title: 3 prime HS1 Inverted HUDEP2 clone G3 H3K27ac-ChIP

extract_protocol:
About 2 million of HUDEP-2 cells upon 5 days of differentiation were harvested and fixed with 1% formaldehyde for 10 minutes at room temperature. Fixation was quenched with 0.125 M glycine. Cells were washed twice with ice-cold PBS, lysed in 0.13 mL of lysis buffer (10 mM Tris pH 8.0, 0.25% SDS, 2 mM EDTA, 1X protease inhibitors) and sonicated in a Covaris microtube with Covaris ultrasonicator (E220, Covaris). Sonicated chromatin was diluted with 0.2 mL of equilibration buffer (10 mM Tris pH 8.0, 233 mM NaCl, 1.66% Triton X-100, 0.166% sodium deoxycholate, 1 mM EDTA, 1X protease inhibitors) and spun down to pellet insoluble materials. Supernatant was mixed with 2 µg of antibody (H3K27ac, D5E4, Cell Signaling) and incubated overnight along with 10 µL of Dynabeads protein A (Thermo Fisher Scientific), which were washed twice with 0.1% BSA/PBS. After overnight rotating, beads were transferred to the tube containing chromatin and incubated for 2 hours. Beads were washed twice with RIPA-LS (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100), twice with RIPA-HS (10 mM Tris pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100), twice with RIPA-LiCl (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with 10 mM Tris pH 8.0. After washing, 48 uL of elution buffer (10 mM Tris pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.4% SDS) with 2 uL of 20 mg/mL of proteinase K (Viagen) were added to the beads and incubated for 1 hour at 55oC followed by overnight incubation at 65oC to decrosslink. Beads were magnetized and supernatant was purified with phenol-chloroform. DNA was precipitated with ice-cold absolute ethanol, washed with 75% ethanol, and eluted with 20 uL of 10 mM of Tris pH 8.0.
Accel-NGS 2S Plus DNA library kit (21096, Swift Bioscience) was used to construct the library followed by 2S combinatorial dual indexing kit (28096, Swift Bioscience).

value: erythroid


title: 42-Tn-CD226-MOINS

status: Public on Oct 30 2020

type: SRA

city: Toulouse

first: ludovic

last: Martinet

address: 2 av Hubert Curien

department: CRCT

country: France

institute: INSERM U1037

description:
Freshly FACS purified
42-Tn-CD226-MOINS

library_source: transcriptomic

data_processing:
Fastq files were aligned to the Ensembl GRCh38 human reference genome using STAR (version 2.3.0, (Dobin et al., 2013))
Gene expression summary was obtained using the Subread featurecount algorithm (version 1.4.6, (Liao et al., 2014)).
Patient gene expression was then normalized using standard procedure from the limma R package(Ritchie et al., 2015), retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.
Supplementary_files_format_and_content: tab-delimited text files include normalized gene xepression values retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.

molecule: total RNA

organism: Homo sapiens

source_name: Tn CD226-

extract_protocol:
RNeasy mini kit (Qiagen)
The RNA-Seq library preparation was performed using TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, Calif) according to the manufacturer’s instructions (High Sample Protocol). The RNA-Seq libraries were checked on the 2200 Tapestation System (Agilent) using the High-Sensitivity DNA 1000 ScreenTape assay. The average fragment size of the final libraries was found to be 230 to 327 bps. Libraries were quantified by qPCR on a LightCycler 480 System (Roche Molecular Diagnostics, Pleasanton, Calif) using KAPA Library Quantification Kit for Illumina platforms (Kapa Biosystems, Boston, Massachusetts). Libraries were then pooled in equal quantities, checked and quantified using same techniques (2200 Tapestation and LightCycler 480).
Paired-end sequencing (2 x 75 bps) of these libraries was performed on a NextSeq 500 Illumina sequencing platform (Illumina) by 5 successive runs using NextSeq 500 High Output kit v2 (Illumina) generating in average 20 million pairs of reads per sample.

tag: gender

value: male

tag: sampling date

tag: tissue

value: peripheral blood

tag: cell type

value: Tn CD226-


title: 25-Temra-CD226-PLUS

description:
Freshly FACS purified
25-Temra-CD226-PLUS

source_name: Temra CD226+

value: female

value: Temra CD226+


title: 61-Temra-CD226-PLUS

description:
Freshly FACS purified
61-Temra-CD226-PLUS


title: 3 prime HS1 inverted HUDEP2 clone A2 H3K27ac-ChIP

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

country: USA

institute: The University of Texas Health Science Center at Houston

library_source: genomic

data_processing:
Reads were aligned to the human genome (hg19) using Bowtie2 (version 2.3.5).
The resulting alignments bam files were indexed, sorted with SAMtools and marked for duplicates with Picard "MarkDuplicates" function.
Reads were then normalized using deeptools bamCoverage with RPGC parameter :bamCoverage --bam SA73051_unique_picard.bam --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2827437033 --extendReads -o dTag_H3K4m3_norm1x.bw
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: Erythroid progenitor

growth_protocol: HUDEP clone 2 (HUDEP-2) cells were cultured as previously described [3]. Cells were expanded in StemSpan serum-free expansion medium supplemented with 1μM dexamethasone (D2915, Sigma), 1μg/mL doxycycline (D9891, Sigma), 50 ng/mL human SCF (300-07, Peprotech), 3 units/mL EPO (Amgen), and 1% penicillin/streptomycin. HUDEP-2 cells were differentiated in a two-phase differentiation protocol consisting of IMDM supplemented with 5% human AB serum (H6914, Sigma), 10μg/mL recombinant human insulin (91077C, Sigma), 330μg/mL holo-transferrin (T4132, Sigma), 3 units/mL EPO (Amgen), 1μg/mL doxycycline (D9891, Sigma), 2 units/mL heparin (H3149, Sigma), and 1% penicillin/streptomycin. 50 ng/mL human SCF (300-07, Peprotech) was included in the phase one of the culture (day 1-3) and withdrawn in the phase two of the culture (day 4 and beyond).

treatment_protocol: Cas9 nuclease (1081058, IDT) were mixed with synthetically modified sgRNAs (synthesized by Synthego) at a 1:3 molar ratio in resuspension buffer T and incubated at 37oC for 10 minutes to form ribonucleoprotein complexes (RNPs). For the CTCF inversion clones, homology-directed repair (HDR) approach was used by adding 2μg of dsDNA homology repair template (synthesized by Gene Universal) to the RNP complexes. dsDNA repair templates were designed to have 90-130 bp of homology arms distal and proximal to the PAM sequence.


title: 14-Tn-CD226-MOINS

description:
Freshly FACS purified
14-Tn-CD226-MOINS


title: 3 prime HS1 inverted HUDEP2 clone A2 2 capture HiC

description: capture HiC

data_processing:
data is aligned by HiC Pro 2.0, .hic file is generated by HiC Pro 2.0 Utility.
Genome_build: hg19
Supplementary_files_format_and_content: .hic

extract_protocol:
Approximately 2 million cells of each HUDEP-2 clone were differentiated for 5 days and fixed in 1% formaldehyde. Hi-C libraries were generated using the Arima-HiC kit, according to the manufacturer’s protocols.
Final amplification cycle numbers for each library were determined by qPCR in the QC2 step of the Arima protocol. Quantification of the libraries was performed with KAPA Library Quantification Kit (Roche, KK4824). For capture HiC 150-500 ng of the previously created Hi-C libraries were diluted to 25 uL and mixed with 2.5 ug Cot-1 DNA and 10 ug salmon sperm DNA and heated to 95°C for 5 minutes, then held at 65°C for at least 5 minutes. 33 uL of prewarmed (to 65°C) hybridization buffer (10X SSPE, 10X Denhardt's buffer, 10mM EDTA, and 0.2% SDS), along with 6 uL of RNA probe mixture (500 ng RNA probes and 20U RNase inhibitor) were added to the DNA mixture and hybridized for 24 hr at 65°C. After the hybridization incubation was complete, 50 uL of Streptavidan T1 beads (Dynabeads, Life Technologies) were washed in Bind-and-Wash buffer (1M NaCl, 10mM Tris-HCl, pH 7.5, and 1mM EDTA), resuspended in 134 uL of the same buffer, and then added to the hybridization mixture. The beads were allowed to bind to the biotinylated, hybridized DNA and RNA mixture for 30 minutes at room temperature before separating and discarding the supernatant. The bead-bound DNA was then washed once with low-stringency wash buffer (1X SSC, 0.1% SDS), for 15 minutes at room temperature, and three times with high-stringency wash (0.1X SSC, 0.1% SDS) for 10 minutes at 65°C, separating the beads on a magnet each time before discarding the supernatant. After the last wash, the beads were resuspended in 21 uL nuclease-free water. 1 uL was diluted 1:1000 and had qPCR performed as for QC2 of the Arima protocol to determine the number of cycles to amplify the enriched libraries. The indexes were already attached during Hi-C library prep, and remain the same.
HiC and Capture HiC


title: 68-Temra-CD226-MOINS

description:
Freshly FACS purified
68-Temra-CD226-MOINS

source_name: Temra CD226-

value: Temra CD226-


title: 3 prime HS1 deleted HUDEP2 clone D3 H3K27ac-ChIP


title: 2-Tn-CD226-MOINS

description:
Freshly FACS purified
2-Tn-CD226-MOINS


title: WT-HUDEP2 cells rep2 H3K27ac-ChIP


title: 67-Temra-CD226-PLUS

description:
Freshly FACS purified
67-Temra-CD226-PLUS


title: 47-Tn-CD226-PLUS

description:
Freshly FACS purified
47-Tn-CD226-PLUS

source_name: Tn CD226+

value: Tn CD226+


title: 3 prime HS1 deleted HUDEP2 clone B6 2 capture HiC

description: capture HiC


title: 62-Temra-CD226-MOINS

description:
Freshly FACS purified
62-Temra-CD226-MOINS


title: WT-HUDEP2 cell 2 capture HiC

description: capture HiC


title: WT-HUDEP2 cells rep1 H3K27ac-ChIP


title: 3 prime HS1 deleted HUDEP2 clone B6 H3K27ac-ChIP


title: 3 prime HS1 inverted HUDEP2 clone A2 HiC

description: HiC


title: 43-Tcm-CD226-PLUS

description:
Freshly FACS purified
43-Tcm-CD226-PLUS

source_name: Tcm CD226+

value: Tcm CD226+


title: 3-Tcm-CD226-PLUS

description:
Freshly FACS purified
3-Tcm-CD226-PLUS


title: 3 prime HS1 deleted HUDEP2 clone B6 HiC

description: HiC


title: WT-HUDEP2 cell HiC

description: HiC


title: 3 prime HS1 Inverted HUDEP2 clone G3 ATAC-seq

description: ATAC-seq

data_processing:
Paired-end reads were trimmed using Trim Galore (version 0.6.1) and aligned to hg19 using Burrows-Wheeler Aligner (bwa-mem, version 0.7.17).
Reads were then normalized using deeptools bamCoverage with RPGC parameter :bamCoverage --bam SA73051_unique_picard.bam --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2827437033 --extendReads -o dTag_H3K4m3_norm1x.bw
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol: Upon 5 days of HUDEP-2 differentiation, 50,000 cells were harvested and permeabilized in 50 uL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The transposition reaction was carried out at 37oC for 30 minutes with agitation in 50uL volume containing 25uL of 2X TD buffer and 2.5uL of Nextera Tn5 transposase. DNA was purified with Qiagen MinElute PCR purification kit. Library amplification was done with KAPA HiFi HotStart ReadyMix PCR kit, and the resulting libraries were purified with Qiagen MinElute PCR Purification Kit.


