title: hESC_Dox5 scRNA-Seq

description:
hESC_Dox5
Read 1 (R1) - Cell barcode (position 1-16bp) and unique molecular identifier (position 17-26bp). Read 2 (R2) - Biological reads.

data_processing:
Illuminla base call (BCL) files were de-multiplexed and converted to fastq format using the mkfastq funcion in CellRanger version 2.1.1
The data was then aligned to the human genome (hg38) and unique molecular identifiers (UMI) were counted using the count function in the CellRanger software.
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 feature barcode matrix files generated using the CellRanger count software. This file contains the UMI counts for each detected gene in each sequenced cell.

extract_protocol:
Non-adherent progenitors at day 22 of differentiation (untreated and 24-hour Dox treatment) were sorted for CD45+ CD34+ and RUNX1C+. Cells were re-suspended in 80 μl at a concentration of 100-1200 cells/μl for evaluation of cell viability prior to loading of 4000 single cells on a Chromium Single Cell Instrument (10X Genomics).
Library generation for scRNA-seq was performed by the Genomics Birmingham Sequencing Facility using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10X Genomics). Libraries were paired-end sequenced on an Illumina NextSeq machine using the cycle parameters recommended by 10X Genomics.

tag: cell line


title: shALKBH5-#1 ActD 8h

status: Public on May 26 2020

type: SRA

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

description: shALKBH5-#1 ActD 8h

library_source: transcriptomic

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the  human GRCh38 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

molecule: total RNA

organism: Homo sapiens

source_name: AML cell line NOMO-1

growth_protocol: NOMO-1 cells were  routinely  kept in RPMI1640 mediun with 10% FBS at 0.5*10^6 cells/ml and were passeged every other day.

extract_protocol:
The total RNA were extracted with QIAzol lysis reagent.
FastTrack MAG Maxi mRNA isolation kit

treatment_protocol: About 1*10^6 cells were infected with lentivirus targeting FTO collected from 6 cm dish with existence of 1ug/ml polybrene for spinoculation (1,200 rpm, 32℃，1 hour). 48 hours later, the positive cells were selected with 1ug/ml puromucin for 1 week. As durg treatment, NOMO-1 cells were seed in 10 cm dishes at 0.5*10^6 cells/ml and treated with 100nM CS1, 500nM CS2 or DMSO for 72 hours.

tag: cell type

value: Acute myeloid leukemia

tag: lentivirus

tag: treatment

value: ActD

tag: time point


title: shALKBH5-#1 ActD 0h

description: shALKBH5-#1 ActD 0h


title: shALKBH5-#2 ActD 12h

description: shALKBH5-#2 ActD 12h


title: shNS ActD 12h Rep2

description: shNS ActD 12h Rep2

value: shNS


title: shALKBH5-#2 ActD 0h

description: shALKBH5-#2 ActD 0h


title: hESC_Dox0 scRNA-Seq

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description:
hESC_Dox0
Read 1 (R1) - Cell barcode (position 1-16bp) and unique molecular identifier (position 17-26bp). Read 2 (R2) - Biological reads.

source_name: hESC H9 cell line

growth_protocol: Culture and enzymatic passaging of hESC lines was conducted as previously reported by Ng et al. (2008) Nat. Protoc. 3, 768–776.

treatment_protocol: Hematopoietic differentiation of human ESCs was performed following the spin Embryo Body (EB) method in STAPEL medium with supplements used as reported  by Ng et al (2016) Blood 120, 4038–4048. with some modifications, detailed below. Albumin was substituted for a 1:1 mixture of albumin from rice endosperm (ScienCell Research Labs cat# OsSA) and Bovostar acid stripped Bovine Serum Albumin (BSA, Bovogen cat# BSAS 0.1). For the first 4 days, 7.5 ng/ml ACTIVIN A (ACT, R&D Systems cat# 338-AC) and 0.5 μM CHIR99021 (Tocris Biosciences cat# 4423) were used and 3.5 µM SB431542 (Sapphire Bioscience cat# 13031) and 3 µM CHIR99021 were added 4-6 hours before the day 2 time point and until day 4. After day 4, 5 ng/ml BMP4 and 10 ng/ml Insulin-like growth factor 2 (IGF2, PeproTech cat# 100-12) were used instead of the original concentrations. Adherent cultures after d8 were supplemented with 20 ng/ml BMP4, 100 ng/ml stem cell factor (SCF, PeproTech cat# 300-07), 100 ng/ml FMS-like tyrosine kinase 3 receptor (FLT3) ligand (PeproTech cat# 300-19), 50 ng/ml Thrombopoietin (TPO, PeproTech cat# 300-18), 50 ng/ml vascular endothelial growth factor (VEGF, PeproTech cat# 100-20), 25 ng/ml Interleukin (IL) 3 (PeproTech cat# 200-03), 25 ng/ml IL6 (PeproTech cat# 200-06), 20 ng/ml IGF2, 10 ng/ml basic Fibroblast Growth Factor (FGF2, PeproTech cat# 100-18B) and 1x Penicillin/Streptomycin (Pen/Strep, 5000 U/ml and 5000 U/ml respectively, Thermo Fisher Scientific cat# 15140122). Plates were toped up with media every 3 days and half-media changes were performed when the media capacity of the plate was reached. Upon Dox treatment, adherent cultures were supplemented with a ‘5-factor’ cytokine mix including 100 ng/ml SCF, 100 ng/ml FLT3 ligand, 50 ng/ml TPO, 25 ng/ml IL3 and 25 ng/ml IL-6. For analysis, EBs were harvested at different time points and dissociated into single-cell suspensions using TryPLE select (Invitrogen) for non-adherent EBs and Collagenase Type 1 or Type 4 (Worthington, CLS-1 or CLS-4) for adherent EB cultures and passed through 23- and 25-gauge needles and a 40µm filter.


title: Runx1cPos_5Dox_Rep3 RNA-Seq

data_processing:
Reads were processed with Trimmomatic v0.32 to remove low quality bases and sequencing adaptors
Processed reads were aligned to the human genome (hg38) using Hisat2 v2.1.0 with default parameters
Gene expression was quantified as Fragments Per Kilobase per Million mapped reads (FPKM) using Stringtie v1.3.3 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited file containing gene symbols and FPKM values

extract_protocol:
Total RNA was extracted using the Bioline Isolate II RNA Mini Kit according to the manufacturers’ instructions. cDNA was reverse-transcribed using random hexamer priming and Tetro cDNA synthesis kit (Bioline) or using Oligo (dT)18 priming and SuperScript™ II Reverse Transcriptase (Thermo Fisher Scientific) according to the manufacturers’ instructions.
RNA-seq libraries were prepared using a TruSeq Stranded mRNA Library Prep (Illumina cat# 20020594) following the Low Sample (LS) workflow according to manufacturer’s instructions.


title: Runx1cPos_5Dox_Rep2 RNA-Seq


title: shNS ActD 8h Rep2

description: shNS ActD 8h Rep2


title: shNS ActD 12h Rep1

description: shNS ActD 12h Rep1


title: shNS ActD 0h Rep2

description: shNS ActD 0h Rep2


title: Runx1cPos_3Dox_Rep3 RNA-Seq


title: Runx1cPos_3Dox_Rep2 RNA-Seq


title: shNS ActD 0h Rep1

description: shNS ActD 0h Rep1


title: Runx1cPos_10Dox_Rep3 RNA-Seq


title: Runx1cPos_3Dox_Rep1 RNA-Seq


title: Runx1cPos_0Dox_Rep3 RNA-Seq


title: Runx1cPos_10Dox_Rep2 RNA-Seq


title: Runx1cPos_0Dox_Rep2 RNA-Seq


title: Runx1cPos_10Dox_Rep1 RNA-Seq


title: shALKBH5 IP

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the hg38 genome assembly using Tophat 2.1.1
peaks were called using MACS2 and exomePeak. Only the peaks called by both the two tools are retained for further analysis.
the m6A peaks were annotated using an ad hoc perl script.
GSEA was used to perform pathway enrichment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization

molecule: polyA RNA

source_name: NOMO1 cells

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
RNA fragmentation, m6A-Seq and library preparation were performed according to previous protocals (Dan et al., 2012)

value: NOMO1 cells

value: AML cell line

tag: antibody

value: m6A antibody

tag: genotype/variation


title: shALKBH5-#2 ActD 8h

description: shALKBH5-#2 ActD 8h


title: HIV_Pos_1_106_BAL

city: Durban

first: Daniel

last: Muema

address: 719 Umbilo Road

country: South Africa

institute: Africa Health Research Institute

data_processing:
The raw data were demultiplexed and processed using Trimmomatic version 0.36 to remove adaptors and leading/trailing low-quality bases.
The sequences were aligned on the human reference genome GRCh37 (hg19) using the TopHat module (version 2.1.1) and bowtie (version 2.2.4).
The mapped reads were then sorted using the Picard SortSam module. Duplicate reads were identified using the Picard MarkDuplicates module and removed.
The Cufflinks module (Version 2.2.1) was used for subsequent analyses. The transcripts for each sample were assembled and the numbers of reads quantified for each transcript. The expression levels were expressed as Fragments Per Kilobase of transcript per Million fragments mapped (FPKM). The assembled transcripts for all samples were merged to obtain a master transcriptome assembly (Cuffmerge) followed by assessment of differential expression (Cuffdiff).
Genome_build: hg19

source_name: Bronchoalveolar lavage cells

extract_protocol:
For work on unsorted cells, total RNA was extracted from RNAlater-stored cellular pellets using Qiagen RNeasy Micro kit (Qiagen, Hilden, Germany). For work on purified CD8+ T cells, cells were sorted into 70% TRIzol LS Reagent (Thermo Fisher Scientific, Waltham, MA, USA)  followed by isolation of both RNA and DNA using the TRIzol/chloroform method. Total RNA was then extracted using Qiagen RNeasy Micro kit. Enrichment for messenger RNA was done using the NEBNext Poly(A) mRNA Magnetic Isolation kit (New England Biolabs, Ipswich, MA, USA).
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) in accordance to the manufacturer's instructions.

tag: tissue

value: Bronchoalveolar lavage cells

value: Bulk (unsorted cells)

tag: disease state

value: HIV positive


title: shALKBH5 Input


title: Negative control shRNA IP

value: Negative control shRNA


title: Runx1cPos_5Dox_Rep1 RNA-Seq


title: 20

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq 1.8.4
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then the gene expression was quantified by RSEM (v1.2.18) against Ensembl GRCh37 reference build.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw count values

source_name: B cell clones

growth_protocol: Peripheral human B cells were immortalized by transduction with BCL6 and BCL-XL and expanded in vitro by culturing with CD40L-expressing murine fibroblasts + IL-21. Clones were obtained by sorting single cells using a FACS ARIA cell sorter and expanded in vitro.

