate the RNA abundance values in transcripts per million (TPM), Salmon (v0.8.1) tool quant was used.
Samtools (v1.3.1), bedtools (v2.26), Python (v3.7.9), and R (v3.3.1) were used to interconvert files for downstream analyses.
DESeq2 (v1.14.1) was used to determine which genes had significantly differential RNA abundance.
PCA plots were generated using the plotPCA function within DESeq2 using all RNA abundance values (TPMs). gProfiler GOSt was used to identify Reactome pathways and p-values associated with differentially expressed genes. Heatmaps of gene TPMs were made using Morpheus. Boxplots were made in Python using seaborn boxplot and stripplot commands using the log2 fold changes between the mean TPMs across replicates between SMARCB1 positive and SMARCB1 negative samples. Upset plot was generated in R with the UpSetR package.
Assembly: hg19
Supplementary files format and content: DESeq2 files contain the DESeq2 analyses for every genes in the titled comparison.
Supplementary files format and content: Expression matrix is a tab-delimited file containing the VST-normalized gene expression for all genes and all samples analyzed in the manuscript.

growth_protocol: The CH22, UM-Chor5, and TTC642 cell lines were cultured in RPMI 1640 (#11875-093, Gibco, Grand Island, NY) and supplemented with 10% FBS (Sigma-Aldrich, St. Louis, MO).  The pIND20+SNF5-HA cell lines were cultured in RPMI 1640, supplemented with 10% TET-FREE FBS (#100-800, GeminiBio, Sacramento, CA) and 400 ug/ml G418/Geneticin 50mg/ml (#10131-035, Gibco, Grand Island, NY). All cells were maintained in a humidified incubator at 37°C with 5% CO2. All were used within 10 passages of their initial arrival to minimize chances of cross-contamination and tested for mycoplasma contamination by DAPI staining and PCR for the detection of mycoplasma ribosomal DNA.

extract_protocol:
RNA was extracted from frozen cell pellets in biological triplicate using Zymo Quick-RNA Miniprep Kit (Zymo cat# R1054).
Total RNA was prepared by Novogene Inc. using the Illumina TruSeq mRNA v2 kit with an input of 500ng of RNA for each sample to produce unstranded RNA libraries following the manufacturer’s protocol. Final RNA libraries were quantified using the Qubit High Sense Reagent kit and Agilent Tapestation HSD1000 tapes. Libraries were equimolar pooled and paired-end sequenced across three lanes of an Illumina HiSeq 4000.

treatment_protocol: For all RNA-seq studies, 2x10^6 CH22- and UM-Chor5- pIND20+fSN5-HA cells were plated into 10cm dishes and induced with DOX (1 μg/μl) for 72 hours.

tag: cancer type

value: chordoma

value: None (parental cell line)


title: UM-Chor5_RNA_parental_Rep2

status: Public on Dec 21 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: CH22_RNA_parental_Rep3


title: Endothelium (Endo) E8.5 [E8.5 Endo_23]

city: Melbourne

first: Jarny

last: Choi

state: Victoria

address: The University of Melbourne

department: Anatomy and Neuroscience

country: Australia

institute: Centre for Stem Cell Systems

description:
32_C4P47ANXX_CAGAGAGG-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

data_processing:
Read alignment was done by Rsubread v1.22.2, using subjunc function with default parameters.
Summarised gene counts file was generated using Rsubread v1.22.2, using featureCounts function with parameters (GTF.featureType="Exon", userMetaFeatures=T) amongst other standard parameters. Ensembl mouse genome version GRCm38.84.chr.gtf was used.
Filtering was performed on raw counts matrix using scater package in R, by applying isOutlier function on both samples and genes using (nmads=3, type="lower", log=T) parameters. Genes were further filtered out for row mean<1.
To calculate the cpm matrix, computeSumFactors function from scran package in R was used.
Genome_build: Ensembl mouse genome version ens84_GRCm38
Supplementary_files_format_and_content: Tab delimited text file contains a matrix with raw gene counts, with Ensembl gene ids as row ids and sample names as column names.

organism: Mus musculus

source_name: C57BL/6 E8.5 yolk sac

growth_protocol: in vivo

extract_protocol:
yolk sac was dissociated with trypsin (E7.25-7.775) or collagenase/dispase (E8.25-E10.5). Cells were sorted by population first then captured on Fluidigm C1 integrated fluidic circuit (IFC) with the capacity for 96 individual cells and a 10-17um capture aperture
Libraries were constructed using the Nextera XT kit and Illumina 96 index kits according  to the Fluidigm protocol modified from the Illumina protocol to use ¼ of the kit per 96  well plate (Illumina Protocol #15031942 Rev C “Nextera XT DNA Sample Preparation  Guide”; Fluidigm Protocol #PN100-7168 G1 “Using the C1 Single Cell Auto Prep  System to Generate mRNA from Single Cells and Libraries for Sequencing”)

tag: strain/genotype

tag: Stage

tag: tissue source

value: Yolk sac

tag: cell type

value: yolk sac endothelium


title: UM-Chor5_RNA_parental_Rep3


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_22]

description:
32_C4P47ANXX_CAGAGAGG-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

source_name: C57BL/6 E8.25 yolk sac

value: yolk sac EMP


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_27]

description:
35_C4P47ANXX_AAGAGGCA-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_24]

description:
32_C4P47ANXX_CAGAGAGG-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: CH22_RNA_parental_Rep1


title: CH22_RNA_parental_Rep2


title: WT Th17 rep2 IP

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
eCLIP
Rep2 CLIP

data_processing:
Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10
Reads were then trimmed with cutadapt (1.9.1). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Trimmed reads were then mapped with STAR (2.4.0i) against a mouse-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir mouse_repbase \  --readFilesIn path/to/read1 path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a mouse genome (mm10). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 /path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.4.1)
Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam
PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam)
Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species mm10 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were annotated by overlapping peak regions with Gencode M10 annotations
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files; tab-delimited text file includes -log10pValues and Log2FoldChange values for each IDR peaks called after cutoff of 3,3 in each parameter

growth_protocol: Th17 cells were polarized from naïve CD4 T cells obtained from 8wk old female mice and treated with anti-CD3, anti-CD28, IL6, and TGFb for 72hrs in culture.

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used.
eCLIPseq

treatment_protocol: UV-mediated crosslinking, lysis, and treatment with limiting amounts of RNases, followed by immunoprecipitation (IP) of the DDX5 containing RNA complexes. RNA fragments protected from RNase digestion were subjected to RNA linker ligation, reverse-transcription and DNA linker ligation to generate eCLIP libraries for high-throughput Illumina sequencing.

tag: chip antibody

value: Anti-DDX5 antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #

tag: strain

tag: genotype

value: wild type


title: TTC642_RNA_DOX_SNF5pos_Rep2

description:
TTC642_SNF5pos.v.SNF5neg_all_genes.txt
chordoma_MRT_SNF5_addback_samples_RNA_combined_VST_expression.txt

value: malignant rhabdoid tumor

value: 24hr doxycycline (SN5 add-back)


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_21]

description:
32_C4P47ANXX_CAGAGAGG-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac Mk


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_44]

description:
33_C4P47ANXX_GCTACGCT-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

source_name: Flk1-GFP/+ E7.25 yolk sac

value: yolk sac mesoderm


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_20]

description:
31_C4P47ANXX_CTCTCTAC-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: TTC642_RNA_DOX_SNF5pos_Rep1