title: 3 prime HS1 inverted HUDEP2 clone A2 ATAC-seq

description: ATAC-seq


title: 26-Temra-CD226-MOINS

description:
Freshly FACS purified
26-Temra-CD226-MOINS


title: 3 prime HS1 deleted HUDEP2 clone D3 ATAC-seq

description: ATAC-seq


title: 4-Tcm-CD226-MOINS

description:
Freshly FACS purified
4-Tcm-CD226-MOINS

source_name: Tcm CD226-

value: Tcm CD226-


title: 3 prime HS1 deleted HUDEP2 clone B6 ATAC-seq

description: ATAC-seq


title: WT-HUDEP2 cells ATAC-seq

description: ATAC-seq


title: Tem CD226-, 22

data_processing:
Fastq files were aligned to the Ensembl GRCh38 human reference genome using STAR (version 2.3.0, (Dobin et al., 2013))
Gene expression summary was obtained using the Subread featurecount algorithm (version 1.4.6, (Liao et al., 2014)).
Patient gene expression was then normalized using standard procedure from the limma R package(Ritchie et al., 2015), retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene expression values retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.

source_name: peripheral blood

value: CD8+ T cells

tag: cell population

value: Tem CD226-

tag: stimulus

value: Freshly purified

tag: date of sample

tag: Sex

tag: age


title: Tem CD226-  Activated, 66

value: Tem CD226-  Activated

value: anti-CD2/CD3/ CD28 microbeads 24 hrs


title: Tem CD226+, 23

value: Tem CD226+


title: 3 prime HS1 Inverted HUDEP2 clone G3 mRNA-seq

description: mRNA-seq

data_processing:
Paired end reads were trimmed with trim galore and aligned to hg19 genome with STAR (v2.7.0f) using the default parameters with the following modifications:1) sjdbOverhang was set to sequence length - 1 as recommended in the STAR manual, 2) twopassMode was set to Basic, 3) outReadsUnmapped was set to None, 4) outSAMtype was set to BAM SortedByCoordinate, and 5) quantMode was set to GeneCounts
Gene expression was quantified using STAR's built-in and counts were imported into R (v4.0) using redDGE function to produce DGE list object
Differential expression (DE) analysis was performed in R with the edgeR package (v3.30.3).
Genome_build: hg19

extract_protocol:
Total RNA was extracted from 1-2 million of cells using TRIzol (Invitrogen) followed by phenol-chloroform extraction.
Sequencing libraries were prepared from 500 ng of total RNA using NEB PolyA mRNA selection kit and Swift Biosciences rapid RNA library kit following the manufacturer's protocol. Libraries were sequenced in the Illumina HiSeq 4000 platform to generate paired end reads of 2X150 bp.

treatment_protocol: Cas9 nuclease (1081058, IDT) were mixed with synthetically modified sgRNAs (synthesized by Synthego) at a 1:3 molar ratio in resuspension buffer T and incubated at 37oC for 10 minutes to form ribonucleoprotein complexes (RNPs). For the CTCF inversion clones, homology-directed repair (HDR) approach was used by adding 2 μg of dsDNA homology repair template (synthesized by Gene Universal) to the RNP complexes. dsDNA repair template was designed to have 90-130 bp of homology arms distal and proximal to the PAM sequence.

value: erthyroid


title: Nalm6-EV input ChIP-seq 2

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: Mnase digested input

data_processing:
Single-end sequencing (75 bp) was performed with Illumina NextSeq 500/550 High Output Kit v2.5, according to the manufacturer’s instructions.
Sequencing reads were quality controlled using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bases with poor quality scores were trimmed (min 97% of positions have a min phred quality score of 10) using the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Duplicate reads were collapsed from ChIP-seq files using fastx (collapse)
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version bowtie/1.2.3 (-v 2 -k 3 -m 1 --best)
bigWig signal files were generated using HOMER software http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bigWig ChIP-seq signal files

source_name: Nalm-6 pre-B-ALL cell line with inducible EV (empty vector) construct

growth_protocol: Cells were cultured in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM  L-glutamine (Gibco, Thermo Fisher), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).

extract_protocol:
Cells were crosslinked with 1/10 of volume of 11% formaldehyde solution (37% formaldehyde (Sigma-Aldrich), 5 M NaCl, 0.5 M EDTA pH 8.0, 0.5 M EGTA, 1 M HEPES) for 10 min gently rotating at 1 million/ml cell concentration in media. The reactions were quenched by adding glycine to a final concentration of 120 mM, and cells were washed twice with ice-cold PBS. Crosslinked lysate was flash frozen with liquid nitrogen and stored at - 80°C. Lysates were thawed, nuclei were extracted, and MNase  treated. 5 U of MNase (Thermo Fisher Scientific) was used and supernatant was diluted with dilution buffer 2.5 times. Samples were pre-cleared with 25 μl per sample Protein G Dynabeads (Thermo Fisher Scientific) for 1h at 4°C on a rotating platform. Subsequently,  input samples were collected. Next, 5 μg of the RUNX1 antibody (cat# ab23980, Abcam) for 10-16 million cells or 2.5 μg of H3K27ac antibody (cat# ab4729, Abcam) for 5-9 million cells were added. Bound chromatin fragments were collected by adding 25 μl of Dynabeads Protein G (Thermo Fisher Scientific) for 1 hour at 4°C rotating. Beads were washed with 1ml of cold wash buffers for 3 minutes.
Beads were eluted twice in elution buffer (1% SDS, 100 mM NaHCO3). Immunoprecipitated chromatin was reverse crosslinked by adding NaCl to a final concentration of 0.2 M. Next, 2,65 mg/ml of RNAse A (Invitrogen) was added to each sample and crosslinks were reversed overnight at 65°C. Proteinase K treatment was performed by adding 31 μl of buffer containing 161 mM EDTA, 645 mM Tris pH 7.4, Proteinase K 0.65 mg/ml (Thermo Fisher Scientific) for 1 h at 50°C. For DNA purification, ChIP DNA Clean & Concentrator (Zymo Research, Irvine, CA, USA) was used according to manufacture´s protocol. ChIP-Seq libraries were prepared  Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adaptor ligation using barcoded adapters (NextFlex, Bioo Scientific) with 13-14 cycles in PCR amplification and size selected for 225 bp-350 bp fragments by gel extraction.

treatment_protocol: Nalm-6 RUNX1 and Nalm-6 Empty vector constructs were induced for 48h before crosslinking cells for ChIP-seq using 500 ng/ml doxycycline (Sigma-Aldrich).

tag: cell line

tag: time

tag: construct

value: Empty vector ctrl

tag: antibody

tag: replicate


title: 3 prime HS1 inverted HUDEP2 clone A2 mRNA-seq

description: mRNA-seq


title: 3 prime HS1 deleted HUDEP2 clone D3 mRNA-seq

description: mRNA-seq


title: Tem CD226+  Activated, 29

value: Tem CD226+  Activated

value: male


title: 3 prime HS1 deleted HUDEP2 clone B6 mRNA-seq

description: mRNA-seq


title: Tem CD226+  Activated, 65

value: peripheral blood


title: Tem CD226-  Activated, 30


title: Tem CD226-, 12

value: female


title: 9-Tcm-CD226-PLUS

description:
Freshly FACS purified
9-Tcm-CD226-PLUS


title: Tem CD226+, 11


title: Tem CD226+  Activated, 35


title: SNU484-5AZA-Input

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

description: Input (background)

data_processing:
For ChIP-Seq, sequencing reads were mapped to the human reference genome (hg19) using BWA-MEM. Reads with MAPQ<10 and potential PCR duplication were filtered using SAMTools. Peaks were predicted using MACS2 or CCAT with default parameters. For RNA-Seq,  sequencing was performed using paired-end 101bp reads. RNA-seq reads were aligned to the human genome (hg19) using TopHat2 (version 2.0.12) using default parameters. Transcript abundances in units of FPKM at the gene level were estimated using Cufflinks. Gene expression values from primary samples showing variation sgreater than zero was corrected for potential batch effects using ComBat.
Genome_build: hg19

source_name: gastric cancer cell line

extract_protocol:
For ChIP-Seq, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and reactions were stopped by adding glycine to a final concentration of 0.2 M. Chromatin was extracted and sonicated to 500 bp. EBF1 (H00001879-M01, Abnova), H3K27me3 (#07-449, Millipore), h3k27AC (ab4729, Abcam), or H3K4me1 (ab8895, Abcam) antibodies were used for chromatin immunoprecipitation (ChIP). Input DNA from cells prior to immunoprecipitation were used to normalize ChIP-seq peak calling.
ChIPed DNA (10-30 ng) was used for ChIP with DNA sequencing (ChIP-seq) library construction following manufacturer protocols (New England Biolabs). For RNA-Seq, sequencing libraries were constructed from total RNA of GC cell lines with 300-400 bp insert lengths
ChIP-seq, RNA-Seq

value: not applicable


title: 10-Tcm-CD226-MOINS

description:
Freshly FACS purified
10-Tcm-CD226-MOINS


title: Tem CD226-, 6


title: WT-HUDEP2 cells rep2 mRNA-seq

description: mRNA-seq


title: patient_TEF 20

type: RNA

city: Rotterdam

first: Erwin

last: Brosens

state: - If in U.S, Select a State -

address: Dr molewaterplein 50

department: Clinical genetics

country: Netherlands

institute: ErasmusMC

description: patient

hyb_protocol: Fragmented biotinylated cRNA was subsequently hybridised onto Affymetrix Human Genome U133 Plus 2.0 microarray chips, which were scanned with the Affymetrix GeneChip Scanner.

scan_protocol: The measured intensity values were analyzed using GeneChip Operating Software (GCOS). The percentage of present calls, background, and ratio of actin and GAPDH 3’ to 5’ all indicated a high quality of samples and an overall comparability. Probe sets that were not present (according to Affymetrix MAS5.0 software) in any of the Genechips were omitted from further analysis. Raw intensities of the remaining probe sets of each chip were log2 transformed and raw expression values were Quantile normalized. Then, the data were transformed back to normal intensity values.

data_processing: Data analysis was carried out using BRB-array tools version 4.6.0 (October 2018) in combination with R version 3.5.1 (July 2018).

label: biotin

source_name: tracheoesophageal fistula

label_protocol: Depending on the availability and/or quality of purified total RNA, cDNA was synthesized from 0.8-15 μg RNA using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA, USA). Biotin-labelled cRNA synthesis, purification and fragmentation were performed according to standard protocols.

extract_protocol: total RNA was isolated following the manufacturer’s instructions, but the phase separation was repeated by adding 200µl of 0.1% DEPC water to increase RNA yield.  RNA was purified using the Rneasy MinElute Cleanup kit (Qiagen, Valencia, CA, USA) and stored at –80°C until further processing.

