title: Set1G990E H3K4me3 repeat2

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: G990E-K4ME3.calibrated.bw


title: wild type nucleosome rep1

status: Public on Jun 15 2016

type: SRA

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

country: USA

institute: Huntsman Cancer Institute

library_source: genomic

data_processing: De-multiplexed Fastq files from the Illumina pipeline were aligned to the Saccharomyces cerevisiae genome release 64 (UCSC SacCer3) using Novoalign version 2.8 (http://www.novocraft.com), allowing for one random repeat, base recalibration, and a minimum alignment quality score of 13. Alignments were converted to sorted, indexed Bam files using samtools. Separate sequence lanes from the same sample were merged using samtools.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MNase-digested mononucleosome

growth_protocol: Yeast were grown in YPAD broth (1% Yeast extract, 2% Peptone, 2% Dextrose, and 0.004% adenine hemisulfate) at 30°C with constant shaking at 225 rpm to an OD A600  of 0.8-1.0.

extract_protocol:
Cells were crosslinked for 20 minutes by addition of formaldehyde to 1% final concentration in the media and quenched by the addition of 1M glycine to 0.1M final concentration. 33 x 10^7 cells were harvested by centrifugation and washed twice with Phosphate-Buffered Saline and once with spheroplasting buffer (1M Sorbitol, 10 mM Tris.Cl pH 7.5, 15 mM 2-mercaptoethanol and protease inhibitors (PIs): 1 mM PMSF, 1μg/ml aprotinin, 1μg/ml leupeptin, 1μg/ml pepstatin A). Cross-linked cells were resuspended in 1ml fresh spheroplasting buffer before adding Lyticase (500 units; Sigma) and incubated in a 37oC water-bath shaker for 15-20 min with gentle agitation. Spheroplasts were washed twice with 25ml wash buffer (50mM Tris pH 7.5, 100mM KCl, 2.5mM MgCl2, 400mM Sorbitol, and PIs), resuspended in MNase digestion buffer (50mm Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 1mM CaCl2 and 0.1% Triton X-100 and PIs) and digested with 10 units of MNase (Micrococcal Nuclease, Worthington Biomedical) at 37oC for 15 min. Digestion was stopped by adding 100μL 10X stop buffer (50mM Tris.Cl pH 7.5, 500mM NaCl, 100mM EDTA, 20mM EGTA, 10% Triton X-100 and 1% Sodium Deoxycholate). After centrifugation, soluble chromatin (500μL) was mixed with an equal amount of elution solution (1% SDS, 100 mM sodium bicarbonate) and NaCl (200mM final concentration), reverse cross-linked for 5h at 65oC and ethanol precipitated overnight at -20oC. After centrifugation, the DNA pellet was washed with cold 70% ethanol, air-dried, dissolved in nuclease-free water. RNase A (2μL of 10mg/ml stock, Qiagen) digestion was performed at 37oC for 30 min followed by Proteinase K digestion (2 μL, Roche) for 1h at 42oC in the presence 1X Proteinase K digestion buffer (10mM Tris.Cl pH 8.0, 5mM EDTA, 0.5% SDS). DNA was purified using Qiagen PCR purification kit and eluted in 50μL nuclease-free water. DNA concentration was measured using NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Scientific).
Equal amount of purified DNA (10ng) was subjected to library construction using the NEBNext®  ChIP-Seq Library Prep Reagent Set for Illumina following the manufacturer's protocol. Adaptor-ligated and index primer-containing amplified DNA corresponding to mononucleosomes was resolved in an 1.5% agarose gel and purified using the Qiagen Gel Extraction Kit, except incubation to melt the gel was performed at 37oC for 30min. The library was then subjected to 50bp single read sequencing in an Illumina Hiseq2000 sequencer.

tag: strain

value: HTABWT

tag: genotype

value: Mat a hta1-htb1D hta2-htb2D lys2-128deltahis3delta200 ura3-52 HTA1-HTB1 (CEN HIS3)


title: jhd2D nucleosome  rep1

value: jhd2_delta::KanMX Mat a hta1-htb1D hta2-htb2D lys2-128deltahis3delta200 ura3-52 HTA1-HTB1 (CEN HIS3)


title: jhd2Δ H3K4me1 repeat2

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: Jhd2-K4ME1.calibrated.bw

data_processing:
De-multiplexed Fastq files from the Illumina pipeline were aligned using Novoalign version 2.8 (http://www.novocraft.com), allowing for one random repeat, base recalibration, and a minimum alignment quality score of 13. Sequences were aligned first to the C glabrata genome; unaligned read sequences were exported and re-aligned to the S cerevisiae genome. To identify orthologous alignments, aligned sequences to the C glabrata genome were exported as fastq and re-aligned to S cerevisae; sequences that aligned to both genomes were considered orthologous. Alignments were converted to sorted, indexed Bam files using samtools. Biological replicates, after comparison, had their alignments were merged using samtools.
Fragment coverage was generated using the BioToolBox bam2wig application (v1.35) by extending each alignment in the 3' direction by 200 bp and counting the coverage. Depth was normalized to reads per million (RPM). Coverage tracks were converted to bigWig files for visualization and analysis using UCSC utilities.
Replicates were compared by generating a Pearson correlation of the coverage files using the UCSC utility bigWigCorrelate with a max threshold of 250. Replicates were merged with samtools and coverage tracks re-generated.
The number of alignments to S cerevisiae and C glabrata were counted using samtools. The number of orthologous alignments were subtracted from C glabrata counts. A normalization factor was derived from the formula (Cg_Ref x Sc_ChIP) / (Sc_Ref x Cg_ChIP), where Cg_Ref is the number of Input alignments to C glabrata, Sc_ChIP is the number of ChIP alignments to S cerevisiae, Sc_Ref is the number of Input alignments to S cerevisiae, and Cg_ChIP is the number ChIP alignments to C glabrata. This normalization scale was then applied to every genomic position represented in a bedGraph file of the ChIP fragment coverage to S cerevisiae using the script manipulate_wig (https://github.com/tjparnell/HCI-Scripts).
Genome_build: SacCer3
Genome_build: Candida glabrata, GCA_000002545.2, Ensembl Fungi release 30
Supplementary_files_format_and_content: BigWig files representing uncalibrated fragment (uniformly extended to 200 bp) coverage depth normalized to reads per million mapped. Filenames have uncalibrated in their name.
Supplementary_files_format_and_content: BigWig files representing the the merged replicate, calibrated fragment coverage depth. Filenames have calibrated in there name. These files are available in a tar archive on the series record.

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: sonicated soluble chromatin

extract_protocol:
Yeast strains were grown to mid-log phase and cross-linked with 1% formaldehyde for 20 min at room temperature. Crosslinking was stopped using 0.125 mM glycine and cells were washed with 1X PBS. Multiple aliquots of 40 × 107 cross-linked cells each were prepared. Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) was grown at 25°C and subjected to formaldehyde crosslinking as described for budding yeast, and individual aliquots containing 20 × 107 cells each were harvested. Cross-linked S. cerevisiae (40 × 107) and C. glabrata (20 × 107) cells were mixed together in FA140+SDS buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 140 mM NaCl, 0.1% SDS) and lysed by bead beating. Lysates from two sets of S. cerevisiae and C. glabrata admixture (i.e., 120 × 107 cells in total) were pooled and sonicated in a Diagenode Bioruptor™ for 30 min (6 cycles of 5 min each, 30 sec ON and 30 sec OFF at high setting). Soluble chromatin was obtained after two sequential high-speed centrifugations of the sonicated lysate (16,100 X g for 5 min and 15 min). SDS was removed by dialysis as follows. Soluble chromatin obtained from four batches of control or mutant budding yeast and candida admixture were pooled, transferred to a 5 ml Float-A-Lyzer G2 dialysis device (3.5 - 5 kD MWCO) (Spectra/Por) and dialyzed initially for 2 h in 1 L FA140 buffer followed by an overnight dialysis in fresh 4 L FA140 buffer. Dialysate was centrifuged at 16,100 X g for 15 min at 4°C. A 100 μl aliquot was set aside for isolating input DNA. The remaining dialysate was split equally into three tubes and pre-cleared using 50 μl blocked Dynabeads® Protein A for 1h at 4°C with end-over-end rotation. Dynabeads® Protein A were blocked with BSA and fish skin gelatin as described above except bead blocking was done for 4 h. Pre-cleared lysate was combined with either α-H3K4me1 (20 μl, Active Motif) or α-H3K4me2 (10 μl, Millipore) or α-H3K4me3 (10 μl, Active Motif) antibody and 100 μl blocked Dynabeads® Protein A, and incubated overnight at 4°C with end-over-end rotation. Beads were initially washed with three times with FA140 buffer by inversion followed by sequential washes (5 min each with end-over-end rotation): FA140 buffer (2 times), FA1000 buffer (2 times), FA500 (2 times), LiCl/NP40 buffer (1 time) and TE (1 time). ChIP DNA was eluted in 400 μl elution solution (1% SDS, 100 mM sodium bicarbonate) and incubated at room temperature with end-over-end mixing for 40 min. The eluate is transferred to a fresh 0.65 ml tube, 18 μl 5 M NaCl is added and mixed well. At this stage, 400 μl elution solution and 18 μl 5 M NaCl is also added to the 50 μl soluble chromatin set aside to isolate ‘‘input’’ DNA. Reverse crosslinking is done by incubation at 65 °C for 5 h in a thermal cycler. The solution was transferred to a fresh 1.5 ml tube, 1 ml ethanol was added, mixed well and precipitation was allowed to occur overnight at -20 °C. The samples were centrifuged at maximum speed in a table-top centrifuge at 4°C. The pellet was washed with 70% ethanol followed by centrifugation at high speed. The pellet was dissolved in 90 μl water, treated with 2 μl 10 mg/ml RNase A and followed by an incubation at 37 °C for 30 min. Proteins were removed by adding 10 μl 10X PNK buffer (100 mM Tris.Cl, pH 8.0, 50 mM EDTA, 5% SDS), 1 μl Proteinase K (Sigma) and incubating at 42°C for 1 h. DNA was purified using Qiaquick PCR Purification kit after addition of 20 μl 3 M Sodium acetate to adjust the pH. DNA was eluted in 50 μl water and stored at -20 °C. DNA concentration was measured using Qubit Fluorometer. Equal amount ChIP or input DNA was used in library construction using NEBNext® Multiplex Oligos (Index Primers Set 1 and Index Primer Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina.
Equal amount of purified DNA (10ng) was subjected to library construction using the NEBNext®  ChIP-Seq Library Prep Reagent Set for Illumina following the manufacturer's protocol. Adaptor-ligated and index primer-containing amplified DNA were resolved in an 2.0% agarose gel and 300-500 bp sized fragments were purified using the Qiagen Minelute Gel Extraction Kit, except incubation to melt the gel was performed at 37oC for 30min.

