title: CVID P2

city: Prague

last: Klocperk

address: V Uvalu 84

department: Department of Immunology

country: Czech Republic

institute: University Hospital in Motol

description: HY3HHBGX5_FRD15_18s000351-1-1_Keller_lane118s000351

data_processing:
Obtained libraries that passed the QC step were pooled in equimolar amounts; 1.8 pM solution of this pool was loaded on the Illumina sequencer NextSeq 500 and sequenced uni-directionally, generating ~500 million reads per sample, each 85 bases long.
The quality control was performed by FastQC to get information about the run itself.
Sequencing reads were aligned using STAR aligner against human genome reference (GRCh37/hg19 with UCSC annotation).
Reads mapping to regions described as “exon” in the reference were counted during the alignment (--quantMode GeneCounts option in STAR).
The read count values were expressed as raw counts.
Genome_build: GRCh37/hg19 with UCSC annotation
Supplementary_files_format_and_content: xlsx file with samples represented by columns, transcripts as rows.

source_name: CXCR5+ CD8 T cells from lymph node of a CVID patient

extract_protocol:
Secondary lymphoid organs were mechanically dissociated, cells were stained with anitbody-fluorochrome conjugates and then sorted on MoFlo Astrios. CD3+CD4-CD8+CXCR5+ cells were then used to isolate mRNA using RNeasy Mini Kits (Quiagen).
Barcoded stranded mRNA-seq libraries were prepared from high quality total RNA samples (~200 ng/sample) using the Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: cell type

value: secondary lymphoid organ cells, sorted


title: HD 1

status: Public on Sep 27 2019

type: SRA

first: Adam

description: HY3HHBGX5_FRD24_18s002989-1-1_Keller_lane118s002989

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: CXCR5+ CD8 T cells from tonsil of a healthy donor


title: srLp B 1

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

description:
Lexogen-4
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

data_processing:
Primary base calling and quality scoring was performed using RTA v1.18.66.4 (Illumina)
demultiplexing and processing with Bcl2fastq v2.18.0.12 (Illumina)
3' adapter were trimmed using cutadapt v1.15 with parameter -m 10
Remaining reads were mapped to the synthetic miRNA reference or customized miRNA reference based on miRBase v21 using Bowtie v1.1.2 with parameter -a and --norc, no mismatches allowed
Reads were counted a custom python script
Genome_build: synthetic miRNA reference and customized miRNA reference based on miRBase v21
Supplementary_files_format_and_content: Raw count table, Downsampled count table, rlog transformed, downsampled count table, Mapping_reference

organism: synthetic RNA

source_name: Synthetic miRNA

extract_protocol:
Synthetic miRNA samples: no RNA extraction needed, human samples: RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
CATS, Small RNA-Seq Library Prep kit (srLp), QIAseq, TailorMix,SMARTer, CleanTag

tag: library prep kit

value: srLp

tag: mix type/state

value: B

tag: replicate

tag: molecule subtype

value: Synthetic miRNA


title: 317E5

city: San Francisco

first: Kimberley

middle: Jane

last: Evason

state: CA

address: 513 Parnassus Ave, Room M545

department: Pathology

country: USA

institute: University of California, San Francisco

description:
15743R_counts.txt
15743X6

data_processing:
The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab-delimited matrix where each column denotes a sample and each row corresponds to a gene.

organism: Danio rerio

source_name: Liver

growth_protocol: Fish were raised following IACUC-approved protocols in insititutional zebrafish facility.

extract_protocol:
Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis (HCC or no HCC). The other half of each dissected liver was flash-frozen on dry ice and stored in -80C prior to RNA extraction. RNA was isolated using TriReagent (Cat# R2050-1-50, Zymo Research) and Direct-Zol RNA Mini prep kit (Cat# R2050, Zymo Research) including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase-/DNase-free water.
Sample quality control, library preparation, sequencing and alignments were performed by the Huntsman Cancer Institute (HCI) High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired-read, 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell.
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10)

treatment_protocol: Larvae were treated with either 0.1% ethanol or 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.

tag: transgenic line

tag: age

value: 6 months post fertilization

tag: treatment at larval stage

value: No treatment

tag: diagnosis

value: HCC


title: HD 3

description: HY3HHBGX5_FRD18_18s000354-1-1_Keller_lane118s000354


title: A2

city: Qingdao

first: Liu

last: Jun

address: Binhai Road 72

country: China

institute: Shandong University

data_processing:
In this project, Oligo(dT) magnetic beads were used to enrich the mRNA with polyA structure in total RNA, and the RNA was interrupted by ion interrupting to a fragment of about 300 bp in length. The first strand of cDNA was synthesized using a 6-base random primer and reverse transcriptase using RNA as a template, and the second strand cDNA was synthesized using the first strand cDNA as a template. After the library construction was completed, the library fragments were enriched by PCR amplification, and then the library selection was performed according to the fragment size, and the library size was 450 bp. Next, the library was subjected to a quality test by Agilent 2100 Bioanalyzer, and the total library concentration and the effective concentration of the library were examined. Then, according to the effective concentration of the library and the amount of data required for the library, the libraries containing different Index sequences (each sample plus a different index, and finally the index data of each sample are classified according to Index) are mixed in proportion. The mixed library was uniformly diluted to 2 nM and denatured by alkali to form a single-stranded library. After RNA extraction, purification, and library construction, these libraries were subjected to Paired-end (PE) sequencing based on the Illumina HiSeq sequencing platform using Next-Generation Sequencing (NGS).
Genome_build: Starmerella bombicola CGMCC 1576 genomic sequence
Supplementary_files_format_and_content: One matrix table in text format including FPKM values for each genes.

organism: Starmerella bombicola

source_name: Cryptococcus

growth_protocol: All strains were first pre-incubated overnight in YEPD medium containing 2% glucose to OD600 = 1, then transferred to fermentation medium and incubated at 30 ° C, 200 rpm for 72 hours.

extract_protocol: Total RNA was prepared from the cells by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.

treatment_protocol: Cell pellet obtained by centrifugation at 4 °

tag: strain

value: bro1 deletion mutant deltabro1

tag: carbon source

value: glucose and oleic acid


title: CVID P1

description: HY3HHBGX5_FRD14_18s000350-1-1_Keller_lane118s000350


title: HCCHepABC [Single-cell]

data_processing:
10x Genomics’ Cell Ranger software (v2.2.0) executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 (26 bp) and R2 (100 bp)  FASTQ files.
Custom transgenic genomic reference was built with ‘cellranger mkref’, but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene_biotypes matching ‘protein_coding’, ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added.
Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘--expect-cells=3000’
In attempt to recover those (perhaps lower quality) GEM partitions, the raw gene-barcode matrices from ‘cellranger count’ (located in ‘outs/raw_gene_bc_matrices’) was processed with the EmptyDrops algorithm (R package DropletUtils v1.2.2) to discriminate cells from background GEM partitions at a false discovery rate (FDR) of 1% (Lun ATL et al., 2019). GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells, while those with at least 10,000 UMI counts were automatically considered to be cells.
Cell-based QC metrics were calculated with R package scater (v1.10.1) using the calculateQCMetrics function (McCarthy DJ et al., 2017). Principal component analysis (PCA) on the cell-based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect (P. Filzmoser et al., 2008). Cells with extremely low UMI counts, extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally, cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis.
Genome_build: GRCz11
Supplementary_files_format_and_content: MTX

extract_protocol:
Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis (HCC or no HCC). The remaining half of each liver was dissociated into single-cell suspensions and prepared for single-tube single-cell RNA sequencing (scRNA-seq) based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum (FBS) in Hank’s Buffered Saline Solution (HBSS) without phenol red, with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re-suspended in 1 mL of 5%FBS+5mM EDTA in HBSS-Free solution. Cells were then filtered through a 40 micron membrane filter, and the filtrate was centrifuged at 1200 RPM, 4C for 5 minutes. The cell pellet was then re-suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single-cell suspension.
Viability and cell count were assessed on Countess I (Thermo Scientific).  The Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 2 (PN-120237) was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier (UMI) according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6,000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip (PN-120236) to form Gel-Bead-In EMulsions (GEMs), the micro-droplets.  Within individual GEMs, cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min.  Subsequent A tailing, end repair, adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode.
Single-cell 3' RNA-Sequencing

treatment_protocol: Larvae for Samples 2 and 3 were treated with 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.


title: A1


title: srLp A 3

description:
Lexogen-3
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: A


title: 317C8

description:
15743R_counts.txt
15743X5

value: Wild Type

value: no HCC


title: CVID P3

description: HY3HHBGX5_FRD13_18s000349-1-1_Keller_lane118s000349


title: srLp A 2

description:
Lexogen-2
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: W3

value: Reference strain wild


title: 317C5

description:
15743R_counts.txt
15743X4


title: srLp B 2

description:
Lexogen-5
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: 317C4

description:
15743R_counts.txt
15743X3


title: HD 2

description: HY3HHBGX5_FRD17_18s000353-1-1_Keller_lane118s000353


title: srLp B 3

description:
Lexogen-6
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: W1


title: 317C2

description:
15743R_counts.txt
15743X2


title: W2


title: CATS E 1

description:
Diagenode-13
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: CATS

value: E


title: M.pardalis x M.guttatus-8DAP-Rep3

city: Raleigh, NC

first: Robert

last: Franks

state: NC

address: Campus Box 7614

department: Plant & Microbial Biology Department

institute: NC State University

data_processing:
RNA reads were mapped to parental pseudogenomes generated by the package Modtools from Illumina sequence data of parental inbred lines.
Raw RNA reads were trimmed with Trimmomatic and mapped them to each parental pseudo-reference using the aligner STAR
We used the lapels/suspenders pipeline to filter reads by mapping position and quality.
Only properly paired, uniquely mapped reads were retained for analyses involving edgeR and DESeq2.

organism: Erythranthe pardalis x Erythranthe guttata

source_name: Flower organs

growth_protocol: Seeds of inbred lines of Mimulus guttatus (CSS4) and the selfing species Mimulus pardalis (SEC39) were cold-stratified for 10 d at 4°C before germinants were transferred to a growth chamber at 18-hour days, 21°C, 30% relative humidity. Total RNA was extracted from ovules and developing hybrid seeds from that had been removed from longitudinal-sectioned fruits. We sequenced a total of 20 samples, including 5 replicates of un-pollinated M. pardalis ovules and 3-5 replicates of M. pardalis x M. guttatus hybrid seeds collected at 2, 4, 6, and 8 DAP. Each replicate contained ~10-20 ovaries or fruits pooled from different plants.

extract_protocol:
RNA was isolated using the Pure Link RNA Mini Kit (Invitrogen) with Trizol according to manufacturer’s instructions. Libraries were constructed with the NEB Ultra Directional Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.The average size of the cDNA fragments was approximately 380 bp. The 20 barcoded libraries were pooled, and 150bp paired-end sequencing was performed in a NextSeq 500 device.