value: tracheoesophageal fistula


title: WT-HUDEP2 cells rep1 mRNA-seq

description: mRNA-seq


title: Tem CD226+, 21


title: AGS-DMSO-Input

description: Input (background)

value: AGS


title: AGS-GSK126-Input

description: Input (background)


title: AGS-5AZA-Input

description: Input (background)


title: Tem CD226-, 34


title: SNU484-GSK126-H3K27me3

description: H3K27me3 ChIP-seq in SNU484

value: #07-449, Millipore


title: WholeSkin_Ivl_mut_rep2

city: St Louis

first: Cristina

last: de Guzman Strong

state: MO

address: 660 South Euclid

department: Dermatology

institute: Washington University in St Louis

data_processing:
Illumina bcl2fastq software was used for basecalls
Reads were aligned to Ensembl release 96 with STAR version 2.0.4b
Junction saturation and read distribution over known gene models were quantified with RSeQC version 2.3
Gene Counts were normalized  for sample differences in library size using EdgeR and TMM normalization size factors.Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Performance of the samples was assessed with Spearman correlations, and a Multi-Dimensional Scaling plot, and hierarchical clustering. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05, and a log2(fold change) > |2|.
Genome_build: Ensembl release 96
Supplementary_files_format_and_content: tab-delimited text files include CPM and RPKM for each gene

organism: Mus musculus

source_name: whole skin

extract_protocol:
Whole Skin tissue was isolated from newborn mice and stored in TriZol
Ribo-Zero RNA sequencing libraries were prepped according to Illumina library kit protocol

tag: strain

value: newborn

tag: genotype

value: Ivl -/-

value: whole skin


title: SNU484-5AZA-H3K27me3

description: H3K27me3 ChIP-seq in SNU484


title: WholeSkin_Ivl_mut_rep3


title: SNU484-GSK126-Input

description: Input (background)


title: SNU484-DMSO-H3K27me3

description: H3K27me3 ChIP-seq in SNU484


title: Tem CD226+, 5

value: CD8+ T cells

value: Freshly purified


title: WholeSkin_923large_het_rep3


title: WholeSkin_923large_het_rep1


title: WholeSkin_923large_mut_rep3


title: Tem CD226-, 58

value: Tem CD226-


title: WholeSkin_923large_het_rep2


title: WholeSkin_923del_het_rep3


title: Tem CD226+, 57

value: Tem CD226+


title: AGS-GSK126-H3K27me3

description: H3K27me3 ChIP-seq in AGS


title: WholeSkin_923large_mut_rep1


title: WholeSkin_923large_mut_rep2


title: Tem CD226-, 24


title: AGS-DMSO-H3K27me3

description: H3K27me3 ChIP-seq in AGS


title: WholeSkin_923del_het_rep2


title: AGS-5AZA-H3K27me3

description: H3K27me3 ChIP-seq in AGS


title: Tem CD226-  Activated, 36

value: Tem CD226-  Activated

value: anti-CD2/CD3/ CD28 microbeads 24 hrs


title: SNU484-DMSO-Input

description: Input (background)


title: WholeSkin_923del_het_rep1


title: Tem CD226-  Activated, 20


title: WholeSkin_Ivl_mut_rep1


title: D425 lnc-HLX-2-7 KD xenograft

city: St. Petersburg

first: Bongyong

last: Lee

state: Florida

address: 501 6th Ave S

institute: The Johns Hopkins University

description:
Xenograft_aggr_matrix.mtx.gz
Xenograft_aggr_barcodes.tsv.gz
Xenograft_aggr_features.tsv.gz

data_processing:
Xenograft single-cell RNA-seq samples were classified into host and graft reads using XenoCell and Xenome v1.0.1.
FASTQ files for graft were aligned to human genome hg38, indexed with GENCODE human annotations v34 and augmented with lncRNA annotations from LNCipedia v5.2, using 10X Genomics cellranger count and STAR v 2.7.0d_0221.
For downstream integrated analysis, both samples were combined and normalized for the number of mapped reads per cell across libraries using 10X Genomics cellranger aggr function. Note: cell barcodes with "-1" and "-2" suffixes correspond to D425 WT xenograft and D425 lnc-HLX-2-7 KD xenograft respectively.
Quality control and downstream analysis of scRNA-seq data were performed using Seurat v3.1.2 and Monocle3 v0.2.2 in R v3.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger aggr output files (filtered) containing count matrix, cel barcodes, and features information

source_name: Intracranial xenograft tumor cell

growth_protocol: D425 cells were cultured in DMEM/F12 with 10% serum and 1% glutamate/penicillin/streptomycin. Intracranial xenografts were established by injecting D425 cells and D425 lnc-HLX-2-7 KD cells into the cerebellum of NOD-SCID mice (Jackson Laboratory). Cerebellar coordinates were -2 mm from lambda, +1 mm laterally, and 1.5 mm deep. After 30 days of injecting D425 cells and D425 lnc-HLX-2-7 KD cells into the cerebellum of NOD-SCID mice, tumors were harvested.

extract_protocol:
Cell suspensions required for generating 8000 single cell gel beads in emulsion (GEM) were loaded onto the Chromium controller (10X Genomics, Pleasanton, CA).
Each sample was loaded onto the single cell 3’ v3.1 chip. The 3’ gene expression library was prepared using a Chromium v3.1 single cell 3’ library kit (10X Genomics).

value: Intracranial xenograft tumor cell of human medulloblastoma cell line

tag: genotype/variation

value: D425 lnc-HLX-2-7 KD


title: AGS_EBF1-R209Q-INPUT

description: Input (background)


title: 44-Tcm-CD226-MOINS

description:
Freshly FACS purified
44-Tcm-CD226-MOINS

tag: gender

value: male

value: peripheral blood

value: Tcm CD226-


title: WholeSkin_923del_mut_rep1


title: D425 WT xenograft

value: D425 WT


title: Tem CD226+  Activated, 19

value: Tem CD226+  Activated


title: WholeSkin_WT_rep3

value: wild type


title: AGS_EBF1-Q196P-INPUT

description: Input (background)

value: AGS

value: not applicable


title: WholeSkin_WT_rep2

value: newborn

value: whole skin


title: HGC27-INPUT-(control for EBF1 ChIP)

description: Input (background)


title: D425 lnc-HLX-2-7 KD xenograft rep2

description:
Sample 8
HLX2_7_KO_Day30_vs_D425_Day30.txt
HLX2-7-KO-Day30-2

data_processing:
Adapter sequences were trimed from reads via Trimmomatic (v0.38), default parameters were used.
Reads were mapped to hg38 via STAR (2.7.0d), default parameters were used.
DESeq2 (v1.22.2) was used to compute the differential expression level between samples, default parameters were used.
samples 5, 6  were compared with sample 3, 4.
sample 7, 8 were compared with samples 5, 6.
sample 7, 8 were compared with sample 5, 6.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include reads

extract_protocol:
Total RNA was prepared from cell line and orthotopic xenograft using a Direct-zol RNA Miniprep kit (Zymo Research). The quality of RNA was determined with the Agilent 2100 Bioanalyzer Nano Assay (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lnc-HLX-2-7 KD


title: WholeSkin_WT_rep1


title: Tem CD226+, 33

value: CD8+ T cells

value: Freshly purified

value: female


title: epidermis, Del_4

data_processing:
ENCODE ATAC-Seq processing pipeline used
Reads mapped with Bowtie2
Unmapped reads, duplicates, and reads mapping to chrM were filtered out.
Peaks were called using MACS2
Biological replicates were included if both the rescue and self-consistency IDR values per genotype were below (or very near) 2
Differential accessibility was assessed using EdgeR within the DiffBind R package
Genome_build: mm10
Supplementary_files_format_and_content: zipped narrow peaks files

source_name: epidermis

extract_protocol:
Whole skin tissue was isolated from newborn mice and epidermal keratinocytes were speperated after treatment with HBSS:Dispase (1:1)
Lysed cells were treated with Illumina Nextera TD enzyme to cut and insert sequencing adapters. Libraries were amplified and treated with AMPure XP beaks to size select,

value: epidermal keratinocytes


title: epidermis, Del_2


title: AGS_EBF1-R209Q-EBF1

description: EBF1 ChIP-seq in AGS


title: WholeSkin_923del_mut_rep3


title: AGS-Input (Control for EBF1 ChIP)

description: Input (background)


title: D425 WT xenograft rep2

description:
Sample 6
HLX2_7_KO_Day30_vs_D425_Day30.txt
D425_Day30_rep2

value: Intracranial xenograft tumor cell of human medulloblastoma cell line

value: WT


title: WholeSkin_923del_mut_rep2


title: shTBX3 rep2

city: Tianjin

first: xiaomeng

last: Li

address: No.22 qixiangtai Road,heping district,Tianjin

country: China

institute: Tianjin medical university

data_processing:
We use  Bowtie2  to map clean reads to reference gene and use  HISAT to reference genome.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using   Bowtie2  parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar,HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
FPKMs were calculated by RSEM, which is the quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores to determine which transcripts are isoforms of the same gene.
Genome_build: hg19

source_name: thyroid cancer

growth_protocol: Cells were cultured in  RPMI 1640  supplemented with 10% fetal bovine serum

extract_protocol:
RNA was harvested using Trizol reagent. First Strand cDNA Synthesis Kit (04 896 866 001, Roche) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

value: thyroid cancer

value: TBX3 knockdown


title: epidermis, Del_3


title: D425 WT xenograft rep1

description:
Sample 5
HLX2_7_KO_Day30_vs_D425_Day30.txt
D425_Day30_rep1


title: shTBX3 rep1


title: epidermis, Del_1


title: D425 lnc-HLX-2-7 KD rep2

description:
Sample 4
D425_HLX2_7_vs_D425.txt
D425-HLX2-7-KO-2

source_name: Medulloblastoma cell line

value: Human medulloblastoma cell line


title: epidermis, WT_4


title: shCtrl rep2

value: Ctrl


title: AGS-EBF1

description: EBF1 ChIP-seq in AGS


title: D425 lnc-HLX-2-7 KD rep1

description:
Sample 3
D425_HLX2_7_vs_D425.txt
D425-HLX2-7-KO-1


title: epidermis, WT_3


title: shCtrl rep1


title: epidermis, WT_1


title: epidermis, Large_4


title: ALL3

data_processing:
Data was aligned with Cell Ranger 3.0.2 to human reference (hg19) version 3.0.0 from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 3.0.2 following alignment.
Genome_build: hg19
Supplementary_files_format_and_content: barcode annotation: 10x Cell Ranger filtered barcode list; feature annotation: 10x Cell Ranger feature list; count matrix: 10x Cell Ranger filtered UMI count matrix