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_21]

description:
31_C4P47ANXX_CTCTCTAC-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_20]

description:
31_C4P47ANXX_CTCTCTAC-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: TTC642_RNA_noDOX_SNF5neg_Rep1

value: no doxycycline


title: TTC642_RNA_noDOX_SNF5neg_Rep2


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_23]

description:
31_C4P47ANXX_CTCTCTAC-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: UM-Chor5_RNA_DOX_SNF5pos_Rep2

description:
UM-Chor5_SNF5pos.v.SNF5neg_all_genes.txt
chordoma_MRT_SNF5_addback_samples_RNA_combined_VST_expression.txt

value: 72hr doxycycline (SN5 add-back)


title: UM-Chor5_RNA_DOX_SNF5pos_Rep3


title: WT Th17 rep1 IP

description:
eCLIP
Rep1 CLIP

value: treated with anti-CD3, anti-CD28, IL6, and TGFb for 72hrs in culture


title: WT Th17 rep1 INPUT

description:
eCLIP
Rep1 INPUT


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_41]

description:
30_C4P47ANXX_TAGGCATG-TATCCTCT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_21]

description:
32_C4P47ANXX_CAGAGAGG-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: UM-Chor5_RNA_DOX_SNF5pos_Rep1


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_40]

description:
30_C4P47ANXX_TAGGCATG-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: UM-Chor5_RNA_noDOX_SNF5neg_Rep3


title: UM-Chor5_RNA_noDOX_SNF5neg_Rep2


title: UM-Chor5_RNA_noDOX_SNF5neg_Rep1


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_20]

description:
30_C4P47ANXX_TAGGCATG-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_19]

description:
30_C4P47ANXX_TAGGCATG-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: CH22_RNA_DOX_SNF5pos_Rep3

description:
CH22_SNF5pos.v.SNF5neg_all_genes.txt
chordoma_MRT_SNF5_addback_samples_RNA_combined_VST_expression.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_22]

description:
30_C4P47ANXX_TAGGCATG-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_42]

description:
31_C4P47ANXX_CTCTCTAC-TATCCTCT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_22]

description:
30_C4P47ANXX_TAGGCATG-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_39]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_38]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: CH22_RNA_DOX_SNF5pos_Rep1


title: CH22_RNA_DOX_SNF5pos_Rep2


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_18]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: CH22_RNA_noDOX_SNF5neg_Rep2


title: CH22_RNA_noDOX_SNF5neg_Rep3


title: CH22_RNA_noDOX_SNF5neg_Rep1


title: Endothelium (Endo) E8.5 [E8.5 Endo_21]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_19]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_17]

description:
29_C4P47ANXX_GGACTCCT-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_36]

description:
29_C4P47ANXX_GGACTCCT-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_37]

description:
29_C4P47ANXX_GGACTCCT-TATCCTCT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_21]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_18]

description:
29_C4P47ANXX_GGACTCCT-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_35]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_34]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_20]

description:
29_C4P47ANXX_GGACTCCT-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_20]

description:
29_C4P47ANXX_GGACTCCT-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_16]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_17]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_18]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_32]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_33]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_15]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_19]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_19]

description:
28_C4P47ANXX_TCCTGAGC-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_16]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_19]

description:
2_C4P47ANXX_CGTACTAG-GCGTAAGA_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_18]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_17]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_18]

description:
27_C4P47ANXX_AGGCAGAA-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_31]

description:
26_C4P47ANXX_CGTACTAG-TATCCTCT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: IR22 (RNA-seq)

city: Memphis

first: Jason

last: Chiang

state: Tennessee

address: 262 Danny Thomas Pl

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
The RNA-seq data were subjected to both adaptor and quality trimming and then aligned to the human reference genome (build hg38) with STAR (v2.7.9a).
The read counts of gene expression data were preprocessed, normalized, and filtered to remove genes with very low expression values (bottom 5%) in more than 90% samples using DESeq2 (v1.32.0).
NetBID (v2.0.3) and SJARACNe-based network reconstruction were then used to infer drivers (transcription factors or signalling factors) from the transcriptomics data by calculating the activity of drivers and gene sets in Ubuntu (v18.04) with Python (v3.6.1).
Differentially expressed genes and differentially activated drivers were then queried against MSigDB (v7.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Brain

extract_protocol:
A PureLink FFPE Total RNA Isolation Kit (Thermo Fisher Scientific) was used for total RNA extraction from diagnostic FFPE tissue. Purified RNA was quantified on a Qubit 3 Fluorometer (Thermo Fisher Scientific) using Qubit™ RNA BR Assay Kit (Thermo Fisher Scientific), and subjected to Total RNA sequencing using the Illumina TruSeq Stranded Total RNA protocol with at least 500 ng of total RNA.
The Illumina Total Stranded RNA protocol was applied.

tag: tissue

value: brain

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

tag: tumor stage

value: tumor

tag: ffpe (yes/no)

value: yes

tag: age (yr)

tag: Sex

value: male

value: non-treated

tag: tumor grade

value: low-grade

tag: risk (low/intermediate/high)

value: intermediate

tag: outcome

value: not progressed after RT


title: IR18 (RNA-seq)

value: female

tag: treatment


title: IR23 (RNA-seq)


title: IR19 (RNA-seq)


title: IR16 (RNA-seq)


title: IR21 (RNA-seq)


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_30]

description:
26_C4P47ANXX_CGTACTAG-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

tag: strain/genotype

tag: Stage

tag: tissue source

value: Yolk sac


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_15]

description:
26_C4P47ANXX_CGTACTAG-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

tag: cell type


title: IR13 (RNA-seq)


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_16]

description:
26_C4P47ANXX_CGTACTAG-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: IR06 (RNA-seq)


title: IR01 (RNA-seq)


title: Endothelium (Endo) E8.5 [E8.5 Endo_17]

description:
26_C4P47ANXX_CGTACTAG-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac endothelium


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_17]

description:
26_C4P47ANXX_CGTACTAG-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: HR34 (RNA-seq)

value: high

value: progression after RT


title: HR35 (RNA-seq)


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_14]

description:
25_C4P47ANXX_TAAGGCGA-TATCCTCT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_29]

description:
25_C4P47ANXX_TAAGGCGA-TATCCTCT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_14]

description:
25_C4P47ANXX_TAAGGCGA-TATCCTCT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac Mk


title: HR32 (RNA-seq)

value: brain

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: 3+ chemo, progressed after RT, dead


title: HR33 (RNA-seq)

value: tumor

value: yes

value: male

value: dead, presumably died of disease


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_15]

description:
25_C4P47ANXX_TAAGGCGA-TATCCTCT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: HR23 (RNA-seq)

value: non-treated

value: low-grade

value: progressed after RT, mets, dead


title: Endothelium (Endo) E8.5 [E8.5 Endo_16]

description:
25_C4P47ANXX_TAAGGCGA-TATCCTCT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: Yolk sac


title: HR10 (RNA-seq)

value: 3+ chemo


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_28]

description:
24_C4P47ANXX_GTAGAGGA-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: HR08 (RNA-seq)

value: female


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_16]

description:
25_C4P47ANXX_TAAGGCGA-TATCCTCT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: IR07 (RNA-seq)

value: intermediate

value: not progressed after RT


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_14]

description:
24_C4P47ANXX_GTAGAGGA-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: HR07 (RNA-seq)

value: brain

value: high

value: progressed after RT


title: Endothelium (Endo) E8.5 [E8.5 Endo_15]

description:
24_C4P47ANXX_GTAGAGGA-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac endothelium


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_27]

description:
24_C4P47ANXX_GTAGAGGA-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: HR06 (RNA-seq)

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: tumor

value: yes

value: male

value: 3+ chemo, metastatic


title: HR03 (RNA-seq)

value: non-treated

value: low-grade

value: dead after one chemo


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_15]

description:
24_C4P47ANXX_GTAGAGGA-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: Yolk sac

value: yolk sac erythrocytes


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_25]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_13]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Sinovial_Cd1c_AR_LS238

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Genome_build: Human sequenced genome GRCh38 v91
Supplementary_files_format_and_content: *.rsem.genes.results.txt: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Sinovial Fluid