value: SEC39 x CSS4

tag: tissue

value: Seeds

value: 8 DAP


title: CATS D 3

description:
Diagenode-12
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: D


title: M.pardalis x M.guttatus-8DAP-Rep4


title: S. aureus COL_pH9 BF2

type: RNA

city: Hull

first: Georgios

last: Efthimiou

address: Hardy Building, Cottingham Road

department: Biomedical and Forensic Sciences

country: United Kingdom

institute: University of Hull

description: Gene expression data from S. aureus COL growing at pH9 in biofilm mode

hyb_protocol: The labelled cDNA samples were hybridised on a GeneChip®S. aureus Genome Array (Cat. No. 900514; Affymetrix, USA), following the procedure suggested by the GeneChip® Expression Analysis Technical Manual (Affymetrix; P/N 702232 Rev. 3). Biological duplicates were used (n=2).

scan_protocol: GeneChip Scanner 3000 7G System (Affymetrix)

data_processing: The raw microarray data were first normalised by using the statistical language R (TM4 protocol at: http://www.tm4.org/normalizing.html). Data filtering was performed by using MeV (MultiExperiment Viewer Quickstart Guide v. 4.2). The selected variance filter value was 50. Finally, the filtered data were exported to Excel and the Log2 ratios of the average gene expression values of the two compared conditions were calculated [Log2(Expr1/Expr2)]. A two-tailed paired T-test was also performed in Excel, using the gene expression values of each gene for the two compared conditions. Gene expression differences were considered to be significant only if the p-value was <0.05. Databases KEGG and Aureowiki were used for confirming gene annotation and function.

label: biotin

organism: Staphylococcus aureus subsp. aureus COL

label_protocol: 1.5 μg of synthesised first-strand cDNA were labelled, following the procedure suggested by the GeneChip® Expression Analysis Technical Manual (Affymetrix; P/N 702232 Rev. 3). Biological duplicates were used (n=2).

growth_protocol: Tryptone Soya Broth (TSB) and Tryptone Soya Agar (TSA) were used for growing S. aureus COL (MRSA) in this study. 100 μL of an overnight pre-culture were used to inoculate 10 mL of the same medium in sterile glass shake flasks. The flasks were incubated for 5 h at 37oC (150 rpm). HCl and NaOH solutions (1 M) were used to adjust the pH. Colony forming units per mL of liquid culture were determined by serial dilutions and colony enumeration (at least three biological replicates in each case). Biomass from these cultures was harvested for RNA isolation, immediately dissolved in RNAlater® reagent (Ambion, USA), as advised by the manufacturer, and strored at -80oC for further use.

extract_protocol: Biomass pellets treated with RNAlater® reagent were dissolved in an aqueous solution of lysostaphin (0.2 U/μL) and incubated at 37oC for 30 min. The samples were transferred into new Eppendorf tubes containing 0.2 g of glass beads (0.6 mm diameter), 750 μL of RA1 lysis buffer (Νucleospin® RNA II kit; Cat. No. 740955.50; Macherey-Nagel, Germany) and 1% β-mercaptoethanol (Sigma-Aldrich, UK). The samples were vortexed thrice for 30 sec and total RNA was then isolated as suggested by the Νucleospin® RNA II kit instructions. Two elution steps were performed at the end of the procedure. The quality of the extracted RNA was determined by spectrophotometry and gel electrophoresis in a 1.4% agarose gel with DEPC-treated distilled water. First-strand cDNA synthesis was performed by using the PrimeScript™ 1st strand cDNA Synthesis Kit (Cat. No. 6110A; Takara, Japan).

treatment_protocol: Four 100 μL drops of a 5-hour pre-culture were pipetted on a nitrocellulose membrane (pore size 0.45 μm; Sartorius, UK), which was placed on TSA with different pH (5, 7 and 9) and allowed to grow statically for 24 h at 37oC. Determination of colony forming units per nitrocellulose disc (at least three biological replicates in each case)and biomass harvestation with RNAlater® reagent were performed as described above.

tag: genotype

value: Wild type


title: S. aureus COL_pH7 PL2

description: Gene expression data from S. aureus COL growing at pH7 in planktonic mode


title: 622

description:
16048R_counts.txt
16048X10

value: 11 months post fertilization

value: 0.1percent ethanol


title: S. aureus COL_pH5 BF2

description: Gene expression data from S. aureus COL growing at pH5 in biofilm mode


title: 609

description:
16048R_counts.txt
16048X9

value: 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.


title: M.pardalis x M.guttatus-8DAP-Rep1


title: M.pardalis x M.guttatus-8DAP-Rep2


title: CATS E 3

description:
Diagenode-15
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: Synthetic miRNA


title: S. aureus COL_pH5 PL2

description: Gene expression data from S. aureus COL growing at pH5 in planktonic mode


title: 624

description:
16048R_counts.txt
16048X8

value: HCC


title: CATS D 2

description:
Diagenode-11
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: M.pardalis x M.guttatus-6DAP-Rep4

value: 6 DAP


title: CATS E 2

description:
Diagenode-14
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: S. aureus COL_pH7 PL1

source_name: S. aureus COL growing at pH7 in planktonic mode


title: 621

description:
16048R_counts.txt
16048X7


title: S. aureus COL_pH9 PL1

description: Gene expression data from S. aureus COL growing at pH9 in planktonic mode


title: CATS C 3

description:
Diagenode-9
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: C


title: CATS D 1

description:
Diagenode-10
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: M.pardalis x M.guttatus-6DAP-Rep3


title: 625

description:
16048R_counts.txt
16048X6


title: CATS C 2

description:
Diagenode-8
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: S. aureus COL_pH5 PL1

source_name: S. aureus COL growing at pH5 in planktonic mode


title: 623

description:
16048R_counts.txt
16048X5


title: 628

description:
16048R_counts.txt
16048X4


title: S. aureus COL_pH5 BF1

source_name: S. aureus COL growing at pH5 in biofilm mode


title: M.pardalis x M.guttatus-4DAP-Rep3

value: 4 DAP


title: M.pardalis x M.guttatus-6DAP-Rep1


title: S. aureus COL_pH9 PL2

source_name: S. aureus COL growing at pH9 in planktonic mode


title: 630

description:
16048R_counts.txt
16048X3

value: no HCC


title: CATS B 2

description:
Diagenode-5
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: B


title: 317C1

description:
15743R_counts.txt
15743X1

value: Wild Type

value: 6 months post fertilization

value: No treatment


title: S. aureus COL_pH7 BF2

description: Gene expression data from S. aureus COL growing at pH7 in biofilm mode


title: 605

description:
16048R_counts.txt
16048X2


title: M.pardalis x M.guttatus-4DAP-Rep2

value: SEC39 x CSS4

value: Seeds


title: CATS B 1

description:
Diagenode-4
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: CATS


title: 604

description:
16048R_counts.txt
16048X1


title: M.pardalis x M.guttatus-4DAP-Rep1


title: CATS A 3

description:
Diagenode-3
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: A


title: rB_wt input

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: input

library_source: genomic

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)

molecule: genomic DNA

organism: Mus musculus

source_name: resting B cell

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).

value: WT

value: spleen

tag: chip antibody

value: input

tag: activation time


title: M.pardalis x M.guttatus-6DAP-Rep2


title: CATS C 1

description:
Diagenode-7
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: Synthetic miRNA


title: aB24h_wt input

description: input

source_name: activated B cell


title: M.pardalis x M.guttatus-2DAP-Rep4

value: 2 DAP


title: S6_Washington

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Raw reads were trimmed and filtered by quality characteristics using Trimmomatic.
The reads for each sample were mapped to a concatonated Potamopyrgus antipodarum transcriptome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-5 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
Genome_build: Transcriptome contigs obtained from http://bioweb.biology.uiowa.edu/neiman/download.php were used as the reference genome.
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Potamopyrgus antipodarum

source_name: Foot tissue

growth_protocol: Potamopyrgus antipodarum individuals were sampled from three lakes; Lake Lytle (Lake 1) in Rockaway Beach, OR (45.6272°N, 123.9392°W), Capitol Lake (Lake 2) in Olympia, WA (47.0384°N, 122.9119°W), and Lake Washington (Lake 3) in Seattle, WA (47.6971°N, 122.2711°W).

extract_protocol:
Genomic DNA from snail foot tissue was prepared as follows. Snail tissue was suspended in 100 μl of 1 x Phosphate Buffered Saline (PBS), then 820 μl DNA extraction buffer (50mM Tris pH8, 10mM EDTA pH8, 0.5% SDS) and 80 μl Proteinase K (20 mg/ml) was added and the sample incubated on a rotator at 55 C for 2-3 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A) was added, the sample mixed and incubated on ice for 15 minutes, then spun at 4 C at 13,000 rpm for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated over night with the same volume 100% isopropanol and 2 μl glycoblue at -20 C. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. Genomic DNA from ten individuals was pooled into a single sample. Three pooled samples were processed for each sampling location.   Methylated DNA Immunoprecipitation (MeDIP) from genomic DNA was performed as follows. For the snail samples approximately 6 μg of each genomic DNA pool was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 5min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube The same volume of Washing Buffer (at least 1 mL) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the washed beads were resuspended in the same volume of 1xIP buffer as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the beads were washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed beads were then resuspended in 250μl digestion buffer (50 mM Tris-HCI pH8, 10mM EDTA pH8, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚C. After incubation the tube was put again into the magnetic rack for 3 minutes and the supernatant removed to a new microfuge tube. The beads were discarded. 250μl of buffered Phenol-Chloroform-Isoamylalcohol solution were added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250μl chloroform were added to the supernatant from the previous step, vortexed for 30sec and centrifuged at 14,000rpm for 5min at room temperature.  The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in  -20˚C freezer for 1 hour to overnight.   The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 25μl H2O or TE. DNA concentration was measured in Qubit with ssDNA kit.
For library preparation we used the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. Next generation sequencing (NGS) was performed at the WSU Spokane Genomic Core laboratory using the Illumina® HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 100 million reads per pool.

treatment_protocol: Samples were obtained by searching the substrate and scraping snails off the underside of rocks and woody debris. The samples were maintained on wet paper towels and kept cool until they reached the laboratory at Washington State University, Pullman, WA. In the laboratory the samples are kept in water in an environmental chamber that is held at 14C with a 12:12 day/night cycle for several days until they were processed for phenotypic and molecular analysis.