molecule: polyA RNA

source_name: Primary pre-B-ALL BM

extract_protocol:
Mononuclear cells (MNC) were extracted from fresh BM at diagnosis using Ficoll-Paque Plus (GE Healthcare, #17-1440-02). Bone marrow MNCs were also extracted from two patients (ALL10 and ALL12) during the induction therapy at day 15 after initiation of therapy. MNCs were viably frozen in 15% DMSO/40% FBS in RPMI in liquid nitrogen. Cells from primary BM samples were processed for scRNA-seq in the Finnish Functional Genomics Center, Turku, Finland, in 4 batches: 1) ALL3, 2) ALL1 3) ALL10 and ALL10-d15, and 4) ALL8, ALL9, ALL12, and ALL12-d15. Before applying the cells into the Chromium cartridge, their viability was checked using Trypan blue. PI-negative (live) cells were selected from sample ALL3 using FACS. Samples ALL1, ALL10, and ALL10-d15 were processed directly after thawing the MNC fraction without further processing. Excess dead cells were depleted from samples ALL8 and ALL9 using bead-based Dead Cell Removal Kit (#130-090-101, MACS miltenyi Biotech), increasing the percentage of viable cells from 43 % to 72 % and from 63 % to 78 %, respectively. For samples ALL12 and ALL12-d15, enrichment of leukemic cells was carried out by depleting non-B-cells using streptavidin-beads (BD Streptavidin Particles Plus, BD Biosciences, Franklin Lakes, NJ, USA) and biotinylated antibodies against human CD16 (clone 3G8), CD14 (HCD-14), CD11c (3.9), CD56 (HCD56), CD3 (UCHT1), and CD66 (G10F5) (Biolegend), all with final concentrations of 2 ug/ml, following the manufacturer's instructions and as previously described (Good et al. 2018 Nat Meth). Depletion efficiency was estimated by flow cytometry using CD3 (BV421, BD Biosciences, #56287, RRID:AB_27378607) and CD19 (Thermo Fisher Scientific, # 25-0199-41, RRID:AB_1582279) antibodies, with a viability dye (eBioscience, Fixable Viability Dye eFluor™ 506, #65-0866-14). Depletion decreased the proportion of T-cells (CD3+) from 30 to 2%, increased the proportion of B-cells (CD19+) from 23 to 50%, and increased the percentage of viable cells from 50 to 80% in a test BM sample.
Cells were combined with reverse transcriptase Master Mix and partitioned into Gel Bead-In EMulsions (GEMs) using 10X GemCode Technology, where the poly-A transcripts are barcoded with an Illumina R1 sequence, a 16 bp 10X barcode and a 10 bp Unique Molecular Identifier (UMI). 11-12 cycles of PCR was used to amplify the cDNA.

treatment_protocol: All cases received standard induction therapy according to the NOPHO ALL-2008 protocol, with prednisolone 60 mg/m2/day p.o. days 1-29, vincristine 2.0 mg/m2 i.v. days 1, 8, 15, 22, and 29, doxorubicin 40 mg/m2 i.v. days 1 and 22, and methotrexate i.t. days 1, 8, 15, and 29

tag: time point

value: bone marrow


title: D425 lnc-HLX-2-7 KD xenograft rep1

description:
Sample 7
HLX2_7_KO_Day30_vs_D425_Day30.txt
HLX2-7-KO-Day30-1


title: AGS_EBF1-Q196P-EBF1

description: EBF1 ChIP-seq in AGS


title: HH800-replicate 1

city: New Haven

first: Alexandre

last: Duprey

state: CT

address: 295 congress avenue

department: Microbial pathogenesis

institute: Yale university

data_processing:
Alignment to reference genome using bowtie 2.2.9
Differential expression analysis using cuffdiff (from cufflinks 2.2.1)
Genome_build: CP001363.1
Supplementary_files_format_and_content: tab-delimited file including FPKM values and differential expression analysis for all genes

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: Pure culture

growth_protocol: Cells were grown in N-minimal medium supplemented with MgCl2 (concentration depending on the condition), 0.1% casamino acids, 0.27% glycerol, and adjusted to pH 7.7, at 37°C

extract_protocol:
RNA was extracted using a QIAGen RNeasy Mini kit. In addition to the included DNase treatment in the kit, DNA was further eliminated by treatment by turbo DNase (Ambion). RNA was finally re-purified using a QIAGen RNeasy Mini kit. rRNA was depleted using a RiboZero kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown until OD600= 0.8 ± 0.1

tag: culture condition


title: HH800-replicate 2


title: HGC27-EBF1

description: EBF1 ChIP-seq in HGC27


title: 119490_ACAGTG_S11_L004

city: Middletown

first: Joseph

last: Coolon

address: 52 Lawn Avenue

department: Biology

institute: Wesleyan University

description: 40 hours APF Replicate 2

data_processing:
FASTQC on each of the 12 raw fastq files
Bowtie2 alignment using the D. melanogaster reference genome available at the time of analysis.
Cuffdiff for quantification and differential expression analysis using the D. melanogaster reference genome available at the time of analysis and gene files available at the time of analysis with geometric library normalization
Genome_build: Drosophila_melanogaster.BDGP6.dna.toplevel.fa
Supplementary_files_format_and_content: Tab-delimited Cuffdiff output in text format

organism: Drosophila melanogaster

source_name: dissected tissue

extract_protocol:
Total RNA was extracted from dissected tissue using the ReliaPrep RNA Tissue Miniprep System.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Different developmental stage eyes were dissected and genome-wide gene expression levels were compared between these two stages

value: CantonS

tag: tissue

value: pupal eye

tag: developmental stage

value: 40 hours APF


title: Chicken cerebellar nuclei

city: Stanford

first: Justus

middle: M

last: Kebschull

state: CA

address: 327 Campus Drive

institute: Stanford University

description: Chicken cerebellar nuclei

data_processing:
Basecalling through Illumina pipeline
STAR alignment to (I) mouse genome GRCm38, Ensembl 92 annotation, (ii) human genome GRCh38, annotation Ensemble 94, (iii) chicken genome GRCg6a Ensembl annotation 99
Count reads in exons and introns using Htseq
Produce count matrix
Analyse in Seurat
Genome_build: GRCm38, GRCh28, GRCg6a
Supplementary_files_format_and_content: seurat v3 object containing count matrix, dimensionality reduction, cluster assignment, metadata

organism: Gallus gallus

source_name: Cerbellar nulcei

extract_protocol:
cerbellar nulcei were dissected from fresh frozen or accute sliced brains, flash frozen. Nuclei were released using standard protocols, stained for NeuN and FACS sorted into 384 well plates
smartseq2

tag: cell type

value: Cerbellar nulcei

tag: breed

value: ADOL Line 6 x Line 7 F1


title: HH-replicate 2

value: 10 mM Mg2+


title: HH-replicate 1


title: 119489_GTCCGC_S10_L004

description: 40 hours APF Replicate 1


title: 8300_rnaseq_Lidia_4years

city: madrid

first: Paulina

middle: G.

last: Eusebi

state: madrid

address: Ave. Puerta del hierro

department: Animal Production

country: Spain

institute: Universidad Complutense de Madrid

data_processing:
Illumina Casava1.7 software used for de-multiplex individual reads
Read quality of the sixteen RNA-seq datasets was checked and trimmed using PRINSEQ v. 0.20.4
Trimmed reads were then mapped to the bovine reference genome (Bos taurus ARS.UCD 1.2) with STAR v.2.7.3a
The SAM files generated by STAR, which contains the count of reads per base aligned to each location across the length of the genome, were converted into a binary alignment/map (BAM) format and sorted using SAMTools v.0.1.18
The aligned RNA-seq reads were assembled into transcripts and their abundance in fragments per kilobase of exon per million fragments mapped (FKPM) was determined with Cufflinks v.2.2.1
Analysis of differential gene expression across aggressive and non-aggressive groups was performed using Cuffdiff
Genome_build: Bos_taurus_ARS.UCD 1.2
Supplementary_files_format_and_content: text files include  gene  transcript values for each Sample

organism: Bos taurus

source_name: brain

extract_protocol:
PFC were removed, preserved with RNA-later and then RNA extacted with Rneasy Lipid tissue Mini kit, and RNApreserved with RNAstable, Illumina TruSeq stranded mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prefrontal cortex

value: 4years (adult)

value: male

value: Lidia


title: DOCA-EVs 2 group

city: Padova

first: Federica

last: Collino

state: TO

address: via Ugo Bassi, 58/B

department: Department of Biomedical Sciences

country: Italy

institute: UNIPD

description: miRNA expression after 8-weeks from UNX

hyb_protocol: 0.1 ug of Cy3-RNA was mixed with the hybridization mix for miRNA microarrays with Hyb Spike-In solution. The hybridization mix was loaded into the SureHyb chamber and hybridized to Agilent rat miRNA Microarrays (G4471A) at 55°C for 20 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (Agilent Technologies), using one color scan setting for 8x15K array slides (Scan Region - Full Agilent Slide, Scan Resolution - 5 um, Tiff dynamic range - 20bit). Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with the Agilent GeneSpring GX Data software (Agilent Technologies), using default parameters for miRNA analysis to obtain background subtracted and spatially detrended Processed Signal intensities. No baseline transformation was applied.
For fold change analysis, data were filtered on Expression (30,0 - 100,0) of the percentile in the raw data and differential expression was determined by a fold change ≥1.5 with respect to DOCA-salt treatment.

organism: Rattus norvegicus

source_name: Renal Cortex, DOCA-EV animal, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using miRNA Complete Labeling and Hyb Kit (Agilent), that generates fluorescently labeled miRNA with a sample input of 100 ng of total RNA. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule. Sample was then dry to continue with the Hybridization procedure

extract_protocol: Kidney cortex extracts were homogenized in lysis buffer and RNA extraction from SHAM, UNX, DOCA and EV-DOCA animals was conducted by using the Absolutely RNA miRNA Kit following the manufacturer's recommendations (400814, Agilent Technologies). Characterization of the input total RNA using the Agilent 2100 bioanalyzer was conducted on the sample quality prior to labeling and hybridization. Moreover, the yield of the extracted RNA was determined spectrophotometrically (Nanodrop-1000, Thermo Scientific). RNA samples with RNA integrity numbers (RINs) >8.0 were used for microarray experiments

treatment_protocol: Rats were nephrectomized and randomly divided into 3 cohorts: (1) the normal salt control-group, that received standard-Na+ diet chow (0.50% w/w Na+) being injected subcutaneously with vehicle (soybean oil, 0.1 ml/animal) (UNX); (2) the high salt-group, that received high-Na+ diet (1.5% w/w Na+) in combination with a subcutaneous administration of deoxycorticosterone acetate (D7000-5G, Sigma-Aldrich) (8 mg/kg, twice a week in soybean oil) and weekly intravenous injection (i.v.) of vehicle, starting from week 2 after nephrectomy (DOCA); (3) the high salt-group that received high-Na+ diet in combination with a subcutaneous administration of deoxycorticosterone acetate, and weekly intravenous injection (i.v.) of ASC-EVs, starting from week 2 after nephrectomy (DOCA-EV). A 4th group of sham-operated rats receiving standard-Na+ diet was added as control (SHAM). Animal were sacrificed at 9 weeks after nephrectomy and renal cortex from all the rats was isolated.