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Stranded library: 200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Low Input library: Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Sinovial Fluid

value: Dendritic Cells Cd1c+

tag: diagnosis

value: Rheumatoid Arthritis

tag: library type

value: Low Input


title: Sinovial_Cd1c_AR_LS237


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_13]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: Sinovial_Mo_AR_LS241

value: Monocytes


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_14]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_14]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac endothelium


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_13]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt

value: yolk sac Mk


title: Sinovial_Cd1c_AR_LS241


title: Sinovial_Mo_Condro_LS225

value: CPPD


title: Sinovial_Mo_AR_LS237


title: Sinovial_Mo_AR_LS238


title: Sinovial_Mo_Condro_LS248


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_24]

description:
22_C4P47ANXX_CGAGGCTG-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: Sinovial_Cd141_Condro_LS225

value: Dendritic Cells Cd141+


title: Sinovial_Cd141_Condro_LS248


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_12]

description:
22_C4P47ANXX_CGAGGCTG-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_26]

description:
23_C4P47ANXX_AAGAGGCA-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_12]

description:
22_C4P47ANXX_CGAGGCTG-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_13]

description:
22_C4P47ANXX_CGAGGCTG-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_12]

description:
22_C4P47ANXX_CGAGGCTG-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Sinovial_Cd141_AR_LS238


title: Sinovial_Cd141_AR_LS237


title: Sinovial_Cd141_AR_LS241


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_23]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Sinovial_Mo_Condro_LS247


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_22]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Sinovial_Cd1c_Condro_LS225


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_11]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Sinovial_Cd1c_Condro_LS248


title: Sinovial_Cd1c_Condro_LS247


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_11]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_11]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_21]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_12]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Sinovial_Cd141_Condro_LS247


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_20]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: w-PA-W1.R2 RNA-seq

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

data_processing:
Cutadapt v1.15 were used to trim adaptor sequence.The sequence of in-vitro samples mapped to genome GRCh38 and the sequence of in-vivo samples mapped to a custom genome(mm10 and GRCh38), using bowtie2 v2.3.4.3.
Aligned reads were counted over gene and given as counts using RefSeq GRCh38 and mm10 annotation.
RPKM(Reads Per Kilobase per Million mapped reads) were calculated by a custom perl script.
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM  for each sample.

source_name: mesenchymal stem cells

growth_protocol: Adult human bone marrow mesenchymal stromal cells (hBMSCs) were purchased from ATCC. Cells were expanded in Human StemMACS MSC Expansion Media Kit XF (Miltenyi Biotec Inc) supplemented with 1 Penicillin/Streptomycin/Glutamine (Gibco™)

extract_protocol:
For cells cultured in vitro, samples were harvested, and RNA extraction was performed using RNeasy Plus Micro Kit (Qiagen). The total RNA was then subjected to the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. For samples harvested in vivo, proper amount of tissues was collected under the mice skins and then homogenized in Trizol with the tissue pellet pestle. Total RNA was then extracted following the Trizol RNA extraction protocol. In brief, every 50-100 mg tissue was homogenized in 1 mL TRIzol then 0.2 mL chloroform. The aqueous phase (with RNA) was collected and pelleted with isoproponal precipitation. We treated the extracted total RNA with DNase to remove residual DNA in the samples.
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mRNA kit.

treatment_protocol: In order to form 3D aggregates, the expanded hBMSCs (P5) were detached using 0.25% Trypsin, counted and reseeded in a 24-well non-adherent plate containing an agarose microwell insert. To create 3D aggregates composed of 200 cells, 400,000 cells in 2ml of either expansion media or differentiation media (detailed information on the content of media is listed in Table S1) were seeded in each well to cover the microwell inserts. After 24h culture in the aforementioned microwells with differentiation media, hBMSCs microaggregates were collected were formed were formed within 24-hour culture in micrcultured in differentiation media for 24 hours. After that, 6000 of microaggregates were washed with 15 µl of DMEM media and incorporated in 65 µl of annealed PA solution (1.25% weight/volume). For the samples without PA hydrogel, the same amount of cell aggregates were diluted with 65 µl of dissolving solution. To improve the stability of cell-laden construct during in vitro culture, hBMSCs aggregates laden-PA hydrogel were loaded on the commercially available bovine collagen (Type I) scaffolds (Helistat), which is the most frequently used clinical-grade scaffold for cell-based therapy in osteochondral defects. The aforementioned ex-vivo 21-day cultured hBMSCs microaggregates encapsulated with or without PA were implanted subcutaneously into the back of anesthetized mice. One week after implantation, animals were sacrificed and the explants (n=3) were retrieved, quickly frozen in liquid nitrogen and then stored in -80°C prior to RNA extraction for RNA-sequencing.

value: bone marrow-derived mesenchymal stem cells

tag: time point

value: 1 week

tag: culture condition


title: w-PA-W1.R1 RNA-seq


title: Material-control-W1.R1 RNA-seq


title: w-o-PA-W1.R2 RNA-seq


title: w-o-PA-W1.R3 RNA-seq


title: w-PA-W1.R3 RNA-seq


title: Endothelium (Endo) E8.5 [E8.5 Endo_13]

description:
22_C4P47ANXX_CGAGGCTG-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_10]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_10]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: 3D72h-Differentiation RNA-seq


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_10]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: w-o-PA-W1.R1 RNA-seq


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_11]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_11]

description:
20_C4P47ANXX_CAGAGAGG-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_18]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: 3D12h-Differentiation RNA-seq


title: 3D24h-Expansion RNA-seq


title: 3D72h-Expansion RNA-seq


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_19]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_12]

description:
21_C4P47ANXX_GCTACGCT-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: 3D12h-Expansion RNA-seq


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_9]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_9]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: 2D72h-Differentiation RNA-seq


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_9]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_10]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: 2D72h-Expansion RNA-seq


title: 2D24h-Expansion RNA-seq


title: 3D24h-Differentiation RNA-seq


title: zfish, embryo, MeHg50, 4-72 hpf, 3 [M5047203]

city: Beijing

first: Ruihong

last: Wang

address: No. 8 Dayangfang, Anwai Beiyuan, Chaoyang District, Beijing

department: State Key Laboratory of Environmental Criteria and Risk Assessment

institute: Chinese Research Academy of Environmental Sciences

data_processing:
Raw RNA-Seq data quality was assessed using FastQC(V0.10.1). In order to remove technical sequences, including adapters, polymerase chain reaction primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Reference genome file (GRCz11) was downloaded from ENSEMBL. Hisat2 (v2.0.1) was used to index reference genome sequence. After that, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Read counts per gene were quantified from the pair-end clean data, using HTSeq (v0.6.1) with default settings.
Differential expression analysis used the DESeq2 Bioconductor package. Padj of genes were setted <0.05 to detect differential expressed genes.
GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05.
Assembly: GRCz11
Supplementary files format and content: The XLS file include FPKM values for each Sample via HTSeq (v0.6.1).

organism: Danio rerio

source_name: whole embryo

extract_protocol:
RNA was harvested using TRIzol reagent protocal. 1 μg total RNA was used for following library constructing.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.Then libraries with different indexs were multiplexed and loaded on the Illumina instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer's instructions.

treatment_protocol: Embryos were respectively exposed to 0, 6, 30, 50 μg/L MeHg at 4 to 72 hpf.