value: Foot tissue

tag: location

value: Lake Washington


title: CD_2D

city: Herts

first: Deborah

last: Guest

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

institute: Royal Veterinary College

description: 2x100 paired-end sequence reads

data_processing:
RNA sequencing was performed on a NovaSeq6000 (Illumina) both by an external provider (Edinburgh Genomics, Edinburgh, UK).
20.2 – 23.8 million reads  of 100 base pair paired end data were generated per sample.
Resulting FASTQ files generated were then quality control (QC) checked using FASTQC and FASTQ Screen (Babraham Bioinformatics, Cambridge, UK).
QC checked reads were then aligned to the Ensemble version v95 EquCab 3.0 transcriptome using the pseudoaligner Salmon in Quasi-mapping based mode with GC-bias correction (-gcBias).
The tximport package (Soneson et al 2015) was then used to import the quantified gene-level abundance data into R (v.3.5.2) and differential expression analysis conducted using R/Bioconductor DSeq2 (v.1.22.2) as described in Love et al., 2014
Genes with adjusted pvalue of less than 0.01 and log2 fold change of ± 2 were considered as differentially expressed.
Genome_build: Ensemble version v95 EquCab 3.0
Supplementary_files_format_and_content: Comma Seperated Value (CSV) files include raw counts of sequencing reads for each sample in a matrix table

organism: Equus caballus

source_name: Tenocytes

growth_protocol: Adult and Fetal cells were cultured in Dulbecco’s modified eagle medium (DMEM) high glucose, 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen, Renfrewshire, UK) and passaged using 0.25% trypsin-EDTA (Sigma-Aldrich) every 3-4 days. Undifferentiated ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts at 37°C, 5% CO2 in ESC medium (DMEM/F12 containing 15% fetal bovine serum, 2 mM L-glutamine, 1% non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol (all from Invitrogen) and 1000 units/ml leukaemia inhibitory factor (LIF) (Sigma-Aldrich). ESCs were passaged mechanically every 5-7 days in the presence of 2 μM thiazovivin (StemGent, Cambridge, USA). To differentiate the ESCs to tenocytes they were cultured without feeders in ESC media lacking LIF and in the presence of 20 ng/ml TGF-β3 (Peprotech, London, UK) for 14 days.

extract_protocol:
RNA was extracted using Tri-reagent (Sigma), purified using an RNeasy mini Kit (Qiagen, Manchester, UK) and contaminating genomic DNA removed using Ambion DNA-free (Life Technologies, Paisley, UK). RNA concentration was measured using a Nanodrop (ThermoFisher, Loughborough, UK) and a Qubit (ThermoFisher). RNA integrity was confirmed on a Tapestation (Agilent, Milton Keynes, UK) by an external provider (Cambridge Genomics, Cambridge, UK).
mRNA libraries were prepared using a TruSeq stranded mRNA kit (Illumina, Cambridge, UK)

value: Adult tenocyte

tag: passages

value: 2-6 years


title: M.pardalis x M.guttatus-2DAP-Rep3


title: M.pardalis x M.guttatus-2DAP-Rep2


title: CATS A 1

description:
Diagenode-1
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CATS B 3

description:
Diagenode-6
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: B


title: S. aureus COL_pH7 BF1

source_name: S. aureus COL growing at pH7 in biofilm mode

value: Wild type


title: S_2D

description: 2x100 paired-end sequence reads

tag: cell type


title: S. aureus COL_pH9 BF1

description: Gene expression data from S. aureus COL growing at pH9 in biofilm mode


title: S5_Washington


title: M.pardalis x M.guttatus-2DAP-Rep1


title: S4_Washington


title: control 3

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

description: polyA RNA crosslinked to viral HSUR 2 ncRNA

data_processing:
A reference sequence file was created by combining the genomic sequences of Callithrix Jaccus (v3.2.1) and Saimiriine herpesvirus 2 (Genbank ID: X64346.1).  A gene annotation file was created by combining Callithrix Jaccus Ensembl annotations (v91) and gene definitions from X64346.1.  The STAR (v2.5.3a) ‘genomeGenerate’ command was used to create an index file using the reference and annotation files described above and with ‘sjdbOverhang’ set to 124.
Reads were processed using cutadapt (v1.6) to remove the first three base pairs at the start of the read and the ends of reads beginning at polyA stretches 10bp or longer. Reads shorter than 10bp after processing were removed from the analysis.
Trimmed reads were aligned to the reference index using STAR and set to report alignment data in bam format.  The Subread ‘featureCount’ command was used to generate read counts for each gene in the annotation file described above, only counting reads on the same strand as the annotation.
DESeq2 (v1.14.1) was used normalize gene counts across the samples and determine differential expression between the enriched and non-enriched groups, controlling for sample.
Genome_build: CalJac3
Supplementary_files_format_and_content: tab-delimited text file containing EnsemblID, Gene Name, Log2 Fold Change, Adjusted P-value, and DESeq2 normalized counts.
Genome_build: X64346.1

molecule: polyA RNA

organism:
Callithrix jacchus
Saimiriine gammaherpesvirus 2

source_name: Herpesvirus saimiri-transformed T cells

growth_protocol: HVS-infected Marmoset T cells were grown at at density of 500,000-1 million cells/ml in RPMI 1640 medium supplemented with 20% FBS, 100 Units of penicllin, 100 µg/ml streptomycin, 1 mM of sodium pyruvate, 2 mM glutaMAX and 0.001% b-mercaptoethanol.

extract_protocol:
Total RNA was extracted with TRIzol following the manufacturer's protocol (Invitrogen).  Poly A+ RNA was selected with oligo-dT magnetic beads following the manufacturer's protocol (New England Biolabs). Ten percent of each sample was saved as input and stored in TRIzol.  Crosslinked-HSUR 2-mRNA complexes were captured with HSUR 2 antisense oligonucleotide and magnetic streptavidin beads (Dynabeads).  Bound RNA was released from the beads with TRIzol.  HSUR 2 and control pull down samples were purified and used directly to library preparation.
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara)

treatment_protocol: Three independent samples of 200 million HVS-infected marmoset T cells each were crosslinked with psoralen at 365 nm for one hour at 4°C.  Samples were then lysed with 6 M guanidium hydrochloride, 0.8% SDS & proteinase K and incubated at 65°C for one hour.  One milliliter of TRIzol was added to each sample and stored at -80°C.

value: Cj319/cj137  T cell lines

tag: transformation

value: Transformed with HVS strain A11

value: Adult marmoset


title: 321d_2D

description: 2x100 paired-end sequence reads

value: Fetal tenocyte

value: 321 day gestatation


title: control 2


title: S3_Lytle

value: Lytle lake


title: S2_Lytle


title: M.pardalis ovules-0DAP-Rep5

organism: Erythranthe pardalis

value: Ovules

value: 0 DAP


title: 320d_2D

description: 2x100 paired-end sequence reads

value: 320 day gestatation


title: control 1


title: M.pardalis ovules-0DAP-Rep4


title: CATS A 2

description:
Diagenode-2
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

tag: library prep kit

value: CATS

tag: mix type/state

value: A

value: Synthetic miRNA


title: S1_Lytle

value: Foot tissue


title: HSUR 2-3


title: M.pardalis ovules-0DAP-Rep3


title: HSUR 2-2


title: P3_Capital

value: Capitol Lake


title: M.pardalis ovules-0DAP-Rep2


title: ES_HJ_diff

description: 2x100 paired-end sequence reads

value: ESC-derived tenocyte


title: TB_2D

description: 2x100 paired-end sequence reads

value: Adult tenocyte

value: 2-6 years


title: M.pardalis ovules-0DAP-Rep1


title: P2_Capital


title: HSUR 2-1

value: Cj319/cj137  T cell lines


title: ES_IG_diff

description: 2x100 paired-end sequence reads


title: P1_Capital


title: Cerebellum, Rotarod_MEF2AD_cKO1 (RNA-seq)

status: Public on Sep 26 2019

city: st. louis

first: Naveen

last: Reddy

state: MO

address: 660 S Euclid Ave

institute: Washington University In St. Louis

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 v2.3.4.2
Data were filtered using a map quality score of >10
Peaks were called using MACS2 on concatenated datasets. Mfold = (2,50); Bandwidth = 200; q-value 0.05
RNA-seq reads were aligned to mm10 genome assembly using RNA STAR 2.6
Genome_build: mm10
Supplementary_files_format_and_content: Text or excel workbooks containing raw read counts or CPM, histone enrichment, or fold change

source_name: Cerebellum

growth_protocol: Brain tissue was taken from MEF2 conditional knockout and control mice maintained under standard housing conditions.

extract_protocol:
RNA was extracted from the cerebella of P22 mice using Trizol (Invitrogen) according to the manufacturer’s instructions. ChIP lysates clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: MEF2AD Conditional Knockout

tag: Sex

value: Female

value: Cerebellum


title: Cerebellum, Rotarod_MEF2AD_cKO2 (RNA-seq)


title: Cerebellum, Rotarod_MEF2AD_Ctrl3 (RNA-seq)

value: MEF2AD Control


title: Cerebellum, Rotarod_MEF2D_cKO2 (RNA-seq)

value: MEF2D Conditional Knockout


title: Cerebellum, Rotarod_MEF2AD_Ctrl1 (RNA-seq)


title: Cerebellum, Rotarod_MEF2AD_cKO3 (RNA-seq)


title: Cerebellum, Rotarod_MEF2D_cKO4 (RNA-seq)


title: Cerebellum, Rotarod_MEF2AD_Ctrl2 (RNA-seq)


title: Cerebellum, Rotarod_MEF2D_cKO1 (RNA-seq)


title: Cerebellum, Rotarod_MEF2D_cKO3 (RNA-seq)


title: ES_PW_diff

description: 2x100 paired-end sequence reads


title: Cerebellum, Rotarod_MEF2AD_cKO4 (RNA-seq)


title: Cerebellum, Rotarod_MEF2D_Ctrl2 (RNA-seq)

value: MEF2D Control


title: Cerebellum, Rotarod_MEF2D_Ctrl3 (RNA-seq)


title: Cerebellum, Rotarod_MEF2D_Ctrl1 (RNA-seq)


title: Cerebellum, Rotarod_MEF2AD_Ctrl4 (RNA-seq)


title: Cerebellum, Rotarod_MEF2D_Ctrl4 (RNA-seq)


title: Cerebellum, Rotarod_MEF2A_cKO4 (RNA-seq)

value: MEF2A Conditional Knockout


title: Cerebellum, Rotarod_MEF2A_cKO3 (RNA-seq)


title: Cerebellum, Rotarod_MEF2A_cKO1 (RNA-seq)


title: Cerebellum, Rotarod_MEF2A_Ctrl4 (RNA-seq)

value: MEF2A Control


title: Cerebellum, Rotarod_MEF2A_Ctrl3 (RNA-seq)


title: Cerebellum, Rotarod_MEF2A_Ctrl1 (RNA-seq)


title: Cerebellum, Rotarod_MEF2A_cKO2 (RNA-seq)


title: Cerebellum, Rotarod_MEF2A_Ctrl2 (RNA-seq)


title: RGS4KO_Brain_CFA_Sample15

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using TopHat (Trapnell, C. et al.)
Counts of reads mapping to genes were obtained using HTSseq-counts (Anders, S. et al.) software against Ensembl v75 (mm10) annotation
Differential expression was done using the DESeq2 (Love, M. I. et al.) package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Brain

extract_protocol:
Four biological replicates per group were used for the RNA-Seq studies. Bilateral thalamus punches from two male mice were pooled per biological replicate (four 12 gauge punches persample). Total RNA was isolated with TRIzol, and the integrity was confirmed with an Agilent 2100 Bioanalyzer
mRNA-Seq libraries were prepared using a TruSeq RNA sample preparation kit version 2 (Illumina).