extract_protocol:
RNA was isolated using the RNeasy micro kit (Qiagen)
RNA libraries were prepared for sequencing using Illumina TruSeq RNA stranded kit

treatment_protocol: Epxanded B cell clones were stimulated with an anti-BCR antibody 4 hours prior to RNA isolation

value: B cell clone

tag: specifitity

value: PLA

tag: donor


title: Runx1cPos_0Dox_Rep1 RNA-Seq


title: Negative control shRNA Input


title: 27

value: TT


title: shNS ActD 8h Rep1

description: shNS ActD 8h Rep1


title: 6


title: Runx1cNeg_5Dox_Rep2 RNA-Seq


title: Runx1cNeg_5Dox_Rep1 RNA-Seq


title: 7

value: unspecified


title: Runx1cNeg_3Dox_Rep3 RNA-Seq


title: 5


title: Runx1cNeg_3Dox_Rep1 RNA-Seq


title: Runx1cNeg_10Dox_Rep2 RNA-Seq


title: 3


title: 2


title: 4


title: 26


title: Runx1cNeg_10Dox_Rep1 RNA-Seq


title: Runx1cNeg_10Dox_Rep3 RNA-Seq


title: 24


title: 23


title: 25


title: Runx1cNeg_0Dox_Rep2 RNA-Seq


title: Runx1cNeg_0Dox_Rep3 RNA-Seq


title: Runx1cNeg_0Dox_Rep1 RNA-Seq


title: H3K4me3_5Dox ChIP-Seq

library_source: genomic

data_processing:
Single-end reads were processed to remove low-quality bases and sequencing adaptors using Trimmomatic v0.32.
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.6 with the parameter --very-sensitive-local.
Peaks were identified using MACS2 v2.1.1 with default settings.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files produced by MACS2

molecule: genomic DNA

extract_protocol:
ChIP was performed on CD34+ magnetic sorted samples (RUNX1-ETO and RUNX) and on non-adhered floating mixed progenitors (H3K4me3 and H3K27ac) after single crosslink. Antibodies were used against the following antigens (manufacturer, cat #): HA tag (Sigma, H6908), RUNX1 (ab23980, Abcam), H3K27ac (Abcam, ab4729), H3K4me3 (Merk, 07-473), H3K79me2 (Abcam, ab3594). For H3K79me2 ChIP, a concentration of at least 0.2% SDS on the chromatin suspension was used and immunoprecipitation was carried overnight.
ChIP libraries for Illumina sequencing were prepared using the KAPA Hyper Prep Kit (Roche, KR0961), as detailed by the manufacturer. Quality control of the libraries was performed using a High Sensitivity DNA chip on an Agilent Technologies 2100 Bioanalyser instrument and libraries were quantified using the RT-qPCR-based method KAPA Library Quantification Kit for Illumina Sequencing Platforms, following the manufacturer’s protocol.

tag: target


title: Runx1cNeg_5Dox_Rep3 RNA-Seq


title: H3K4me3_0Dox ChIP-Seq


title: 22


title: 21


title: Runx1cNeg_3Dox_Rep2 RNA-Seq


title: H3K27ac_0Dox ChIP-Seq


title: H3K27ac_5Dox ChIP-Seq


title: 19


title: 16


title: RUNX1_0Dox ChIP-Seq


title: 15


title: RUNX1_5Dox ChIP-Seq


title: 17


title: 1


title: HA-RUNX1-ETO_0Dox ChIP-Seq

value: HA-tagged RUNX1-ETO


title: Input ChIP-Seq

description: Input

value: Input DNA


title: Runx1cPos_5Dox ATAC-Seq

data_processing:
Single-end reads from ATAC-Seq experiments were processed to remove low-quality bases and sequencing adaptors using Trimmomatic.
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.6 with the parameter --very-sensitive-local. Reads that aligned to the mitochondrial genome were removed from further analysis.
Potential PCR duplicated reads were identified and removed from the alignments using Picard v2.10.5
Open chromatin regions (peaks) were identified using MACS2 v2.1.1 using the settings --nomodel --nolambda -B --trackline.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files generated by MACS v2.1.1

extract_protocol:
50,000 single-cell sorted hematopoietic progenitors were pelleted and snap-frozen upon resuspension in 5 μl sucrose freezing buffer, consisting of 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris pH 7.4 and 1.5 M sucrose.
Transposition reaction was performed for 30 minutes at 37°C upon addition of 45 μl of ATAC reaction mix consisting of 25 μl Tagmentation DNA Buffer (Illumina cat# FC-121-1030, Nextera DNA Library Prep Kit), 2.5 μl Tn5 Transposase enzyme (Illumina cat# FC-121-1030, Nextera DNA Library Prep Kit), 1 μl of 0.5% Digitonin (Promega cat# G9441) and 16.5 μl water. DNA was purified using a MinElute Reaction Cleanup Kit (Qiagen cat# 28204). Purified DNA fragments were amplified using Customized Nextera PCR Primer Adaptors and NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs cat# M0541). Adaptor dimers were cleaned up from the libraries using AMPure magnetic beads (Beckman Coulter) prior to validation. Libraries were evaluated using a High Sensitivity DNA chip on an Agilent Technologies 2100 Bioanalyser™ instrument and concentration was measured using a RT-qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms). Libraries were also validated by RT-qPCR evaluation of the ratio of open (TBP promoter) to closed regions of DNA (chromosome 18) and active gene body (β-actin).


title: Runx1cPos_3Dox ATAC-Seq


title: HA-RUNX1-ETO_5Dox ChIP-Seq


title: 12


title: 14


title: Runx1cPos_10Dox ATAC-Seq


title: 10


title: Runx1cPos_0Dox ATAC-Seq


title: Runx1cNeg_3Dox ATAC-Seq


title: Runx1cNeg_5Dox ATAC-Seq


title: 8


title: 18


title: Runx1cNeg_10Dox ATAC-Seq


title: Runx1cNeg_0Dox ATAC-Seq


title: XT0106_CD8_HC

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
PolyAtail selected messenger RNA
Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD8 T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).
RNA-Seq (HISeq 2500 illumina, Single-end 50bp)

treatment_protocol: No specific treatment involved

tag: disease group

value: Healthy

tag: cell subset

value: Memory CD3+CD8+ T cells


title: XT0123_CD8_HC


title: XT0134_CD8_LTBI


title: XT0082_CD8_HC


title: 13


title: TU0110_CD8_HC


title: 11


title: X6_5 - CBE+GZ-667161

city: Rehovot

first: Anthony

last: Futerman

address: Herzl

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome.
The pipeline quantifies the genes annotated in Gencode (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Read count was performed with HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis is done for genes having minimum 5 reads in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg
Fdr correction: - The pipeline computes the fractions of the p-values between 0.25 and 1, and uses them to recompute the fractions for the following bins: (0.25,0.5], (0.5,0.75], and (0.75,1). If the result is not between 0.28 and 0.38 for at least one of these bins, we apply the fdrtool (R package, DOI: 10.1186/1471-2105-9-303) correction, to compensate for the uneven distribution of p values between 0.25 and 1. - The fdrtool correction is also applied if the fraction of the p-values between 0 and 0.25 is less than 0.2, since that could indicate an over-estimation of the negative binomial dispersion.
Differentially expressed genes (DEGs) were selected using a 2-fold change and adjusted p value for multiple gene testing (<0.05) between two populations (with one exception when a 1.4-fold change was used) (Kohen et al. 2019).
UTAP: User-friendly Transcriptome Analysis Pipeline. Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran and Dena Leshkowitz (in revision BMC Bioinformatics).
Genome_build: mm10
Supplementary_files_format_and_content: Raw reads were mapped to the Mus musculus genome (mm10) using hisat (version 0.1.6). Only reads with unique mapping were considered for further analysis.

organism: Mus musculus

source_name: Whole brain

extract_protocol:
Brain tissues were homogenized using a GentleMACS dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) and mRNA was isolated using an RNeasy mini kit (Qiagen, Hilden, Germany).
A bulk variation of MARSseq (Jaitin et al. 2014) was used to construct RNAseq libraries.

tag: agent

tag: strain

tag: age

value: post natal 40


title: TU0085_CD8_HC


title: X6_3 - CBE+GZ-667161


title: TU0094_CD8_HC


title: X5_4 - CBE

value: CBE


title: 9


title: X5_3 - CBE

value: post natal 34


title: TU0070_CD8_LTBI

value: Latent tuberculosis infection


title: TU0071_CD8_HC


title: X1_5 - PBS

value: PBS


title: TU0075_CD8_LTBI


title: X1_4 - PBS


title: TU0063_CD8_LTBI


title: TU0059_CD8_HC


title: NOMO1 shNS Rep1

description: NOMO1 shNS Rep1

value: Acute myeloid leukemia

value: shNS

tag: cell line


title: TU0057_CD8_HC


title: X1_2 - PBS


title: TU0056_CD8_HC


title: X6_4 - CBE+GZ-667161


title: TU0053_CD8_HC


title: TU0052_CD8_HC


title: X6_2 - CBE+GZ-667161


title: X5_6 - CBE


title: TU0050_CD8_HC


title: Tdgf1GFPplus, Bulk RNA-seq, Replicate 1

city: Boston

first: Richard

middle: I

last: Sherwood

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics, Department of Medicine

institute: Brighan and Women's Hospital and Harvard Medical School

data_processing:
barRNA-seq transcriptome reads were mapped using the 10X cellranger pipeline (v1.3.1) to mm10 (v.1.2.0).
barRNA-seq barcodelet reads were mapped using the 10X cellranger pipeline (v1.3.1) modified with a custom mapping step that first aligns and trims the common right flanking sequence, and then maps the remaining sequence to the known pool of unique barcodelet sequences. The alignment allows for 4 mismatches in the right flanking sequence, and 2 mismatches in the unique subsequence. The output of the pipeline is UMI-unique barcodelet counts for each cell.
To assign each cell a treatment combination, we inspect the top k most abundant barcodelet species in the count data, where k is the number of barcodelets each cell was labeled with, and compute the summed count fraction of these top k barcodelets. We expect that invalid combinations observed are due to noise. Since we also know the expected fraction of invalid combination based on the size of the starting pool of barcodelets, we can estimate the false positive rate at any given summed count fraction. To ensure labeling fidelity, we set the threshold on the summed count fraction at a false positive rate of 1%, and assign all cells above that threshold for which the barcodelet combination was valid. We retain the set of cells which have been assigned a treatment combination and that also have a high quality transcriptome for downstream analysis.
Bulk RNA-seq reads were mapped using the Quantseq 3' mRNA mapping pipeline as described by lexogen to mm10. Briefly, reads were first trimmed using bbduk from the bbmap suite (v37.75) trimming for low quality tails, poly-A read-through and adapter contamination using the recommended parameters. Then, reads were mapped using the STAR aligner (v2.5.2b) with the recommended modified-Encode settings. Finally, HT-seq (v0.9.1) count was used to obtain per-gene counts.
Genome_build: mm10
Genome_build: germlayer_bcd.fa (reference for germlayer_bcd.possorted_genome_bam.bam)
Genome_build: mesendoderm_bcd.fa (reference for mesendoderm_bcd.possorted_genome_bam.bam)
Genome_build: mixed_bcd.fa (reference for mixed_bcd.possorted_genome_bam.bam)
Supplementary_files_format_and_content: Gene-barcode matrices are stored as matrices in *mtx files, with gene and barcode metadata in *tsv files. These are generated by 10X, and more information on the format can be found here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/1.3/output/matrices. Filtered gene-barcode matrices are provided for transcriptomic reads, while raw gene-barcode matrices are provided for the barcodelet reads.
Supplementary_files_format_and_content: Treatment group assignments are stored in *assignments.csv files.