tag: tissue

value: whole embryo

tag: genotype

value: WT

value: 50 ug/L MeHg


title: zfish, embryo, MeHg30, 4-72 hpf, 3 [M3047203]

value: 30 ug/L MeHg


title: zfish, embryo, MeHg50, 4-72 hpf, 2 [M5047202]


title: zfish, embryo, MeHg30, 4-72 hpf, 1 [M3047201]


title: zfish, embryo, MeHg30, 4-72 hpf, 2 [M3047202]


title: zfish, embryo, MeHg50, 4-72 hpf, 1 [M5047201]


title: zfish, embryo, MeHg6, 4-72 hpf, 3 [M647203]

value: 6 ug/L MeHg


title: 2D24h-Differentiation RNA-seq


title: zfish, embryo, MeHg6, 4-72 hpf, 2 [M647202]


title: zfish, embryo, control, 4-72 hpf, 3 [MC47203]

value: Untreated


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_8]

description:
19_C4P47ANXX_CTCTCTAC-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: Yolk sac


title: 2D12h-Differentiation RNA-seq


title: Endothelium (Endo) E8.5 [E8.5 Endo_8]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_9]

description:
19_C4P47ANXX_CTCTCTAC-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_8]

description:
19_C4P47ANXX_CTCTCTAC-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_14]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_15]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_7]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_7]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_17]

description:
19_C4P47ANXX_CTCTCTAC-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: 2D12h-Expansion RNA-seq


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_10]

description:
1_C4P47ANXX_TAAGGCGA-GCGTAAGA_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_8]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_9]

description:
19_C4P47ANXX_CTCTCTAC-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_16]

description:
19_C4P47ANXX_CTCTCTAC-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: zfish, embryo, control, 4-72 hpf, 2 [MC47202]


title: 0h-control RNA-seq


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_8]

description:
18_C4P47ANXX_TAGGCATG-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_13]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: zfish, embryo, control, 4-72 hpf, 1 [MC47201]


title: OE rep2

city: Qingdao

first: Anming

last: Ding

state: Shandong

address: No.11 Keyuanjingsi Rd.

institute: Tobacco Research Institute of CAAS

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: rosette leaves of 28-d-old plants

extract_protocol:
Total RNA was extracted from leaves using Plant RNA Purification Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

tag: developmental stage

value: 28-d-old plants

tag: position

value: rosette

tag: genotype/variation

value: over expression


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_12]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_6]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: OE rep1


title: zfish, embryo, MeHg6, 4-72 hpf, 1 [M647201]


title: WT rep2

value: wild type


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_6]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_7]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac Mk


title: WT rep1


title: Endothelium (Endo) E8.5 [E8.5 Endo_7]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac endothelium


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_10]

description:
16_C4P47ANXX_TCCTGAGC-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_7]

description:
17_C4P47ANXX_GGACTCCT-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_5]

description:
16_C4P47ANXX_TCCTGAGC-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_11]

description:
16_C4P47ANXX_TCCTGAGC-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_6]

description:
16_C4P47ANXX_TCCTGAGC-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_6]

description:
16_C4P47ANXX_TCCTGAGC-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: INPUT_NTDChIP_Rep3_2hr

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+dm6 for Native cChIP and mm10+hg19 for cross-linked cChIP) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
Sequencing datasets were calibrated to the spike-in Drosophila or human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of dm6 or hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools. Biological replicates correlated well with each other and were merged for subsequent analysis. Genome coverage tracks were generated using the pileup function from MACS2.
Assembly: mm10; dm6; hg19
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: Input sample for total RNA Pol II ChIP-seq indTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B.

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
Native cChIP-seq was performed as described previously (Fursova et al. 2019). In brief, 5 x 107 ESCs were mixed with 2 x 107 Drosophila SG4 cells and nuclei were released by resuspending in RSB (10 mM Tris HCl pH 8, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40. Nuclei were pelleted at 1500xg for 5 min and then washed and resuspended in 1 ml MNase digestion buffer (RSB with 0.25 M Sucrose, 3 mM CaCl2, 1x PIC). Each sample was incubated with 200 units of MNase (Fermentas) at 37⁰C for 5 minutes, with gentle inversion. Digestion was stopped by addition of 4 mM EDTA. Following centrifugation at 1500xg for 5 min, the supernatant (S1 fraction) was retained and the remaining pellet was resuspended in 300 μl nucleosome release buffer (10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x PIC), rotated at 4⁰C for 1 hr and then passed five times through a 27G needle using a 1 ml syringe. Following centrifugation at 1500xg for 5 min, the supernatant (S2) was combined with S1 fraction, aliquoted, snap frozen and stored at -80°C. For each IP, 100 μl S1/S2 nucleosomes were diluted to 1 ml total volume in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris HCl, pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1 % Triton-X100, 1x PIC) and immunoprecipitated with 3 µl H3K4me3 antibody (Klose Lab) overnight at 4⁰C. IPs were all set up in duplicate for each sample. 100 μl diluted chromatin was also set aside as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in native ChIP incubation buffer, overnight at 4⁰C. 40 μl slurry of pre-blocked agarose beads were used to capture antibody-bound nucleosomes at 4⁰C for 1 hr. Beads were then washed 4x with Native ChIP wash buffer (20 mM Tris HCl, pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1 % Triton-X100, 1x PIC) and 1x TE buffer, pH 8. DNA was eluted by vortexing for 30 min in elution buffer (1% SDS and 0.1 M NaHCO3) and DNA was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). For each ChIP, DNA from the matched input control (10% of the IP) was also purified. Purified DNA was analysed using ChIP-qPCR.    For double cross-linked T7-SET1A ChIP and ZC3H4-T7 ChIP, 5 x 107 ESCs were fixed with 2 mM DSG (disuccinimidyl glutarate, Thermo Fisher Scientific) for 50 min at 25⁰C and then 1% formaldehyde (methanol-free, Thermo Fisher Scientific) for 10 min. Alternatively, for single cross-linked RNA Pol II ChIP, 5 x 107 ESCs were fixed with 1% formaldehyde for 10 min at 25⁰C. Fixation was quenched using glycine added to 125 mM. Cells were then pelleted at 1000xg for 5 min and washed with PBS. Cross-linked ESCs were mixed with 1 x 105 cross-linked HEK 293T/T7-SCC1 cells (1% formaldehyde, 15 min for SET1A ChIP; a gift from Martin Houlard, Nasmyth lab) or 2 x 106 cross-linked HEK 293T cells (1% formaldehyde, 10 min for RNA Pol II ChIP). Chromatin was prepared by incubation in 1 ml FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x PIC, 1 mM AEBSF. For RNA Pol II ChIP, EDTA concentration was increased to 2 mM and 10 mM NaF was added fresh) on ice for 10 min. Chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode) at 4⁰C. Sonication was performed using 23-30 cycles of 30s on/30s off at full power, shearing genomic DNA to an average size of 0.5 kb. The sonicated material was pelleted at 20,000xg for 20 min, and the supernatant taken as sonicated chromatin. 300 μg chromatin was used per IP. Chromatin was diluted to 1 ml total volume per IP in FA-lysis buffer. An additional volume of diluted chromatin was taken to use as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in 1x TE buffer at 4⁰C for 1 hr. Chromatin was pre-cleared with agarose beads (40 μl slurry beads per ChIP) at 4⁰C for 1 - 2 hr. The input sample was taken from the pre-cleared chromatin, and the remainder was immunoprecipitated overnight at 4⁰C with the appropriate amount of antibody: T7 (Cell Signalling, D9E1X, 10µl) or RNA Pol II N-terminal domain (Cell Signalling, D8L4Y, 15µl). Antibody-bound chromatin was precipitated for 3 hr at 4⁰C using 40 μl slurry of blocked Protein A agarose beads. Washes were carried out for 5 min each at 4⁰C, using FA-lysis buffer, FA-lysis buffer with 500 mM NaCl, 1x DOC buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 1 mM EDTA (2 mM EDTA for RNA Pol II ChIP), 0.5% NP-40, 0.5% Na-deoxycholate), and 2 washes with TE buffer (1x PIC and 1 mM AEBSF were added fresh to all wash buffers. 10 mM NaF was also added for RNA Pol II ChIP). DNA was eluted by vortexing for 30 min in elution buffer (1% SDS and 0.1 M NaHCO3). Cross-links were reversed for ChIPs and inputs at 65⁰C overnight with 200 mM NaCl and 2 μl RNase A (Sigma). Samples were then incubated with 20 μg Proteinase K for 1 hr at 45⁰C. DNA for ChIPs and inputs was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). Purified DNA was analysed using ChIP-qPCR.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate on Illumina NextSeq 500 platform.