value: Brain

value: RGS4 KO

tag: treatment

value: CFA

tag: region

value: ventral posterolateral thalamic nuclei


title: RGS4KO_Brain_CFA_Sample16


title: WT_Brain_CFA_Sample12

value: WT


title: RGS4KO_Brain_CFA_Sample13


title: RGS4KO_Brain_Naive_Sample5

value: Naive


title: RGS4KO_Brain_Naive_Sample8


title: WT_Brain_CFA_Sample9


title: WT_Brain_Naive_Sample4


title: WT_Brain_CFA_Sample11


title: RGS4KO_Brain_Naive_Sample6


title: RGS4KO_Brain_CFA_Sample14


title: WT_Brain_Naive_Sample3


title: WT_Brain_Naive_Sample2


title: WT_Brain_Naive_Sample1


title: Stag2KO_SC2_LinNeg

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

growth_protocol: Whole BM was negatively selected for lineage markers using antibodies conjugated to magnetic beads and separated using EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).

extract_protocol:
RNA was isolated by TRIzol extraction
RNA-sequencing libraries were generated by 3' sequencing and SMART-Seq2 amplification for GMP and CFU-E populations and by SMARTer amplification of full transcripts for LSK cells.

value: lineage depleted bone marrow (LinNegBM)

tag: genotype/variation


title: Stag2KO_RM4_LinNeg


title: Stag2WT_RI1_LinNeg


title: Stag2WT_SP3_LinNeg


title: RNA_LSK_Stag2WT_rep4

extract_protocol:
RNA was isolated by TRIzol extraction from sorted cell populations.
RNA-sequencing libraries were generated by 3' sequencing and SMART-Seq2 amplification for GMP and CFU-E populations and by SMARTer amplification of full transcripts for LSK cells.

value: sorted LSK


title: RNA_LSK_Stag2WT_rep3


title: Stag2WT_SH1_LinNeg


title: RNA_LSK_Stag2WT_rep1


title: RNA_LSK_Stag2KO_rep3


title: RGS4KO_Brain_Naive_Sample7


title: RNA_LSK_Stag2WT_rep2


title: WT_Brain_CFA_Sample10


title: RNA_LSK_Stag2KO_rep2


title: RNA_LSK_Stag2KO_rep1


title: srLp A 1

description:
Lexogen-1
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: srLp

value: A

tag: replicate

tag: molecule subtype

value: Synthetic miRNA


title: ChIP_Stag2KO_Smc3_IGO_09396_2

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to bigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA) for CTCF, Stag1, and Stag2 and Swift Accel-NGS 2S Plus (Swift) for Smc1a and Smc3.

treatment_protocol: The cells were sorted from murine bone marrow and spleen in Stag2 wild type and knockout mice

value: hematopoietic stem and progenitor cells (HSPCs)

value: Stag2 KO

value: Smc3 (Bethyl, A300-060A)


title: ChIP_Stag2KO_Smc3_IGO_09396_1


title: ChIP_Stag2WT_Smc1a_IGO_09396_6

value: Stag2 WT

value: Smc1a (Active Motif, 61067)


title: ChIP_Stag2WT_Input_4055_IGO_09396_9


title: ChIP_Stag2WT_Smc3_IGO_09396_3


title: Stag2KO_RM2_LinNeg


title: ChIP_Stag2KO_Smc1a_IGO_09396_8


title: ChIP_Stag2KO_Smc1a_IGO_09396_7


title: ChIP_Stag2KO_Input_4056_IGO_09396_10

description: ChIP_Stag2KO_Input_4056_IGO_09396_10_S10


title: ChIP_LinNegSpleen_Stag2WT_Stag1_11839

description: ChIP_LinNegSpleen_Stag2WT_Stag1_11839_TS12_A12_CTTGTA_BH5HNHBCXY_L001_001

value: Stag1 (Bethyl, A302-579A)


title: ChIP_LinNegSpleen_Stag2KO_Stag2_11843

description: ChIP_LinNegSpleen_Stag2KO_Stag2_11843_TS18_A12_GTCCGC_BH5HNHBCXY_L001_001

value: Stag2 (Bethyl, A302-580A)


title: ChIP_LinNegSpleen_Stag2KO_Input_11843

description: ChIP_LinNegSpleen_Stag2KO_Input_11843_TS21_A12_GTTTCG_BH5HNHBCXY_L002_001


title: ChIP_LinNegSpleen_Stag2WT_Input_11839

description: ChIP_LinNegSpleen_Stag2WT_Input_11839_TS19_A12_GTGAAA_BH5HNHBCXY_L002_001


title: ChIP_LinNegSpleen_Stag2KO_Stag1_11843

description: ChIP_LinNegSpleen_Stag2KO_Stag1_11843_TS14_A12_AGTTCC_BH5HNHBCXY_L001_001


title: ChIP_LinNegBM_Stag2WT_CTCF_rep1_YS5

description: ChIP_LinNegBM_Stag2WT_CTCF_rep1_YS5_09330_2_S49

value: CTCF (Cell Signaling, 3418S)


title: ChIP_LinNegSpleen_Stag2WT_Stag2_11839

description: ChIP_LinNegSpleen_Stag2WT_Stag2_11839_TS15_A12_ATGTCA_BH5HNHBCXY_L001_001


title: ChIP_LinNegBM_Stag2WT_Input_YS7

description: ChIP_LinNegBM_Stag2WT_Input_YS7_09330_6_S53


title: ChIP_LinNegBM_Stag2KO_Input_YS6

description: ChIP_LinNegBM_Stag2KO_Input_YS6_09330_5_S52


title: ChIP_LinNegBM_Stag2WT_CTCF_rep2_YS7

description: ChIP_LinNegBM_Stag2WT_CTCF_rep2_YS7_09330_4_S51


title: ChIP_LinNegBM_Stag2KO_CTCF_rep2_YS6

description: ChIP_LinNegBM_Stag2KO_CTCF_rep2_YS6_09330_3_S50


title: 317E6

description:
15743R_counts.txt
15743X7

tag: transgenic line

tag: age

value: 6 months post fertilization

tag: treatment at larval stage

value: No treatment

tag: diagnosis

value: HCC


title: ATAC_LinNegBM_Stag2WT_rep2

description: ATAC_LinNegBM_Stag2WT_rep2_VS5_AT_A12_TAGGCATG_IGO_08482_5_S58

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

extract_protocol:
Cells (1e4) were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo).
Samples were eluted in 20uL of elution buffer and PCR-amplified using the NEBNext 2X Master Mix (NEB) for 10 cycles and sequenced on a HiSeq 2500 (Illumina).


title: ChIP_LinNegBM_Stag2KO_CTCF_rep1_YS4

description: ChIP_LinNegBM_Stag2KO_CTCF_rep1_YS4_09330_1_S48

tag: genotype

tag: chip antibody


title: ATAC_LinNegBM_Stag2WT_rep1

description: ATAC_LinNegBM_Stag2WT_rep1_VW2_AT_A12_GGACTCCT_IGO_08482_4_S57


title: ChIP_Stag2WT_Smc1a_IGO_09396_5


title: ChIP_Stag2WT_Smc3_IGO_09396_4


title: ATAC_LSK_Stag2WT_rep1

description: ATAC_LSK_Stag2WT_rep1_ZA1_AT_A11_CGAGGCTG_IGO_09381_1_S72

extract_protocol:
Cells (1e4) were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo).
Samples were eluted in 20uL of elution buffer and PCR-amplified using the NEBNext 2X Master Mix (NEB) for 10 cycles and sequenced on a NextSeq 500 for GMP and CFU-E populations and on the HiSeq 2500 for the LSK cells (Illumina).


title: ATAC_LSK_Stag2WT_rep3

description: ATAC_LSK_Stag2WT_rep3_ZR3_AT_A11_GTCGTGAT_IGO_09381_4_S75


title: ATAC_LSK_Stag2KO_rep1

description: ATAC_LSK_Stag2KO_rep1_ZR1_AT_A11_AAGAGGCA_IGO_09381_2_S73


title: ATAC_LSK_Stag2WT_rep2

description: ATAC_LSK_Stag2WT_rep2_ZA2_AT_A11_ACCACTGT_IGO_09381_5_S76


title: ATAC_LinNegBM_Stag2KO_rep1

description: ATAC_LinNegBM_Stag2KO_rep1_VN1_AT_A12_CGTACTAG_IGO_08482_1_S54


title: ATAC_LSK_Stag2KO_rep3

description: ATAC_LSK_Stag2KO_rep3_ZA3_AT_A11_TGGATCTG_IGO_09381_6_S77


title: ATAC_LSK_Stag2KO_rep2

description: ATAC_LSK_Stag2KO_rep2_ZR2_AT_A11_GTAGAGGA_IGO_09381_3_S74


title: Th0+Dopa_3

city: Boston

first: Xingbin

last: Ai

state: MA

address: 75 Francis St

department: Medicine

institute: Brigham and Women's Hospital

description:
Sample was split into 2 lanes and tested paired-end
Th0Dopa-3_CGCTCATT-TAATCTTA
processed data file: genes_list_2.fpkm_table.txt

data_processing:
Base calling:  RTA-1.18.64.0
FASTQ generation:  bcl2fastq-1.8.4
Read trimming:  trimmomatic-0.35
Read QC:  fastQC-0.10.1
Alignment:  STAR-2.4.2
Mapping statistics:  bamtools-2.3.0
Differential expression:  cufflinks-2.2.1
Genome_build: Mus musculus UCSC version mm10
Supplementary_files_format_and_content: FPKM_Table File

source_name: splenic naïve CD4+ T cells_Th0+Dopa

extract_protocol:
Naïve mouse CD4+ T cells in Th0 culture with and without dopamine treatment were harvested on day 4. Total RNA was purified with a RNeasy kit (Qiagen) followed with DNase I treatment.
The TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina) was used for library construction. This kit captures coding RNA and multiple forms of non-coding RNA, while depleting cytoplasmic rRNA, mitochondrial rRNA, and globin mRNA.