source_name: Mouse embryonic stem cells

growth_protocol: Culture and differentiation of 129P2/OlaHsd male mouse embryonic stem cells was modified slightly from previously published protocols (Sherwood et al., 2014). mESCs were grown at 37 degrees Celsius in mESC media: Knockout DMEM supplemented with 15% ES-tested fetal bovine serum, 0.1 mM nonessential amino acids, Glutamax, 0.55 mM 2-mercaptoethanol (all from Thermo Fisher), 1X ESGRO LIF, 5 µM GSK3 inhibitor XV, and 50 µM UO126 (Millipore).

extract_protocol:
For Foxa2GFPplus, Foxa2GFPminus and Tdgf1GFPplus samples, cell populations were flow cytometrically isolated prior to RNA isolation
3’-enriched RNA-sequencing was performed using the Lexogen Quantseq 3’ mRNA-seq kit using manufacturer-suggested protocols and sequenced using Illumina Nextseq

treatment_protocol:
To induce differentiation, cells were grown for 48 hours in mESC media without GSK3 inhibitor XV and UO126 and then seeded at 104 cells/cm2 in mESC media without GSK3 inhibitor XV and UO126. After 24 hours, media was replaced with serum-free differentiation media: Advanced DMEM supplemented with N-2, B27 Supplement without vitamin A, and Glutamax (Thermo Fisher). After 24 hours, media was replaced with differentiation media: Advanced DMEM with 2% ES-tested FBS and Glutamax. After 24 hours in differentiation media, cells were treated in differentiation media with combinatorial treatment conditions for 24 hours. To induce mesendoderm differentiation, cells were treated for 24 hours in differentiation media with CD 2665, Activin A, GSK3 inhibitor XV, Dorsomorphin, and Fgf2 and then exposed to combinatorial treatment conditions for 24 hours in differentiation media. Control conditions did not receive combinatorial treatments.
Transfection of barcodelets was performed using TransIT-mRNA (Mirus) 2-16 hours before harvest for single cell RNA-seq. Each well of a 96-well plate received 200 ng total barcodelet RNA mixed equally among the 2-5 component barcodelet species. Barcodelets for each well were diluted in 5 µL OptiMEM with 0.1 µL mRNA-Boost reagent. This mixture was mixed well with a mixture of 5 µL OptiMEM + 0.1 µL TransIT-mRNA reagent, incubated at room temperature for 2-5 minutes, and pipetted onto cells in differentiation media with combinatorial treatment conditions.

tag: cell type

value: Mouse embryonic stem cells


title: X5_2 - CBE


title: Foxa2GFPminus, Bulk RNA-seq, Replicate 2


title: Foxa2GFPminus, Bulk RNA-seq, Replicate 1


title: Foxa2GFPplus, Bulk RNA-seq, Replicate 4


title: TU0046_CD8_LTBI


title: TU0035_CD8_LTBI


title: TU0033_CD8_LTBI


title: Foxa2GFPplus, Bulk RNA-seq, Replicate 3


title: X1_3 - PBS


title: Foxa2GFPplus, Bulk RNA-seq, Replicate 2


title: TU0024_CD8_LTBI


title: TU0022_CD8_LTBI


title: Foxa2GFPplus, Bulk RNA-seq, Replicate 1


title: TU0010_CD8_LTBI


title: Barcodelet72h, Bulk RNA-seq, Replicate 2


title: TU0013_CD8_LTBI


title: Barcodelet72h, Bulk RNA-seq, Replicate 1


title: Barcodelet24h, Bulk RNA-seq, Replicate 2


title: Barcodelet24h, Bulk RNA-seq, Replicate 1


title: TP0013_CD8_LTBI


title: Untransfected, Bulk RNA-seq, Replicate 2


title: TU0005_CD8_LTBI


title: XT0103_CD8_HC


title: Mixed, barRNA-seq barcodelets

description: 5 pathways + control, 144 conditions, 2-4 replicates, starting state: mESC and mesendoderm

extract_protocol:
For each dataset, cells were mixed at equal concentrations and resulting pool was prepared for 10X Chromium scRNA-seq XXh later. Cells were prepared by trypsinization, resuspension in PBS + 0.04% BSA, and repeated filtering through a 70 µM cell strainer. Cells were then counted and loaded onto the 10X Genomics Chromium Single Cell Gene Expression chip using the manufacturer’s protocol, aiming for 10,000 cells.
Library prep was performed according to manufacturer's protocol with modified SPRI purification to prepare transcriptome (long cDNA > 500bp) and barcodelet (short cDNA <500bp) libraries. The transcriptome is pooled with the barcodelet at a molar ratio of 9:1 for Illumina Nextseq sequencing.


title: TU0146_CD8_HC


title: Mixed, barRNA-seq transcriptome


title: TP0001_CD8_LTBI


title: TP0007_CD8_LTBI


title: TU0119_CD8_HC


title: TU0079_CD8_HC


title: Mesendoderm, barRNA-seq barcodelets

source_name: Mouse embyonic stem cells


title: Mesendoderm, barRNA-seq transcriptome


title: Germ layer, barRNA-seq barcodelets


title: TP0015_CD8_LTBI


title: TU0084_CD8_HC


title: TP0003_CD8_LTBI


title: TP0004_CD8_LTBI


title: XT0101_CD8_HC


title: Untransfected, Bulk RNA-seq, Replicate 1


title: Tsc1foxo_Normal_rep3

first: Avantika

last: Gupta

state: Zurich

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

data_processing:
Sequencing reads were trimmed for adapters and low quality using trimmomatic
Reads were mapped to the Drosophila genome (BDGP6) using STAR aligner
Mapped reads were assigned to genomic features using featurecounts with the paramters -M -O -s 2 --fraction
Genome_build: BDGP6
Supplementary_files_format_and_content: comma-separated values file with read counts for all libraries

organism: Drosophila melanogaster

source_name: Larval eye imaginal disc cells

growth_protocol: Flies were crossed at 25°C for two days on normal food. Thereafter, they were transferred to egg laying chambers and allowed to lay eggs on agar plates containing yeast overnight. For clone induction, a 11 min heat shock at 37°C was applied 36 h AEL, after which the L1 larvae were transferred to normal food or nutrient restriction (NR) food. Normal fly food is composed of 100 g fresh yeast, 55 g cornmeal, 10 g wheat flour, 75 g sugar, 8 g bacto agar, and 1.5% antimicrobial agents (33 g/L nipagin and 66 g/L nipasol in ethanol) in 1 L water. NR food was prepared by reducing the amount of yeast to 10% with 1.5% nipagin (100 g/L in ethanol).

extract_protocol:
Eye imaginal discs were dissected in HBSS and mounted in a 0.5 µL drop of HBSS on FrameSlide PET (Carl Zeiss AS). Single clones of approximately 50 cells were microdissected using a Zeiss PALM-Microdissection system and captured into the caps of AdhesiveCap (Carl Zeiss AS) microcentrifuge tubes. The samples were frozen in liquid nitrogen and stored at -80°C until RNA isolation.
RNA isolation and cDNA library preparation from the microdissected samples were done according to the Ovation SoLo RNA-seq Systems kit (NuGEN Cat#0502-32).

treatment_protocol: Temporal knockdown of foxo was achieved by shifting larvae to 30°C 12 h before dissection.

tag: genotype

value: Tsc1[Q87X] foxoRi

tag: food

value: Normal

tag: temperature


title: TU0021_CD8_LTBI


title: Germ layer, barRNA-seq transcriptome


title: foxo_Normal_rep3

value: foxoRi


title: Tsc1foxo_Normal_rep1


title: Tdgf1GFPplus, Bulk RNA-seq, Replicate 2


title: foxo_Normal_rep4


title: foxo_Normal_rep2


title: TP0005_CD8_LTBI


title: Tsc1foxo_Normal_rep4


title: Tsc1foxo_Normal_rep2


title: foxo_Normal_rep1


title: Tsc1_Normal_rep4


title: TP0008_CD8_LTBI


title: Tsc1_Normal_rep1


title: Tsc1_Normal_rep3


title: WT_Normal_rep4

value: WT


title: WT_Normal_rep1


title: WT_Normal_rep2


title: slh1∆ [SM025Fd]

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: Ribosome-protected RNA 54-68 nt

data_processing:
Library strategy: Ribo-Seq
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, treated with RNase I, and run over sucrose gradients to extract either the monosome or the disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.


title: hel2∆ [SM024Fd]

description:
Ribosome-protected RNA 40-80 nt
Biological replicate of SM016Fd


title: Tsc1foxo_Starv_rep4

value: Nutrient restriction


title: WT [SM023Fd]

description:
Ribosome-protected RNA 40-80 nt
Biological replicate of SM015Fd
end3SM015Fd23Fd_minus.wig
end3SM015Fd23Fd_plus.wig


title: HGPS SMC_d4_biological rep2

type: RNA

city: Coimbra

first: Lino

last: Ferreira

state: Azinhaga de Santa Comba,

address: Pólo das Ciências da Saúde,Unidade Central

country: Portugal

institute: Faculty of Medicine

description: Gene expression data from HGPS SMC derived from HGPS iPSCs in flow conditions

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Human Gene 2.1 ST Array Strip from Affymetrix.