value: jhdelta2_delta::KanMX Mat a hta1-htb1delta hta2-htb2delta lys2-128deltahis3delta_200 ura3-52 HTA1-HTB1 (CEN HIS3)


title: Set1G990E H3K4me1 repeat2

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: G990E-K4ME1.calibrated.bw

value: AdeltaH1p-FlagSET1G990E::URA3 Mat a hta1-htb1delta hta2-htb2delta lys2-128deltahis3delta_200 ura3-52 HTA1-HTB1 (CEN HIS3)


title: jhd2Δ H3K4me3 repeat2

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: Jhd2-K4ME3.calibrated.bw


title: wild type H3K4me2 repeat2

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: WT-K4ME2.calibrated.bw

value: Mat a hta1-htb1delta hta2-htb2delta lys2-128deltahis3delta_200 ura3-52 HTA1-HTB1 (CEN HIS3)


title: wild type input repeat1

description:
genomic DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file:


title: Set1G990E H3K4me3 repeat1


title: Set1G990E input repeat1


title: jhd2Δ input repeat1


title: jhd2Δ H3K4me3 repeat1


title: wild type H3K4me2 repeat1


title: wild type H3K4me3 repeat1

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: WT-K4ME3.calibrated.bw


title: jhd2Δ H3K4me2 repeat1

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: Jhd2-K4ME2.calibrated.bw


title: Set1G990E H3K4me2 repeat1

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: G990E-K4ME2.calibrated.bw


title: polysome Ct rep4

status: Public on Jun 14 2016

city: Dundee

first: Victoria

last: Cowling

address: Dow Street

department: School of Life Sciences

country: United Kingdom

institute: University of Dundee

description: polysomal RNA

library_source: transcriptomic

data_processing:
Base calling performed using the BCL2Fastq2
Reads were aligned to the mm10 genome assembly using STAR 2.5.1b using --quantMode GeneCounts parameters to count number of reads per gene using htseq-count tool.  Counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse).
Differential expression analysis was performed using edgeR Bioconductor package. Counts per million (CPM) were calculated using normalized library sizes.
Genome_build: mm10
Supplementary_files_format_and_content: Number  reads  per  gene was counted with STAR --quantMode GeneCounts option and counts for all samples saved to a tab delimited file.

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: 46C ESCs (expressing Sox1-GFP) derived from strain 129Ola mice were cultured on 0.1% gelatin-coated dishes in Glasgow Minimal Essential Medium (GMEM) (Sigma), 10% knockout serum replacement, 1% modified Eagle’s medium (MEM) non-essential amino acids, 1mM sodium pyruvate (Life Technologies), 0.1 mM 2-Mercaptoethanol (Sigma) and 100 Units/ml recombinant human leukaemia inhibitory factor (LIF; prepared in-house).

extract_protocol:
Cells were incubated in 100 µg/ml cycloheximide for 10 min, washed in ice cold PBS supplemented with 100 µg/ml cycloheximide  and extracts were collected in polysome lysis buffer: 15 mM Tris (pH7.5), 15 mM MgCl2, 0.3 M NaCl, 1 mM DTT, 1% Triton X-100, 100 mg/ml cycloheximide, 100 U/ml RNasin. 10% of extracts was kept as input and the rest layered onto 10 ml of 10%–50% sucrose steps and centrifuged at 18 000 x g for 2 hr at 4ºC. 0.5 ml fractions were collected and OD254 nm monitored. Fractions 17-22 (polysome) were purified by Phenol:Chloroform:Isoamyl Alcohol (25:24:1) (Ambion), pooled, and RNA precipitated with 2M of LiCl (Sigma). RNA from inputs was purified using Trizol Reagent (Invitrogen) according to manufacturer’s instructions.
Libraries were prepared according to Illumina's TruSeq Stranded Total RNA with Ribo-Zero Gold for Human/Mouse/Rat (RS-122-2303). Briefly, the first step involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The Ribo-Zero Gold Human/Mouse/Rat kit depletes samples of cytoplasmic rRNA and mitochondrial rRNA. Following purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments are then 'A' tailed followed by ligation of the Illumina adapter. The products are purified and enriched by PCR to create the final cDNA library.

treatment_protocol: 2.5x10^6 cells was transfected with 70 pM RAM siRNA or non-targetting control (siGenome, Dharmacon) for 48 hrs using Lipofectamine RNAiMAX (Invitrogen).

tag: cell type

value: 46C embryonic stem cells

tag: treatment

value: Control siRNA


title: polysome siRAM rep1

description: polysomal RNA

value: RAM siRNA


title: polysome siRAM rep3

description: polysomal RNA


title: polysome siRAM rep2

description: polysomal RNA


title: polysome siRAM rep4

description: polysomal RNA


title: MC

city: Wuhan

first: Xiaoming

last: Sun

state: Hubei

address: Lumo road, No. 1

country: China

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean reads were obtained by discarding read lengths shorter than 18 nt or longer than 30 nt, while removing the adaptors, low quality tags, and contaminants from the raw reads. The read length distributions of unique and total reads were summarized. Small RNA tags were mapped to the Vitis vinifera cv. Pinot Noir (PN40024) genomes using the SOAP2 program. The program was performed using the following parameters: soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap.
The matched sequences were then queried against snRNAs, snoRNAs, scRNAs, rRNAs, and tRNAs from NCBI Genbank database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) and Rfam database (http://www.sanger.ac.uk/Software/Rfam) by Blastn search with the parameters, blastall -p blastn -F F -e 0.01.
Genome_build: 12× Vitis vinifera cv. Pinot Noir (PN40024)
Supplementary_files_format_and_content: novel_miRNA.stat.txt: statistic of predicted novel miRNAs of all samples. STAR format
*clean.fa: clean tags, 18-30 nt, tab delimited | raw counts | sequence

organism: Vitis vinifera

growth_protocol: Micropropagated ‘Muscat Hamburg’ (V. vinifera) plantlets were grown on 1/2 B5 medium with 30 g L−1 of sucrose in a growth chamber at 26 °C. The average photosynthetic photon flux (PPF) was 100 μmol m-2 s−1 with a 16 h light and 8 h dark cycle.

extract_protocol:
The samples harvested at 0 h (none cold-treated, NCT) and 4 h (cold-treated, CT) were used to construct small RNA libraries. Total RNA was extracted from collected samples using Column Plant RNAOUT 2.0 kit (Tiandz, Beijing, China), following the instructions of the manufacturer. RNA concentration and quality were detected using Agilent 2100 Bioanalyzer.
Total RNA was purified by electrophoretic separation on a 15% TBE urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5’-adaptor and a 3’- adaptor sequentially by T4 RNA ligase (New England Biolabs, USA). The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript III Reverse Transcriptase (Invitrogen, USA) and then PCR-amplified for 17 cycles using the adaptor primers. The PCR products were purified for high-throughput sequencing.

treatment_protocol: Six-week old plantlets were treated at 4 °C for 4 h and the plantlets grew at 26 °C as a control.

tag: cultivar

value: Muscat Hamburg

tag: age

value: 6-week old

tag: treated at

value: 26 °C as a control

tag: tissue

value: leaf


title: wild type H3K4me1 repeat1

description:
ChIP DNA
contains DNA from Candida glabrata (Anderson) Meyer et Yarrow Strain Designation: NCYC 388 (ATCC® 36909) used as calibration genome
calibrated processed data file: WT-K4ME1.calibrated.bw


title: jhd2Δ H3K4me1 repeat1


title: polysome Ct rep3

description: polysomal RNA


title: MT

source_name: leaf_cold treatment

value: 4°C for 4h (cold treatment)


title: input Ct rep3

description: cytoplasmic RNA


title: input Ct rep4

description: cytoplasmic RNA


title: polysome Ct rep1

description: polysomal RNA


title: input siRAM rep1

description: cytoplasmic RNA


title: input siRAM rep2

description: cytoplasmic RNA


title: input siRAM rep4

description: cytoplasmic RNA


title: input siRAM rep3

description: cytoplasmic RNA


title: polysome Ct rep2

description: polysomal RNA


title: Set1G990E H3K4me1 repeat1


title: T47D_MK2206_H3K4me3_48

city: Boston

first: Koen

last: Dreijerink

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls were performed with FastQC version 0.10.0.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7.
Data were filtered according to mappable reads with 2 mismatches at most allowed.
Peaks were called using MACS version 2.0 with the following settings: band width (300), model fold (5, 50), qvalue cut-off (1*10e-2), range for calculating regional lambda (1000bps and 10000bps)
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using MACS version 2.0, scores represent -LOG10(qvalue)

organism: Homo sapiens

source_name: T47D breast cancer cells

growth_protocol: Cells were maintained at 37oC and 5% CO2 in RPMI or DMEM + 10% FBS and Pen-Strep.

extract_protocol:
Cells were crosslinked, lysed in SDS lysis buffer, and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics

treatment_protocol: The medium was changed to medium containing either MK2206 or DMSO for 24 hours.