tag: strain

tag: tissue

value: Spleen

value: CD4+ T cells

tag: culture condition

value: under Th0 condition with dopamine treatment


title: Th0_3

description:
Sample was split into 2 lanes and tested paired-end
Th0-3_CGCTCATT-CCTATCCT
processed data file: genes_list_2.fpkm_table.txt

source_name: splenic naïve CD4+ T cells_Th0

tag: cell type

value: under Th0 condition


title: Th0+Dopa_2

description:
Sample was split into 2 lanes and tested paired-end
Th0Dopa-2_CGCTCATT-AGGCGAAG
processed data file: genes_list_1.fpkm_table.txt


title: Th0_2

description:
Sample was split into 2 lanes and tested paired-end
Th0-2_CGCTCATT-ATAGAGGC
processed data file: genes_list_1.fpkm_table.txt


title: 319d_2D

description: 2x100 paired-end sequence reads

value: Fetal tenocyte

tag: passages

value: 319 day gestatation


title: ChIPseq_H3K27ac_HDAC3ΔIEC_ZT20

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

data_processing:
Sequence data were mapped against the mm10 genome using BowTie2 and signals were normalized by the total numbers of aligned reads and visualized by the UCSC Genome Browser. Peaks were detected by MACS with a cutoff of peak length >100 and –log10 (P values) > 50. Peaks of the same mark were merged across CV and/or GF samples from all time points. Spatial analysis between different peaks and genomic features were performed using “countOverlaps” function in R. Circadian analysis was performed by first counting read intensities at peaks. Circadian characteristics were further calculated using ARSER. Heat maps were generated by first counting reads across consecutive 50 bp bins across each peak and plotting the values using “heatmap.2” function in R.
genome build: mm10
supplementary files format and content: Comma-delimited file with peaks and p values

source_name: ileum epithelial cells

extract_protocol:
Mouse ileum was washed with ice-cold PBS and IECs were extracted in 10 mM EDTA. Cells were washed with ice-cold PBS twice and fixed in 1% formaldehyde at room temperature for 10 min. Cells were then quenched in 125 mM glycine for 10 min, washed twice with PBS, resuspended in 0.5 ml lysis buffer (20 mM Tris-HCl, pH 8, 60 mM KCl, 1 mM EDTA, 0.5% NP-40 with protease inhibitors), and incubated at 4oC for 15 min. Nuclei were pelleted and resuspended in 250 μl RIPA buffer (Thermo Scientific 89900) with protease inhibitors and sonicated with a Bioruptor Pico sonication device (Diagenode) for 20 cycles (30 sec on, 30 sec off). The supernatant was pre-cleared with 10 μl protein G magnetic beads for 1 h and then incubated with 3 μg of primary antibodies overnight at 4oC. The antibodies used were: anti-H3K9ac (Abcam ab4441), anti-H3K27ac (Abcam ab4729), anti-HDAC3 (Abcam ab7030), anti-PGC-1α (Millipore, ST1204), anti-ERRα (Millipore 17-603). 50 μl protein G beads were added and incubated for 1.5 h at 4oC. Beads were washed four times with LiCl wash buffer (100 mM Tris-HCl pH 7.5, 500 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and finally with TE buffer. DNA was eluted in 150 μl TES buffer (TE with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) by resuspending the beads at 65oC for 8 h. DNA was purified using ChIP DNA Clean & Concentrator (Zymo Research D5205).
ChIP-seq libraries were generated using a KAPA Hyper Prep Kit (kapabiosystems KK8502) and library sizes and concentrations were evaluated by Bioanalyzer and RT-qPCR.

value: C57BL/6 Hdac3 {delta}IEC

tag: diet

value: Chow diet

value: H3K27ac, Abcam ab4729


title: ChIPseq_H3K27ac_HDAC3fl/fl_ZT20

value: C57BL/6 Hdac3 fl/fl


title: ChIPseq_H3K27ac_HDAC3ΔIEC_ZT8


title: ChIPseq_H3K27ac_CV_ZT16


title: ChIPseq_H3K27ac_HDAC3fl/fl_ZT8


title: ChIPseq_H3K27ac_CV_ZT8


title: ChIPseq_H3K27ac_CV_ZT12


title: ATAC_LinNegBM_Stag2KO_rep3

description: ATAC_LinNegBM_Stag2KO_rep3_VW1_AT_A12_TCCTGAGC_IGO_08482_3_S56

value: lineage depleted bone marrow (LinNegBM)


title: ChIPseq_H3K27ac_CV_ZT0


title: ChIPseq_H3K27ac_GF_ZT14


title: ChIPseq_H3K27ac_CV_ZT4


title: ChIPseq_H3K27ac_GF_ZT20


title: ChIPseq_H3K27ac_GF_ZT2


title: ChIPseq_H3K27ac_GF_ZT8


title: ChIPseq_H3K9ac_nr1d1_ZT20

value: C57BL/6 Nr1d1 knockout

value: H3K9ac, Abcam ab4441


title: ChIPseq_H3K9ac_nr1d1_ZT8


title: ATAC_LinNegBM_Stag2KO_rep2

description: ATAC_LinNegBM_Stag2KO_rep2_VN2_AT_A12_AGGCAGAA_IGO_08482_2_S55


title: ChIPseq_H3K9ac_myd88_ZT8

value: C57BL/6 Myd88 knockout


title: ChIPseq_H3K9ac_HDAC3fl/fl_ZT8


title: ChIPseq_H3K9ac_HDAC3ΔIEC_ZT8


title: ChIPseq_H3K9ac_HDAC3fl/fl_ZT20


title: ChIPseq_H3K9ac_myd88_ZT20


title: ChIPseq_H3K27ac_CV_ZT20


title: ChIPseq_H3K9ac_CV_ZT16


title: ChIPseq_H3K9ac_HDAC3ΔIEC_ZT20


title: ChIPseq_H3K9ac_CV_ZT20


title: ChIPseq_H3K9ac_CV_ZT12


title: ChIPseq_H3K9ac_CV_ZT4


title: ChIPseq_H3K9ac_CV_ZT0


title: ChIPseq_H3K9ac_GF_ZT2


title: ChIPseq_H3K9ac_GF_ZT20


title: MRL_Surg_02

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

data_processing:
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10) with the STAR software package
Differential expression based on counts per million mapped reads was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: edgeR

source_name: Supraspinatus muscle

extract_protocol:
Muscles were finely minced and RNA was isolated using an miRNeasy kit (Qiagen, Valencia, CA, USA), supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop (ThermoFisher Scientific, Waltham, MA, USA), and quality was assessed using an Agilent Bioanalyzer System (Agilent, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MRL/MpJ

tag: surgical  group

value: Supraspinatus tenectomy and denervation


title: ChIPseq_H3K9ac_GF_ZT8


title: MRL_Surg_03


title: MRL_Surg_01


title: RNAseq_GF_ZT20

data_processing:
Reads were mapped against mm10 using tophat with default parameters and FPKMs were caluclated using cuffdiff with default parameters
genome build: mm10
supplementary files format and content: Comma-delimited file with fpkm for each sample

extract_protocol:
RNA was extracted from intestinal epithelial cells isolated by laser capture microdissection. Extracted RNA was purified using PicoPure RNA Isolation Kit (Life Technology 12204-01).
Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina)


title: RNAseq_GF_ZT2


title: RNAseq_GF_ZT8


title: ChIPseq_H3K9ac_GF_ZT14


title: MRL_NoSurg_03

value: Unoperated control


title: MRL_NoSurg_01


title: MRL_NoSurg_02


title: MRL_Surg_04


title: BL6_Surg_04


title: RNAseq_GF_ZT14


title: MRL_NoSurg_04


title: ChIPseq_H3K9ac_CV_ZT8


title: BL6_Surg_03


title: BL6_Surg_01


title: BL6_Surg_02


title: BL6_NoSurg_03


title: BL6_NoSurg_04


title: BL6_NoSurg_01


title: BL6_NoSurg_02


title: mESC_0hr_5hmC

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

description: Peak calling not performed for this sample.

data_processing:
Library strategy: 5hmC-Enrichment followed by sequencing
Fastq files were aligned to the mm9 genome using Bowtie aligner using default parameters.
BAM and index files was generated using samtools toolkit view and index commands respecitvely.
Peak calling bed files was generated using macs2 call peak command between target and input bam files with a p-value cutoff of 1e-4.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak file obtained from macs2 peak calling

source_name: V6.5 Mouse Embryonic Stem Cells

growth_protocol: MEF derived pre-iPSCs or mESCs were cultured in ESC Media (knockout DMEM, 15% FBS, L-glutamine, Pen/Strep, NEAA, 2-mercaptoethanol, and leuemia inhibitory factor) with or without Ascorbic acid,  CHIR-99021, and PD-032501).

extract_protocol:
Samples were harvested at day 0, 2, and 10 and DNA was harvest by treatment of DNA lysis buffer and proteinase K. DNA was purified by isopropanol perceipitation followed by 70% EtOH washes and resuspended in TE buffer. Samples were sonicated using Covaris S220 to 200-500 bp fragments.
50ug of Sonicated DNA was labeled with UDP-6-N3_Glc at a final concentration of 10uM using T4-BGt for 1 hour at 37C. UDP-labelled DNA was purified and treated with DBCO-S-S-PEG3_biotin at a final concetration of 150mM at 37C for 2 hours.
Biotin labelled DNA was quantified and normalized and 5hmC capture was performed by incubation with 50uL of equilibrated Dynabeads MyOne streptavidin C1 beads for 15 minutes at room temperature.
Captured DNA was eluted using 50mM of DTT for 2 hours and DNA was purified by Micro Bio-Spin5 Columns and Qiagen MinElute PCR purifition kit.
Library was prepared by Nugen Ultra Low Library Systems via manufacture's protocol with 14 cycles of amplification.

treatment_protocol: Reprogramming cultures were treated with 50ug/mL ascorbic acid, CHIR-99021 and PD-0325901 (2i). Media containing chemicals was replaced on every two days and culture was split on day 4 to prevent overcrowding

value: V6.5 Mouse Embryonic Stem Cells

tag: timepoint

tag: treatment


title: Pre-iPSC_Input_5hmC

source_name: MEF derived pre-iPSCs

value: MEF derived pre-iPSCs

value: Day 0


title: mESC_72hr_5hmC


title: mESC_12hr_5hmC


title: KO2-D2_5hmC

value: Day 2


title: KO1-D2_5hmC


title: WT-D2_RepC_5hmC


title: WT-D10_RepC_5hmC

value: Day 10


title: KO1-D10_5hmC


title: KO1-D0_5hmC


title: WT-D10_RepB_5hmC


title: WT-D0_RepB_5hmC


title: WT-D2_RepB_5hmC


title: WT-D10_RepA_5hmC


title: WT-D0_RepC_5hmC


title: mESC_RNA

data_processing:
Reads from fastq file were trmmed (first 10bp), and filtered by quality (quality score > 28) using FASTX toolkit
Quality reads were aligned to the mm9 reference genome constructed to include only annotated sequences (i.E. NM_ Refseqs) by Bowtie2 alignment.
Gene expression of aligned reads was quantified using RSEM.
Genome_build: mm9
Supplementary_files_format_and_content: text file containing genes, transcript ID, length, counts, transcripts per million (TPM), and FPKM.