scan_protocol: The microarrays were scanned by a GeneAtlas system from Affymetrix.

data_processing: The raw data were analyzed using Expression Console™ Software from Affymetrix which uses RMA (Robust Multiarray Averaging). Differentially expressed genes were identified also using Affymetrix® Expression Console™ Software

label: biotin

source_name: HGPS SMC from HGPS iPSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in Smooth Muscle Growth Medium-2 (SmGM-2) medium. Cell cultures were maintained at 37 ºC, 5 % CO2 in a humidified atmosphere, with media changed every 2 days

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

treatment_protocol: Cells were applied to the entry port of an IBIDI channel and allowed to flow inside by capillary force. After 4 h, a confluent cell layer was formed, which was then perfused with SmGM-2 medium at arterial flow rate. All tests were performed at day 0 and day 4 on flow culture conditions

tag: mutation

value: mutation in the LMNA gene, G608G

tag: conditions

value: flow 4 days


title: MKN7_WT_CDDP_ATF3_ChIPseq

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: Anti-ATF3 (#sc-188X, Santa Cruz Biotechnology, Lot#E0316)

data_processing:
Low quality reads were removed by using fastq_quality_fileter (fastx_toolkit v0.0.14) with parameters -q 20 -p 80
Reads were aligned to hg19 genome assembly with Hisat v2.2.1.0 for RNA-Seq and Bowtie2 (version 2.2.3) for ChIP-Seq.
Reads with more than two mismatches were removed form aligned reads for RNA-Seq and ChIP-Seq. Then, multiply mapped reads were removed for ChIP-Seq followed by PCR duplicates by using picard-tools-1.1119.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1for RNA-seq and Aligned reads were converted to BedGraph format with bedtools v2.20.1 for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Bedgraph files are generated from bedtools and converted to bigwig file.

growth_protocol: MKN7_WT, MKN7_EB, NCC24 and SNU719 cells were cultured in RPMI1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
ChIP samples were purified by QIAquick PCR purification kit (Qiagen, Hilden, Germany) and total RNAs were collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for ChIP-seq. TruSeq Stranded mRNA Sample Prep Kit (Illumina) were used for RNA-seq following the manufacturer’s protocol.

value: gastric cancer cell line

tag: genotype/variation

value: ATF3 induced expression


title: SNU719_shATF3_RNAseq

value: ATF3-targeted shRNA


title: hvSMC_d0_biological rep1

description: Gene expression data from healthy human vascular SMC in static conditions

source_name: hvSMC

value: no mutation

value: static


title: SNU719_shNON_RNAseq

value: non-targeted shRNA


title: HGPS SMC_d0_biological rep1

description: Gene expression data from HGPS SMC derived from HGPS iPSCs in static conditions


title: hvSMC_d0_biological rep2


title: HGPS SMC_d0_biological rep3


title: hvSMC_d4_biological rep3

description: Gene expression data from healthy human vascular SMC in flow conditions


title: hvSMC_d4_biological rep2


title: Tsc1foxo_Starv_rep3


title: healthy SMC_d4_biological rep1

description: Gene expression data from healthy SMC derived from iPSCs in flow conditions

source_name: healthy SMC from iPSCs


title: NCC24_shNON_RNAseq


title: HGPS SMC_d4_biological rep4


title: WT_Normal_rep3


title: healthy SMC_d4_biological rep3


title: Tsc1foxo_Starv_rep2


title: Tsc1foxo_Starv_rep1


title: HGPS SMC_d0_biological rep2


title: healthy SMC_d0_biological rep1

description: Gene expression data from healthy SMC derived from iPSCs in static conditions


title: healthy SMC_d0_biological rep3


title: TBT 100 nM R2

city: Barcelona

first: Rubén

middle: Francisco

last: Martínez López

state: Cataluña

address: Carrer Jordi Girona, 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

data_processing:
Real Time Analysis (RTA 1.13.48) software was used for basecalling and the quality scoring of the run.
Generation of FASTQ sequence files was carried out with CASAVA software.
RNA-seq reads were aligned to the GRCz10 genome reference using STAR version 2.5.1b
Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters
Differential expression analysis between all TBT conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option (Li and Dewey, 2011; Love et al., 2014)
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads values (normalized counts) for each sample.

organism: Danio rerio

source_name: Whole larvae

growth_protocol: Zebrafish (Danio rerio) embryos were obtained by natural mating following standard procedures. At 2 hours post fertilization (hpf), eggs were collected, rinsed and fertilized viable eggs were transferred to embryo water (90 µg/ml of Instant Ocean -Aquarium Systems, Sarrebourg, France-, 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water) and kept under standard conditions (28.5 ºC and 12L:12D photoperiod).

extract_protocol:
ZF embryos were taken in an Eppendorf (10 larvae per replicate) and flash frozen on dry ice. Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA). Then, total RNA was assayed for quantity and quality using Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent Technologies).
Libraries for RNA-Seq were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500 ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters (Illumina) were added by ligation. The ligation product was enriched through 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2x76bp. We generated on average 42 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina) following the manufacturer’s protocol.

treatment_protocol: The exposure of the larvae was driven through the water: tributyltin chloride (TBT, Sigma-Aldrich, St. Louis, MO, USA) stock solutions (1.5, 15 and 50 µM) were prepared in DMSO and stored at -20 °C. During the exposure period, fresh working solutions were prepared everyday by dissolving the stock solutions in fish water, with a final concentration of DMSO of 0.2% (v/v). The final TBT working concentrations were: 0 (control), 3, 30 and 100 nM.

value: wild type

value: 5 days post fertilization

tag: Stage

value: eleutheroembryo

tag: condition

value: 100 nM TBT

tag: exposure time

value: from 2 to 5 dpf

tag: nº larvae/replicate


title: TBT 100 nM R1


title: TBT 30 nM R3

value: 30 nM TBT


title: foxo_Starv_rep3

value: foxoRi


title: NCC24_shATF3_RNAseq


title: TBT 30 nM R1


title: foxo_Starv_rep2


title: foxo_Starv_rep1


title: TBT 3 nM R3

value: 3 nM TBT


title: TBT 3 nM R2


title: TBT 3 nM R1


title: HGPS SMC_d4_biological rep5


title: TBT 30 nM R2


title: TBT 100 nM R3


title: Tsc1_Starv_rep3

value: Nutrient restriction


title: TBT Ctrl R3

value: Control


title: WT_Starv_rep4

value: WT


title: Tsc1_Starv_rep1


title: EXP145-6A

city: EVRY

first: Mario

last: Amendola

address: 1 rue de l'internationale

department: research and development

country: France

institute: genethon

data_processing:
demultiplexing and quality trimming using cutadapt 1.18 : cutadapt -q 30,30 -e 0.25 --no-trim --no-indels -g file:{TAGS} -m 30:20 --pair-filter=both
Linker trimming using cutadapt 1.18 : cutadapt -a "GTCCCTTAAGCGGAGCCCT;max_error_rate=0.16;min_overlap=6" -G "AGGGCTCCGCTTAAGGGAC;max_error_rate=0.1;min_overlap=10" -m 93:93 -q 30,30
Discard provirus contining reads : cutadapt -g "TGGCGCCCGAACAGGGACTTGAAAGCGAAAGGGAAACCAGAGG;max_error_rate=0.1;min_overlap=42" --no-indels --no-trim
Trim 3'LTR  : cutadapt -g TAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTA --no-indels
Align on genome using bowtie2 (2.3.4.2) : bowtie2 -k 15 --no-unal --gbar 10
filter alignments using samtools 1.9. Unique alignements were those with a mapping quality greater than 255 and multiple hits with mapping quality lower than 1 and XS tag.
Convert alignments in BAM to bed using bedtools 2.27.1 and extract insertion sites as first nucleotide of the alignment
Using R 3.6.0, for multi hit alignments, sort by increasing score (editing distance) and select alignement with loer score. If ties, keep all aligments and consider as 'true' multi hits. If a single lower score alignment exist, convert to unique hit alignment.
Aggregate alignments based on genomic coordinates, considering single and multi-hits read counts.
Annotate IS to genes using R bioconductor 'annotatr' package and hg19 UCSC known genes database ('TxDb.Hsapiens.UCSC.hg19.knownGene' package)
Genome_build: hg19
Supplementary_files_format_and_content: tsv files contain the annotated IS detected for each sample together with the number of reads mapping uniquely to each position and number of reads mapping multiple times in he genome including this position. The CLISS column correspond to the cluster name of each insertion site determined based on a 500bp window.

source_name: K562 human cell line

growth_protocol: K562 (ATCC® CCL243) were maintained in RPMI 1640 medium containing 2 mM glutamine and supplemented with 10% fetal bovine serum (FBS, BioWhittaker, Lonza), 10 mM HEPES, 1 mM sodium pyruvate (LifeTechnologies) and penicillin and streptomycin (100U/ml each, LifeTechnologies)

extract_protocol:
DNA was extracted using Qiagen DNA mini kit and quantified at Nanodrop.
LTR vector-genome junctions were amplified by LM-PCR as previously described (Poletti V, Mol Therapy Meth, 2018). 1 ug genomic DNA was fragmented with Tru91 (Roche) and ligated to a TA-protruding double-stranded DNA linker. After SacI digestion, multiple nested PCRs were performed with specific primers annealing to the linker and vector LTR. Amplicons ranging from 200 to 500 kb were purified by NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel). 1 mg of the final libraries was subsequently processed with MiSeq Reagent Kit v3 (2 x 300-bp pair-end sequencing) and sequenced to saturation on Illumina MiSeq System (IGA Technology Services, Udine, Italy).

treatment_protocol: K562 cells were infected with an IDLV expressing GFP under the control of human phosphoglycerate kinase 1 (PGK) promoter (MOI 100) and subsequently nucleofected with 30 pmol of Cas9:gRNA complex (1:2). Two weeks later GFP positive cells were sorted using MoFlocell sorter (Beckman Coulter) and genomic DNA was extracted after expansion.

tag: guiderna


title: Tsc1_Starv_rep4


title: EXP144-1B


title: EXP144-2B


title: EXP145-5A


title: EXP144-3A


title: WT_Starv_rep3


title: TBT Ctrl R2


title: WT_Starv_rep1


title: Dam DamID-seq, rep 2

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
Library strategy: DamID-seq
Two biological replicates of Dam-only or Dam-HP1 DamID-seq reads were adapter clipped, mapped to the dm3 genome assembly by bowtie2 (Langmead 2012) and counted by ‘HTSeq-count’ software (Anders et al., 2015) on the 500-bp genomic bins. The resulted counts of Dam-HP1 samples were converted to RPM, normalized to the Dam-only samples counts and log2-transformed. The domain calling was performed with the 3-state HMM algorithm without taking into account the heterochromatin portion of dm3 genome assembly.
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: bedgraph files were generated using htseq-count software and R via Rstudio, counts represent RPM values per 500-nt bins.
Supplementary_files_format_and_content: bed files represent HP1 domains in somatic cells of Drosophila ovaries after performing 3-state HMM domain calling via custom script in R.