tag: chip antibody

value: H3K4me3 Abcam (Ab8580)


title: input Ct rep1

description: cytoplasmic RNA


title: T47D_DMSO_KDM5A

value: KDM5A #1416 (gift Kaelin Lab DFCI)

value: DMSO


title: T47D_MK2206_KDM5A


title: DMSO24h_2_s4_ctrl

data_processing:
Basecalls were performed with FastQC version 0.10.0.
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Genome_build: hg19

extract_protocol:
RNA was extracted using RNeasy
Libraries were made from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit


title: T47D_DMSO_H3K4me3_24


title: T47D_MK2206_H3K4me3_24


title: MK24h_2_s1_treat

value: AKT inhibitor MK2206


title: T47D_DMSO_H3K4me3_48


title: r873sU-I3_hs_rna_sr_Wiese_F_3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using Bowtie2 v2.1.0 to mm10. Data were conversed and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 2x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; normalised text file and raw data txt files

growth_protocol: cells were cultures as monolayers

extract_protocol:
High Pure RNA Isolation Kit according to manufacturers instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

treatment_protocol: RNA was isolated from two independent biological replicates of KNS42 and UW479 cells after treatment with ICG-001 or vehicle for 48h

tag: cell line

tag: developmental stage

value: pediatric

value: ICG

tag: treatment period


title: MK24h_2_s2_treat


title: r873sU-I2_hs_rna_sr_Wiese_F_2


title: r873sU-D3_hs_rna_sr_Wiese_E_3

value: Control


title: DMSO24h_1_s3_ctrl


title: r873sU-D2_hs_rna_sr_Wiese_E_2


title: input Ct rep2

description: cytoplasmic RNA


title: wild type H3K4me1 repeat2

value: HTABWT


title: TG.Pin1.KO_1

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Read alignment with tophat 2.0.8: tophat -p 8 -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded R1.fastq R2.fastq
Genome_build: mm9
Supplementary_files_format_and_content: csv file with RPKM

source_name: spleen

growth_protocol: primary mouse samples

extract_protocol:
Total RNA from B cells was purified using RNeasy Mini kit (Qiagen) according to the manufacturers protocol, including the on-column DNase I digestion step. 1µg total RNA was retro-transcribed into cDNA using the reverse transcriptase ImPromII (Promega) and oligodT and random primers. 10ng of cDNA were used for each quantitative reverse transcriptase PCR (qRT-PCR) analysis. Amplification was performed with the FAST SYBR Green Master Mix and quantified using the 7500 Fast Real-Time PCR machine (both Applied Biosystems).   For RNA sequencing, 5µg of total RNA of good quality (RNA integrity number ≥ 7.5) were treated according to the Ribozero rRNA removal kit (Epicentre) and purified on RNeasy MinElute columns (Qiagen). RNA integrity and successful removal of ribosomal RNA were assessed with the Agilent 2100 Bioanalyser (Agilent Technologies) or the LabChip® GX II Gel Electrophoresis (PerkinElmer).
RNA-seq libraries were prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol starting from the RNA fragmentation step.

treatment_protocol: B220+ cells were purified from the spleens of control or pre-tumoral (6-8 weeks old) Eµ-myc mice using the MACS B cell isolation kit (Miltenyi Biotec)according to the manufacturers protocol.

value: spleen

value: E-mu-myc Pin1-/-


title: S_1036

city: Gothenburg

first: Adil

last: Mardinoglu

state: Gothenburg

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
standard Illumina RNA-Seq protocol was used for processing.
processed reads were mapped to the human genome (GRCh37) using Tophat v2.0.8b (C. Trapnell et al., Bioinformatics, 2009)
fragments per kilobase of exon model per million mapped reads (FPKM) values were calculated using Cufflinks v2.1.1 (C. Trapnell et al., Nat. Biotechnol. 2010) and the gene models from Ensembl build 75 were used in Cufflinks.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Subcutaneous fat tissue of obese patient

extract_protocol:
Samples were obtained from obese subjects undergoing bariatric surgery.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Subcutaneous fat

tag: bmi


title: TG.Pin1.KO_4


title: TG.Pin1.KO_5


title: r873sS-I2_hs_rna_sr_Wiese_D_2


title: r873sU-D1_hs_rna_sr_Wiese_E_1


title: TG.Pin1.KO_3


title: r873sS-D3_hs_rna_sr_Wiese_C_3


title: G1_165kb_B2_1_1_k562_I1_MS

city: Rehovot

first: Omer

last: Schwartzman

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.k562_I1

data_processing:
The data was processed using our UMI-4C pipeline. With default parameters.
Processed reads were mapped with bowtie2 with the parameters:  --reorder --end-to-end.
Genome_build: hg19
Supplementary_files_format_and_content: The processed adj files are a 3 columns tab delimited table with headers: fragment end id1 (fend1), fragment end id2 (fend2), UMI count (count)

source_name: K-562 cells

growth_protocol: Human leukemia cell lines, CMK, CMY, CHRF, and K562 were grown in RPMI (GIBCO) supplemented with 10% FBS, 1% glutamine (GIBCO), penicillin (100 U/mL), and streptomycin (100 μg/mL). Wi38 cells were grown in DMEM supplemented with 10% FBS, 1 mM sodium pyruvate, 1% glutamine (GIBCO), penicillin (100 U/mL), and streptomycin (100 μg/mL). (GIBCO) All cell lines were grown at 37°C and 5% CO2.

extract_protocol:
10^7 cells used to generate the primary 3C template. Cells are collected, centrifuged at 1200rpm, the supernatant is removed and are resuspended in PBS/10% FBS. Then the cells are cross-linked with formaldehyde to final concentration of 2% for 10min. The reaction is quenched by addition of glycine to final concentration of 0.125M. The cells are then centrifuged and resuspended in cold lysis buffer (50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100, 1 tbl Protease inhibitor). The nuclei are extracted and resuspended in 450µl UPW. For digestion, we add 60µl DpnII buffer, 15µl 10% SDS and incubate on a Thermomixer (Eppendorf) 37c, 60 minutes. 75µl of 20% TX-100 are added and the tube is incubated again 37c, 60 minutes. The chromatin is then digested with HC DpnII (NEB R0543M) in three rounds as following: 200U for 2 hours, 200U overnight and 200U for 2 hours. An aliquot is taken from the tube and run on gel to inspect digestion efficiency. The enzyme is then inactivated by incubating 65c, 20min. Next, the chromatin is ligated with 15µl of HC T4 ligase (NEB M0202M), with 10x ligase buffer to final volume of 7mL and incubated overnight at 16c. Aliquot is taken from the sample and ran on gel to inspect ligation efficiency. The chromatin is then reverse cross-linked overnight at 65c with 30ul proteinase K (Sigma-Aldrich), and then 30ul  of RNase A are added and incubated for 45 minutes, 37c. The 3C DNA is then extracted with Phenol-Chloroform resuspended in 10mM Tris-Hcl pH 8 and stored in -20c.
5-10ug DNA in 200µl Elution Buffter (EB, 10mM Tris-HCl, pH 8) of 3C template is sonicated at 4°c using Bioruptor program: 5 cycles of 30s on, 60s off. The sonicated material is inspected by running 10µl on agarose gel to assure size distribution of 450-550 bps. The sonicated DNA is subjected to end-repair reaction - 20µl 10X end-repair buffer and 10µl end-repair mix (NEB E6050L) are added to the mix and incubated at 20°c for 30 minutes. The DNA is cleaned by x2.2 AmpureXP beads (Beckman Coulter) and eluted in 76µl EB. Two nested PCR reactions are used for UMI-4C library construction. The PCR reactions are performed in 50ul volume with the following reagents: 10ul GoTaq Flexi buffer (promga M792A), 3ul MgCl 25mM (promega A3511), 0.2mM dNTPs, 2µl 10mM bait primer (0.4mM final concentration), 2µl 10mM Illumina enrichment primer 2 (0.4mM final concentration), 1ul GoTaq (promga M3008) and 200ng UMI-4C DNA template. PCR program is 2 minutes 95°c, 20 cycles of 30s 95°c, 30s 56°c, 60s 72°c, final extension of 5min 72°c. Following the PCR reaction we clean the amplified DNA with x1 SPRI beads and use 75% of the eluate to a second PCR reaction. The second PCR reaction is identical to the first. The only difference is the use of the bait primer with the Illumina dangling adapter (As shown in figure 1B). In the second PCR reaction 15-18 cycles are used instead of 20. Then, A-tailing reaction is performed with 10µl NEBbuffer2, 4µl Klenow (NEB M0212M), and 10µl 10nM dATP. Following A-tailing, the 5’ ends of the DNA are dephosphorylated with 2µl of Alkaline Phosphatase (NEB M0290S) 50°c for 60 minutes, and the DNA is cleaned with AmpureXP beads (x2) and eluted in 67µl EB. The DNA template is ligated with 5µl 15µM Illumina indexed adapters (final concentration 0.4µM), 10µl ligase mix and 80µl 10X buffer (NEB M2200). To release the non-ligated strand of the adapter, the DNA is denatured at 95°c for 2 minutes and cleaned with SPRI beads x1.

value: Mega-Erythroleukemia

tag: linage

value: Hematopoietic

tag: viewpoint


title: S2R+ 110k rep1 (EV)

city: Montreal

first: Fabio

middle: Alexis

last: Lefebvre

state: Quebec

address: 110 Ave des Pins

department: RNA biolog

country: Canada

institute: IRCM

data_processing:
Read quality was confirmed using FastQC v0.10.1 and trimming was performed with Trimmomatic when deemed necessary.
Read alignment was performed using Tophat v2.0.10 on the human GRCh37/hg19 and the Drosophila BDGP5.78/dm3 genomes, respectively.
Ribosomal RNA sequences were filtered out by first mapping the reads to FASTA files of genes annotated as rRNA in Ensembl.  Remaining reads were then re-aligned to reference genomes with Tophat.
BAM files were used for expression analyses with Cuffdiff v2.2.1 without effective length correction.
Genome_build: GRCh37/hg19 (human) and BDGP5.78/dm3 (Drosophila)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Drosophila melanogaster

source_name: S2R+ EV

growth_protocol: Human HepG2 and A431 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 1% of a 1:100 solution of penicillin and streptomycin (pen/strep) and 10% fetal bovine serum (depleted FBS) (Wisent). Before use, FBS was depleted of bovine EVs by ultracentrifugation (110,000 g, 18h, 4°C). Human cells were cultured at 37 °C, in an atmosphere of 5% CO2 in T-flasks of 175 cm2 and routinely detached using 0.25% trypsin upon reaching 80% confluence. Drosophila D17 and S2R+ cells were respectively maintained in Shield and Sang Insect Medium (M3) and in Schneider medium. Both media were supplemented with 1% of a 1:100 pen/strep solution and 10% depleted FBS. M3 medium additionally contained insulin (20 μg/mL). Droso¬phila cells were cultured at 25°C.