extract_protocol:
Samples were harvest and RNA was extraced using Qiagen Rneasy Mini kit.
Single-end cDNA library was constructed usign 2ug of RNA via TruSeqRNA Sample preparation kit according to manufacturer's istuction

value: wildtype


title: KO-DMSO_RepB_RNA

value: Kdm3b KO


title: KO-D2_RepB_RNA


title: WT-D0_RepA_5hmC


title: WT-D2_RepA_5hmC


title: KO2-D10_5hmC


title: WT-D10_RepB_RNA


title: WT-DMSO_RepB_RNA


title: KO-D10_RepA_RNA


title: WT-D10_RepA_RNA


title: WT-DMSO_RepA_RNA


title: KO2-D0_5hmC


title: WT-D2_RepA_RNA


title: 2D_3

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
2D_p_fdr.txt
CT21

data_processing:
Sequence read quality was assessed using fastqc
5’ and 3’ adapters flanking the sgRNA sequences were trimmed off using cutadapt v1.11. Error tolerance for adapter identification was set to 0.25, and minimal required read length after trimming was set to 10 bp
Trimmed reads were aligned to the GeCKO mouse library using Bowtie2 in the local mode with a seed length of 11, an allowed seed mismatch of 1 and the interval function set to 'S,1,0.75'.
Reads with the primary alignment score not exceeding the secondary score by at least 5 points were discarded as ambiguous matches
Read counts were normalized. All of this was done using implementations in the PinAPL-Py webtool, with detailed code available at https://github.com/LewisLabUCSD/PinAPL-Py
Genome_build: mm10
Supplementary_files_format_and_content: sgRNA counts and differential expressed sgRNAs

source_name: Msi2-reporter KPf/fC cell line 3 following selection in standard conditions (2D)

extract_protocol:
Total gDNA was extracted using the Qiagen Blood and Cell Culture DNA Midi Kit
Guide RNA's were amplified from total genomic DNA and barcoded by PCR for Next Generation Sequencing
CRISPR library guide RNA sequencing

value: Mixed C57BL/6, Agouti

value: Pancreatic adenocarcinoma

value: 10-12 week old endstage KPf/fC mice

value: Msi2-reporter het; Ptf1a-Cre het; KrasG12D het; p53f/f


title: 3D_1

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
3DV_p_fdr.txt
A3DV

source_name: Msi2-reporter KPf/fC cell line 1 following growth in stem cell conditions (3D)


title: 2D_1

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
2D_p_fdr.txt
AT21

source_name: Msi2-reporter KPf/fC cell line 1 following selection in standard conditions (2D)


title: T0_2

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
3DV_p_fdr.txt
2D_p_fdr.txt
BTO

source_name: Msi2-reporter KPf/fC cell line 2 following CRISPR library transduction


title: T0_1

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
3DV_p_fdr.txt
2D_p_fdr.txt
AT0

source_name: Msi2-reporter KPf/fC cell line 1 following CRISPR library transduction


title: T0_3

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
3DV_p_fdr.txt
2D_p_fdr.txt
CTO

source_name: Msi2-reporter KPf/fC cell line 3 following CRISPR library transduction


title: 2D_2

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
2D_p_fdr.txt
BT21

source_name: Msi2-reporter KPf/fC cell line 2 following selection in standard conditions (2D)


title: KO-DMSO_RepA_RNA


title: Chicken_Liver_LateEmbryo1

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

country: France

institute: CNRS, Université Claude Bernard Lyon 1

data_processing:
Reads were aligned on the corresponding genomes with HISAT2 version 2.0.5.
We used Ensembl release 94 annotations as a reference and we assembled additional gene models with StringTie 1.3.5.
We estimated gene expression levels with Kallisto 0.45.0 (TPM and estimated read counts).
We normalized per.gene TPM levels among samples with a median scaling approach, using the 100 least-varying genes as a reference (Brawand et al., Nature, 2011)
We also computed uniquely mapped read counts using the Rsubread library in R (featureCounts) version 1.32.4, in R version 3.5.
Genome_build: mm10, rn6, galGal5
Supplementary_files_format_and_content: tab-separated files containing TPM and read count values for each gene and sample. Genes are in rows, samples in columns.

organism: Gallus gallus

source_name: Liver

extract_protocol:
RNA was extracted using the RNeasy plus kit from Qiagen.
Libraries were constructed using  the Illumina TruSeq Stranded mRNA protocol, with polyA selection.

value: white Leghorn

tag: developmental stage


title: KO-D2_RepA_RNA


title: Chicken_Liver_EarlyEmbryo2


title: Chicken_Liver_LateEmbryo2


title: 3D_3

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
3DV_p_fdr.txt
C3DV

source_name: Msi2-reporter KPf/fC cell line 3 following growth in stem cell conditions (3D)


title: 3D_2

description:
guide RNA amplification from total gDNA
sgRNA_counts.csv
3DV_p_fdr.txt
B3DV

source_name: Msi2-reporter KPf/fC cell line 2 following growth in stem cell conditions (3D)


title: Chicken_Liver_EarlyEmbryo1


title: Chicken_Kidney_EarlyEmbryo2

source_name: Kidney


title: Chicken_Kidney_EarlyEmbryo1


title: Chicken_Brain_LateEmbryo2

source_name: Brain


title: WT-D2_RepB_RNA


title: Chicken_Brain_EarlyEmbryo2


title: KO-D10_RepB_RNA


title: Chicken_Brain_LateEmbryo1


title: Chicken_Kidney_LateEmbryo2


title: 16Sseq_HDAC3dIEC_3

data_processing:
Library strategy: 16SDNA-seq
Sequences were joined, depleted of barcodes then sequences <150bp removed, sequences with ambiguous base calls removed.  Sequences were denoised, OTUs generated and chimeras removed.  Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity).  Final OTUs were taxonomically classified using BLASTn against a curated database derived fromRDPII and NCBI (www.ncbi.nlm.nih.gov,  http://rdp.cme.msu.edu).
genome build: RDPII and NCBI
supplementary files format and content: Tab-delimited file with OTU counts for each sample

source_name: feces

extract_protocol:
Fecal DNA was extracted and purified from freshly collected feces using the FastDNA Spin Kit (MP Biomedicals 116560-200)
Sequencing libraries were prepared using the HotStarTaq Plus Master Mix Kit (Qiagen)

value: C57BL/6 Hdac3 {delta}IEC

value: Chow diet


title: 16Sseq_HDAC3dIEC_1


title: Chicken_Kidney_LateEmbryo1


title: 16Sseq_HDAC3dIEC_2


title: 16Sseq_HDAC3fl/fl_1

value: C57BL/6 Hdac3 fl/fl


title: 16Sseq_HDAC3fl/fl_3


title: 16Sseq_HDAC3ΔIEC_HFD_3

data_processing:
Library strategy: 16SDNA-seq
Taxonomic classification and Operational taxonomic units (OTUs) abundance analysis was done using CLC Bio microbial genomics module (https://www.qiagenbioinformatics.com/plugins/clc-microbial-genomics-module/). Individual sample reads were annotated with Greengene database and taxonomic features were determined. Alpha and beta diversity analysis was done to understand the within and between sample diversity, respectively. Abundance data was used for numeric Principal Component Analysis (PCA) in SVS, Golden Helix Software. Raw fastq files from this study will be submitted to SRA and are also available on request.
genome build: Greengene
supplementary files format and content: Tab-delimited file with OTU counts for each sample

extract_protocol:
Fecal DNA was extracted and purified from freshly collected feces using the FastDNA Spin Kit (MP Biomedicals 116560-200)
The hypervariable region V3 & V4 of bacterial 16S rRNA gene were captured using Illumina Nextera protocol (Part # 15044223 Rev. B). A single amplicon of about 460bp was amplified using 16S Forward Primer 5'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG and 16S Reverse Primer = 5'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC as described in Illumina protocol. PCR product was cleaned using Agencourt AmpureXP beads from Beckman Counter Genomics. Illumina adapter and barcode sequences were ligated to amplicon in order to attach them to MiSeqDx flow cell and for multiplexing. Quality and quantity of each sequencing library was assessed using Bioanlyzer and picogreen measurements, respectively. About 6pM of pooled libraries was loaded onto a MiSeqDX flow cell and sequenced using PE300 (Paired end 300 bp) v3 kit. Raw fastq files were demultiplexed based on unique barcodes and assessed for quality. Samples with more than 50K QC pass sequencing reads were used for downstream 16S OTU analysis.

value: High fat diet


title: 16Sseq_HDAC3ΔIEC_HFD_5


title: 16Sseq_HDAC3ΔIEC_HFD_2


title: 16Sseq_HDAC3ΔIEC_HFD_4


title: 16Sseq_HDAC3fl/fl_2


title: 16Sseq_HDAC3ΔIEC_HFD_1


title: GFP neg cells from P14 uterus, biological rep1

city: Singapore

first: Ryo

last: Seishima

address: 8A Biomedical Grove

country: Singapore

institute: A*STAR Institute of Medical Biology

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix G3000 GeneArray Scanner.

data_processing: The data was preprocessd by RMA alogrithm implemented in an R package, oligo, and then corrected for batch effects by limma using default parameters

source_name: mouse P14 uterus

label_protocol: Biotinylated cDNA were prepared according to the protocol of Nugen Encore Biotin module (Nugen Technologies) from 5ug total RNA .

growth_protocol: Uterine horns were harvested from Lgr5-2A-EGFP mice and minced by using scalpel blades. Tissues were then incubated in chelation buffer with 5mM EDTA, 2mg/ml collagenese I and 1mM DTT at 37C for 1h followed by resuspention in mixture of TrypLE and 0.8U/ul DNaseI at 37C for 10min. The suspension was then filtered through 40um strainer, stained with Epcam antibody. Cells were then sorted by BD Influx Cell Sorter (BD Biosciences) after adding 1 μg/ml propidium iodine.

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

value: uterus

tag: facs-sorted cells

value: GFP neg cells


title: 16Sseq_HDAC3fl/fl_HFD_1


title: 16Sseq_HDAC3ΔIEC_Chow_5


title: 16Sseq_HDAC3fl/fl_HFD_4


title: Chicken_Brain_EarlyEmbryo1


title: GFP neg cells from P14 uterus, biological rep2


title: GFP high cells from P14 uterus, biological rep3

value: GFP high cells


title: GFP high cells from P14 uterus, biological rep2


title: GFP high cells from P14 uterus, biological rep1


title: 16Sseq_HDAC3fl/fl_HFD_5


title: 16Sseq_HDAC3fl/fl_HFD_2


title: 16Sseq_HDAC3fl/fl_HFD_3


title: GFP neg cells from P14 uterus, biological rep3


title: 16Sseq_HDAC3ΔIEC_Chow_4


title: Meh-TCDD-PTX+Veh

city: Columbia

first: Philip

middle: Brandon

last: Busbee

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

hyb_protocol: Labeled samples were hybridized to miRNA 3.0 chips overnight (16h, 48°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0002 protocol.

scan_protocol: Chips were scanned on a Affymetrix GCS 3000 system scanner.

data_processing: Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was RMA-DABG. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. MicroRNAs were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05

label: Biotin

source_name: Spleen CD4+

label_protocol: 500ng total RNA was used as starting material for labeling according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manufacturer protocol.

growth_protocol: Mice were first injected intraperitoneally (ip) with vehicle (corn oil, CO), or TCDD (25 µg/kg body weight) then injected i.p. with 400 ng/mouse PTX . Twenty-four hours later (Day 1), the mice were rechallenged with the same dose of PTX by i.p. injection. On Day 4, mice were euthanized and CD4+ selected cells were isolated from spleens for miRNA analysis.

extract_protocol: Total RNA was isolated with Qiagen miRNeasy micro kit.

treatment_protocol: Splenocytes were excised from experimental groups followed by CD4+ immunomagnetic selection prior to total RNA isolation.