treatment_protocol: Cell lines expressing dTAG fusion proteins were treated with 100 nM dTAG-13 (produced by Behnam Nabet and Nathanael Gray1 or Carole Bataille and Angela Russell) to induce protein depletion.

tag: cell line

tag: condition

value: 100 nM dTAG13

tag: treatment time

tag: replicate

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: type of chip

value: cross-linked

tag: ChIP

value: Input

tag: antibody


title: INPUT_NTDChIP_Rep1_2hr

value: Input sample for total RNA Pol II ChIP-seq indTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B.

tag: treatment


title: INPUT_NTDChIP_Rep2_0hr

source_name: Input sample for total RNA Pol II ChIP-seq in untreated dTAG-SET1A/B cells.

value: untreated


title: INPUT_NTDChIP_Rep2_2hr


title: INPUT_NTDChIP_Rep1_0hr

value: Input sample for total RNA Pol II ChIP-seq in untreated dTAG-SET1A/B cells.


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_4]

description:
15_C4P47ANXX_AGGCAGAA-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

tag: strain/genotype

tag: Stage

tag: tissue source

value: Yolk sac

tag: cell type


title: NTDChIP_Rep3_2hr

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in. Total RNA Pol II ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B.

value: Total RNA Pol II

value: anti-Rbp1-NTD (Cell Signalling D8L4Y)


title: NTDChIP_Rep2_2hr

value: Mouse embryonic stem cells with human HEK293T cells spike-in. Total RNA Pol II ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B.


title: NTDChIP_Rep3_0hr

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in. Untreated control for total RNA Pol II ChIP-seq in dTAG-SET1A/B cells.


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_9]

description:
15_C4P47ANXX_AGGCAGAA-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_5]

description:
15_C4P47ANXX_AGGCAGAA-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: NTDChIP_Rep2_0hr

value: Mouse embryonic stem cells with human HEK293T cells spike-in. Untreated control for total RNA Pol II ChIP-seq in dTAG-SET1A/B cells.


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_5]

description:
15_C4P47ANXX_AGGCAGAA-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: Endothelium (Endo) E8.5 [E8.5 Endo_5]

description:
15_C4P47ANXX_AGGCAGAA-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: NTDChIP_Rep1_0hr


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_5]

description:
15_C4P47ANXX_AGGCAGAA-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: Input_T7SET1AChIP_Rep3_2hr

source_name: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Input sample for the T7-SET1A ChIP-seq in dTAG-SET1A cells depleted of SET1A.

value: HEK293T; Scc1-T7


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_8]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: Input_T7SET1AChIP_Rep3_0hr

source_name: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Input sample for the untreated control for T7-SET1A ChIP-seq in dTAG-SET1A cells.


title: Input_T7SET1AChIP_Rep2_2hr

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Input sample for the T7-SET1A ChIP-seq in dTAG-SET1A cells depleted of SET1A.


title: INPUT_NTDChIP_Rep3_0hr


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_6]

description:
16_C4P47ANXX_TCCTGAGC-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt

value: yolk sac Mk


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_7]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_3]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Input_T7SET1AChIP_Rep2_0hr

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Input sample for the untreated control for T7-SET1A ChIP-seq in dTAG-SET1A cells.

value: Homo sapiens


title: Input_T7SET1AChIP_Rep1_0hr

value: cross-linked

value: Input


title: Input_T7SET1AChIP_Rep1_2hr

value: 100 nM dTAG13


title: T7SET1AChIP_Rep3_2hr

source_name: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. T7-SET1A ChIP-seq in dTAG-SET1A cells depleted of SET1A.

value: anti-T7 (Cell Signalling D9E1X)


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_4]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: Yolk sac


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_4]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: NTDChIP_Rep1_2hr

value: Total RNA Pol II


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_4]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_5]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: T7SET1AChIP_Rep3_0hr

source_name: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Untreated control for T7-SET1A ChIP-seq in dTAG-SET1A cells.

value: untreated


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_3]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: T7SET1AChIP_Rep1_2hr

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. T7-SET1A ChIP-seq in dTAG-SET1A cells depleted of SET1A.


title: T7SET1AChIP_Rep2_0hr

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Untreated control for T7-SET1A ChIP-seq in dTAG-SET1A cells.


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_6]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: T7SET1AChIP_Rep1_0hr


title: T7SET1AChIP_Rep2_2hr


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_3]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: Endothelium (Endo) E8.5 [E8.5 Endo_3]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac endothelium


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_3]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: JLat106_HuEpi_gDNA2

city: Seattle

first: Emily

last: Hsieh

state: WA

address: 1100 Fairview Ave N, Mail Stop C2-023

institute: Fred Hutchinson Cancer Center

description: gDNA

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software. This was followed by generation of fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Samples were demultiplexed using FASTX toolkit v0.0.13. Specifically, FASTX barcode splitter was used to separate reads by barcode matching.
Reads were trimmed and aligned to a custom human epigenome guide library using Bowtie v1.0.0, followed by tabulation of read counts using R.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform differential guide analysis between various groups of interest. PMID: 25476604.
Assembly: HuEpi guide RNA library generated by Emerman lab. The library targets 841 human epigenome genes and 252 non-targeting controls.
Supplementary files format and content: *.counts.txt: Tab-delimited files with read counts for each guide sequence.
Library strategy: CRISPR

growth_protocol: J-Lat 10.6 ZAP KO and J-Lat 5A8 ZAP KO are grown in RPMI-1640 supplemented with 10% FBS, 10nM HEPES, and Pen/Strep. Cells are passaged between 2 x 10^5 cells/mL and 2 x 10^6 cells/mL.

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen, Cat No 51183).
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the 5,309 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

treatment_protocol: 3 x 10^6 (>500X coverage) J-Lat 10.6 ZAP KO and J-Lat 5A8 ZAP KO cells were each transduced with the HuEpi library (MOI of 0.4) and selected in 0.4 ug/mL puromycin for 10-14 days. For each cell line, knockout cell pools are treated with or without 10 nM of AZD5582 for 24 hours. Each condition is performed with two replicates. After the treatment, cells and viral supernatants were harvested.

value: Jurkat

tag: group


title: HuEpi_Plasmid_1

description: Plasmid

library_source: other

molecule: other

source_name: Plasmid

extract_protocol:
Plasmid
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the 5,309 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

value: Plasmid


title: JLat106_HuEpi_gDNA1

description: gDNA


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_4]

description:
12_C4P47ANXX_GTAGAGGA-GCGTAAGA_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_1]

description:
12_C4P47ANXX_GTAGAGGA-GCGTAAGA_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

source_name: C57BL/6 E8.5 yolk sac


title: JLat5A8_HuEpi_gDNA2

description: gDNA

source_name: J-Lat 5A8

value: J-Lat 5A8


title: JLat5A8_HuEpi_gDNA1

description: gDNA


title: Endothelium (Endo) E8.5 [E8.5 Endo_4]

description:
14_C4P47ANXX_CGTACTAG-CTCTCTAT_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Jlat106_HuEpi_AZD5582_vRNA2

description: viral RNA (vRNA)

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen, Cat No 52904).
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the 5,309 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

tag: time

value: 24 hrs


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_2]

description:
12_C4P47ANXX_GTAGAGGA-GCGTAAGA_L004
processed data file:
counts.Unfiltered.3.0.txt

value: yolk sac Mk


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_2]

description:
12_C4P47ANXX_GTAGAGGA-GCGTAAGA_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

source_name: C57BL/6 E8.25 yolk sac


title: Jlat106_HuEpi_AZD5582_vRNA1

description: viral RNA (vRNA)