extract_protocol:
EVs and corresponding cellular pellets were resuspended in 1 mL of TRIzolTM reagent (Ambion) and processed according to the manufacturer's instructions RNA extracts were purified with the RNA Clean & ConcentratorTM-5 system (Zymo Research).  In-column DNase I (New England BioLabs) treatment, RNA washes and elution steps were performed according to the manufacturer's instructions. One additional centrifugation step was included (5 min at 16,000×g) to ensure complete removal of the washing buffer.  RNA samples were eluded in 12 μL of RNAse-free water (Wisent). Absorbance distributions were immediately quantified using a NanoDrop 2000c spectrophotometer.  RNA samples were  pure ( A260/A280 ≥ 2.0)( 2.00 ≤ A260/A230 ≤ 2.25). Aliquots of ~5 ng were submitted to capillary electrophoresis on a Bioanalyzer 2100 machine (Agilent). RNAse protection assay was performed to confirm the intraluminal topology of exRNA within EVs.  D17 and HepG2 cellular RNA extracts were used as controls. RNAse A (Qiagen) was inactivated by heat (10 min at 65 ºC) and RNA was extracted as described above.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For EV isolation, cells were kept at low passage (P<10) and cultured for approximately 48h starting from ~10^7 cells.  EVs were isolated according to an established differential ultracentrifugation protocol (Thery, C., et al. Curr Protoc Cell Biol, 2006. ). Briefly, fresh culture supernatants (~80 mL) were cleared of floating (10 min at 400×g) and dead cells (10 min at 2000×g) using a 5810 R centrifuge (Eppendorf). Cell debris were removed (30 min at 10,000×g) and EVs were pelleted (70 min at 110,000×g) using the Sw28 and the Sw32 Ti rotor (Beckman Coulter) in an L8-70M machine (Beckmann). Preparations were extensively washed with PBS and pelleted (70 min at 110,000×g) using a RP100-AT4 rotor (Sorvall) and a RC-M100 micro ultracentrifuge (Sorvall). All steps were performed at 4 °C and EVs were immediately processed for analysis.

value: S2R+ embryonic cell line

tag: cell passages

tag: rna source

value: EV


title: r873sS-I3_hs_rna_sr_Wiese_D_3


title: r873sS-D2_hs_rna_sr_Wiese_C_2


title: r873sS-I1_hs_rna_sr_Wiese_D_1


title: TG.Pin1.WT_1

tag: strain

value: E-mu-myc Pin1+/+


title: r873sK-I3_hs_rna_sr_Wiese_B_3


title: r873sS-D1_hs_rna_sr_Wiese_C_1


title: r873sU-I1_hs_rna_sr_Wiese_F_1


title: Pin1.WT_2

tag: genotype


title: TG.Pin1.WT_2

tag: cell type


title: Pin1.KO_2


title: Pin1.WT_5


title: TG.Pin1.WT_3


title: Pin1.KO_1


title: r873sK-I2_hs_rna_sr_Wiese_B_2

tag: treatment


title: r873sK-D2_hs_rna_sr_Wiese_A_2


title: r873sK-I1_hs_rna_sr_Wiese_B_1


title: Pin1.WT_1


title: r873sK-D1_hs_rna_sr_Wiese_A_1


title: T47D_MK2206_H3K4me3_72


title: CTRL-13

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

description: HD CTRL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl human transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 1 --library-type fr-unstranded -initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample.

extract_protocol:
TRIzol method (standard).
RNA libraries were prepared for sequencing using standard Illumina mRNA stranded protocols

value: brain BA4

tag: diagnosis

value: HD CTRL


title: T47D_DMSO_H3K4me3_72

value: H3K4me3 Abcam (Ab8580)


title: CTRL-12

description: HD CTRL

tag: age


title: Cell_213

city: Beijing

first: Haofei

last: Luo

address: Tsinghua Univ. Beijing

institute: Tsinghua university

data_processing:
RNAseq: After removing bacodes, adapters and low-quality reads, clean reads were mapped to the Mouse genome (mm10 version) with Tophat (Langmead et al., Genome Biology, 2009, 10, R25) allowing 2 mismatches.Gene expression level was calculated as reads per kilobases per million reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: The expression level (RPKM) of genes in each sample. The columns means for different single cells and rows for genes.

molecule: polyA RNA

source_name: Postnatal day 7 mouse tibia growth plate structures

extract_protocol:
Growth plates were isolated by microdissection and full length Ploy(A) RNA was extracted using Clonetech Smarter kit protocol
cDNA was prepared with Illumia Nextera XT DNA library construction kit according to the manufacture's protocol

tag: genotype/variation

value: Wild type

value: tibia growth plate

value: Postnatal day 7


title: Cell_215

tag: tissue


title: Cell_217


title: r873sK-D3_hs_rna_sr_Wiese_A_3

value: pediatric


title: Cell_212


title: CTRL-9

description: HD CTRL


title: Pin1.WT_4


title: CTRL-8

description: HD CTRL


title: Cell_211


title: Cell_208


title: Cell_210


title: CTRL-3

description: HD CTRL


title: HD-288

description: HD grade 3

value: HD grade 3


title: HD-290

description: HD grade 3


title: Cell_207


title: HD-68

description: HD grade 2

value: HD grade 2


title: Cell_206


title: Cell_209


title: HD-283

description: HD grade 4

value: HD grade 4


title: Cell_214


title: Cell_205


title: HD-61

description: HD grade 3


title: Cell_204


title: Cell_216


title: CTRL-4

description: HD CTRL


title: Cell_203


title: CTRL-11

description: HD CTRL


title: HD-58

description: HD grade 3


title: Cell_202


title: Cell_201


title: Cell_199


title: HD-57

description: HD grade 2


title: Cell_198


title: Cell_197


title: Cell_200


title: Cell_195


title: Cell_190


title: Cell_191


title: Cell_192


title: Cell_188


title: Cell_193


title: Cell_194


title: Cell_187


title: Cell_186


title: Cell_196


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_95

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description:
manuscript figure: New supplemental data
Nov11_95
adult heart derived, approx 5 months of age

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Reads were aligned with Bowtie v1.0.0, with parameters ³-p4 aS -X 800 --offrate 1 --chunkmbs 256 --nofw².  The Bowtie index was constructed from the UCSC Known Genes transcript sequences for the mm10 genome, downloaded in November 2014.  The index was created using the ³--offrate 1² parameter to bowtie-build.
Genes were quantified with eXpress v1.5.1, using the ³--rf-stranded² parameter.  Gene level expression values were calculated by summing the estimated TPM for each transcript associated with the gene in question.
Genome_build: mm10; gene models per UCSC
Supplementary_files_format_and_content: Expression values for each gene for each cell are provided in tab-delimited text file of calculated expression values for each sample using Log2(TPM+1)

extract_protocol:
Single cell suspensions were processed using Fluidigm C1 protocols
RNA libraries were prepared for sequencing using Clontech UltraLow SMARTer amplification chemistry, and Illumina/Nextera tagmentation-barcoding as per Fluidigm recommendations (2014)

value: C57BL/6 (backcross N=6)

value: heart

value: fibroblasts

value: approx 5 months of age

tag: cell classification


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_94

description:
manuscript figure: New supplemental data
Nov11_94
adult heart derived, approx 5 months of age


title: Cell_184


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_93

description:
manuscript figure: New supplemental data
Nov11_93
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_92

description:
manuscript figure: New supplemental data
Nov11_92
adult heart derived, approx 5 months of age


title: Cell_182


title: Cell_181


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_91

description:
manuscript figure: New supplemental data
Nov11_91
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_90

description:
manuscript figure: New supplemental data
Nov11_90
adult heart derived, approx 5 months of age


title: Cell_180


title: S_1104

value: Subcutaneous fat


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_89

description:
manuscript figure: New supplemental data
Nov11_89
adult heart derived, approx 5 months of age


title: Cell_189


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_88

description:
manuscript figure: New supplemental data
Nov11_88
adult heart derived, approx 5 months of age


title: Cell_178


title: Cell_179


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_87

description:
manuscript figure: New supplemental data
Nov11_87
adult heart derived, approx 5 months of age


title: Cell_177


title: Cell_176


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_84

description:
manuscript figure: New supplemental data
Nov11_84
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_86

description:
manuscript figure: New supplemental data
Nov11_86
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_85

description:
manuscript figure: New supplemental data
Nov11_85
adult heart derived, approx 5 months of age


title: Cell_185


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_82

description:
manuscript figure: New supplemental data
Nov11_82
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_81

description:
manuscript figure: New supplemental data
Nov11_81
adult heart derived, approx 5 months of age


title: Cell_183


title: Cell_171


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_76

description:
manuscript figure: New supplemental data
Nov11_76
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_77

description:
manuscript figure: New supplemental data
Nov11_77
adult heart derived, approx 5 months of age


title: Cell_170


title: Cell_169


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_79

description:
manuscript figure: New supplemental data
Nov11_79
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_75

description:
manuscript figure: New supplemental data
Nov11_75
adult heart derived, approx 5 months of age


title: Cell_168


title: Cell_167


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_74

description:
manuscript figure: New supplemental data
Nov11_74
adult heart derived, approx 5 months of age


title: Cell_165


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_72

description:
manuscript figure: New supplemental data
Nov11_72
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_71

description:
manuscript figure: New supplemental data
Nov11_71
adult heart derived, approx 5 months of age


title: Cell_173


title: Cell_163


title: Cell_175


title: Cell_174


title: Cell_166


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_73

description:
manuscript figure: New supplemental data
Nov11_73
adult heart derived, approx 5 months of age


title: Cell_164


title: Cell_172


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_70

description:
manuscript figure: New supplemental data
Nov11_70
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_68

description:
manuscript figure: New supplemental data
Nov11_68
adult heart derived, approx 5 months of age


title: Cell_161


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_67

description:
manuscript figure: New supplemental data
Nov11_67
adult heart derived, approx 5 months of age


title: Cell_162


title: Cell_160


title: Cell_157


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_69

description:
manuscript figure: New supplemental data
Nov11_69
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_65

description:
manuscript figure: New supplemental data
Nov11_65
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_8

description:
manuscript figure: Fig7-f
Jul24_8
adult heart derived, approx 5 months of age

value: Resident Tcf21traced/Tcf21+ (uninjured)