tag: gender

value: Female

value: 6-8 weeks

value: Spleen CD4+


title: Meh-TCDD-PTX+TCDD

tag: age


title: 16Sseq_HDAC3ΔIEC_Chow_3


title: 16Sseq_HDAC3fl/fl_Chow_5


title: 16Sseq_HDAC3fl/fl_Chow_4


title: 16Sseq_HDAC3ΔIEC_Chow_1


title: 16Sseq_HDAC3fl/fl_Chow_3


title: 16Sseq_HDAC3fl/fl_Chow_1


title: Mock-KYSE150 clone 4

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

data_processing:
SequSequenced reads were mapped to hg19 whole genome using Torrent Suite Software version 4.0.2.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Strand NGS v2.8 Software.
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.25.0; tab-delimited text files include RPKM values for each gene;

source_name: Esophageal squamous cell carcinoma

extract_protocol:
Total RNA was prepared from stable transfectants by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I. Ribosomal RNA (rRNA) was removed from total RNA using Low Input RiboMinus Eukaryote System v2 (Life Technologies).
RNA-seq libraries were prepared for sequencing using Ion Total RNA-Seq Kit v2 and multiplexed by using Ion Xpress™ RNA-seq Barcoding 01-16 Kit according to the manufacturer’s instructions.

value: Esophagus

value: Esophageal squamous cell carcinoma

tag: cell line

tag: transfection

value: KYSE150 clone stably transfected with pIRES2-EGFP vector


title: Mock-KYSE150 clone 5


title: Mock-KYSE150 clone 1


title: NCCRP1-KYSE150 clone 6

value: KYSE150 clone stably transfected with human NCCRP1-expression vector


title: 16Sseq_HDAC3ΔIEC_Chow_2

tag: genotype


title: RHCG-KYSE30

data_processing:
SequSequenced reads were mapped to hg19 whole genome using Torrent Suite Software version 4.0.2.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Strand NGS v2.8 Software.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.25.0; tab-delimited text files include RPKM values for each gene;

source_name: Esophageal squamous cell carcinoma_KYSE30_RHCG

value: Stable transfectants with human RHCG-expression vector


title: NCCRP1-KYSE150 clone 1


title: NCCRP1-KYSE150 clone 17


title: P204_O1 (bulk RNAseq)

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
CelSeq2 RNA sequencing reads were mapped to the GRCm38 mouse genome and GRCh38 human genome using the Subread aligner and assigned to genes using scPipe with ENSEMBL v86 annotation. Gene counts were exported as a matrix by scPipe with UMI-aware counting and imported into R.
For 100 cell bulk samples, cells were removed from further analysis if they failed to achieve 5000 total counts. In single cell samples, cells were removed using the detect_outlier function from the scPipe. In 100 cell bulk samples, genes were filtered out if they failed to achieve 5 counts per million in 3 samples and in single cells genes were required to be expressed in at least 5 samples and an average of 2 or more counts in those samples.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: comma-separated files containing gene counts accounting for unique moleculat identifiers

source_name: young blood

extract_protocol:
Single cell suspensions from mouse and human thymus were obtained by mechanically grinding the organs through a 70mm sieve. Single cell suspensions of mouse thymus were  stained with PE-mouse MR1-5-OP-RU tetramers prior to magnetic bead enrichment using anti-PE microbeads as per manufacturer’s instructions (Miltenyi Biotec). Single cell suspensions of human thymus were enriched for TRAV1.2+ cells by staining for TRAV1.2-PE antibody, followed by magnetic bead enrichment using anti-PE microbeads (Miltenyi Biotec). Human blood cell suspensions were obtained through Ficoll gradient separation. After staining with a panel of flow cytometry surface markers, cells were sorted into a chilled 384-well PCR plate (Greiner #785290) containing 1.2μl of primer/lysis mix.
RNA libraries were prepared and described fully in the methods section of the manuscript..

tag: sample index

value: CTCAAGAC

tag: plate number

tag: well position

tag: donor id

value: Thymus donor blood CD161+ MAIT cells

tag: cell number


title: P204_N1 (bulk RNAseq)

source_name: thymus

value: GCGCTTAA

tag: cell type

value: Human thymus stage 3 MAIT cells


title: P204_N7 (bulk RNAseq)

value: CGTAGTGT

value: Human thymus stage 1 MAIT cells


title: P204_N4 (bulk RNAseq)

value: TGACCATG

value: Human thymus stage 2 MAIT cells


title: P204_N14 (bulk RNAseq)

value: AACGTCAC


title: Mock-KYSE30

source_name: Esophageal squamous cell carcinoma_KYSE30_mock

tag: tissue

value: Stable transfectants with pIRES2-EGFP vector


title: P204_N11 (bulk RNAseq)

value: CAGTACCA


title: P203_M3 (bulk RNAseq)

value: TCAAGCAC


title: P203_M8 (bulk RNAseq)

value: GGCCAATT


title: P203_M6 (bulk RNAseq)

value: ATGTCCAG


title: P204_N17 (bulk RNAseq)

value: GTCAGTAC


title: P203_M12 (bulk RNAseq)

value: TGCGGTTA


title: 16Sseq_HDAC3fl/fl_Chow_2

value: C57BL/6 Hdac3 fl/fl

tag: diet

value: Chow diet


title: P202_F4 (bulk RNAseq)

value: GTCGCTAA


title: P203_M10 (bulk RNAseq)

value: GATTGGTC


title: P204_O5 (bulk RNAseq)

value: TCACACGA

value: Thymus donor blood CD161+ MAIT cells


title: P202_F1 (bulk RNAseq)

value: ATTCGCAG

value: Human thymus stage 1 MAIT cells


title: P203_M14 (bulk RNAseq)

value: TAAGCTGC


title: P203_M16 (bulk RNAseq)

value: ATTGCCGA

value: Human thymus stage 2 MAIT cells


title: P130_D2 (bulk RNAseq)

value: CCATCAAG

value: Human thymus stage 3 MAIT cells


title: P130_B2 (bulk RNAseq)

value: AGTCTTGG


title: G12 YB85 S3 P9 (bulk RNAseq)

data_processing:
CelSeq2 RNA sequencing reads were mapped to the GRCm38 mouse genome and GRCh38 human genome using the Subread aligner and assigned to genes using scPipe with ENSEMBL v86 annotation. Gene counts were exported as a matrix by scPipe with UMI-aware counting and imported into R.
Cells were removed from further analysis if they failed to achieve 5000 total counts. Genes were filtered out if they failed to achieve 5 counts per million in 3 samples and in single cells genes were required to be expressed in at least 5 samples and an average of 2 or more counts in those samples.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: comma-separated files containing gene counts accounting for unique moleculat identifiers

extract_protocol:
Single cell suspensions from mouse thymus, mouse spleen and human thymus were obtained by mechanically grinding the organs through a 70mm sieve. Single cell suspensions of mouse thymus were  stained with PE-mouse MR1-5-OP-RU tetramers prior to magnetic bead enrichment using anti-PE microbeads as per manufacturer’s instructions (Miltenyi Biotec). Single cell suspensions of human thymus were enriched for TRAV1.2+ cells by staining for TRAV1.2-PE antibody, followed by magnetic bead enrichment using anti-PE microbeads (Miltenyi Biotec). Human blood cell suspensions were obtained through Ficoll gradient separation. After staining with a panel of flow cytometry surface markers, cells were sorted into a chilled 384-well PCR plate (Greiner #785290) containing 1.2μl of primer/lysis mix.
RNA libraries were prepared and described fully in the methods section of the manuscript..

value: GTGTAGCT

tag: strain

tag: umi position

value: 1 to 6 in R1

tag: index position

value: 7 to 14 in R1


title: I14 YB87 P12 (bulk RNAseq)

value: CTCTCTCT


title: P130_B4 (bulk RNAseq)

value: TCACAGAC


title: I1 Thy87 S3 P10 (bulk RNAseq)

value: ATTGGCGT


title: G1 Thy85 S3 P8 (bulk RNAseq)

value: GGCTAATC


title: G14 YB85 P11 (bulk RNAseq)

value: TGTCGATG


title: E6 Thy84 S2 P7 (bulk RNAseq)

value: GTACTTGG


title: P202_F10 (bulk RNAseq)

value: GTTCCAAG

value: Thymus donor blood CD161+ MAIT cells


title: G7 Thy85 S1 P6 (bulk RNAseq)

value: GAATCGTC

value: Human thymus stage 1 MAIT cells


title: G4 Thy85 S2 P7 (bulk RNAseq)

value: GATTCGCA

value: Human thymus stage 2 MAIT cells


title: p53 mutant R158L knockout, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.12 software was used to estimate raw read counts using Ensemble transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains raw counts for each gene

source_name: NCI-H441 cell line

extract_protocol:
Total mRNA was extracted from cells transfected with control or p53-targeted siRNA using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions
Libraries were prepared using the Lexogen mRNA sample preparation kit

tag: p53 mutation

tag: replicate

tag: experiment


title: I7 Thy87 S1 P8 (bulk RNAseq)

value: ACAGCACT


title: p53 mutant R158L control, replicate 2

tag: cell line

value: siCtrl


title: p53 mutant V157F knockout, replicate 2

source_name: NCI-H2087 cell line


title: p53 mutant V157F knockout, replicate 1


title: I4 Thy87 S2 P9 (bulk RNAseq)

value: TACGGATC


title: p53 mutant R158L knockout, replicate 2


title: p53 mutant R158L control, replicate 1


title: p53 mutant V157F control, replicate 2


title: P202_F7 (bulk RNAseq)

value: ACACAGCT

value: Human thymus stage 3 MAIT cells


title: E8 Thy84 S1 P6 (bulk RNAseq)

value: AGCTTGCA

value: 1 to 6 in R1

value: 7 to 14 in R1


title: p53 mutant V157F control, replicate 1


title: E2 Thy84 S3 P8 (bulk RNAseq)

value: TGCGACTA


title: p53 mutant R158P knockout, replicate 2

source_name: NCI-H2110 cell line


title: C1 CTRL

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
TrimGalore
STAR
RSEM
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression values (TPM and FPKM) generated by RSEM

source_name: iPSC-CM

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol:
Total RNA was isolated using micro RNeasy kit (QIAGEN) in accordance to manufacturer’s instructions, followed by DNAse treatment.
RNA-seq library was constructed from 100 ng of the total RNA using the KAPA stranded RNA-seq kit with RiboErase following manufacturer's instructions

treatment_protocol: iPSC-CMs were treated with trastuzumab (1 μM) or IgG as a control for a period of 7 days.