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_2]

description:
13_C4P47ANXX_TAAGGCGA-CTCTCTAT_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Jlat5A8_HuEpi_AZD5582_vRNA2

description: viral RNA (vRNA)


title: HuEpi_Plasmid_2

description: Plasmid


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_3]

description:
11_C4P47ANXX_AAGAGGCA-GCGTAAGA_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

source_name: Flk1-GFP/+ E7.25 yolk sac


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_2]

description:
12_C4P47ANXX_GTAGAGGA-GCGTAAGA_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: JLat106_HuEpi_NoTreat_vRNA2

description: viral RNA (vRNA)


title: Jlat5A8_HuEpi_AZD5582_vRNA1

description: viral RNA (vRNA)


title: JLat106_HuEpi_NoTreat_vRNA1

description: viral RNA (vRNA)


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_1]

description:
11_C4P47ANXX_AAGAGGCA-GCGTAAGA_L004
processed data file:
counts.Unfiltered.3.0.txt


title: Endothelium (Endo) E8.5 [E8.5 Endo_1]

description:
11_C4P47ANXX_AAGAGGCA-GCGTAAGA_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: JLat5A8_HuEpi_NoTreat_vRNA1

description: viral RNA (vRNA)


title: JLat5A8_HuEpi_NoTreat_vRNA2

description: viral RNA (vRNA)


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_1]

description:
11_C4P47ANXX_AAGAGGCA-GCGTAAGA_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: HT-29 cells, TRIM40, rep2

city: Seoul

first: Sujin

last: Kang

address: 50, Yonsei-ro, Seodaemun-gu

department: Department of Systems Biology

country: South Korea

institute: Yonsei University

description:
Sample 4
transcript_2.txt

data_processing:
RNA-seq paired-end reads were mapped to UCSC hg19 homo sapiens genome using HISAT2 version 2.1.0
The expression level of each gene was quantified as FPKM using StringTie tool v1.3.4d
Assembly: UCSC hg19
Supplementary files format and content: transcript_1.txt represents FPKM values of sample 1-2. transcript_2.txt represents FPKM and TPM values of sample 3-4.

growth_protocol: HT-29 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA preparation kits (GeneAll). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Standed mRNA LT Sample Prep Kit following manufacturer's protocols.

value: colon cancer cells

tag: genotype

value: TRIM40 overexpression


title: HT-29 cells, Control, rep2

description:
Sample 3
transcript_2.txt

tag: cell line

value: WT


title: HT-29 cells, TRIM40, rep1

description:
Sample 2
transcript_1.txt


title: HT-29 cells, Control, rep1

description:
Sample 1
transcript_1.txt


title: Erythro-Myeloid Progenitors (EMP) E8.5 [E8.5 HPC_0]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L005
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: Yolk sac


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_1]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L007
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_0]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Megakaryocytes (Mk) E8.5 [E8.5 PreDPFC_0]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L004
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: DTP_137

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

description: DTP

data_processing:
Cell Ranger (v2.0, 10X Genomics) was used to process barcodes, remove empty “cells”, align reads to GRCh38-mm10 genomes, and generate gene-cell matrices following their standard pipeline
Seurat (v2.3.4) was used for further quality-control, cell filtering, normalization.
Assembly: GRCh38 + mm10
Supplementary files format and content: CSV count matrices

source_name: Xenograft

growth_protocol: Human primary lung tumors grown in the subcutaneous pocket at the flank of NOD SCID mice to form xenograft tumors

extract_protocol:
10XGenomics;Baseline and DTP tumors were digested with liberaseTM (Sigma Aldrich). Single-cell libraries were prepared using 10X Genomics Single Cell 3’ Reagent Kits v2. Volumes for each sample were calculated for target capture of 1000 (DTP) or 6000 (BL) cells
10X Genomics Single Cell 3’ Reagent Kits v2 user guide

treatment_protocol: Treatment was applied to the DTP cells prior to extraction: DTP PDXs were treated daily with 50 mg/kg erlotinib (UHN Shanghai, Toronto, Canada) by oral gavage (excluding weekends) for 30 days.

tag: host strain

value: NOD SCID mice

tag: histology

value: LUAD

value: erlotinib

value: DTP cells


title: BL_137

description: BL

value: control

value: Baseline (BL) cells


title: Endothelium (Endo) E8.5 [E8.5 Endo_2]

description:
12_C4P47ANXX_GTAGAGGA-GCGTAAGA_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac endothelium


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_0]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac EMP


title: Endothelium (Endo) E8.5 [E8.5 Endo_0]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L002
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: Primitive erythrocytes (EryP) E8.5 [E8.5 EryP_0]

description:
10_C4P47ANXX_CGAGGCTG-GCGTAAGA_L001
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac erythrocytes


title: fetal pancreas pool_4_151820_PCW_HTO library

city: London

first: Oladapo

middle: Edward

last: Olaniru

address: Hodgkin building, Guy's campus

department: Department of Diabetes

institute: King's College London

description: Totalseq B HTO library of of single cells from 3 fetal pancreases at 15, 18 and 20 PCW

data_processing:
Generation of FASTQ files and alignment of raw sequencing reads were carried out using CellRanger (version 6.0.0, 10x Genomics).
Raw sequence data from HTO libraries were processed using CITE-Seq-Count, version 1.4.5
Genome_build: hg38
Supplementary_files_format_and_content: csv files contain de-hashing result of the pooled samples into their indvidual gestation age
Supplementary_files_format_and_content: final_matrix.csv.gz is a five-column filtered gene-count-matrix file from Cellranger output contatining 10x Genomics cellular barcode, feature ID, feature name, feature type and UMI count

source_name: human fetal pancreas

extract_protocol:
Human fetal pancreases were dissociated into single cells by collagenase and trypsin/EDTA treatment. Each batch contains 3 samples from different gestational stages which were stained with oligonucleotide-conjugated antibodies from BioLegend and pooled
Single cell mRNA and antibody (HTO) libraries were prepared according to the manufacturer’s protocol and paired-end sequencing was carried out on an Illumina NextSeq 2000, except for batch 15, 18 and 20 PCW batch which was sequenced on a HiSeq 2500.

tag: tissue

value: pancreas

tag: developmental stage


title: Flk1-GFP+ E7.25 extraembryonic mesoderm [E7.5 Flk1_2]

description:
11_C4P47ANXX_AAGAGGCA-GCGTAAGA_L006
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt

value: yolk sac mesoderm


title: Erythro-Myeloid Progenitors (EMP) E8.25 [E8.5 PreHPC_1]

description:
11_C4P47ANXX_AAGAGGCA-GCGTAAGA_L003
processed data file:
counts.Unfiltered.3.0.txt
counts.3.0.txt
cpm.Size.3.0.txt


title: HUPEC_15_G0G0_D1 [small RNA]

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

description:
15_D1
small RNA

data_processing:
miRge 3.0 with default parameter and option to analyze tRNA fragment and halves.
Genome_build: Human small-RNA annotation libraries from miRge3.0.
Supplementary_files_format_and_content: miR.Counts.xlsx: Matrix table with raw microRNA counts for every RNA and every sample.
Supplementary_files_format_and_content: tRF.Counts.xlsx: Matrix table with raw transfer RNA fragment counts for every RNA and every sample.

source_name: podocyte-like epithelial cells (HUPEC)

growth_protocol: Undifferentiated podocytes were cultured in RPMI 1640 medium (Gibco, ThermoFisher Scientific, Gaithersburg, MD), supplemented with 10% fetal bovine serum and insulin/transferrin/selenium (Gibco, Thermo Fisher Scientific, Gaithersburg, MD) at 33 °C, 95% air and 5% CO2) for expansion.