value: renal cortex

tag: Sex


title: DOCA-EVs 1 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, DOCA-EV animal, replicate 1


title: 119487_GTGGCC_S8_L004

description: 21 hours APF Replicate 2

value: 21 hours APF


title: DOCA 2 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, DOCA animal, replicate 2


title: 8298_rnaseq_Lidia_4years

tag: age


title: 119486_TAGCTT_S7_L004

description: 21 hours APF Replicate 1


title: UNX 2 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, UNX animal, replicate 2


title: 8295_rnaseq_Lidia_4years


title: UNX 1 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, UNX animal, replicate 1


title: DOCA 1 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, DOCA animal, replicate 1


title: 119491_GCCAAT_S12_L004

description: 40 hours APF Replicate 3


title: SHAM 2 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, Sham animal, replicate 2


title: S2.1

city: Townsville

first: Craig

last: McFarlane

state: Queensland

address: 1 James Cook Drive, Building 142-309

department: Molecular & Cell Biology

country: Australia

institute: James Cook University

description: adjacent sample from patient - technical replicate 1

hyb_protocol: 750ng of cRNA generated from amplification and labeling were hybridized into one Human HT-12 beadchip. The BeadChips were incubated at 58°C, with rotation speed 5 for 18 hrs for hybridization.

scan_protocol: The BeadChips were scanned on the iScan (Illumina).

data_processing: The data files were quantified in GenomeStudio Version 2011.1 (Illumina). All samples passed Illumina's sample dependent and independent QC metrics. Data from the beadchips were quantified separately in GenomeStudio.

source_name: adjacent

label_protocol: Two hundred nanograms from samples were label using Illumina TotalPrep-96 RNA Amplification kit Lot # 1206032 (Ambion) as per amplification protocol.

extract_protocol: Tumor tissue, adjacent normal tissue and resected overlying skin tissue biopsies were stored in RNAlater (Ambion) prior to RNA extraction. Total RNA was isolated from each tissue using QIAzol lysis reagent (Qiagen), as per the manufacturer’s instructions. The integrity of isolated RNA was evaluated using the Agilent 2100 Bioanalyzer system and the RNA 6000 Nano Kit (Agilent). All samples were stored at -80 degrees Celsius prior to further use.

value: adjacent


title: SK1.1

description: skin sample from patient - technical replicate 1

source_name: skin

value: skin


title: SK1.2

description: skin sample from patient - technical replicate 2


title: SHR rep6

city: Beijing

first: Xiaoyan

last: Liu

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

institute: Beijing Chao-Yang Hospital

data_processing:
bcl2fastq2.17 software used for basecalling.
Raw data (raw reads) of fastq format went through preprocessing first to trim 3’ and 5’ adapter and next to clear away low-quality reads to obtain clean reads. By classifying clean reads, we can obtain the components and expression information of all kinds of small RNA including miRNA in the sample.
miRNA expression levels were estimated by RPM (the number of reads per million).
Genome_build: rno6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

source_name: spontaneously hypertensive rat_plasma exosomes

extract_protocol:
Exosomes from prefiltered plasma were isolated with exoEasy Maxi Kit (Qiagen Hilden, Germany, catalog no. 76064) following the manufacturer’s instructions, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spontaneously hypertensive rats (SHRs)

value: 10 weeks

value: blood

tag: rna extracted from

value: plasma exosomes


title: 8292_rnaseq_Lidia_4years


title: DRG Lumbar treated 4

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences, Inc.

description: 8382-643 GLD1 P0906 5F

data_processing:
Fastq reads were clipped from illumina barcodes and poor quality bases
Clipped fastq files were aligned to a reference genome using STAR_2.5.3a with these options:--outSAMtype BAM SortedByCoordinate --outSAMattributes NH --outSAMunmapped Within --alignSJoverhangMin 8 --sjdbScore 3 –twopassMode Basic
Genes were quantified using featureCounts
Genome_build: Macaca fascicularis 5.0.94
Supplementary_files_format_and_content: processed data is a matrix of read counts produced by featureCounts

organism: Macaca fascicularis

source_name: Dorsal Root Ganglia (Lumbar)

extract_protocol:
Samples were stored in RNAlater. RNA was extracted using the Qiagen miRNeasy mini kit
Samples were created using the Illumina TruSeq stranded mRNA kit. Sequencing was performed using an Illumina HiSeq 2500, 50bp paired-end reads

value: Dorsal Root Ganglia (Lumbar)

tag: treatment

value: High (6 mg/kg/day)

value: Female


title: DRG Lumbar treated 3

description: 8382-643 GLD1 P0904 5F


title: SHR rep5


title: 8326_rnaseq_Lidia_4years


title: SHR rep4


title: SHR rep3


title: DRG Lumbar treated 2

description: 8382-643 GLD2 P0403 5M

value: Male


title: 8150_rnaseq_Lidia_4years


title: T1.1

description: tumor sample from patient - technical replicate 1

source_name: tumor

value: tumor


title: NPAHi1

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_105827

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify quality problems before and after alignment.
We used the Tuxedo Suite software package for alignment
Reads were aligned to the reference genome (UCSC mm10)  using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: brain tumor infiltrating immune cells

growth_protocol: High grade gliomas were generated by the Sleeping Beauty (SB) Transposase system, which is used to integrate genetic lesions into the genomic DNA of brain cells of neonatal mice. Tumors then develop intracranially de novo from neural progenitor cells. The plasmids encoding the different genetic lesions used in this study were: (i) pT2C-LucPGK-SB100X, encoding SB transposase and luciferase, (ii) pT2CAG-NRAS-G12V, encoding a constitutively active mutant of NRAS, NRAS-G12V (iii) pT2-shATRX53-GFP4, encoding a short hairpin against ATRX (iv) pT2-shp53, encoding a short hairpin against p53 and (v) pKT-H3.3(G34R)-IRES-Katushka, encoding H3.3-G34R mutation.

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit (cat# 74104)
RiboGone and the TruSeq stranded Library prep kit with 100ng input and 13 cycles of PCR; HiSeq4000, Ribodepleted, stranded TruSeq. H4K PE50 Cycle, Pico kit

treatment_protocol: Mouse were euthanized at symptomatic stage and the tumor was dissected and smashed through a 70 μm strainer. After red blood cell, cells were resuspended in 90 μL of cold BSA-EDTA buffer (0.5% BSA, 2 mM Ethylenediaminetetraacetic acid in DPBS pH 7.2). CD45+ cells were labeled with 10 μL of CD45 MicroBeads (Miltenyi Biotec) per 107 total cells and sorted using a MACS column (Miltenyi Biotec) placed in the magnetic field of a suitable MACS Separator (Miltenyi Biotec). Tumor cell-enriched and CD45+ cell-enriched fractions were procesed for RNA purification. Cell purity was assessed by flow cytometry (Garcia-Fabiani et al., 2020).

value: brain tumor infiltrating immune cells

value: overexpression of NRASG12V + shorthair pin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R


title: DRG Lumbar treated 1

description: 8382-643 GLD1 P0406 5M


title: 8142_rnaseq_Lidia_4years

value: Prefrontal cortex

value: 4years (adult)

value: male


title: NPAi4

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_105825

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX


title: NPAi3

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_105824


title: DRG Lumbar control 4

description: 8382-643 GLD1 P0504 1F

value: Control (0 mg/kg/day)


title: NPAHi2

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_107902

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R


title: SHR rep1

value: spontaneously hypertensive rats (SHRs)


title: 8134_rnaseq_Lidia_4years

value: Lidia


title: NPAHi4

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_105828


title: NPAi2

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_105823


title: 8174_rnaseq_Lidia_3years

value: 3 years (young)


title: T1.2

description: tumor sample from patient - technical replicate 2


title: NPAi1

description:
rawCounts2_HTSeq.txt
rawCounts_Cufflinks2.txt
Sample_105822


title: WKY rep6

source_name: normotensive WKYs_plasma exosomes

value: Wistar-Kyoto (WKY) rats

value: 10 weeks

value: blood

value: plasma exosomes


title: SHR rep2


title: DRG Lumbar control 2

description: 8382-643 GLD2 P0004 1M

value: Dorsal Root Ganglia (Lumbar)

value: Male


title: S2.2

description: adjacent sample from patient - technical replicate 2

value: adjacent


title: WKY rep5


title: 8171_rnaseq_Lidia_3years


title: DRG Lumbar control 3

description: 8382-643 GLD1 P0501 1F

value: Female


title: NPAHt4

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105821

source_name: brain tumor cells

value: brain tumor cells


title: DRG Lumbar control 1

description: 8382-643 GLD1 P0003 1M


title: 8165_rnaseq_Lidia_3years

value: Prefrontal cortex


title: 119488_AGTCAA_S9_L004

description: 21 hours APF Replicate 3

source_name: dissected tissue

value: CantonS

value: pupal eye

value: 21 hours APF


title: WKY rep4


title: NPAHt3

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105352

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R


title: SHAM 1 group

description: miRNA expression after 8-weeks from UNX

source_name: Renal Cortex, Sham animal, replicate 1

value: renal cortex

value: male


title: DRG Cervical treated 4

description: 8382-643 GCD2 P0905 5F

source_name: Dorsal Root Ganglia (Cervical)

value: Dorsal Root Ganglia (Cervical)

value: High (6 mg/kg/day)


title: 8162_rnaseq_Lidia_3years

source_name: brain

value: 3 years (young)

value: Lidia


title: WKY rep3

value: Wistar-Kyoto (WKY) rats

value: 10 weeks

value: blood

value: plasma exosomes


title: DRG Cervical treated 3

description: 8382-643 GCD1 P0906 5F

value: Female


title: 8324_rnaseq_Lidia_3years


title: NPAt4

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105348

value: brain tumor cells

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX


title: WKY rep2


title: WKY rep1


title: DRG Cervical treated 2

description: 8382-643 GDC1 P0403 5M

value: Male


title: 8320_rnaseq_Lidia_3years

value: Prefrontal cortex


title: NPAt3

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105347


title: DRG Cervical treated 1

description: 8382-643 GDC1 P0402 5M


title: 8314_rnaseq_Lidia_3years


title: NPAt2

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105346


title: 8312_rnaseq_Lidia_3years


title: DRG Cervical control 4

description: 8382-643 GCD1 P0504 1F

value: Control (0 mg/kg/day)


title: JWH176_SEMmCas9_USF2sgRNA3_USF2_CUT&RUN

city: Memphis

first: Chunliang

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

data_processing:
Cut&Run ChiP-seq reads from each species were aligned using Bowtie2  2.3.4
bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. DeepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016)) was used to convert apping .bam file to .bw file
Genome_build: hg19

source_name: B cell precursor leukemia

growth_protocol: SEM cells were maintained in RPMI-1640 containing 10% fetal bovine serum (FBS) (HyClone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Invitrogen). All cells were maintained at 37°C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Cut&Run ChiP-seq was performed according the the protocol in, Skene PJ, Henikoff S.  2017.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites on Elife. Antibodies against USF2 for a pulldown assay. USF2 antibody from NBP1-92649, Novus was used for immunoprecipitation.
NEBNext Ultra II DNA Library Prep Kit from New England Biolabs (E7645S)

value: B cell precursor leukemia

tag: cell line

value: SEM

tag: chip antibody

value: USF2 (NBP1-92649, Novus)


title: DRG Cervical control 3

description: 8382-643 GCD1 P0501 1F

value: Dorsal Root Ganglia (Cervical)


title: JWH172_SEMhCas9_USF2sgRNA3_USF2_CUT&RUN


title: JWH175_SEMmCas9_USF2sgRNA2_USF2_CUT&RUN


title: DRG Cervical control 2

description: 8382-643 GDC1 P0004 1M


title: Mark3-KO rep2

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
fastq files were QC'd using FASTQC
fastq files were aligned using HISAT2 v 2.0.5
Raw read counts were generated using Stringtie
Differential expression analysis was performed using DESeq2
Genome_build: GRCm38

source_name: primary osteoblasts

growth_protocol: Primary osteoblasts were isolated from the calvaria of 1d old Mark3 flox/flox pups, and plated in 6-well dishes. Cells were grown in 10% FBS aMEM and placed in  5% CO2 37 °C incubator.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-Seq libraries were constructed using TruSeq RNA Library Prep Kit v2 sample prep kits (Illumina).