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_64

description:
manuscript figure: New supplemental data
Nov11_64
adult heart derived, approx 5 months of age


title: Untraced Activated CD31- CD45- cells from scar_cell-idNov11_66

description:
manuscript figure: New supplemental data
Nov11_66
adult heart derived, approx 5 months of age


title: Cell_159


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_9

description:
manuscript figure: Fig7-f
Jul24_9
adult heart derived, approx 5 months of age


title: Cell_156


title: Cell_154


title: Cell_155


title: Cell_158


title: Cell_153


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_5

description:
manuscript figure: Fig7-f
Jul24_5
adult heart derived, approx 5 months of age


title: Cell_152


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_4

description:
manuscript figure: Fig7-f
Jul24_4
adult heart derived, approx 5 months of age


title: Cell_151


title: Cell_149


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_32

description:
manuscript figure: Fig7-f
Jul24_32
adult heart derived, approx 5 months of age


title: Cell_148


title: Cell_150


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_29

description:
manuscript figure: Fig7-f
Jul24_29
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_7

description:
manuscript figure: Fig7-f
Jul24_7
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_28

description:
manuscript figure: Fig7-f
Jul24_28
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_31

description:
manuscript figure: Fig7-f
Jul24_31
adult heart derived, approx 5 months of age


title: Cell_147


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_26

description:
manuscript figure: Fig7-f
Jul24_26
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_3

description:
manuscript figure: Fig7-f
Jul24_3
adult heart derived, approx 5 months of age


title: Cell_146


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_25

description:
manuscript figure: Fig7-f
Jul24_25
adult heart derived, approx 5 months of age


title: Cell_145


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_23

description:
manuscript figure: Fig7-f
Jul24_23
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_18

description:
manuscript figure: Fig7-f
Jul24_18
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_24

description:
manuscript figure: Fig7-f
Jul24_24
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_12

description:
manuscript figure: Fig7-f
Jul24_12
adult heart derived, approx 5 months of age


title: Resident Tcf21traced/Tcf21+ (uninjured)_cell-idJul24_1

description:
manuscript figure: Fig7-f
Jul24_1
adult heart derived, approx 5 months of age


title: Cell_141


title: Cell_142


title: Cell_139


title: Resident Postn- CD31- CD45-_cell-idJul24_33

description:
manuscript figure: Fig3-g and 7-f
Jul24_33
adult heart derived, approx 5 months of age

value: Resident Postn- CD31- CD45-


title: Cell_137


title: Resident Postn- CD31- CD45-_cell-idJul24_27

description:
manuscript figure: Fig3-g and 7-f
Jul24_27
adult heart derived, approx 5 months of age


title: Cell_138


title: Resident Postn- CD31- CD45-_cell-idJul24_21

description:
manuscript figure: Fig3-g and 7-f
Jul24_21
adult heart derived, approx 5 months of age


title: Cell_135


title: Cell_136


title: Cell_144


title: Resident Postn- CD31- CD45-_cell-idJul24_2

description:
manuscript figure: Fig3-g and 7-f
Jul24_2
adult heart derived, approx 5 months of age


title: Resident Postn- CD31- CD45-_cell-idJul24_30

description:
manuscript figure: Fig3-g and 7-f
Jul24_30
adult heart derived, approx 5 months of age


title: Resident Postn- CD31- CD45-_cell-idJul24_20

description:
manuscript figure: Fig3-g and 7-f
Jul24_20
adult heart derived, approx 5 months of age


title: Cell_134


title: Cell_132


title: Resident Postn- CD31- CD45-_cell-idJul24_19

description:
manuscript figure: Fig3-g and 7-f
Jul24_19
adult heart derived, approx 5 months of age


title: Resident Postn- CD31- CD45-_cell-idJul24_17

description:
manuscript figure: Fig3-g and 7-f
Jul24_17
adult heart derived, approx 5 months of age


title: Cell_131


title: Resident Postn- CD31- CD45-_cell-idJul24_15

description:
manuscript figure: Fig3-g and 7-f
Jul24_15
adult heart derived, approx 5 months of age


title: Cell_143


title: Resident Postn- CD31- CD45-_cell-idJul24_14

description:
manuscript figure: Fig3-g and 7-f
Jul24_14
adult heart derived, approx 5 months of age


title: Cell_130


title: Cell_129


title: Resident Postn- CD31- CD45-_cell-idJul24_13

description:
manuscript figure: Fig3-g and 7-f
Jul24_13
adult heart derived, approx 5 months of age


title: Cell_140


title: Cell_128


title: Resident Postn- CD31- CD45-_cell-idJul24_11

description:
manuscript figure: Fig3-g and 7-f
Jul24_11
adult heart derived, approx 5 months of age


title: Postn+ Resident Tcf21+_cell-idJul24_6

description:
manuscript figure: New supplemental data
Jul24_6
adult heart derived, approx 5 months of age

source_name: Postn+ Resident Tcf21+_cell-idJul24_6

value: Postn+ Resident Tcf21+


title: Cell_127


title: Postn+ Resident Tcf21+_cell-idJul24_16

description:
manuscript figure: New supplemental data
Jul24_16
adult heart derived, approx 5 months of age

source_name: Postn+ Resident Tcf21+_cell-idJul24_16


title: Cell_124


title: Cell_125


title: Cell_126


title: Postn+ Resident Tcf21+_cell-idJul24_10

description:
manuscript figure: New supplemental data
Jul24_10
adult heart derived, approx 5 months of age

source_name: Postn+ Resident Tcf21+_cell-idJul24_10


title: Postn+ resident CD31- CD45-_cell-idJul24_22

description:
manuscript figure: New supplemental data
Jul24_22
adult heart derived, approx 5 months of age

value: Postn+ resident CD31- CD45-


title: Cell_133


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_9

description:
manuscript figure: Fig7-f
Nov4_9
adult heart derived, approx 5 months of age

value: Activated Tcf21 Traced/ Act. TCF21+


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_63

description:
manuscript figure: Fig7-f
Nov4_63
adult heart derived, approx 5 months of age


title: Cell_122

value: Wild type


title: Cell_121

value: tibia growth plate


title: Cell_123

value: Postnatal day 7


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_58

description:
manuscript figure: Fig7-f
Nov4_58
adult heart derived, approx 5 months of age


title: Cell_119


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_56

description:
manuscript figure: Fig7-f
Nov4_56
adult heart derived, approx 5 months of age


title: Cell_117


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_55

description:
manuscript figure: Fig7-f
Nov4_55
adult heart derived, approx 5 months of age


title: Cell_116


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_54

description:
manuscript figure: Fig7-f
Nov4_54
adult heart derived, approx 5 months of age


title: Cell_115


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_53

description:
manuscript figure: Fig7-f
Nov4_53
adult heart derived, approx 5 months of age


title: Cell_120


title: Cell_113


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_52

description:
manuscript figure: Fig7-f
Nov4_52
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_51

description:
manuscript figure: Fig7-f
Nov4_51
adult heart derived, approx 5 months of age


title: Cell_112


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_5

description:
manuscript figure: Fig7-f
Nov4_5
adult heart derived, approx 5 months of age


title: Cell_114


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_47

description:
manuscript figure: Fig7-f
Nov4_47
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_61

description:
manuscript figure: Fig7-f
Nov4_61
adult heart derived, approx 5 months of age


title: Cell_108


title: Cell_110


title: Cell_107


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_45

description:
manuscript figure: Fig7-f
Nov4_45
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_44

description:
manuscript figure: Fig7-f
Nov4_44
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_59

description:
manuscript figure: Fig7-f
Nov4_59
adult heart derived, approx 5 months of age


title: Cell_118


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_41

description:
manuscript figure: Fig7-f
Nov4_41
adult heart derived, approx 5 months of age


title: Cell_106


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_38

description:
manuscript figure: Fig7-f
Nov4_38
adult heart derived, approx 5 months of age


title: Cell_103


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_50

description:
manuscript figure: Fig7-f
Nov4_50
adult heart derived, approx 5 months of age


title: Cell_102


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_36

description:
manuscript figure: Fig7-f
Nov4_36
adult heart derived, approx 5 months of age


title: Cell_111


title: Cell_101


title: Cell_109


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_34

description:
manuscript figure: Fig7-f
Nov4_34
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_33

description:
manuscript figure: Fig7-f
Nov4_33
adult heart derived, approx 5 months of age


title: Cell_099


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_32

description:
manuscript figure: Fig7-f
Nov4_32
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_31

description:
manuscript figure: Fig7-f
Nov4_31
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_40

description:
manuscript figure: Fig7-f
Nov4_40
adult heart derived, approx 5 months of age


title: Cell_105


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_3

description:
manuscript figure: Fig7-f
Nov4_3
adult heart derived, approx 5 months of age


title: Cell_104


title: Cell_096


title: Cell_095


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_27

description:
manuscript figure: Fig7-f
Nov4_27
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_25

description:
manuscript figure: Fig7-f
Nov4_25
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_4

description:
manuscript figure: Fig7-f
Nov4_4
adult heart derived, approx 5 months of age


title: Cell_093


title: Cell_094


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_24

description:
manuscript figure: Fig7-f
Nov4_24
adult heart derived, approx 5 months of age


title: Cell_092


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_37

description:
manuscript figure: Fig7-f
Nov4_37
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_22

description:
manuscript figure: Fig7-f
Nov4_22
adult heart derived, approx 5 months of age


title: Cell_089


title: Cell_091


title: Cell_100


title: Cell_090


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_20

description:
manuscript figure: Fig7-f
Nov4_20
adult heart derived, approx 5 months of age


title: Cell_088


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_2

description:
manuscript figure: Fig7-f
Nov4_2
adult heart derived, approx 5 months of age


title: Cell_087


title: Cell_098


title: Cell_086


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_14

description:
manuscript figure: Fig7-f
Nov4_14
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_15

description:
manuscript figure: Fig7-f
Nov4_15
adult heart derived, approx 5 months of age