extract_protocol:
Cells were resuspended with QIAzol (QIAGEN, Hilden, Germany) and RNA was extracted (Zymo Direct-zol RNA miniprep kit).
Libraries were size selected after 3′ ligation and 5′ linker-ligation. cDNA generated with Superscript IV reverse transcriptase was amplified with Q5 Polymerase (NEB) in a low cycle PCR (12 cycles). Pippin prep was used to remove ligated linker-linker (143–185 bp). Pilot PCR on 10% of pippin-prepped cDNA was performed to determine appropriate number of additional PCR cycles. Tapestation (Agilent) was used to determine quality and concentration of the resulting libraries.

treatment_protocol: Podocytes were differentiated by culturing in the same medium formulation at 37°C for 14 days, exchanging medium every 2-3 days.

tag: differentiation status

value: Differentiated

value: APOL1 G0/G0


title: HUPEC_13_G1G2_D3 [small RNA]

description:
13_D3
small RNA

value: APOL1 G1/G2


title: HUPEC_15_G0G0_D3 [small RNA]

description:
15_D3
small RNA


title: HUPEC_13_G1G2_D2 [small RNA]

description:
13_D2
small RNA


title: fetal pancreas pool_4_151820_PCW_Gene expression

description: Gene expression of single cells from 3 fetal pancreases at 15, 18 and 20 PCW. Cells were tagged with oligonucleotide-conjugated antibodies, pooled, sequenced in a single 10x reaction and demultiplexed afterwards.


title: HUPEC_15_G0G0_D2 [small RNA]

description:
15_D2
small RNA


title: HUPEC_12_G1G2_D2 [small RNA]

description:
12_D2
small RNA


title: HUPEC_12_G1G2_D1 [small RNA]

description:
12_D1
small RNA


title: HUPEC_10_G0G0_D3 [small RNA]

description:
10_D3
small RNA


title: HUPEC_10_G0G0_D2 [small RNA]

description:
10_D2
small RNA


title: HUPEC_10_G0G0_D1 [small RNA]

description:
10_D1
small RNA


title: DTP, 137_RES, 8

type: RNA

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data were normalized using quantile normalization and log2 transformation,background correction with the lumi package in R

label: biotin

label_protocol: Biotinylated cRNA were prepared with the DASL Assay kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: lung adenocarcinoma (LUAD)

value: LUAD patient-derived xenograft (PDX) tumor


title: HUPEC_15_G0G0_UD3 [small RNA]

description:
15_UD3
small RNA

value: Undifferentiated


title: HUPEC_15_G0G0_UD2 [small RNA]

description:
15_UD2
small RNA


title: HUPEC_15_G0G0_UD1 [small RNA]

description:
15_UD1
small RNA


title: HUPEC_13_G1G2_D1 [small RNA]

description:
13_D1
small RNA


title: DTP, 137_RES, 5


title: HUPEC_12_G1G2_D3 [small RNA]

description:
12_D3
small RNA


title: HUPEC_13_G1G2_UD3 [small RNA]

description:
13_UD3
small RNA


title: DTP, 137_RES, 6


title: DTP, 137_RES, 7


title: BL, 137_RES, 2

value: baseline (BL) cells


title: Stable clone of NIM1 cell line transfected with TIMP3 replicate 2

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Human Gene 2.0 ST arrays (Thermo Fisher Scientific,Affymetrix, Waltham, MA, USA), according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied using Brainarray CDF (Chip Definition File) version 20 for gene annotations, (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp),  as previously described (Ronchetti D., et al. SciRep 2018).

source_name: stable clone

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA)

growth_protocol: NIM1-EV and NIM-T23 stable clones were maintained in DMEM medium containing 10% FCS, 2 mM glutamine and 100U/ml penicillin/streptomycin, with the addition of G418 (Lifetechnologies, Invitrogen, Carlsbad, CA, USA) selection (400 μg/ml)

extract_protocol: RNA extraction was performed with Nucleospin RNA II purification kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) according to the manufacturer’s instructions


title: BL, 137_RES, 4


title: Stable clone of NIM1 cell line transfected with TIMP3 replicate 3


title: BL, 137_RES, 3


title: Stable clone of NIM1 cell line transfected with TIMP3 replicate 1


title: HUPEC_13_G1G2_UD2 [small RNA]

description:
13_UD2
small RNA


title: HUPEC_13_G1G2_UD1 [small RNA]

description:
13_UD1
small RNA


title: Stable clone of NIM1 cell line transfected with empty vector replicate 1


title: Stable clone of NIM1 cell line transfected with empty vector replicate 2


title: CONTROL HBEM1

type: genomic

city: Dammam

first: Noor

middle: B

last: Almandil

address: C1 West Campus

department: Department of Clinical Pharmacy

country: Saudi Arabia

institute: Imam Abdulrahman Bin Faisal University

description:
CONTROL
Genomic DNA was genotyped using The Human Exome Bead Chip Kit v1.0 and v1.1 (Illumina).

hyb_protocol: According to the hybridazation protocol in manufacture's Reference Guide of The Human Exome Bead Chip Kit v1.0 and v1.1 Illumina

scan_protocol: According to the scan protocol in manufacture's Reference Guide

data_processing:
GenomeStudio 2,0 software
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

source_name: Buccal cells

label_protocol: standard Illumina protocol using C-Bio and A-DNP

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from  buccal cell using Gentra Puregene Cell Kit

treatment_protocol: Samples are buccal cell

tag: gender

value: Female


title: CONTROL DCY221


title: CONTROL DCY222


title: CONTROL CDY30


title: CONTROL DCY215


title: CONTROL DCY213


title: HUPEC_12_G1G2_UD2 [small RNA]

description:
12_UD2
small RNA


title: HUPEC_12_G1G2_UD3 [small RNA]

description:
12_UD3
small RNA


title: Stable clone of NIM1 cell line transfected with empty vector replicate 3


title: HUPEC_12_G1G2_UD1 [small RNA]

description:
12_UD1
small RNA


title: CONTROL DCY200


title: CONTROL DCY212


title: HUPEC_10_G0G0_UD3 [small RNA]

description:
10_UD3
small RNA


title: BL, 137_RES, 1


title: CONTROL PDY50


title: CONTROL PDY47


title: HUPEC_10_G0G0_UD2 [small RNA]

description:
10_UD2
small RNA


title: HUPEC_10_G0G0_UD1 [small RNA]

description:
10_UD1
small RNA


title: CONTROL PDY44


title: CONTROL PDY43


title: CONTROL PDY48


title: CONTROL PDY41


title: Dys0100_2

city: Buffalo

first: Michael

last: Farkas

state: NY

address: 3495 Bailey Ave, Bldg 20, Mail Stop 151

department: Ophthalmology

institute: State University of New York at Buffalo

data_processing:
Base calling was performed using RTA v2
Reads were aligned to human genome version hg38 using STAR v2.5.2b
Counts were generated for each transcript using Rsubread v1.32.4
RPKM values for each transcript were calculated to determine overall expression
Differential expression analsis was perfromed using DESeq
Genome_build: hg38
Supplementary_files_format_and_content: raw counts for each sample from Rsubread, includes isoform ID, length, and count
Supplementary_files_format_and_content: tables containing DESeq normalized counts and rpkm values for all samples

source_name: induced pluripotent stem cell-derived retinal pigment epithelium

growth_protocol: Human iPSC (line ) were seeded at 500,000 cells in a 10-cm dish coated with Matrigel. Cells were maintained in TeSR-E8 media (Stem Cell Technologies) with Rock Inhibitor (Y-27632 dihydrochloride, Santa Cruz Biotechnology) at a final concentration of 1 μM/mL. Media was changed daily. To differentiate iPSC cells toward RPE, the culture was maintained in RDM until day 80, when RPE was dissected and passaged.