treatment_protocol: Primary osteoblasts were affected by GFP or CRE adenovirus for 24h.

value: primary osteoblasts

value: CRE-adenovirus 24h


title: JWH171_SEMhCas9_USF2sgRNA2_USF2_CUT&RUN


title: DRG Cervical control 1

description: 8382-643 GDC1 P0003 1M


title: NPAHt1

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105349

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R


title: Mark3-KO rep3


title: Spinal Cord Lumbar treated 4

description: 8382-643 SC6 P0905 5F

source_name: Spinal Cord (Lumbar)

value: Spinal Cord (Lumbar)

value: High (6 mg/kg/day)


title: Spinal Cord Lumbar treated 3

description: 8382-643 SC5 P0904 5F


title: WT-rep2

value: wild-type

value: GFP-adenovirus 24h


title: JWH169_SEMhCas9_lucsgRNA_USF2_CUT&RUN

value: sgLuc


title: JWH170_SEMhCas9_USF2_CUT&RUN

value: wt


title: Mouse_Stromal_rep 2 (S2) bulkRNAseq

city: Edinburgh

first: Philippa

middle: TK

last: Saunders

address: 47 Little France Crescent

department: College of Medicine and Veterinary Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
TruSeq DNA Nano gel free library
Illumina HiSeq 4000 (4 lanes)

data_processing:
Illumina software for basecalling
Sequenced reads were trimmed for adaptor sequence and low quality sequence using cutadapt, then mapped to assembly GRCm38 annotation version 84 using STAR2 version 2.5.2b specifying paired-end reads and '-outSAMtype BAM Unsorted. All other parameters were left at default
Output BAM files for each sample were merged using samtools (4 lanes).
Reads were assigned to exon features and grouped by gene ID in the reference genome using featurecounts3
Genome_build: GRCm38 version 84
Supplementary_files_format_and_content: Text file with featurecounts3 output
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Uterus

extract_protocol:
Enzymatic digestion and FACS
Uteri were removed and mesenchymal cells isolated using FACS
TruSeq DNA Nano gel free library

value: Pdgfrb-BAC-eGFP

value: Healthy uterus

tag: cell population

value: GFPdim cells

value: F


title: WT-rep1

tag: strain


title: Mouse_Stromal_rep 4 (S4) bulkRNAseq


title: Mark3-KO rep1

tag: genotype


title: Mouse_Stromal_rep 3 (S3) bulkRNAseq


title: Mouse_Stromal_rep 5 (S5) bulkRNAseq


title: Spinal Cord Lumbar treated 2

description: 8382-643 SC5 P0403 5M

value: Male


title: JWH161_SEM_USF2_CUT&RUN

data_processing:
library strategy: Cut&Run ChIP-seq
Cut&Run ChiP-seq reads from each species were aligned using Bowtie2  2.3.4
bamCoverage (PMID: 27079975. Nucleic Acids Research (2016)) was used to convert apping .bam file to .bw file
Genome_build: hg19

value: SEM

value: human B-cell lymphoblastic leukemia (B-ALL) cell line


title: Mouse_Stromal_rep 6 (S6) bulkRNAseq


title: Human cerebellar nuclei

description: Human cerebellar nuclei

source_name: Cerbellar nulcei

value: Cerbellar nulcei


title: WT-rep3

value: primary osteoblasts


title: Spinal Cord Lumbar treated 1

description: 8382-643 SC5 P0402 5M


title: Mouse_Naive_rep 6 (N6) bulkRNAseq

value: GFPtotal cells


title: Spinal Cord Lumbar control 4

description: 8382-643 SC5 P0504 1F

value: Control (0 mg/kg/day)

value: Female


title: Mouse_Stromal_rep 1 (S1) bulkRNAseq


title: NPAt1

description:
rawCounts1_HTSeq.txt
rawCounts_Cufflinks1.txt
Sample_105345

value: brain tumor cells

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX


title: IgG

city: Boston

first: Cloud

middle: Peter

last: Paweletz

state: MA

address: 360 Longwood Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The raw sequencing reads were processed using the 10X Genomics CellRanger bioinformatics pipeline v3.0.2.
The assembled matrix was  fed into the standard workflow of the R package, Seurat v2.1.0. Genes that were expressed in at least 3 cells, and only cells that expressed at least 200 genes, were kept for downstream processing. Additionally, cells expressing more than 7000 genes, and cells with more than 18% of UMIs mapping to mitochondrial genes, were removed from the analysis.
The filtered matrix was log-normalized using global scaling in Seurat. The normalized matrix was scaled and centered gene-wise, and then underwent dimensionality reduction using principal component analysis (PCA) on the highly varying genes. After visual inspection of the PCA elbow plot, the top 18 PCs were chosen for further analysis. Clustering was performed on the chosen PCs using the shared nearest neighbor algorithm in Seurat, with default parameters.
A t-SNE map was computed and plotted using the RunTSNE and TSNEPlot modules of Seurat.
Cluster differential expression analysis was performed in Seurat using the FindMarkers command using the Wilcoxon Rank Sum test without thresholds. To further characterize these clusters, pathway analysis was carried out using the ClusterProfiler R package. To estimate pathway scores for single cells, the z-normalized expression values for pathway genes in each cell were summed.  Scores using this method correlated highly with those generated using the AUCell R package (data not shown).  Pathway scores were then added to the MetaData slot of Seurat objects (Aibar et al., 2017).
Genome_build: mm10

source_name: cells after 6 days of ex vivo growth

growth_protocol: Fresh MC38 tumor specimens were dissociated, S2 fraction (40-100um) was re-suspended in a 2.8 mg/mL collagen matrix and loaded into the DAX-1 3-D cell culture chip (AIM Biotech).

extract_protocol:
mDOTS were isolated from the microfluidic device on day 6 of treatment after a 15-minute collagenase treatment. The spheroids were then treated with trypsin in a 37°C incubator for 5 minutes to obtain single cell suspensions. The tumor cells were isolated via FACS, washed, assessed for viability, and loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions.
Single-cell RNA libraries were generated using the Single Cell 3’ Reagent Kit (10X Genomics) per user guide. Quality control of the completed libraries was performed using Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: Drug treatments were performed by diluting drugs in full media and adding 300 µL to each well of the chip.

value: C57BL/6 albino

value: IgG (clone 2A3, 10ug/mL)


title: Mouse_Naive_rep 5 (N5) bulkRNAseq


title: Spinal Cord Lumbar control 3

description: 8382-643 SC5 P0501 1F

value: Spinal Cord (Lumbar)


title: JWH174_SEMmCas9_lucsgRNA_USF2_CUT&RUN

value: B cell precursor leukemia

tag: genotype/variation

value: sgLuc

value: USF2 (NBP1-92649, Novus)


title: aPD-1

value: aPD-1 (clone RMP1-14, 10ug/mL)


title: Mouse_Naive_rep 4 (N4) bulkRNAseq

value: Pdgfrb-BAC-eGFP

value: Healthy uterus

value: F


title: Spinal Cord Lumbar control 2

description: 8382-643 SC6 P0004 1M

value: Male


title: Mouse_Naive_rep 3 (N3) bulkRNAseq


title: Spinal Cord Lumbar control 1

description: 8382-643 SC5 P0003 1M


title: Cancer-associated fibroblasts 2 monoculture, replicate 2

city: Moscow

first: Olga

last: Rakitina

address: 117997, Russian Federation, Moscow, GSP-7, Ulitsa Miklukho-Maklaya, 16/10

department: Department of Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

description:
Sample 25
CAF2 - rep2

data_processing:
The raw reads were mapped on the human reference genome (hg38) using HISAT2 (Galaxy Version 2.1.0+galaxy5)
The featureCounts (Galaxy Version 1.6.4+galaxy1) was used for counting reads to GENCODE release 33 annotated genes.
Mitochondrial genes were removed from the featureCounts output
The obtained read counts were analyzed with DESeq2 (Galaxy Version 2.11.40.6+galaxy1)
Genome_build: hg38
Supplementary_files_format_and_content: .txt format, matrix table with DESeq2 rLog-Normalized counts

source_name: Colorectal tumor

growth_protocol: All the used cell lines were grown in a three-dimensional tumor model based on type I rat tail collagen for 5 days at 37°C in a 5% CO2 humidified atmosphere. Collagen type I was derived from the rat tails according to the standard protocol. To obtain a three-dimensional collagen matrix model, we mixed 3,5 volumes of collagen solution (1.5 mg/ml) with one volume of the reagents mixture (10x Medium 199, NaOH, Na2CO3, glutamine and 1x HEPES). For obtaining the co-culture, tumor cells and fibroblasts were mixed in a ratio of 1: 1.2. Then a suspension of cells was mixed with a collagen gel in a ratio of 1:10. The total cell concentration was 1*10^5 cells/ml with a final concentration of collagen gel 1.2 mg/ml. Then 500 μl of the mixture was immediately pipetted and added to a 35 mm^2 glass-bottom dish and incubated for 30 min at 37°C. Then 2 ml of culture medium (DMEM medium (Gibco, Life Technologies, USA) supplemented with 10% FBS (HyClone, USA), 2 mM glutamine, 10 mg/mL penicillin and 10 mg/mL streptomycin) was added and routinely changed once in two days.

extract_protocol:
At least 250 000 cells were collected by centrifugation and lysed using ExtractRNA (Evrogen, Russia). The cell lysates were stored at – 70°C until RNA extraction. RNA was extracted with RNA Clean & ConcentratorTM-5 (Zymo Research, United States). DNase I treatment was performed in-column manner during the clean-up. The quality of the extracted RNA was determined using TapeStation 2200 (Agilent Technologies, Santa Clara, California, United States) with Agilent High Sensitivity RNA ScreenTape (Agilent Technologies, United States). Since the RINe was greater than 7 for all samples, poly(A) RNA isolation was performed with a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, Massachusetts, United States).
The NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® with Sample Purification Beads (New England BioLabs, United States) and a NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1-3) (New England BioLabs, United States) were used for the preparation of single-indexed libraries. After the preparation, the individually indexed libraries were mixed in equimolar amounts; the final mixture was analyzed with TapeStation using Agilent High Sensitivity DNA ScreenTape (Agilent Technologies, United States). The sequencing was performed with an Illumina NovaSeq 6000 System (Illumina, SP-type, single-end reads, 100 bp).

treatment_protocol: Prior to co-cultivation, NFs were stained in order to separate co-cultured cancer cells and NFs, NFs were stained before co-culturing with CMFDA (Sigma-Aldrich) in serum free medium for 20 min, washed in complete medium and mixed with cancer cells. After 5 days co-culturing cells were detached with trypsin solution and counterstained with propidium iodide for 10-30 min to discriminate dead cells. Live NFs and cancer cells were sorted with FACSAria III sorter (BD Biosciences) into falcon tubes filled with complete medium. After sorting cells were washed once with PBS and processed for RNA isolation.