title: Cell_083


title: Cell_082


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_16

description:
manuscript figure: Fig7-f
Nov4_16
adult heart derived, approx 5 months of age


title: Cell_085


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_13

description:
manuscript figure: Fig7-f
Nov4_13
adult heart derived, approx 5 months of age


title: Cell_097


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_11

description:
manuscript figure: Fig7-f
Nov4_11
adult heart derived, approx 5 months of age


title: Cell_084


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_12

description:
manuscript figure: Fig7-f
Nov4_12
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_29

description:
manuscript figure: Fig7-f
Nov4_29
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_10

description:
manuscript figure: Fig7-f
Nov4_10
adult heart derived, approx 5 months of age


title: Cell_080


title: Activated Postn+ CD31- CD45-_cell-idNov4_8

description:
manuscript figure: Fig3-g
Nov4_8
adult heart derived, approx 5 months of age

value: Activated Postn+ CD31- CD45-


title: Cell_079


title: Activated Postn+ CD31- CD45-_cell-idNov4_7

description:
manuscript figure: Fig3-g
Nov4_7
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_62

description:
manuscript figure: New supplemental data
Nov4_62
adult heart derived, approx 5 months of age


title: Cell_077


title: Cell_076


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_1

description:
manuscript figure: Fig7-f
Nov4_1
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_21

description:
manuscript figure: Fig7-f
Nov4_21
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_60

description:
manuscript figure: New supplemental data
Nov4_60
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_6

description:
manuscript figure: New supplemental data
Nov4_6
adult heart derived, approx 5 months of age


title: Activated Tcf21 Traced/ Act. TCF21+_cell-idNov4_19

description:
manuscript figure: Fig7-f
Nov4_19
adult heart derived, approx 5 months of age


title: Cell_075


title: Cell_078


title: Cell_074


title: Activated Postn+ CD31- CD45-_cell-idNov4_57

description:
manuscript figure: Fig3-g
Nov4_57
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_49

description:
manuscript figure: New supplemental data
Nov4_49
adult heart derived, approx 5 months of age


title: Cell_081


title: Cell_073


title: Activated Postn+ CD31- CD45-_cell-idNov4_42

description:
manuscript figure: New supplemental data
Nov4_42
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_46

description:
manuscript figure: Fig3-g
Nov4_46
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_39

description:
manuscript figure: New supplemental data
Nov4_39
adult heart derived, approx 5 months of age


title: Cell_071


title: Cell_070


title: Activated Postn+ CD31- CD45-_cell-idNov4_48

description:
manuscript figure: New supplemental data
Nov4_48
adult heart derived, approx 5 months of age


title: Cell_072


title: Activated Postn+ CD31- CD45-_cell-idNov4_26

description:
manuscript figure: New supplemental data
Nov4_26
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_30

description:
manuscript figure: New supplemental data
Nov4_30
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_35

description:
manuscript figure: Fig3-g
Nov4_35
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_43

description:
manuscript figure: Fig3-g
Nov4_43
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_18

description:
manuscript figure: Fig3-g
Nov4_18
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_23

description:
manuscript figure: Fig3-g
Nov4_23
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_28

description:
manuscript figure: New supplemental data
Nov4_28
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov4_17

description:
manuscript figure: Fig3-g
Nov4_17
adult heart derived, approx 5 months of age


title: Cell_069


title: Cell_068


title: Activated Postn+ CD31- CD45-_cell-idNov11_83

description:
manuscript figure: Fig3-g
Nov11_83
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idNov11_78

description:
manuscript figure: Fig3-g
Nov11_78
adult heart derived, approx 5 months of age


title: Cell_067


title: Cell_065


title: Cell_066


title: huCB stem miR-126/OE_rep3

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

description:
crs1_r3_1395_c
processed data file: Processed_file_cd38_negative_kd_oe.xlsx

data_processing:
alignment with SOAPSplice 1.9
count reads with HT-Seq 0.5.3 with Ensembl72 gtf annotation
cord blood cells study: Differential expression analysis with DESeq2
murine leukemic blasts study: Differential expression analysis with limma/voom
Genome_build: hg19 (coord blood cells study); mm10 (murine leukemic blasts study)
Supplementary_files_format_and_content: xlsx files were generated from txt output from DESeq2 (*kd_oe.xlsx) and from limma voom (*blasts.xlsx)

source_name: huCB stem miR-126/OE

growth_protocol: StemSpan supplemented with rhSCF (100ng/ml, rhFLT3L (100ng/ml), rhIL6 (20ng/ml), rhTPO (20ng/ml)

extract_protocol:
RNA from sorted murine blasts was extracted using RNeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Amplification of cDNA from total RNA (starting amount =200 ng per sample) was performed using the Ovation RNA-Seq system V2 (Nugen). Then, cDNA was fragmented and ligated into a sequencing library using Encore TM NGS Multiplex system (Nugen)

treatment_protocol: huCB-derived CD34+ cells, sorted for CD133+38-, stimulated for 18h, transduced with LV, kept in culture for72h then collected

value: human cord blood HSPC (CD34+CD133+CD38-)

value: miR126 overexpression


title: Cell_064


title: Cell_063


title: Activated Postn+ CD31- CD45-_cell-idJul29_78

description:
manuscript figure: New supplemental data
Jul29_78
adult heart derived, approx 5 months of age


title: Activated Postn+ CD31- CD45-_cell-idJul29_82

description:
manuscript figure: New supplemental data
Jul29_82
adult heart derived, approx 5 months of age


title: huCB progenitors miR-126/KD_rep3

description:
cbs1_r6_2435_C
processed data file: Processed_file_cd38_positive_kd_oe.xlsx

source_name: huCB progenitors miR-126/KD

treatment_protocol: huCB-derived CD34+ cells, sorted for CD133+38+, stimulated for 18h, transduced with LV, kept in culture for72h then collected

value: human cord blood progenitor cells (CD34+CD133+CD38+)

value: miR126 knockdown


title: huCB progenitors miR-126/KD_rep2

description:
cbs1_r6_2435_B
processed data file: Processed_file_cd38_positive_kd_oe.xlsx


title: Cell_062


title: huCB stem miR-126/OE_rep1

description:
crs1_r3_1395_a
processed data file: Processed_file_cd38_negative_kd_oe.xlsx


title: huCB progenitors miR-126/OE_rep3

description:
cbs1_r6_1395_C
processed data file: Processed_file_cd38_positive_kd_oe.xlsx

source_name: huCB progenitors miR-126/OE


title: Activated Postn+ CD31- CD45-_cell-idJul29_72

description:
manuscript figure: New supplemental data
Jul29_72
adult heart derived, approx 5 months of age

value: C57BL/6 (backcross N=6)

value: heart


title: Cell_060


title: Activated Postn+ CD31- CD45-_cell-idJul29_77

description:
manuscript figure: New supplemental data
Jul29_77
adult heart derived, approx 5 months of age

value: fibroblasts

value: approx 5 months of age


title: huCB progenitors miR-126/KD_rep1

description:
cbs1_r6_2435_A
processed data file: Processed_file_cd38_positive_kd_oe.xlsx


title: Activated Postn+ CD31- CD45-_cell-idJul29_47

description:
manuscript figure: New supplemental data
Jul29_47
adult heart derived, approx 5 months of age


title: Cell_061


title: Activated Postn+ CD31- CD45-_cell-idJul29_43

description:
manuscript figure: New supplemental data
Jul29_43
adult heart derived, approx 5 months of age


title: huCB progenitors miR-126/OE_rep2

description:
cbs1_r6_1395_B
processed data file: Processed_file_cd38_positive_kd_oe.xlsx


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_90

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_90
adult heart derived, approx 5 months of age


title: Cell_059


title: Activated Postn+ CD31- CD45-_cell-idNov11_80

description:
manuscript figure: Fig3-g
Nov11_80
adult heart derived, approx 5 months of age


title: huCB stem miR-126/OE_rep2

description:
crs1_r3_1395_b
processed data file: Processed_file_cd38_negative_kd_oe.xlsx


title: Cell_058


title: huCB progenitors miR-126/OE_rep1

description:
cbs1_r6_1395_A
processed data file: Processed_file_cd38_positive_kd_oe.xlsx


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_89

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_89
adult heart derived, approx 5 months of age


title: Cell_057


title: huCB progenitors ctrl_rep2

description:
cbs1_r6_1394_B
processed data file: Processed_file_cd38_positive_kd_oe.xlsx

source_name: huCB progenitors ctrl

value: control vector


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_85

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_85
adult heart derived, approx 5 months of age


title: huCB progenitors ctrl_rep1

description:
cbs1_r6_1394_A
processed data file: Processed_file_cd38_positive_kd_oe.xlsx


title: Cell_055


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_81

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_81
adult heart derived, approx 5 months of age


title: Cell_054


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_83

description:
manuscript figure: not used
Jul29_83
adult heart derived, approx 5 months of age


title: huCB stem miR-126/KD_rep2

description:
cbs1_r3_2435_b
processed data file: Processed_file_cd38_negative_kd_oe.xlsx

source_name: huCB stem miR-126/KD


title: huCB stem miR-126/KD_rep1

description:
cbs1_r3_2435_a
processed data file: Processed_file_cd38_negative_kd_oe.xlsx


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_80

description:
manuscript figure: not used
Jul29_80
adult heart derived, approx 5 months of age


title: huCB stem miR-126/KD_rep3

description:
cbs1_r3_2435_c
processed data file: Processed_file_cd38_negative_kd_oe.xlsx


title: huCB stem ctrl_rep2

description:
cbs1_r3_1394_b
processed data file: Processed_file_cd38_negative_kd_oe.xlsx

source_name: huCB stem ctrl


title: Cell_050


title: Cell_051


title: huCB stem ctrl_rep3

description:
cbs1_r3_1394_c
processed data file: Processed_file_cd38_negative_kd_oe.xlsx


title: Cell_052


title: huCB progenitors ctrl_rep3

description:
cbs1_r6_1394_C
processed data file: Processed_file_cd38_positive_kd_oe.xlsx


title: Cell_053


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_84

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_84
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_74