source_name: Ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
160-200 ovaries from 0-4 days old females were manually dissected using dissection needles in PBS at 4°C. Isolation of genomic DNA was performed by DNeasy Blood and Tissue kit (Qiagen), following the protocol for cultured cells. DNA was concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g and its concentration was measured using a NanoDrop spectrophotometer. For the selective amplification of methylated GATC-GATC fragments, genomic DNA was first digested by DpnI, followed by ligation of adaptors, DpnII digestion and PCR-amplification as described previously (Vogel et al. 2007) with a minor modification: ~0.5 µg instead of 2.5 µg of genomic DNA was used as an input. We applied 16 cycles of PCR (1 min at 94°C, 1 min at 65°C, 2 min at 68°C) for Dam-only and Dam-HP1 DNA samples. Adaptors were removed by DpnII digestion for 2 h at 37°C. The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (Qiagen), concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g, and quantified on a NanoDrop spectrophotometer.
0.5 µg of Dam-only and Dam-HP1 DNA samples (each in two biological replicates) were subjected to next generation sequencing (NGS) on Illumina HiSeq 2500 resulting in ~30 million 100 nt single-end reads per sample.

value: F1 from hsp70-FLP x STOP#1-Dam

tag: tissue

value: Ovaries

tag: Sex

value: Female

tag: biological replicate


title: EXP145-4A


title: Dam-HP1 DamID-seq, rep 2

tag: strain

value: F1 from hsp70-FLP x STOP#1-Dam-HP1


title: EXP144-1A-A5

tag: cell line


title: Dam-HP1 DamID-seq, rep 1


title: EXP144-1A


title: Dam DamID-seq, rep 1


title: TBT Ctrl R1

tag: age


title: 20170926_PM3_XZ4704-1_S6

first: Xuemei

last: Xie

address: 811 Enders Building, 320 Longwood Ave.

department: Transfusion Medicine

institute: Boston Children's Hospital

description: processed data file: 2019Granulocyte_bulk_matrix.csv

data_processing:
QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
Gene differential expression analysis were using EdgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.

source_name: Bone marrow neutrophil

extract_protocol:
Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.

tag: strain/background

tag: cell type

value: PM neutrophils


title: healthy SMC_d4_biological rep2

value: no mutation

value: flow 4 days


title: 20170926_PM2_XZ4704-1_S5


title: healthy SMC_d0_biological rep2

value: static


title: siASCC3-R1

city: London

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

description: TTchem-seq

data_processing:
Library strategy: TT-seq as Gregersen et al., 2020
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 89 transcript annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig files representing alignment read depth coverage.

source_name: lung fibroblast cell line

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS , 100 U/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the strand-specific TruSeq total RNA kit (Illumina) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

treatment_protocol: cells were successively transfected with siRNAs twice to increase knockdown efficiency, and harvested for different analyses 72 hours after the second transfection. 20 µM siRNA was mixed with Lipofectamine RNAiMAX (Thermo Fisher Scientific, 13778150) at a ratio of 1:2 (v/v) according to the manufacturer’s protocol, and the final concentration of siRNAs in antibiotic-free medium was 20 nM. Nascent RNA labelling by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest.

value: Human SV40-transformed lung fibroblast cell line

tag: sirna sequence

value: GAACAUCAUUGCAACAGUA

tag: treatment

value: 15 min 4-thiouridine pulse

tag: molecule type

value: Nascent RNA


title: Tsc1_Normal_rep2

tag: genotype

tag: food

value: Normal

tag: temperature


title: siASCC3-R2

description: TTchem-seq


title: Tsc1_Starv_rep2


title: siCon-R2

description: TTchem-seq

value: UGGUUUACAUGUCGACUAA


title: siCon-R1

description: TTchem-seq


title: 20170926_MM4_XZ4704-1_S12

value: MM neutrophils


title: 20170926_MM1_XZ4704-1_S10


title: 20170926_PM_1_8_17_XZ4704-1_S4


title: HIPSC_MT_BATCH1

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Replicates of CMs and CMECFs were pre-processed separately. In both cases, undetected genes (genes with a count of one in less than two cells) and the 50 cells with the lowest number of transcripts were removed from further analysis. This resulted in 6810 cells and 12823 genes for the CMs dataset, and 9497 cells and 13958 genes for the CMECFs dataset.
Counts were normalized with the scran package in R
Celltypes were assigned by hierachical clustering
Genome_build: GRch38
Supplementary_files_format_and_content: count_matrix: matrix of UMI counts where cells are columns and genes rows; barcode_list: list of 12bp barcodes corresponding to the columns of matrix; gene_list: HUGO and ensembl identifiers corresponding to the rows of matrix; processed-table.tsv.gz: Compressed table of normalized expression and cell types.

growth_protocol: CM differentiation was performed as follow: Briefly, 25 × 103 cells per cm2 (CTRL1, CTRL2, CTRL3) were seeded on plates coated with 75 µg/ml matrigel growth factor reduced (Corning) the day before differentiation (day -1). At day 0, cardiac mesoderm was induced by changing E8 to BPEL medium (Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids; 5, supplemented with a mixture of cytokines (20 ng/ml BMP4, R&D Systems; 20 ng/ml ACTIVIN A, Miltenyi Biotec; 1.5 μM GSK3 inhibitor CHIR99021, Axon Medchem). After 3 days, cytokines were removed and a Wnt inhibitor (5 μM XAV939, Tocris) was added for 3 days. BPEL medium was refreshed every 3 days.

extract_protocol:
2D CMs were dissociated on differentiation day 20 into single cells for single-cell RNAseq. MTs were incubated in 290 U/mg of pre-warmed collagenase type II (Worthington) in HBSS solution (Sigma Aldrich). Single cells were used for single-cell RNAseq.
10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol. Libraries were sequenced on a NextSeq500 in Mid Output mode using a version 2, 150 cycles kit (Illumina).

treatment_protocol: Prior to MT formation, hiPSC-ECs and hiPSC-CFs were prepared as follow: briefly, 2-3 days before MT formation, a vial of cryopreserved hiPSC-ECs and a vial of cryopreserved hiPSC-CFs were thawed and cultured either in BPEL medium supplemented with VEGF on plates coated with fibronectin (hiPSC-ECs), or in FGM3 medium on uncoated plates (hiPSC-CFs). The day of MT formation (day 0), hiPSC-ECs, hiPSC-CFs, SFs, ACFs, Cx43-sh-RNA CFs, SFs Empty LV and SFs CX43 LV were detached using TrypLE 1X for 5 min at 37 oC, 5% CO2, centrifuged for 3 min at 1100 rpm, resuspended in BPEL medium and counted. hiPSC-CMs at day 14-21 that showed > 80% purity, measured as the percentage of troponin positive cells by FACS analysis, were dissociated using the Multi Tissue Dissociation Kit 3 (Miltenyi Biotec) following the manufacturer’s instructions, resuspended in BPEL medium and counted. For CMECs: cell suspensions were combined together to 5000 cells (85% cardiomyocytes and 15% endothelial cells) per 50μl BPEL medium supplemented with VEGF (50 ng/ml). For microtissues (CMECFs), cell suspensions were combined together to 5000 cells (70% cardiomyocytes, 15% endothelial cells and 15% cardiac fibroblasts) per 50μl BPEL medium supplemented with VEGF (50 ng/ml) and FGF2 (5 ng/ml).  For all microtissues, cell suspensions were seeded on V-bottom 96 well microplates (Greiner bio-one) and centrifuged for 10 min at 1100 rpm. MTs were incubated at 37 oC, 5% CO2 for 21 days with media refreshed every 3-4 days. Dibutyryl cAMP (dbcAMP) treatment was performed on CMECFs in BPEL medium supplemented with 0.5 mM dbcAMP for 7 days (from day 14 to day 21). scRNAseq analysis of all MTs was performed after 21 days.

tag: cell type source

value: hiPSCs

value: 3D cardiac microtissues (MT)


title: HIPSC_CM_BATCH1

value: cardiomyocytes (CM)


title: 20170926_MC_1_8_17_XZ4704-1_S7

value: MC neutrophils


title: 20170926_MB3_XZ4704-1_S3

value: MB neutrophils


title: 20170926_MC3_XZ4704-1_S9


title: 20170926_MB2_XZ4704-1_S2


title: p4_unstim_ininh

city: Amsterdam

first: Jeffrey

last: Kroon

address: Meibergdreef 9

department: Experimental Vascular Medicine

institute: Amsterdam UMC, location AMC

data_processing:
Reads were aligned to human genome hg38 with STAR 2.5.2b
Mapped reads were filtered on MAPQ >= 30
Reads were counted in exons and aggregated per gene using HOMER’s (v4.9.1) analyzeRepeats.pl script with the following parameters: -count exons -raw. RPKM values were obtained using the same script with the -rpkm flag instead of -raw.
Genome_build: hg38
Supplementary_files_format_and_content: Text file containting a count matrix of raw reads.

source_name: HAECs; Lonza

extract_protocol:
TriPure (Roche, Basel, Switzerland)
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: Human Arterial Endothelial Cells (HAECs; Lonza)

value: Unstimulated


title: p4_5mg_uninh

value: 5 mg/dl Lp(a)


title: p4_100mg_pfk158

value: 100 mg/dl Lp(a) + PFK158


title: p4_100mg_uninh

value: 100 mg/dl Lp(a)


title: 20170926_BM_NEU3_XZ4704-1_S15

value: BN/SN neutrophils


title: 20170926_MB1_XZ4704-1_S1


title: 20170926_BM_NEU2_XZ4704-1_S14


title: p3_100mg_pfk158


title: p3_5mg_pfk158

value: 5 mg/dl L(a) + PFK158


title: p3_100mg_uninh


title: B1411 MZ ATAC

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

country: Germany

institute: Medical Center - University of Freiburg

description:
DNA after Transposase reaction
Follicular B cells were isolated from WT NOD mice for ATAC-Seq