value: Cancer-associated fibroblasts

tag: sample type

value: CAFs monoculture


title: Spinal Cord Thoracic treated 3

description: 8382-643 SC3 P0904 5F

source_name: Spinal Cord (Thoracic)

value: Spinal Cord (Thoracic)

value: High (6 mg/kg/day)


title: GFP-positive tanycytes P45 KO rep1 (scRNA-seq)

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

data_processing:
Raw scRNA-seq data were processed with the Cell Ranger software (version 3.1) for formatting reads, demultiplexing samples, genomic alignment, and produce the cell-by-gene count matrix.
Using the Seurat R package, we created Seurat objects for each sample with the cell-by-gene count matrix using the function ‘CreateSeuratObject’ (min.cells = 3, min.features = 200).  After visual analysis of the violin plot of the total counts for each cell, we filtered out cells with nCount_RNA < 600 or nCount_RNA > 6000.  Next, we calculated the fraction of mitochondrial genes for each cell and filtered out the cells with a mitochondrial fraction > 8%.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation and raw data matrix txt files

source_name: GFP-positive tanycytes

growth_protocol: P8, P17, and P45 Rax-CreER;Nfialox/lox;Nfiblox/lox;Nfixlox/lox;CAG-lsl-Sun1-GFP mutant mice and control Rax-CreER;CAG-lsl-Sun1-GFP mice were sacrificed by cervical dislocation and brains were dissected.

extract_protocol:
2 mm thick coronal slices including the hypothalamic protruding median eminence (ME) were collected using adult mouse brain matrix (Kent Scientific).  The mediobasal hypothalamic region was microdissected using a surgical scalpel, dampened in Hibernate-A media supplemented with 0.5 mM GlutaMax and 2% B-27 (HABG) and chopped with a razor blade.
Brain tissues were transferred into pre-equilibrated papain/Dnase-I mix (Worthington Papain Dissociation System, #LK003150) and incubated for 30 min at 37°C with frequent agitation using a fire-polished glass pipette.  Dissociated cells were filtered through a 40 μm strainer and subjected to density gradient centrifugation to remove the cell debris as suggested in the manufacturer’s protocol. Cells were resuspended cells with ice-cold PBS containing 0.04% BSA and 0.5 U/μl RNase inhibitor, and 10,000-15,000 cells were loaded on a 10x Genomics Chromium Single Cell system (10X Genomics, Redwood City, CA), using the v3 chemistry following the manufacturer’s instructions, and libraries were sequenced on an Illumina NextSeq with ~200 million reads per library.  Sequencing results were processed through the Cell Ranger 3.1 pipeline (10x Genomics, Redwood City, CA) with default parameters.
single cell RNAseq

value: KO

value: GFP-positive tanycytes

tag: replicates


title: GFP-positive tanycytes P45 KO rep2 (scRNA-seq)

treatment_protocol: P8, P17, and P45 Rax-CreER;Nfialox/lox;Nfiblox/lox;Nfixlox/lox;CAG-lsl-Sun1-GFP mutant mice and control Rax-CreER;CAG-lsl-Sun1-GFP mice


title: GFP-positive tanycytes P45 Ctrl (scRNA-seq)

value: Ctrl


title: GFP-positive tanycytes P8 KO (scRNA-seq)


title: GFP-positive tanycytes P17 KO (scRNA-seq)


title: Mouse_Naive_rep 2 (N2) bulkRNAseq

value: GFPtotal cells


title: Cancer-associated fibroblasts 1 monoculture, replicate 2

description:
Sample 23
CAF1 - rep2


title: Spinal Cord Thoracic treated 4

description: 8382-643 SC3 P0905 5F

value: Female


title: Cancer-associated fibroblasts 2 monoculture, replicate 1

description:
Sample 24
CAF2 - rep1


title: Mouse_Naive_rep 1 (N1) bulkRNAseq


title: Spinal Cord Thoracic treated 1

description: 8382-643 SC3 P0402 5M


title: Atrium

first: Yang

address: 300 George St., Room 8300C 8th floor

department: Pathology

institute: Yale University

description: Transcriptome

data_processing:
DBiT (Deterministic barcoding in tissue)-seq
Illumina Casava 1.8.2 software used for basecalling.
The submitted raw data have been transformed from the original read data. Read 1 contains the barcode and UMI. Read 2 is the biological read. The submitted format is compatible with the software st-pipeline: https://github.com/SpatialTranscriptomicsResearch/st_pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv: Tab-delimited text files include counts for each pixels for each Sample.

source_name: Mouse atrium

extract_protocol:
FFPE samples of adult mouse and mouse embryo were obtained from Zyagen (San Diego, CA). According to Zyagen protocol, the mice used in this project were purchased from Charles River Laboratories. Adult mice were sacrificed upon arrival, and the aorta, atrium and ventricle were collected. The embryo (E10.5) were collected the day the pregnant mouse was received. The FFPE tissues were processed following standard protocols, which includes fixation (10% formalin), dehydration (ethanol series: 70%-100%), clearing (100% xylene), paraffin infiltration and embedding. FFPE sample was sectioned with a thickness of ~10 µm and placed onto a poly-L-lysine coated glass slide. After receiving the sectioned FFPE slides, the tissue sections were stored at -20 °C in a sealed bag until use.
Sequencing library was built using standard Nextera kit from Illumina

value: Untreated

value: Mouse atrium

tag: spatial resolution

value: 25 um


title: Spinal Cord Thoracic treated 2

description: 8382-643 SC3 P0403 5M

tag: tissue


title: Ventricle

description: Transcriptome

source_name: Mouse ventricle

value: Mouse ventricle


title: Normal skin fibroblasts co-cultured with SW480, replicate 3

description:
Sample 21
NFs co-cultured with SW480 cells - rep3

source_name: Skin fibroblasts co-cultured with SW480

value: Skin fibroblasts

value: NFs co-cultured with SW480


title: GFP-positive tanycytes P17 Ctrl (scRNA-seq)


title: GFP-positive tanycytes P8 Ctrl (scRNA-seq)


title: Aorta

description: Transcriptome

source_name: Mouse aorta

value: Mouse aorta


title: GFP-positive tanycytes P8 KO (scATAC-seq)

data_processing:
Raw scRNA-seq data were processed with the Cell Ranger software (version 3.1) for formatting reads, demultiplexing samples, genomic alignment, and produce the cell-by-gene count matrix.  First, the ‘cellranger mkfastq’ function was used to generate fastq files from BCL files.  Second, the ‘cellranger count’ function was used to process fastq files for each library using default parameters and the mm10 mouse reference index provided by 10x Genomics.  Finally, we obtained the cell-by-gene count matrix for each library, and used this for all downstream analysis.
We generated the cell-by-peaks matrix for each sample using the same method as described in Satpathy, A. T. et al .First, we constructed 2.5-kb tiled windows across the mm10 genome using the local script.  Next, a cell-by-window sparse matrix was computed by counting the Tn5 insertion overlaps for each cell, and this matrix was then binarized and inputted to Signac package (0.2.5) to create a Seurat object using ‘CreateSeuratObject.’  Second, we normalized the cell-by-window matrix by TF-IDF methods using ‘RunTFIDF’ and ran a singular value decomposition (SVD) on the TF-IDF normalized matrix with ‘RunSVD.'  We retained the 2nd to 30th dimensions, and identified clusters using SNN graph clustering with 'FindClusters' with a resolution of 0.3.  Third, to identify high-quality peaks for each cluster in each sample, we called peaks for each cluster by MACS2 with the command: '-shift -75 --extsize 150 --nomodel --callsummits --nolambda --keep-dup all -q 0.05'.  The peak summits were then extended to 250 bp on either side to a final width of 500 bp and then filtered by the mm10 v2 blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10blacklist.v2.bed.gz). The top 50,000 peaks for each cluster in each sample were kept, converted to Granges, and merged into a union peak set with the function ‘reduce’ in the GenomicRanges package.
We calculate the TSS enrichment, unique fragments, and nucleosome banding for each cell using the Signac package.  The cell-by-peak sparse matrices were inputted to the ‘CreateSeuratObject’ function to create a Seurat object with default parameters. Then we filtered the cells using the following criteria: 1) The number of unique nuclear fragments > 1000; 2) TSS enrichment score > 2; 3) nucleosome banding score < 4; 4) blacklist_ratio < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: cell_annotation.txt, raw_matrix.mtx

extract_protocol:
2 mm thick coronal slices including the hypothalamic protruding median eminence (ME) were collected using adult mouse brain matrix (Kent Scientific).  The mediobasal hypothalamic region was microdissected using a surgical scalpel, dampened in Hibernate-A media supplemented with 0.5 mM GlutaMax and 2% B-27 (HABG) and chopped with a razor blade.
Single cell ATAC-Seq was performed using the 10x Genomic single cell ATAC reagent V1 kit following the manufacturer’s instructions.  Briefly, FACS-sorted cells (~30k cells) were centrifuged at 300xg for 5 min at 4oC. The cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min.  Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 4oC. The nuclei pellet was resuspended in 250 ul of 1x Nuclei buffer.  Cell nuclei were then counted using Trypan blue staining.  Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on an Illumina NextSeq with ~200 million reads per library.  Sequencing data were processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) with default parameters.
single cell ATACseq


title: Spinal Cord Thoracic control 4

description: 8382-643 SC3 P0504 1F

value: Control (0 mg/kg/day)


title: Cancer-associated fibroblasts 1 monoculture, replicate 1

description:
Sample 22
CAF1 - rep1

value: Cancer-associated fibroblasts


title: Normal skin fibroblasts co-cultured with SW480, replicate 2

description:
Sample 20
NFs co-cultured with SW480 cells - rep2


title: Spinal Cord Thoracic control 3

description: 8382-643 SC3 P0501 1F


title: FFPE-2

description: Transcriptome

source_name: Mouse embryo E10.5

value: Mouse embryo E10.5


title: GFP-positive tanycytes P8 Ctrl (scATAC-seq)


title: Normal skin fibroblasts co-cultured with SW480, replicate 1

description:
Sample 19
NFs co-cultured with SW480 cells - rep1


title: FFPE-1

description: Transcriptome


title: Spinal Cord Thoracic control 2

description: 8382-643 SC3 P0004 1M

value: Spinal Cord (Thoracic)

value: Male


title: Spinal Cord Thoracic control 1

description: 8382-643 SC3 P0003 1M


title: Microglia_KO_2

city: Montreal

first: Stephane

last: Richard

address: 3755 Côte Ste-Catherine Road

country: Canada

institute: McGill University

data_processing:
Illumina HiSeq 4000
Sequenced reads were trimmed with Trimmomatic v0.39
STAR v2.7.1a was then used to align the reads to the mouse genome (mm10/GRCm38)
Gene expression was quantified across all samples with HOMER v4.11.1, and the normalization was carried out through the regularized logarithm (rlog) transformation of DESeq2 v1.26.0
Differential expression was calculated through DESeq2 v1.26.0, and the gene expression was considered significantly different if the absolute value of the log-fold-change (LFC) was higher than 2, the base means larger than 10 and the false discovery rate (FDR) less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: rlog table with fold change and p value