extract_protocol:
RNA was isolated using the Rneasy plus mini kit
RNA-sequencing libraries were prepared using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing kit according to the manufacturer’s protocol using 100 ng total RNA, and each sample was indexed for multiplexing

value: Smith-Lemil-Opitz syndrome (SLOS) cell line

tag: cell source id

tag: disease state

value: control/ normal WT


title: CWISLOS_5

value: CWI

value: mild

value: compound heterozygous, consisting of 278C>T (T93M) and splicing acceptor variant c.964-1G>C (commonly known as IVS8G-C) point mutations in the DHCR7 gene


title: Dys0100_1


title: Dys0100_4


title: Dys0100_6


title: CONTROL PDY40


title: CWISLOS_6


title: CWISLOS_4


title: CWISLOS_2


title: CWISLOS_1


title: CWISLOS_3


title: CONTROL PDY36


title: CONTROL PDY31


title: CONTROL CDY16


title: CONTROL PDY34


title: CONTROL PDY28


title: A2SLOS_6

value: severe

value: homozgous for IVS8G-C (splice acceptor variant, in 5' region of exon 9)


title: CONTROL CDY13


title: CONTROL PDY22


title: A2SLOS_5


title: A2SLOS_4


title: CONTROL CDY20


title: A2SLOS_2


title: CONTROL CDY11


title: CONTROL PDY12


title: A2SLOS_1


title: CONTROL PDY15


title: CONTROL PDY10


title: TCR repertoire of P7-post [P7-post-TCR]

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

description:
P7-post-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells
An antigen stimulation experiment using Dynabeads Human T-Activator CD3/CD28 was performed on T cells obtained from patient #7. "P7-post" indicates post-stimulated.

data_processing:
Library strategy: TCR repertoire
10x Genomics cellranger (4.0.0) mkfastq used for basecalling.
Sequenced reads were processed with cellranger (4.0.0) count using the GRCh38 reference dataset (version 2020-A; downloaded from 10x Genomics) to derive gene expression and feature barcode UMI count matrix.
Sequenced reads were processed with cellranger (4.0.0) vdj using the GRCh38 reference dataset (version 4.0.0; downloaded from 10x Genomics) to derive TCR clonotype data.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_matrix.mtx.gz: MatrixMarket format files include UMI count matrixes of gene expressions and feature barcodes for each sample. Row and column names of matrix are separately recorded in following two files.
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Tab-separated text files include cell barcodes for each sample.
Supplementary_files_format_and_content: *_features.tsv.gz: Tab-separated text files include gene names and feature barcode names for each sample.
Supplementary_files_format_and_content: *_filtered_contig_annotations.csv.gz: Comma-separated text files include TCR clonotype data for each sample.

source_name: CD62Llow CD4+ T cells

extract_protocol:
Manufactured protocol of Chromium system (10x Genomics).
Manufactured protocol of Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 with Feature Barcoding technology (10x Genomics).

treatment_protocol: Pre-treatment samples.

tag: diagnosis

value: Lung cancer

value: CD62Llow CD4+ T cells


title: CONTROL PDY9


title: CONTROL CDY2


title: scRNAseq of P7-post [P7-post-GEX]

description:
P7-post-GEX, P7-post-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells
An antigen stimulation experiment using Dynabeads Human T-Activator CD3/CD28 was performed on T cells obtained from patient #7. "P7-post" indicates post-stimulated.

data_processing:
10x Genomics cellranger (4.0.0) mkfastq used for basecalling.
Sequenced reads were processed with cellranger (4.0.0) count using the GRCh38 reference dataset (version 2020-A; downloaded from 10x Genomics) to derive gene expression and feature barcode UMI count matrix.
Sequenced reads were processed with cellranger (4.0.0) vdj using the GRCh38 reference dataset (version 4.0.0; downloaded from 10x Genomics) to derive TCR clonotype data.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_matrix.mtx.gz: MatrixMarket format files include UMI count matrixes of gene expressions and feature barcodes for each sample. Row and column names of matrix are separately recorded in following two files.
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Tab-separated text files include cell barcodes for each sample.
Supplementary_files_format_and_content: *_features.tsv.gz: Tab-separated text files include gene names and feature barcode names for each sample.
Supplementary_files_format_and_content: *_filtered_contig_annotations.csv.gz: Comma-separated text files include TCR clonotype data for each sample.


title: scRNAseq of P7-pre [P7-pre-GEX]

description:
P7-pre-GEX, P7-pre-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells
An antigen stimulation experiment using Dynabeads Human T-Activator CD3/CD28 was performed on T cells obtained from patient #7. "P7-pre" indicates pre-stimulated.


title: TCR repertoire of P7-pre [P7-pre-TCR]

description:
P7-pre-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells
An antigen stimulation experiment using Dynabeads Human T-Activator CD3/CD28 was performed on T cells obtained from patient #7. "P7-pre" indicates pre-stimulated.


title: CONTROL PDY6


title: CONTROL AUN121M1


title: AUTISM AUN121

description:
AUTISM
Genomic DNA was genotyped using The Human Exome Bead Chip Kit v1.0 and v1.1 (Illumina).


title: scRNAseq of P6 [P6-GEX]

description:
P6-GEX, P6-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells

source_name: CD4+ T cells

value: CD4+ T cells


title: TCR repertoire of P4 [P4-TCR]

description:
P4-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells


title: TCR repertoire of P6 [P6-TCR]

description:
P6-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells


title: CONTROL AUNC121F1


title: scRNAseq of P4 [P4-GEX]

description:
P4-GEX, P4-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells


title: CONTROL AUNC66F1


title: AUTISM AUN88


title: AUTISM AUN87


title: scRNAseq of P3 [P3-GEX]

description:
P3-GEX, P3-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells


title: A2SLOS_3


title: Blood_Mo_BK43

source_name: Blood

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Stranded library: 200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Low Input library: Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

value: Monocytes

value: Control

tag: library type

value: Stranded


title: Blood_Mo_BK42


title: AUTISM AUN85


title: AUTISM AUN81


title: AUTISM AUN77


title: CONTROL AUNC34


title: CONTROL PDY8


title: Blood_Cd141_BK43

value: Dendritic Cells Cd141+

value: Low Input


title: Blood_Cd1c_BK42

value: Dendritic Cells Cd1c+


title: Blood_Cd1c_BK43


title: Blood_Cd141_BK42


title: AUTISM AUN73

value: Female


title: AUTISM AUN72


title: Blood_Mo_BK32


title: AUTISM AUN70


title: Blood_Cd1c_BK32


title: CONTROL AUNC33


title: TCR repertoire of P3 [P3-TCR]

description:
P3-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells


title: Blood_Cd141_BK32


title: AUTISM AUN68


title: Blood_Cd1c_BK114


title: Blood_Mo_BK114


title: AUTISM AUN69


title: CONTROL AUNC32


title: AUTISM AUN57


title: Blood_Mo_ARC382

value: Rheumatoid Arthritis


title: CONTROL AUNC27


title: AUTISM AUN50


title: Blood_Cd141_BK114


title: Blood_Cd141_ARC382


title: Blood_Cd1c_ARC382


title: CONTROL AUNC26


title: Blood_Cd1c_ARC376


title: AUTISM AUN40


title: CONTROL AUNC22


title: Blood_Mo_ARC376


title: Blood_Cd141_ARC376


title: Blood_Mo_ARC338


title: Blood_Cd1c_ARC338


title: Blood_Cd141_ARC338


title: AUTISM AUN33


title: Blood_Mo_ARC255


title: AUTISM AUN31


title: Blood_Cd1c_ARC255


title: AUTISM AUN27


title: CONTROL AUNC20


title: Blood_Cd141_ARC255


title: CONTROL AUNC19