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were quality filtered and adapter trimmed using bbmap v36.27 with the following options: ktrim=r k=28 mink=13 hdist=1, minlen=25.
Filtered reads were aligned to the mouse genome using bowtie2
Enrichment was quanitifed using Homer v4.8 findPeaks.pl with following options: -style dnase -i WT
Motifs discovery was carried out using findMotifsGenome.pl with options: -size 100 -mask
Genome_build: mm9
Supplementary_files_format_and_content: Peak files are in the original HOMER output format (http://homer.salk.edu/homer/). Column headers are: PeakID, chromosome, starting position, ending position, strand (+/-), normalized tag counts, region size, peak score, statistics.

source_name: CD23-positive Marginal Zone B cells isolated from WT NOD mouse

extract_protocol:
MZ or FO B cells were FACS-sorted and treated with Transposase, with Illumina adapters inserted into open chromatin regions.
Illumina adapter specific PCR primers were used to amplify the library

value: B-cell

tag: cell subtype

value: Marginal Zone B cells

value: positive

value: negative

tag: model

value: wildtype

tag: derivation


title: 20170926_BM_NEU1_XZ4704-1_S13


title: WT MZ ATAC

description:
DNA after Transposase reaction
Marginal zone B cells were isolated from WT NOD mice for ATAC-Seq

source_name: CD21-positive Marginal Zone B cells isolated from WT NOD mouse


title: HIPSC_MT_BATCH2

value: hiPSCs


title: p3_5mg_uninh


title: 20170926_MM3_XZ4704-1_S11

value: MM neutrophils


title: WT_Starv_rep2

value: WT

value: Nutrient restriction


title: HIPSC_CM_BATCH2

value: cardiomyocytes (CM)


title: p3_unstim_ininh

value: Human Arterial Endothelial Cells (HAECs; Lonza)


title: WT FO ATAC

description:
DNA after Transposase reaction
Marginal zone B cells were isolated from B1411 B cell model for ATAC-Seq

source_name: CD21-positive Follicular B cells isolated from B1411 mouse

value: Follicular B cells

value: nuclear transfer


title: B1411 FO ATAC

description:
DNA after Transposase reaction
Follicular B cells were isolated from B1411 B cell model for ATAC-Seq

source_name: CD23-positive Follicular B cells isolated from B1411 mouse


title: p4_5mg_pfk158


title: p2_5mg_pfk158


title: WT MZ RNA

description: Marginal zone B cells were isolated from WT NOD mice for mRNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were quality filtered and adapter trimmed using bbmap v36.27 with the following options: ktrim=r k=28 mink=13 hdist=1, minlen=25.
Filtered reads were aligned to the mouse genome using RNA-STAR v2.5.2b with the following options:  --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 --sjdbScore 1
Reads were quanitifed using Homer v4.8 using the analyzeRepeats.pl script with the following options: -count exons -strand - -condenseGenes
Normalized abundance calculated from EdgeR called by Homer v4.8 using the script getDiffExpression.pl
Genome_build: mm10
Supplementary_files_format_and_content: Tab deliminated text file of normalized abundance measurements from EdgeR for each sample (column)

extract_protocol:
MZ or FO B cells were FACS-sorted and RNA was isolated using RNA Nucleospin XS kit, treated with Dnase (Machery-Nagel)
RNA was processed into RNA-Seq libraries using Truseq Stranded mRNA-Seq sample prep kit(Illumina) following manufacturer’s instructions


title: p2_5mg_uninh

value: 5 mg/dl Lp(a)


title: 20170926_MC2_XZ4704-1_S8

value: MC neutrophils


title: p2_100mg_pfk158

value: 100 mg/dl Lp(a) + PFK158


title: p1_100mg_pfk158


title: B1411 FO RNA

description: Follicular B cells were isolated from B1411 B cell model for RNA-Seq


title: B1411 MZ RNA

description: Follicular B cells were isolated from WT NOD mice for RNA-Seq


title: WT FO RNA

description: Marginal zone B cells were isolated from B1411 B cell model for mRNA-Seq


title: p1_5mg_pfk158

value: 5 mg/dl L(a) + PFK158


title: p1_100mg_uninh

value: 100 mg/dl Lp(a)


title: p2_unstim_ininh

value: Unstimulated


title: p1_5mg_uninh


title: SW620

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

country: China

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

description: high-metastatic

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: GRCh37/hg19

source_name: colon cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
The ribosome-bound RNAs were harvested using Trizol reagent. The ribosome-bound RNAs were used for the construction of sequencing libraries.
Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) was used to remove rRNA, and rRNA free residue was cleaned up by ethanol precipitation. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer’s instructions.In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The purified libraries were validated by the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

value: colon cancer cell line

value: cell line from metastatic colon cancer tissue


title: p1_unstim_ininh


title: p2_100mg_uninh


title: SW480

description: low-metastatic

value: cell line from primary colon cancer tissue


title: Sample 80277 MDAMB468 Meox1 siRNA B2

city: Ann Arbor

first: Duxin

last: Sun

state: MI

address: 1600 Huron Parkway

institute: University of Michigan

data_processing:
Fastq generation was performed using Illumina’s bcl2fastq software version 2.17.
The sequencing reads were mapped to human transcripts annotated in GENCODE using Bowtie. Only uniquely mapped reads were used for further analysis.
Gene expression levels were estimated as reads/kilobase/million mapped reads (RPKM) using rSeq. Genes with average RPKM less than 1.0 across all the samples were removed from analysis.
Differentially expressed genes were detected using edgeR. Genes with a log2 fold change > 1.5 and FDR < 0.05 were considered significant.
Supplementary_files_format_and_content: Each row is a gene. Column A is the Ensemble ID of the gene, followed by the name of the gene. Columns B to Q are expression values of the gene in all the samples, the expression values are measured in the RPKM unit. Genes having average RPKM less than 1.0 across all the samples are removed from the analysis. Columns R to Y are log2(1+RPKM) gene expression values for BT-549. The columns are renamed and reordered by sample names. Columns Z to AB are the log2 fold changes, p-values, and false discovery rates, respectively, for Meox1 vs Control, in BT-549, estimated using software edgeR. Columns AC to AM are similar, but for MDA-MB-468.

source_name: triple negative breast cancer MDA-MB-468

growth_protocol: BT-549 cells were grown in RPMI Gibco Life Technologies base media supplemented with antibiotic-antimycotic, 10% fetal bovine serum, 0.85µg/mL insulin, 1mM sodium pyruvate, and 10mM HEPES. MDA-MB-468 cells were grown in DMEM Gibco Life Technologies base media supplemented with antibiotic-antimycotic, 10% fetal bovine serum, and 1mM sodium pyruvate.

extract_protocol:
RNA was extracted using RNeasy Kit (Qiagen #74104).
Libraries were prepared by the University of Michigan DNA Core using just mRNA, non-strand-specific, polyA-selection, fragment lengths of ~120 nucleotides.

treatment_protocol: Cells were treated with 50nM Negative Control siRNA (Qiagen #1027281) and 50nM Meox1 siRNA (Qiagen #1027416, four different Meox1 siRNA pool mixture). Cells were transfected using Lipofectamine RNAiMAX Reagent (Invitrogen #13778-150), transfections were conducted according manufacturer protocol. Following 72 hours of siRNA transfection, cells were harvested to extract RNA.

value: Meox1 knockdown


title: Sample 80273 MDAMB468 Meox1 siRNA A2

value: triple negative breast cancer MDA-MB-468


title: Sample 80269 BT549 Meox1 siRNA B2

source_name: triple negative breast cancer BT-549

value: triple negative breast cancer BT-549


title: Sample 80270 MDAMB468 Negative Control siRNA A1

value: Control


title: CD4+ T cells, HAM3947

city: Kagoshima-Shi

first: Daisuke

last: Kodama

state: Kagoshima-Ken

address: Sakuragaoka 8-35-1

department: Joint Research Center for Human Retrovirus Infection, Kagoshima University Campus

institute: Kagoshima University

description: Gene expression in CD4+ T cells without incubation from a patient with HTLV-1-associated myelopathy

hyb_protocol: Using Agilent Gene Expression Hybridization Kit (Agilent Technologies), microarray Hybridization was performed on the GPL4133 Platform Agilent-14850 Whole Human Genome cDNA microarray 44k×4plex G4112F (Feature number version, 85 columns x 532 rows) (Agilent Technologies)

scan_protocol: Raw images were acquired by an Agilent DNA microarray scanner and Feature Extraction Software 10.5.1(Agilent Technologies).

data_processing: The fluorescent intensity data extracted from the raw images were imported into Agilent GeneSpring GX Software ver. 7.3.1.(Agilent Technologies). Unreliable probes were determined by filtering on flag and were removed. For all other reliable probes, raw signal intensities (Agilent pProcessedSignal) less than 5 were set to 5.0 (thresholding). After per chip normalization (scaling to 50th percentile) and per gene normalization (baselining) were performed, all signal intensities were converted to base 2 logarithms.

source_name: CD4+ T cells

label_protocol: 50 μg of total RNA was pre-amplified and labelled by Cyanine 3-CTP (Cy3) using Agilent Low RNA Input Linear Amplification Kit PLUS, One-color (Agilent Technologies).

growth_protocol: PBMC samples were cryopreserved until use and were used for microarray experiment without incubation.

extract_protocol: CD4+ T cells were separated from PBMC using microbeads by Human CD4+ T cell Isolation Kit (Miltenyi Biotech KK., Tokyo, JAPAN). Total RNA was extracted using PureLink RNA Mini Kit (Thermo Fisher Scientific K.K., Tokyo, JAPAN). Quality check of the total RNA was done using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, U.S.A.).

treatment_protocol: PBMCs were purified from blood samples obtained from HTLV-1 negative controls, HTLV-1 asymptomatic carriers, and patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). These PBMCs were cryopreserved in liquid nitrogen until use.

tag: individual

value: CD4+ T cells

tag: gender

value: Female


title: Sample 80268 BT549 Meox1 siRNA B1


title: CD4+ T cells, HAM4874

value: a patient with HTLV-1-associated myelopathy

value: Male


title: CD4+ T cells, HAM5317


title: Sample 80275 MDAMB468 Negative Control siRNA B2


title: CD4+ T cells, AC5623

description: Gene expression in CD4+ T cells without incubation from a HTLV-1 asymptomatic carrier

value: HTLV-1 asymptomatic carrier


title: CD4+ T cells, AC5915


title: Sample 80267 BT549 Negative Control siRNA B2


title: Sample 80274 MDAMB468 Negative Control siRNA B1


title: CD4+ T cells, NC5022

description: Gene expression in CD4+ T cells without incubation from a HTLV-1 negative individual

value: HTLV-1 negative control


title: Sample 80266 BT549 Negative Control siRNA B1


title: CD4+ T cells, NC5036


title: CD4+ T cells, HAM5215


title: DN1 lymphoma T-cell subpopulation, replicate 1

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Gene expression data from aged Wild type mouse, 4 Gy irradiated