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_74
adult heart derived, approx 5 months of age


title: Cell_047


title: Cell_048


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_73

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_73
adult heart derived, approx 5 months of age


title: Cell_056


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_70

description:
manuscript figure: not used
Jul29_70
adult heart derived, approx 5 months of age


title: Cell_046


title: huCB stem ctrl_rep1

description:
cbs1_r3_1394_a
processed data file: Processed_file_cd38_negative_kd_oe.xlsx


title: Cell_049


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_68

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_68
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_76

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_76
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_67

description:
manuscript figure: not used
Jul29_67
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_63

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_63
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_75

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_75
adult heart derived, approx 5 months of age


title: Cell_045


title: Cell_043


title: Cell_044


title: Cell_042


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_62

description:
manuscript figure: not used
Jul29_62
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_61

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_61
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_50

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_50
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_54

description:
manuscript figure: not used
Jul29_54
adult heart derived, approx 5 months of age


title: Cell_039


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_58

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_58
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_51

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_51
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_71

description:
manuscript figure: not used
Jul29_71
adult heart derived, approx 5 months of age


title: Cell_041


title: Cell_038


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_45

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_45
adult heart derived, approx 5 months of age


title: Cell_035


title: Cell_037


title: Cell_036


title: Cell_034


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_41

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_41
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_38

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_38
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_86

description:
manuscript figure: Fig3-g
Jul29_86
adult heart derived, approx 5 months of age

value: Activated Postn- CD31- CD45-


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_37

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_37
adult heart derived, approx 5 months of age


title: Cell_033


title: Activated Postn- CD31- CD45-_cell-idJul29_88

description:
manuscript figure: Fig3-g
Jul29_88
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_79

description:
manuscript figure: Fig3-g
Jul29_79
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_69

description:
manuscript figure: Fig3-g
Jul29_69
adult heart derived, approx 5 months of age


title: Cell_040


title: Activated Postn- CD31- CD45-_cell-idJul29_87

description:
manuscript figure: Fig3-g
Jul29_87
adult heart derived, approx 5 months of age


title: Cell_027


title: Cell_030


title: Cell_029


title: Cell_032


title: Cell_026


title: Activated Postn- CD31- CD45-_cell-idJul29_65

description:
manuscript figure: Fig3-g
Jul29_65
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_64

description:
manuscript figure: Fig3-g
Jul29_64
adult heart derived, approx 5 months of age


title: Cell_025


title: Activated Postn- CD31- CD45-_cell-idJul29_60

description:
manuscript figure: Fig3-g
Jul29_60
adult heart derived, approx 5 months of age


title: Activated Postn traced Postn+ CD31- CD45-_cell-idJul29_42

description:
manuscript figure: Fig4-d Postn+WT1- Fibroblasts
Jul29_42
adult heart derived, approx 5 months of age


title: Cell_031


title: Cell_023


title: Cell_024


title: Cell_022


title: Activated Postn- CD31- CD45-_cell-idJul29_59

description:
manuscript figure: Fig3-g
Jul29_59
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_56

description:
manuscript figure: Fig3-g
Jul29_56
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_55

description:
manuscript figure: Fig3-g
Jul29_55
adult heart derived, approx 5 months of age


title: Cell_028


title: Cell_021


title: Cell_020


title: Cell_019


title: Activated Postn- CD31- CD45-_cell-idJul29_53

description:
manuscript figure: Fig3-g
Jul29_53
adult heart derived, approx 5 months of age


title: Cell_018


title: Activated Postn- CD31- CD45-_cell-idJul29_52

description:
manuscript figure: Fig3-g
Jul29_52
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_49

description:
manuscript figure: Fig3-g
Jul29_49
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_48

description:
manuscript figure: Fig3-g
Jul29_48
adult heart derived, approx 5 months of age


title: Cell_016


title: Cell_014


title: Activated Postn- CD31- CD45-_cell-idJul29_66

description:
manuscript figure: Fig3-g
Jul29_66
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_57

description:
manuscript figure: Fig3-g
Jul29_57
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_46

description:
manuscript figure: Fig3-g
Jul29_46
adult heart derived, approx 5 months of age


title: Cell_017


title: Cell_015


title: Cell_013


title: Cell_012


title: Activated Postn- CD31- CD45-_cell-idJul29_40

description:
manuscript figure: Fig3-g
Jul29_40
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_39

description:
manuscript figure: Fig3-g
Jul29_39
adult heart derived, approx 5 months of age


title: Cell_008


title: Activated Postn- CD31- CD45-_cell-idJul29_36

description:
manuscript figure: Fig3-g
Jul29_36
adult heart derived, approx 5 months of age


title: Cell_011


title: Activated Postn- CD31- CD45-_cell-idJul29_34

description:
manuscript figure: Fig3-g
Jul29_34
adult heart derived, approx 5 months of age


title: Activated Postn- CD31- CD45-_cell-idJul29_35

description:
manuscript figure: Fig3-g
Jul29_35
adult heart derived, approx 5 months of age


title: Cell_010


title: Cell_005


title: murine miR-126/OE blasts tet-off_Dox72h_rep1

description:
t72_Doxy_dxdx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

source_name: murine miR-126/OE blasts tet-off_Dox72h

growth_protocol: in vivo

treatment_protocol: murine miR-126/OE tet ALL blasts (CD45.2) transplanted into recipient C57 mice (CD45.1). After ALL development into recipient animals, treatment was administrated then cells were sorted for CD45.2 and collected

tag: recipient strain

tag: transplanted with

value: sorted CD45.2 murine leukemic B-ALL blasts

tag: treated with

value: Doxycyline for 72hrs


title: Cell_009


title: murine miR-126/OE blasts tet-off_PBS72h_rep1

description:
t72_PBS_dx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

source_name: murine miR-126/OE blasts tet-off_PBS72h

value: murine miR-126/OE tet ALL blasts (CD45.2)

value: PBS for 72hrs


title: Activated Postn- CD31- CD45-_cell-idJul29_44

description:
manuscript figure: Fig3-g
Jul29_44
adult heart derived, approx 5 months of age


title: murine miR-126/OE blasts tet-off_PBS48h_rep2

description:
t48_PBS_sxdx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

source_name: murine miR-126/OE blasts tet-off_PBS48h

value: PBS for 48hrs


title: murine miR-126/OE blasts tet-off_PBS48h_rep1

description:
t48_PBS_sx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_Dox72h_rep3

description:
t72_Doxy_sxdx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: Cell_007

value: Wild type

value: tibia growth plate

value: Postnatal day 7


title: Cell_002


title: Cell_001


title: Cell_006


title: murine miR-126/OE blasts tet-off_Dox48h_rep3

description:
t48_Doxy_dxdx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

source_name: murine miR-126/OE blasts tet-off_Dox48h

value: Doxycyline for 48hrs


title: murine miR-126/OE blasts tet-off_Dox48h_rep2

description:
t48_Doxy_dx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_PBS24h_rep2

description:
t24_PBS_dxdx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

source_name: murine miR-126/OE blasts tet-off_PBS24h

value: PBS for 24hrs


title: Cell_003


title: murine miR-126/OE blasts tet-off_Dox72h_rep2

description:
t72_Doxy_no
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_Dox48h_rep1

description:
t48_Doxy_dx2
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_Dox24h_rep1

description:
t24_Doxy_dx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

source_name: murine miR-126/OE blasts tet-off_Dox24h

value: Doxycyline for 24hrs


title: Cell_004


title: murine miR-126/OE blasts tet-off_untreated_rep2

description:
t0_sx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_untreated_rep3

description:
t0_dx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_untreated_rep1

description:
t0_no
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_PBS24h_rep3

description:
t24_PBS_sx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: murine miR-126/OE blasts tet-off_Dox24h_rep2

description:
t24_Doxy_sx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: A5_3

status: Public on Jun 13 2016

city: Bern

first: Oliver

last: Muehlemann

address: Freiestrasse 6

country: Switzerland

institute: University of Bern

description: RNA from SH-SY5Y FUS KO cells. A5 clone.

data_processing:
Mapping: TopHat v2.0.9
Counting: HTSeq-count, –r name –s reverse –a 0 –m union
Genome_build: GRCh38.81
Supplementary_files_format_and_content: Counts: Ensembl gene id, reads count

extract_protocol:
Total RNA was extracted from biological replicates.
PolyA transcripts were selected. Stranded Illumina library kit was employed.

treatment_protocol: Three wells of a six well plate containing 80 % confluent SH-SY5Y neuroblastoma cells were each transfected with 2.7 μg FUS knockout ZeoR matrix (GeneArt, Life Technologies) and 1.3 μg of plasmid coding for the Cas9 endonuclease and the guide RNAs which target the first intron of FUS

value: neuroblastoma cell line

tag: cell line


title: murine miR-126/OE blasts tet-off_Dox24h_rep3

description:
t24_Doxy_sxdx
processed data file: Processed_file_murine_leukemic_blasts.xlsx


title: A5_2

source_name: RNA from SH-SY5Y FUS KO cells. A5 clone.


title: A4_1

description: RNA from SH-SY5Y FUS KO cells. A4 clone.


title: A4_3

source_name: RNA from SH-SY5Y FUS KO cells. A4 clone.


title: wt_2

description: WT RNA from SH-SY5Y cells

source_name: WT RNA from SH-SY5Y cells


title: A4_2


title: A5_1


title: CDK9_WT_UT

city: New York

first: Yingli

last: Shang

state: NY

address: 535E 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalls performed using Real Time Analysis.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.5
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
Peaks were called using MACS (version1.4.2) with the following setting: P-value < 10^-5)
Annotation was done by using script annotatePeaks.pl in HOMER
Genome_build: mm10

source_name: Macrophages

growth_protocol: Bone marrows cells from C57BL/6 mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
Lysates were clarified from sonicated nuclei and CDK9-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs  were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for 1 hour.