tag: treatment

value: Control

value: iPSC-CM


title: C2 CTRL


title: C2 TRZ

value: trastuzumab


title: P115_J10 (scRNAseq)

value: AGGCCATT

value: CD138+ Thymus Maits


title: P115_I4 (scRNAseq)


title: C1 TRZ


title: P115_I8 (scRNAseq)

value: ATCTACGG


title: P115_I5 (scRNAseq)

value: AGCAACTC


title: P115_J1 (scRNAseq)

value: CACTGCAA


title: p53 mutant R158P control, replicate 2


title: P115_I24 (scRNAseq)

value: CGTAACTG


title: P115_J11 (scRNAseq)

value: CGACCTAA


title: P115_I3 (scRNAseq)

value: CTAGACCA


title: P115_I23 (scRNAseq)

value: TCGACCAA


title: P115_I20 (scRNAseq)

value: ATGCACCA


title: P115_I6 (scRNAseq)

value: AAGTCGCT


title: P115_I21 (scRNAseq)

value: GTGACACT


title: P115_I18 (scRNAseq)

value: GCAAGCTT


title: C3 CTRL


title: P115_I13 (scRNAseq)

value: AACCGTAC


title: P115_I16 (scRNAseq)

value: CTAAGCCA


title: P115_I17 (scRNAseq)

value: AAGGAGGA


title: P115_I22 (scRNAseq)

value: ATTGCTGG


title: P115_I15 (scRNAseq)

value: AGCCTAAC


title: P115_I14 (scRNAseq)

value: CTCTCTCT

value: CD138+ Thymus Maits


title: C3 TRZ

value: trastuzumab

value: iPSC-CM


title: P115_I12 (scRNAseq)

value: ATGCAGCT


title: P115_I7 (scRNAseq)

value: ACAGCACT


title: P115_I11 (scRNAseq)

value: CAATCCAG


title: P115_I10 (scRNAseq)

value: AAGCTCCA


title: P115_H9 (scRNAseq)

value: AGTCGTAC

value: CD138- CD319- DN Thymus Maits


title: P115_I19 (scRNAseq)

value: CACAGTAC


title: P115_H8 (scRNAseq)

value: GGAACTCT


title: P115_H6 (scRNAseq)

value: GTAACGCT


title: P115_H7 (scRNAseq)

value: CGAACACT


title: P115_H4 (scRNAseq)

value: GTGCATGT


title: P115_H2 (scRNAseq)

value: GTTGCGAT


title: P115_H22 (scRNAseq)

value: CCTTCTTC


title: P115_H21 (scRNAseq)

value: ACGAACTC

value: LEF1+ DN Thymus Maits


title: P115_H20 (scRNAseq)

value: AACGCTGT


title: P115_H12 (scRNAseq)

value: CAGTCCAA


title: P115_H11 (scRNAseq)

value: ATTGGCAC


title: P115_H19 (scRNAseq)

value: GGAGTCTT


title: P115_H18 (scRNAseq)

value: GCGTTGTA


title: P115_G8 (scRNAseq)

value: GTAGGTCT


title: P115_H1 (scRNAseq)

value: TGCACTGA


title: P115_H23 (scRNAseq)

value: CATACGTG

value: CD138- CD319- DN Thymus Maits


title: P115_H10 (scRNAseq)

value: ACGGTTAC


title: P115_G9 (scRNAseq)

value: GATTCGGT


title: P115_G3 (scRNAseq)

value: CGAACTGT


title: P115_H13 (scRNAseq)

value: TCCTTCTC


title: P115_H15 (scRNAseq)

value: ACGACATC


title: P115_G6 (scRNAseq)

value: CCGATAGT


title: P115_G24 (scRNAseq)

value: ACAGCTAC


title: P115_G23 (scRNAseq)

value: GGCTTAAC


title: P115_H17 (scRNAseq)

value: CATGGTTG


title: P115_G4 (scRNAseq)

value: GATTCGCA


title: P115_G7 (scRNAseq)

value: GAATCGTC


title: P115_G22 (scRNAseq)

value: AACCAGTC


title: P115_G21 (scRNAseq)

value: ATAGCGTC


title: P115_G2 (scRNAseq)

value: CACGAGTT


title: P115_G20 (scRNAseq)

value: CGACATAC

value: LEF1+ DN Thymus Maits


title: P115_G19 (scRNAseq)

value: GTACGACT


title: P115_G14 (scRNAseq)

value: TGTCGATG


title: P115_G18 (scRNAseq)

value: CGATTCAG

value: CD138- CD319- DN Thymus Maits


title: P115_G15 (scRNAseq)

value: CCAACTAG


title: P115_G5 (scRNAseq)

value: ACCGTTAG


title: P115_F6 (scRNAseq)

value: GAGAGGAA


title: P115_G13 (scRNAseq)

value: GGTCAATC


title: P115_F5 (scRNAseq)

value: ATAGGCTC


title: P115_F8 (scRNAseq)

value: CGACGTAT


title: P115_G11 (scRNAseq)

value: GTTGTGAC


title: P115_F3 (scRNAseq)

value: AGGAGGAA


title: P115_G12 (scRNAseq)

value: GTGTAGCT


title: P115_G10 (scRNAseq)

value: TGGCATCA


title: P115_G17 (scRNAseq)

value: GCTACAAC


title: P115_F23 (scRNAseq)

value: AGCGTTAC


title: P115_F20 (scRNAseq)

value: CTGCAACA


title: P115_F21 (scRNAseq)

value: GTAGACCT


title: P115_F7 (scRNAseq)

value: ACACAGCT


title: P115_F2 (scRNAseq)

value: TAACCGTG


title: P115_F18 (scRNAseq)

value: TACCACGA

value: CD138- CD319- DN Thymus Maits


title: P115_F19 (scRNAseq)

value: ACACACGT


title: P115_G1 (scRNAseq)

value: GGCTAATC


title: P115_F17 (scRNAseq)

value: GCTGCATA

value: LEF1+ DN Thymus Maits


title: P115_F14 (scRNAseq)

value: TACAGGCT


title: P115_F12 (scRNAseq)

value: TGATGCTG


title: P115_G16 (scRNAseq)

value: AATCCGCA


title: P115_F13 (scRNAseq)

value: TACCGATG


title: P115_E7 (scRNAseq)

value: TAGGTGCT


title: P115_F24 (scRNAseq)

value: GTAGTCCA


title: P115_E9 (scRNAseq)

value: AGTGACTC


title: P115_E6 (scRNAseq)

value: GTACTTGG


title: P115_F10 (scRNAseq)

value: GTTCCAAG


title: P115_F1 (scRNAseq)

value: ATTCGCAG


title: P115_E20 (scRNAseq)

value: TCGTTGGA


title: P115_E18 (scRNAseq)

value: CACAAGTC


title: P115_E12 (scRNAseq)

value: CGACACAT


title: P115_E4 (scRNAseq)

value: GGCATGTT

value: CD138- CD319- DN Thymus Maits


title: P115_E5 (scRNAseq)

value: ACGATGTC


title: P115_E23 (scRNAseq)

value: CGACTACA

value: LEF1+ DN Thymus Maits


title: P115_E16 (scRNAseq)

value: GTACTGTG


title: P115_E17 (scRNAseq)

value: CGATTGTG


title: P115_D9 (scRNAseq)

value: CAGTGCTA

value: CD319+ Thymus Maits


title: P115_E10 (scRNAseq)

value: TACGAGTC


title: P115_E11 (scRNAseq)

value: GTGCGTAT


title: P115_E15 (scRNAseq)

value: ATGGTGCT


title: P115_E13 (scRNAseq)

value: TCGACTAG


title: P115_E24 (scRNAseq)

value: ATCCGTAG


title: P115_D8 (scRNAseq)

value: GACTACCA


title: P115_D5 (scRNAseq)

value: GCTAAGCT


title: P115_E14 (scRNAseq)

value: TCACGGTA


title: P115_F11 (scRNAseq)

value: GCGTGATT


title: P115_D6 (scRNAseq)

value: ATGCCAGT


title: P115_D3 (scRNAseq)

value: ATTGCGTG


title: P115_D7 (scRNAseq)

value: CATCCAGA


title: P115_D4 (scRNAseq)

value: CTACGCAA


title: P115_E19 (scRNAseq)

value: CAACTGAC

value: LEF1+ DN Thymus Maits


title: P115_E2 (scRNAseq)

value: TGCGACTA


title: P115_D24 (scRNAseq)

value: GAAGGAAG

value: CD319+ Thymus Maits


title: P115_D22 (scRNAseq)

value: TGGCGATT


title: P115_D21 (scRNAseq)

value: AGGTTCCA


title: P115_D14 (scRNAseq)

value: GTGCGTTA


title: P115_D20 (scRNAseq)

value: CAGCTTAG


title: P115_D11 (scRNAseq)

value: GGTAACTC


title: P115_D15 (scRNAseq)

value: GGATGCTT


title: P115_D12 (scRNAseq)

value: CACTAGCA


title: P115_D17 (scRNAseq)

value: TAGCTCAG


title: P115_D2 (scRNAseq)

value: CCATCAAG


title: P115_D10 (scRNAseq)

value: CGTGAATC


title: P115_D18 (scRNAseq)

value: TAGCGATC


title: P115_C23 (scRNAseq)

value: TCCTCTTC


title: P115_C5 (scRNAseq)

value: ACGCGTTA


title: P115_C22 (scRNAseq)

value: GACCATCA


title: P115_D1 (scRNAseq)

value: ACAACGTC


title: P115_C21 (scRNAseq)

value: TGACTCAG


title: P115_C8 (scRNAseq)

value: ATCACGAC

value: CD319+ Thymus Maits


title: P115_C24 (scRNAseq)

value: ACTGTGAC


title: P115_C2 (scRNAseq)

value: TGTCGCAA


title: P115_C3 (scRNAseq)

value: GGACTTAC


title: P115_C15 (scRNAseq)

value: CTCACGAA


title: P115_C18 (scRNAseq)

value: GGCACTTA


title: P115_C4 (scRNAseq)

value: CTATCGGA


title: P115_C16 (scRNAseq)

value: AGTCACGT


title: P115_C17 (scRNAseq)

value: CACGGTAT


title: P115_C19 (scRNAseq)

value: TGCACGTA


title: P115_C14 (scRNAseq)

value: GCTAGTGT


title: P115_C13 (scRNAseq)

value: TGCGTAGT


title: P115_C12 (scRNAseq)

value: GCGATATC


title: P115_D16 (scRNAseq)

value: TCAGGTGT


title: P115_C10 (scRNAseq)

value: ACTGTTGG


title: P115_C1 (scRNAseq)

value: AGTGTGCT


title: P115_C6 (scRNAseq)

value: TACGCTGA


title: P115_B8 (scRNAseq)

value: CGTGTCAA

value: CD319+ Thymus Maits


title: P115_B5 (scRNAseq)

value: CCTGTAAG


title: P115_B9 (scRNAseq)

value: GCCTTAAG


title: P115_B3 (scRNAseq)

value: AGCAGCTT


title: P115_B7 (scRNAseq)

value: CTCTCCTT


title: P115_B22 (scRNAseq)

value: CAGTCATG


title: P115_B4 (scRNAseq)

value: TCACAGAC


title: P115_B21 (scRNAseq)

value: TACTGGCA


title: P115_B2 (scRNAseq)

value: AGTCTTGG


title: P115_B20 (scRNAseq)

value: ATGCTGAC


title: P115_B17 (scRNAseq)

value: GTTGCTGA


title: P115_B19 (scRNAseq)

value: ACCGACAT


title: P115_B16 (scRNAseq)

value: GTGGTTGT


title: P115_B18 (scRNAseq)

value: CCTGGATA