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 2.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Murine lymphoma out of thymus, replicate 1

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Sublethally irradiated Lck-Cre transgene mice were transplanted with retroviral infected bone marrow cells. Thereby, NPM-ALK is retroviral and lineage-specific expressed in early T-cells. ALCL developing mice were sacrificed when moribund. Mouse housing was in accordance with national and institutional guidelines for animal care and experiments.

extract_protocol: Extraction of total RNA was performed by RNeasy Micro Kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: Harvested lymphomas or healthy bone marrow were flushed in DMEM (+10% FCS) followed by lysis of erythrocytes for 5 minutes at room temperature and staining for stem cell and T-cell markers (CD4, CD8, CD25, CD44, IL7Rα, cKIT, SCA1, Lineage markers). Lymphoma subpopulations (DN1, DN2, DN3, DN4, CLP) or LSK cells were sorted using Coulter MoFlo XDP and and cell pelletts were stored at -80°C.

tag: tissue

value: lymphoma out of thymus

value: DN1 lymphoma T-cell subpopulation

value: moribund mouse

value: Lck-Cre transgene


title: CD4+ T cells, NC2628


title: DN1 lymphoma T-cell subpopulation, replicate 2

source_name: Murine lymphoma out of thymus, replicate 2


title: DN1 lymphoma T-cell subpopulation, replicate 3

source_name: Murine lymphoma out of thymus, replicate 3


title: Sample 80272 MDAMB468 Meox1 siRNA A1

tag: cell line


title: Sample 80271 MDAMB468 Negative Control siRNA A2


title: DN2 lymphoma T-cell subpopulation, replicate 1

value: DN2 lymphoma T-cell subpopulation

tag: age


title: DN2 lymphoma T-cell subpopulation, replicate 2


title: Sample 80264 BT549 Meox1 siRNA A1


title: CD4+ T cells, AC5726


title: Sample 80263 BT549 Negative Control siRNA A2


title: Sample 80262 BT549 Negative Control siRNA A1


title: CD4+ T cells, NC5015


title: DN2 lymphoma T-cell subpopulation, replicate 3


title: DN3 lymphoma T-cell subpopulation, replicate 2

value: DN3 lymphoma T-cell subpopulation


title: EC_3

description:
hiPSC-ECs
RPKM_normalized.csv

data_processing:
LUMC BIOPET Gentrap pipeline was used to process raw data (https://github.com/biopet/biopet). Trimming of low-quality read ends was done with Sickle (v1.2). Cutadapt (v1.1) was used for adapters clipping. Using GSNAP (gmap-2014-12-23)   reads were aligned to the human reference genome GRCh38. Gene read quantification was done with with htseq-count (v0.6.1p1) against the Ensembl v87 annotation. The R package cqn (v1.24.0) was used to normalize gene length and GC content bias.
Genome_build: GRCh38

source_name: hiPSCs

growth_protocol:
Generation and culture of 3D cardiac MTs: Prior to MT formation, hiPSC-ECs and hiPSC-CFs were prepared as follow: briefly, 2-3 days before MT formation, a vial of cryopreserved hiPSC-ECs and a vial of cryopreserved hiPSC-CFs were thawed and cultured either in BPEL medium supplemented with VEGF on plates coated with fibronectin (hiPSC-ECs), or in FGM3 medium on uncoated plates (hiPSC-CFs). The day of MT formation (day 0), hiPSC-ECs and hiPSC-CFs were detached using TrypLE 1X for 5 min at 37 °C, 5% CO2, centrifuged for 3 min at 1100 rpm, resuspended in BPEL medium, and incubated at 37 oC, 5% CO2 while hiPSC-CMs were dissociated and counted as follow: briefly, CMs were dissociated using the Multi Tissue Dissociation Kit 3 (Miltenyi Biotec) following the manufacturer’s instructions, resuspended in BPEL medium and counted. For MT-CMEC: cell suspensions were combined together to 5000 cells (85% cardiomyocytes and 15% endothelial cells) per 50μl BPEL medium supplemented with VEGF (50 ng/ml). For MT-CMECF: cell suspensions were combined together to 5000 cells (70% cardiomyocytes, 15% endothelial cells and 15% cardiac fibroblasts) per 50μl BPEL medium supplemented with VEGF (50 ng/ml) and FGF2 (5 ng/ml). For both MT-CMEC and MT-CMECF, cell suspensions were seeded on V-bottom 96 well microplates (Greiner bio-one) and centrifuged for 10 min at 1100 rpm. MTs were incubated at 37 oC, 5% CO2 for 21 days with media refreshed every 3 days. RNAseq analysis of MTs was performed after 21 days, when hiSPC-CMs were approximately 35-42 days old. MTs comprising primary fibroblasts were prepared as described for MT-CMECF.
Human fetal heart ECs and fibroblasts: RNA from human fetal heart ECs and fibroblasts were isolated at passage 1 (P1) after isolation from fetal heart samples at the gestation stage E12.5, W15 and W21. Human fetal tissue samples were obtained from elective abortion material (vacuum aspiration) without medical indication, with approval by the Medical Ethical Committee of the Leiden Medical University Center (P08.087). Informed consent was obtained and the study was conducted in accordance with the Declaration of Helsinki by the World Medical Association.

extract_protocol:
Rotal RNA was purified using the NucleoSpin RNA Kit  (Bioke’) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
TrueSeq RNA-Seq library, about 160 bp short-insert library

value: Endothelial cells


title: Sample 80265 BT549 Meox1 siRNA A2

value: Meox1 knockdown


title: CM_3

description:
hiPSC-CMs
RPKM_normalized.csv

value: Cardiomyocytes

value: day 20


title: EC_1

description:
hiPSC-ECs
RPKM_normalized.csv


title: Primary_SF

description:
SFs
RPKM_normalized.csv

source_name: Skin

value: Fibroblast

value: adult


title: hiPSC_CF

description:
hiPSC-CFs
RPKM_normalized.csv


title: Primary_CF

description:
ACs
RPKM_normalized.csv

source_name: Heart


title: EC_2

description:
hiPSC-ECs
RPKM_normalized.csv


title: Human cord blood, CD34+Lin-, replicate 2

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

department: Diagnostic Sciences

country: Belgium

institute: Ghent University

description:
miRNA expression data from ex vivo isolated cord blood CD34+Lin HPCS
Expi 173 - M_CB1 34+ na SORT Dag 0

data_processing:
Normalization of the microRNA expression data was done using the global mean normalization method (Mestdagh P. Genome Biol. 2009).
Cq values above 32 were removed and samples were mean centered. Next, miRNAs expressed in less than two samples were removed and missing values were imputed by the highest value for each miRNA and multiplied by -1.
Matrix normalized worksheet reports global mean normalization.

label: FAM

label_protocol: miRNA profiling was performed using stem-loop reverse transcriptase primers for miRNA complementary DNA (cDNA) synthesis followed by a pre-amplification step and TaqMan PCR analysis (Applied Biosystems).

growth_protocol: CD34+ thymocytes were cultured on OP9 stromal cells in the presence of SCF, IL7 and FLT3L for 5 days or 10 days.

extract_protocol: Total RNA was harvested using the miRNeasy Mini Kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: CD34+ thymocytes were used immediately for miRNA expression profiling or cultured on OP9 stromal cells for 5 - 10 days and sorted for CD45+.

value: cord blood

tag: origin

value: ex vivo isolated


title: CM_2

description:
hiPSC-CMs
RPKM_normalized.csv

tag: cell type


title: Sample 80276 MDAMB468 Meox1 siRNA B1

value: triple negative breast cancer MDA-MB-468


title: Human cord blood, CD34+Lin-, replicate 1

description:
miRNA expression data from ex vivo isolated cord blood CD34+Lin HPCS
Expi 173 - L_CB2 34+ na SORT Dag 0


title: CM_1

description:
hiPSC-CMs
RPKM_normalized.csv


title: MT.CMEC_ASF_3

description:
MT-CMEC SFs
RPKM_normalized.csv

value: 3D microtissues

value: day 21


title: DN3 lymphoma T-cell subpopulation, replicate 1

value: lymphoma out of thymus


title: CLP lymphoma T-cell subpopulation, replicate 3

description: Gene expression data from aged NIPA KO mouse

value: CLP lymphoma T-cell subpopulation


title: DN4 lymphoma T-cell subpopulation, replicate 3

description: Gene expression data from aged Wild type mouse

value: DN4 lymphoma T-cell subpopulation

value: moribund mouse


title: DN4 lymphoma T-cell subpopulation, replicate 2

value: Lck-Cre transgene


title: CLP lymphoma T-cell subpopulation, replicate 1

description: Gene expression data from aged NIPA KO mouse, 4 Gy irradiated


title: Healthy LSK cells, replicate 3

source_name: Bone marrow, healthy control, replicate 3

value: bone marrow

value: LSK

value: 18 month old mouse

value: wildtype


title: Healthy LSK cells, replicate 2

source_name: Bone marrow, healthy control, replicate 2


title: Healthy LSK cells, replicate 1

source_name: Bone marrow, healthy control, replicate 1


title: CLP lymphoma T-cell subpopulation, replicate 2


title: Human thymus, CD34+, OP9JAG2 cultured, 10d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG2 (10d)
Expi 173 - K_KT34+ na MACS op OP9-J2 Dag 10

value: thymus

tag: agent

tag: time point


title: DN3 lymphoma T-cell subpopulation, replicate 3

value: DN3 lymphoma T-cell subpopulation


title: Human thymus, CD34+, OP9JAG1 cultured, 10d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG1 (10d)
Expi 173 - J_KT34+ na MACS op OP9-J1 Dag 10


title: MT.CMEC_ASF_2

description:
MT-CMEC SFs
RPKM_normalized.csv


title: Human thymus, CD34+, OP9DLL4 cultured, 10d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL4 (10d)
Expi 173 - I_KT34+ na MACS op OP9-DL4 Dag 10


title: MT.CMEC_ASF_1

description:
MT-CMEC SFs
RPKM_normalized.csv


title: MT.CMEC_ACF_3

description:
MT-CMEC ACFs
RPKM_normalized.csv


title: Human thymus, CD34+, OP9JAG2 cultured, 5d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG2 (5d)
Expi 173 - F_KT34+ na MACS op OP9-J2 Dag 5


title: MT.CMEC_ACF_2

description:
MT-CMEC ACFs
RPKM_normalized.csv


title: Human thymus, CD34+, OP9DLL1 cultured, 10d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL1 (10d)
Expi 173 - H_KT34+ na MACS op OP9-DL1 Dag 10


title: MT.CMEC_ACF_1

description:
MT-CMEC ACFs
RPKM_normalized.csv


title: Human thymus, CD34+, OP9JAG1 cultured, 5d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG1 (5d)
Expi 173 - E_KT34+ na MACS op OP9-J1 Dag 5


title: MT.CMECF_4

description:
MT-CMECF
RPKM_normalized.csv


title: CD4+ T cells, AC5821

value: HTLV-1 asymptomatic carrier

value: CD4+ T cells

value: Female


title: Human thymus, CD34+, OP9DLL4 cultured, 5d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL4 (5d)
Expi 173 - D_KT34+ na MACS op OP9-DL4 Dag 5


title: Human thymus, CD34+, OP9LIE cultured, 5d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9LIE (5d)
Expi 173 - B_KT34+ na MACS op OP9-LIE Dag 5


title: NEDD8-deficient BMMs, LPS treatment for 4h

city: Beijing

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

description: KL; KO LPS4h

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing:
Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.
Rosetta Resolvers computed normalized intensities, average of technical replicates.

source_name: Primary BMMs

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: BMMs were generated by flushing bone marrow cells from femurs and tibiae of mice. Cells were cultured in RPMI 1640 medium containing 15% (v/v) FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, and 50 µM β-mercaptoethanol with 100 ng/ml M-CSF (Cetus) for 7 days.