source_name: Microglia

extract_protocol:
Brains were digested, and myelin were removed using 30% percoll gradient. Microglia was isolated using Facs sorting method using CD45 and CD11B surface markers
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adult 4-5 weeks

value: QKIflfl; Cx3cr1cre-ert2

value: Microglia


title: Microglia_KO_3


title: Spinal Cord Cervical treated 4

description: 8382-643 SC1 P0905 5F

source_name: Spinal Cord (Cervical)

value: Spinal Cord (Cervical)

value: High (6 mg/kg/day)


title: SW480 co-cultured with NFs, replicate 3

description:
Sample 18
Co-cultured SW480 cells - rep3

source_name: colorectal cancer cell line co-cultivated with NFs

value: Colorectal cancer (mesenchymal)

value: SW480 co-culture with NFs


title: Microglia_KO_1


title: SW480 co-cultured with NFs, replicate 1

description:
Sample 16
Co-cultured SW480 cells - rep1


title: SW480 co-cultured with NFs, replicate 2

description:
Sample 17
Co-cultured SW480 cells - rep2


title: Spinal Cord Cervical treated 3

description: 8382-643 SC2 P0904 5F

value: Female


title: Normal skin fibroblasts co-cultured with HT29, replicate 3

description:
Sample 15
NFs co-cultured with HT29 cells - rep3

source_name: Skin fibroblasts co-cultured with HT29

value: NFs co-cultured with HT29


title: Microglia_WT_2

value: QKIfl/fl


title: Microglia_WT_3


title: Spinal Cord Cervical treated 1

description: 8382-643 SC1 P0402 5M


title: Normal skin fibroblasts co-cultured with HT29, replicate 2

description:
Sample 14
NFs co-cultured with HT29 cells - rep2

value: Skin fibroblasts


title: Spinal Cord Cervical control 4

description: 8382-643 SC1 P0504 1F


title: Spinal Cord Cervical treated 2

description: 8382-643 SC1 P0403 5M


title: Pchabaudi - replicate 3 [P3]

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 2.0.1
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and its built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

extract_protocol:
Bioline RNA kit extraction protocol
RNA-seq libraries were prepared from effector memory gd T cell : 1 ng of total RNA using the Illumina Truseq RNA-seq kit (Illumina).

treatment_protocol: N/A (no in vitro treatment. Cells were assessed ex vivo)

tag: strain background

value: Pchabaudi

value: spleen

value: Splenocytes

tag: cell subtype

value: CD62L-CD44+γδ T cells (EM)


title: Pchabaudi - replicate 4 [P4]

tag: cell type


title: Spinal Cord Cervical control 3

description: 8382-643 SC1 P0501 1F

value: Control (0 mg/kg/day)

tag: Sex


title: Pchabaudi - replicate 2 [P2]


title: Normal skin fibroblasts co-cultured with HT29, replicate 1

description:
Sample 13
NFs co-cultured with HT29 cells - rep1


title: Naive - replicate 4 [N8]

value: Naive


title: HT29 co-cultured with NFs, replicate 3

description:
Sample 12
Co-cultured HT29 cells - rep3

value: Colorectal cancer (epithelial)

value: HT29 co-cultured with NFs


title: Naive - replicate 3 [N7]


title: Naive - replicate 5 [N9]


title: Pchabaudi - replicate 1 [P1]


title: HT29 co-cultured with NFs, replicate 2

description:
Sample 11
Co-cultured HT29 cells - rep2


title: 460_WholeSpleen

first: Tawaun

middle: Autry

last: Lucas

address: 1201 Welch Rd

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim galore
Trimmed reads were mappped to the mm10 genome using STAR --outSAMunmapped Within  --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1
Aligned reads were quantified using RSEM
Counts were modified using cellular deconvoultion and re-adjusted to reflect purity
Differential expression analysis conducted using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: excel file of differential expression for genes that include our expression cutoffs include FPKM values for each Sample ...

source_name: Whole Spleen

extract_protocol:
Spleens were dissected, minced and resuspended in 4ml of dissociation buffer and incubated with constant agitation or 1 h. After the hour, Dispase II (2mg/ml) was added and the samples were incubated for an additional 30 min. Upon completion, 5 mM EDTA was added to the sample and incubated at room temperature for 5 min and subsequently centrifuged. Red blood cells were lysed and samples were diluted with 13 ml of cold PBS + FBS before another centrifugation at . The cell pellets were resuspended in of PBS +  FBS and passed through a cell strainer. After washing, the remaining cells on the filter (size-selected), were lysed using RLT buffer.
Libraries were prepared using standard Illumina protocols

value: Spleen


title: Pchabaudi - replicate 5 [P5]


title: 460_SizeSelected

source_name: Spleen Glia


title: Naive - replicate 2 [N6]


title: 447_WholeSpleen


title: Microglia_WT_1

tag: age

value: Adult 4-5 weeks

value: Microglia


title: Spinal Cord Cervical control 2

description: 8382-643 SC1 P0004 1M

value: Spinal Cord (Cervical)

value: Male


title: Naive - replicate 1 [N5]

value: Female


title: HT29 co-cultured with NFs, replicate 1

description:
Sample 10
Co-cultured HT29 cells - rep1


title: Liver treated 4

description: 8382-643 LI1 P0905 5F

source_name: Liver

value: Liver

value: High (6 mg/kg/day)


title: Normal skin fibroblasts monoculture, replicate 3

description:
Sample 9
Monocultured NFs - rep3

source_name: monocultured skin fibroblasts

value: Skin fibroblasts

value: NFs monoculture


title: 445_WholeSpleen


title: Normal skin fibroblasts monoculture, replicate 2

description:
Sample 8
Monocultured NFs - rep2


title: Liver treated 1

description: 8382-643 LI1 P0402 5M


title: 447_SizeSelected


title: 436_WholeSpleen


title: ATAC_WT_REP2

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Str. 10

department: Cancer Research

country: Germany

institute: MDC Berlin

data_processing:
ATAC read alignment Bowtie2
ATAC peak calling: MACS2
ATAC differential peak detection: DiffBind (version 2.14.0)
Genome_build: mm10
Supplementary_files_format_and_content: differential peaks dKO:dKOLAPSTAR; WT:dKO

extract_protocol:
For each cell line, three independent RNA samples were isolated at different time points. 50,000 cells were sorted into 500 μL PBS and immediately processed as described under "library construction protocol"
To prepare the ATAC sequencing libraries, 50,000 cells were sorted into 500 μL PBS. The libraries were prepared as previously described (Buenrostro et al., 2013) with slight modifications (Lara-Astiaso et al., 2014). Briefly, the cells were lysed with 25 μL cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM MgCl2, 0.1% Igepal CA-630) and the nuclei were pelleted by centrifugation for 25 min at 4°C and 500 g in a swing rotor with low acceleration and brake settings. The pellet was resuspended in 25 μL reaction mix containing 2 μL Tn5 transposase and 12.5 μL TD buffer (Nextera DNA library preparation kit, Illumina), and incubated at 37°C for 1 h. Next, 5 μL cleanup buffer (900 mM NaCl, 30 mM EDTA) with 2 μL 5% SDS and 2 μL Proteinase K (NEB) were added, and the samples were incubated at 40°C for 30 min. Subsequently, the DNA was purified using AMPure XP beads (Beckman Coulter) and PCR-amplified with Kapa HiFi HotStart ReadyMix (Kapa Biosystems) and indexing primers published previously (Buenrostro et al., 2013). Then, the DNA library fragments were selected for <600-bp fragments and purified using AMPure XP beads. The concentration and fragment size of the final libraries were measured using a Qubit fluorometer (Life Technologies) and TapeStation (Agilent Technologies). The samples were sequenced with an average of 25 million reads per sample using a NextSeq 500 (Illumina).

treatment_protocol: MLL-ENL transformed cell lines were maintained in IMDM with 10% FCS, supplied with murine IL-3 (10 ng/ml). Cultures were passaged three times a week or when the cell number exceeded 1.5x10^6 per 1 ml.

value: MLL-ENL transformed fetal liver cells

value: wild-type


title: ATAC_WT_REP1


title: Normal skin fibroblasts monoculture, replicate 1

description:
Sample 7
Monocultured NFs - rep1


title: 445_SizeSelected

institute: Stanford University


title: Liver treated 3

description: 8382-643 LI1 P0904 5F


title: Liver control 4

description: 8382-643 LI1 P0504 1F


title: 436_SizeSelected


title: ATAC_LAPS_REP2

value: Cebpa KO, Cebpb KO

tag: exogenous expression

value: GFP, rat CEBP/b isoform LAP*


title: SW480 monoculture, replicate 1

description:
Sample 4
Monocultured SW480 cells - rep1

source_name: monocultured colorectal cancer cell line

value: Colorectal cancer (mesenchymal)

value: SW480 monoculture


title: ATAC_LAPS_REP1


title: ATAC_dKO_REP2

value: GFP


title: SW480 monoculture, replicate 3

description:
Sample 6
Monocultured SW480 cells - rep3


title: SW480 monoculture, replicate 2

description:
Sample 5
Monocultured SW480 cells - rep2


title: 435_WholeSpleen

value: Spleen


title: HT29 monoculture, replicate 3

description:
Sample 3
Monocultured HT29 cells - rep3

value: Colorectal cancer (epithelial)

value: HT29 monoculture


title: Liver control 3

description: 8382-643 LI1 P0501 1F

tag: treatment

value: Control (0 mg/kg/day)


title: 435_SizeSelected

value: Male


title: Liver control 2

description: 8382-643 LI1 P0004 1M


title: RNA_C2_WT_REP3

data_processing:
RNA read alignment: STAR (version 2.5.3a)
RNA read quantification: HTSeq (version 0.10.0)
RNA differential gene expression: DESeq2 (version 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: RNA: normalized read count, csv

extract_protocol:
For each cell line, three independent RNA samples were isolated at different time points.
The total RNA was isolated from cells using the RNeasy Kit (Qiagen). The Qiagen RLT lysis buffer was additionally supplied with β-mercapthethanol (10μl per 1ml buffer). The cell lysates were thoroughly homogenized by passing through syringe with 20-G needle. The concentration and purity of the extracted RNA was measured on Qubit 3 Fluorometer (Thermo Fisher Scientific). For each cell line, three independent RNA samples were isolated at different time points. The further analyze of RNA quality and integrity was assessed on Bioanalyzer 2100 (Agilent Technologies), using the Eukaryote Total RNA Nano assay. The subsequent libraries preparation and Next Generation Sequencing (NGS) on the NextSeq500 platform (Illumina) was performed in collaboration with Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin (Dr. Tatiana A. Borodina)


title: Liver treated 2

description: 8382-643 LI1 P0403 5M


title: 427_WholeSpleen


title: Liver control 1

description: 8382-643 LI1 P0003 1M


title: ATAC_dKO_REP1


title: HT29 monoculture, replicate 1

description:
Sample 1
Monocultured HT29 cells - rep1


title: HT29 monoculture, replicate 2

description:
Sample 2
Monocultured HT29 cells - rep2


title: 427_SizeSelected


title: RNA_C2_WT_REP1