value: Bone marrow-derived macrophages

tag: antibody

value: CDK9 (H-169)X, Santa Scruz, Cat # sc-8338x, Lot #:J2813


title: A5_4


title: A4_4


title: CDK9_WT_LPS1h


title: Cr-DJ K27me3

city: yichang

first: chao

last: zhou

address: No.8,daxuelu Street

institute: CTGU

data_processing:
Quality Control: fastqc
Remove low quality data:BS-seq raw data, ChIP-seq raw data and RNA-seq raw data's low quality reads were removed from raw data by Trimmomatic. smRNA sequence raw data were cleaned by removing adaptor contamination and low qualityReads by CutAdaptor (Martin, 2011). miRNA (http://www.mirbase.org/ftp.shtml), tRNA(http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), rRNA (Rice GenomeAnnotation MSU7.0), snoRNA and snRNA (http://www.arb-silva.de/no_cache/download/archive/release_111/Exports/) were also removed.
Mapping: BS-seq clean data were mapped to MSU7.0 rice reference genome (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) by BatMeth (Lim et al., 2012).The RNA-seq clean data were mapped against the MSU7.0 rice genome with corresponding annotation by Tophat2.0(Kim et al., 2013) (http://tophat.cbcb.umd.edu/) using default parameters.And then, the genes’ count were calculated with htseq-count, and the differentially expression’s genes (|log (FC)|>=2 && qvalue < 0.05) were calculated by DESeq2.ChIP-seq Clean reads were aligned to the rice MSU7.0 reference genome by Bowtie (Langmead et al., 2009) allowing 0 mismatches and unique mapping.The ChIP-seq clean reads were mapped to the rice genome (RGAP version 7) by default allowing up to 2 mismatch using Bowtie2 (version 2.1.0).Only uniquely mapped reads were retained for further analysis.
Two types of small RNA abundance was calculated by 21-nt or 24-nt reads number falling into 1 kb windows/regions throughout the whole genomes and windows containing more than 3 reads were tested by EdgeR (Robinson et al., 2010) between samples. Windows with corrected p-value ≤0.01, were defined as differential smRNA regions.
ChIP-seq's peaks calling were used with MACS software with default parameters.
The Differentially Methylated Cytosines (DMCs) between any two genotypes were defined by binomial test (methylSig) (Park et al., 2014). Only cytosine sites whose adjusted q-values ≤ 0.01 and DNA methylation difference of 0.7, 0.5 and 0.1 between any two genotypes were designated for DMCs (Stroud et al., 2013). The Differentially Methylated Regions (DMRs), Differentially Methylated Genes (DMGs) were calculated as DMCs.
Genome_build: MSU7.0:  bulid_all genome.fa
Supplementary_files_format_and_content: wig and peaks' xls files were generated using MACS software;

organism: Oryza sativa Japonica Group

source_name: DongJin

growth_protocol: ere germinated and grown on the hormone-free, half-strength Murashige & Skoog (MS) medium under 16/8 hrs light/dark at 30/25°C,Twelve-day-old seedling leaves from each genotype were harvested for chromatin, genomic DNA or total RNA extraction

extract_protocol:
Rice seedling total RNA samples were isolated using TRIzol reagent (Invitrogen).Seedling were crosslinked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200-750 bp by sonication, and ChIP was performed using the following antibodies: H3K27me3 (a2363, AbclonalABclonal ).The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
RNA libraries were prepared according to the protocol strictly (http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf).  Briefly, 1-4 μg of total RNAs were used for mRNA purification and cDNA synthesis. After single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments of the double strand cDNAs, indexing adapters are ligated to the ends of the cDNA. PCR are performed to amplify the DNA fragments. The amplified DNA fragments were purified and sequenced with the Illumina Hiseq-2000 system.The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
RNA-Seq
ChIP-Seq
Bs-seq

value: 12 day seedling

tag: mutant

value: DJ


title: Hes1_OE_UT

growth_protocol: Bone marrows cells from C57BL/6 mice were cultured for 2 days in DMEM supplemented with 10% FBS and 20% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor，then infected with retrovirus which express pMX-Hes1.Two days later, using 2ug/ml puromycin to select the BMDMs overexpressing pMX-Hes1.

extract_protocol:
Lysates were clarified from sonicated nuclei and Hes1-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs overexpressing pMX-Hes1 were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for 1 hour.

value: Bone marrow-derived macrophages transduced with pMX-Hes1 retrovirus

value: HES1 (H-140), Santa Cruzï¼? Cat # sc-25392, Lot # :I2413


title: murine miR-126/OE blasts tet-off_PBS24h_rep1

description:
t24_PBS_dx
processed data file: Processed_file_murine_leukemic_blasts.xlsx

value: sorted CD45.2 murine leukemic B-ALL blasts


title: wt_4

description: WT RNA from SH-SY5Y cells


title: Cr-DJ smRNA seq


title: ZH11 k9me2


title: Hes1_OE_LPS1h


title: osdrm2  RNA seq repeat1


title: osdrm2  RNA seq repeat2


title: CSF1R-7_L5.N702

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample

source_name: LysM.Cre (D+/+)

extract_protocol:
Cells were homogenized in 700 µl Qiazol reagent (Qiagen). 140 ul of chloroform was added to the homogenate and the mixture centrifuged at 16,000 x g for 5 min at 4°C in Phase Lock Tubes (Qiagen). RNA was subsequently extracted from the aqueous phase using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using the RNase free DNase set (Qiagen) during the extraction. RNA was quality controlled on Agilent RNA 6000 pico chips (Agilent Technologies). High quality RNA (RIN >7) was obtained for all samples. SMARTer ultra low RNA kit for Illumina sequencing (Clontech) was used to prepare and amplify cDNA from two ng of total RNA according to manufacturer’s instructions.
One ng of amplified cDNA was then subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: To explore the role of DICER in the development, activation and immunological functions of TAMs, we crossed homozygous LysM-Cre (Clausen et al., 1999) with Dicerlox/lox (Harfe et al., 2005) mice to obtain mice with myeloid-cell-specific Dicer1 gene deletion (LysM-Cre;Dicer–/–, referred to as D–/–). These mice were then backcrossed to LysM-Cre to obtain the control LysM-Cre mice; Dicer+/+ mice (referred to as D+/+). Both LysM-Cre and Dicerlox/lox mutations were always homozygous in our experiment. We then inoculated Lewis lung carcinoma (LLC) cells subcutaneously (s.c.) in D–/– and control D+/+ mice. Once the tumors were established, we isolated by fluorescence-activated cell sorting (FACS) tumor-associated macrophages (F4/80+ cells).

value: control

tag: protocol

value: inoculated Lewis lung carcinoma (LLC) cells subcutaneously in mice


title: osdrm2  smRNA seq


title: CSF1R-4_L5.N706

value: tumor-associated macrophages (F4/80+ cells)


title: Cr-DJ-2 RNA seq repeat2

value: DJ(osdrm2 WT)


title: Zeb2 cKO_pooled sciatic nerves 2

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

description:
processed data files:
P7Zeb2cKO1~mouse_cufflinks.txt, gene_exp_control2vsZeb2cKO2diff.xlsx

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options.
Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (genes.fpkm tracking); Differential gene expression analysis Cuffdiff output file

source_name: Zeb2 cKO_pooled sciatic nerves

extract_protocol:
Sciatic nerves were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed

value: postnatal day 7

value: Zeb2 cKO

value: sciatic nerves


title: wt_1

description: WT RNA from SH-SY5Y cells


title: CSF1R-6_L5.N704


title: control_pooled sciatic nerves 2

description:
processed data files:
P7ctrl1~mouse_cufflinks.txt, gene_exp_control2vsZeb2cKO2diff.xlsx

source_name: control_pooled sciatic nerves

value: Control


title: CSF1R-3_L4.N709

source_name: Dicer_x_LysM.Cre (D–/–)

value: myeloid-cell-specific Dicer1 gene deletion


title: Zeb2 cKO_pooled sciatic nerves 1


title: M4-48-52h_after_hatching_male

city: Bronx

first: Byunghyuk

last: Kim

address: 1300 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Illumina Casava (version 1.8) software used for basecalling.
Raw FASTQ files were trimmed for adapter sequences using quart.
Alignment to the reference genome was performed using gsnap (version 2012-07-20)
Assignment of reads to genes is performed by htseq-count (version v0.5.3p3)
Genome_build: WS190/ce6
Supplementary_files_format_and_content: Tab-delimited text files include read count data for each gene. These data are not normalized.

organism: Caenorhabditis elegans

source_name: Whole-animal

growth_protocol: Worms were grown at 20C on standard nematode growth media (NGM) plates with OP50 E.coli as a food source until sampling.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen); DNA was removed with TURBO DNA-free (Life Technologies).
For each sample, a total of 1 ug of RNA was used for library preparation according to standard Illumina protocols (detailed protocol available at http://wasp.einstein.yu.edu)

tag: Sex

value: Male

tag: time

value: young adult:48-52h after hatching


title: M5-54-58h_after_hatching_male

tag: genotype

value: young adult:54-58h after hatching


title: Cr-DJ-2 RNA seq repeat1

value: 12 day seedling


title: CSF1R-2_L4.N710

tag: cell type


title: M3-42-46h_after_hatching_male

value: late L4:42-46h after hatching


title: control_pooled sciatic nerves 1


title: osddm1a/1b  RNA seq repeat2


title: Hes1_KO_LPS_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.0.1
Reads have passed Illumina filters, and been trimmed using Sickle using quality threshold >20
Peaks were called using ChIPseeqer with the following setting: p < 10~-15, FDR <0.02)
Annotation and downstream analysis was done using ChIPseeqer
Genome_build: mm10
Supplementary_files_format_and_content: wig

growth_protocol: Bone marrows cells from WT and DKO mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and DKO BMDMs were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, Sigma) for 1 hour.

value: Bone marrow-derived macrophages

tag: strain

tag: chip antibody

value: RNA Pol II


title: Cr-DJ-1 RNA seq repeat2

value: DJ(osddm1a/1b WT)


title: M2-36-40h_after_hatching_male

value: early L4:36-40h after hatching


title: CSF1R-5_L4.N711

tag: genotype/variation

value: control

value: inoculated Lewis lung carcinoma (LLC) cells subcutaneously in mice

value: tumor-associated macrophages (F4/80+ cells)


title: osddm1a/1b  RNA seq repeat1

tag: tissue


title: Hes1_KO_UT_rep2


title: WT_LPS_rep2


title: Cr-DJ-1 RNA seq repeat1


title: WT_UT_rep2


title: H5-54-58h_after_hatching_herma

value: Hermaphrodite


title: Hes1_KO_LPS_rep1


title: osddm1b Bs-seq

source_name: Hwayoung