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: With or without 100ng/ml LPS (Sigma) treatment for 4 hours.

tag: strain background

tag: genotype/variation

value: KO; NEDD8-deficient

value: Bone marrow mononuclear cells (BMM)

tag: stimulated with

value: 100ng/ml LPS for 4 hrs


title: Human thymus, CD34+, control ex vivo isolated, replicate 2

description:
miRNA expression data from ex vivo isolated CD34+ thymocytes
Expi 173 - A_KT34+ na MACS Dag 0

value: control ex vivo isolated

value: ex vivo isolated


title: MT.CMECF_3

description:
MT-CMECF
RPKM_normalized.csv

value: 3D microtissues

value: day 21


title: MT.CMECF_1

description:
MT-CMECF
RPKM_normalized.csv


title: MT.CMEC_2

description:
MT-CMEC
RPKM_normalized.csv


title: NEDD8-deficient BMMs, no stimulation

description: KO; KO oh

value: none (unstimulated control)


title: NEDD8-sufficient BMMs, LPS treatment for 4h

description: WL; WT LPS4h

value: WT; NEDD8-sufficient


title: Human thymus, CD34+, OP9JAG1 cultured, 10d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG1 (10d)
Expi 166 - J_KT34+ na MACS op OP9-J1 Dag 10


title: Human thymus, CD34+, OP9DLL4 cultured, 10d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL4 (10d)
Expi 166 - I_KT34+ na MACS op OP9-DL4 Dag 10


title: MT.CMEC_3

description:
MT-CMEC
RPKM_normalized.csv


title: Human thymus, CD34+, OP9JAG2 cultured, 10d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG2 (10d)
Expi 166 - K_KT34+ na MACS op OP9-J2 Dag 10


title: EG.F.2

description:
hiPSC-CFs
RPKM_normalized.csv

value: Fibroblast


title: MT.CMEC_1

description:
MT-CMEC
RPKM_normalized.csv


title: Human thymus, CD34+, OP9DLL1 cultured, 5d, replicate 2

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL1 (5d)
Expi 173 - C_KT34+ na MACS op OP9-DL1 Dag 5


title: EG.F.1

description:
hiPSC-CFs
RPKM_normalized.csv


title: Human thymus, CD34+, OP9JAG2 cultured, 5d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG2 (5d)
Expi 166 - F_KT34+ na MACS op OP9-J2 Dag 5


title: EG.EP.3

description:
hiPSC-EPI
RPKM_normalized.csv

value: Epicardial cells


title: BMMs from Uba3(flox/flox) mouse No.3, no stimulation

hyb_protocol: MOA v2.1 arrays were pre-heated at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridized on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent Microarray Scanner (G2505C) 0.1 XDR protocol and quantify the fluorescence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amersham).

tag: strain/background

value: Bone marrow-derived macrophages (BMMs)

tag: treatment

tag: mouse id

value: WT 3


title: Human thymus, CD34+, OP9JAG1 cultured, 5d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9JAG1 (5d)
Expi 166 - E_KT34+ na MACS op OP9-J1 Dag 5

value: thymus


title: Human thymus, CD34+, OP9DLL4 cultured, 5d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL4 (5d)
Expi 166 - D_KT34+ na MACS op OP9-DL4 Dag 5


title: EG.F.3

description:
hiPSC-CFs
RPKM_normalized.csv


title: BMMs from Uba3(flox/flox) mouse No.1, LPS 4h

value: LPS 4hr

value: WT 1


title: BMMs from Uba3(flox/flox) mouse No.2, LPS 4h

value: WT 2


title: BMMs from Uba3(flox/flox) mouse No.2, no stimulation


title: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.3, LPS 4h

value: Uba3(flox/flox; lyz2-cre)

value: KO 3


title: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.2, LPS 4h

value: KO 2


title: BMMs from Uba3(flox/flox) mouse No.1, no stimulation


title: EG.EP.2

description:
hiPSC-EPI
RPKM_normalized.csv


title: Human thymus, CD34+, OP9DLL1 cultured, 10d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL1 (10d)
Expi 166 - H_KT34+ na MACS op OP9-DL1 Dag 10


title: NEDD8-sufficient BMMs, no stimulation

description: WO; WT oh

value: Bone marrow mononuclear cells (BMM)


title: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.1, LPS 4h

value: KO 1


title: BMMs from Uba3(flox/flox) mouse No.3, LPS 4h


title: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.3, no stimulation


title: F.21

description:
huF-CFs
RPKM_normalized.csv

value: wk 21


title: Human thymus, CD34+, OP9LIE cultured, 5d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9LIE (5d)
Expi 166 - B_KT34+ na MACS op OP9-LIE Dag 5


title: adipose tissue, BI37

city: Évora

first: André

middle: Filipe Barreto

last: Albuquerque

address: Rua Ramalho Ortigao, 15

institute: Universidade de Évora

data_processing:
Obtained sequence reads were trimmed for three consecutive times for Ilumina adapters, poli-A and poli-T tails using Trim Galore (version 0.5.0) while removing resulting low quality nucleotides (Phred Score, Q<20) and short length reads (<40).
Reads were aligned to the reference pig genome version Sscrofa11.1 (Ensembl release 94) using HISAT2 version 2.1.0
Generated SAM files were then converted to BAM with Samtools version 1.9
HTSeq-count version 0.11.1 was used to count and merge reads based on overlapping paired-end reads
Gcount files were run with the R package DESeq2 with a filtering of a minimum 50 reads per group. Genes were considered as differentially expressed when presenting a false discovery rate (FDR) lower than 0.05
Genome_build: reference pig genome version Sscrofa11.1 (Ensembl release 94)
Supplementary_files_format_and_content: Comma Separated Values (CSV) files that include log2FoldChange and associated p-adjusted values

organism: Sus scrofa

source_name: adipose tissue

extract_protocol:
Adipose tissue samples were collected. Total RNA was obtained through extraction following Ambion RiboPure Kit with Trizol and was stored at -80°C
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Bisaro

value: adipose tissue

tag: carcass weight


title: adipose tissue, BI36


title: adipose tissue, BI34


title: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.2, no stimulation


title: F.15

description:
huF-CFs
RPKM_normalized.csv

value: wk 15


title: Human thymus, CD34+, control ex vivo isolated, replicate 1

description:
miRNA expression data from ex vivo isolated CD34+ thymocytes
Expi 166 - A_KT34+ na MACS Dag 0

value: control ex vivo isolated

value: ex vivo isolated


title: F.12.5

description:
huF-CFs
RPKM_normalized.csv

value: Fibroblast


title: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.1, no stimulation

value: Bone marrow-derived macrophages (BMMs)


title: adipose tissue, BI25


title: EG.EP.1

description:
hiPSC-EPI
RPKM_normalized.csv

value: Epicardial cells


title: Human thymus, GD+CD3+CD1+, replicate 1

description:
miRNA expression data from ex vivo isolated GD+CD3+CD1+ thymocytes
DONOR2_GD+CD3+CD1+

source_name: Human thymus, GD+CD3+CD1+, replicate 1

treatment_protocol: Cell suspension from child thymus was stained for specific cell surface markers in order to sort out dinsinct T cell subsets.

value: thymus


title: Human thymus, GD+CD3+CD1+, replicate 2

description:
miRNA expression data from ex vivo isolated GD+CD3+CD1+ thymocytes
DONOR3_GD+CD3+CD1+

source_name: Human thymus, GD+CD3+CD1+, replicate 2


title: adipose tissue, AL63

value: Alentejano


title: Human thymus, CD34+, OP9DLL1 cultured, 5d, replicate 1

description:
miRNA expression data from CD34+ thymocytes cultured on OP9DLL1 (5d)
Expi 166 - C_KT34+ na MACS op OP9-DL1 Dag 5


title: Human thymus, GD+CD3+CD1-, replicate 2

description:
miRNA expression data from ex vivo isolated GD+CD3+CD1- thymocytes
DONOR3_GD+CD3+CD1-

source_name: Human thymus, GD+CD3+CD1-, replicate 2


title: EC.21

description:
huF-ECs
RPKM_normalized.csv

value: Endothelial cells


title: adipose tissue, AL52


title: Human thymus, GD+CD3+CD1-, replicate 1

description:
miRNA expression data from ex vivo isolated GD+CD3+CD1- thymocytes
DONOR2_GD+CD3+CD1-

source_name: Human thymus, GD+CD3+CD1-, replicate 1


title: EC.12.5

description:
huF-ECs
RPKM_normalized.csv


title: EC.15

description:
huF-ECs
RPKM_normalized.csv


title: adipose tissue, AL44


title: Human thymus, CD8+CD3+, replicate 2

description:
miRNA expression data from ex vivo isolated CD8+CD3+ thymocytes
DONOR3_CD8+CD3+

source_name: Human thymus, CD8+CD3+, replicate 2


title: Human thymus, CD8+CD3+, replicate 1

description:
miRNA expression data from ex vivo isolated CD8+CD3+ thymocytes
DONOR2_CD8+CD3+

source_name: Human thymus, CD8+CD3+, replicate 1