title: rdr2

status: Public on Mar 08 2019

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

country: Israel

institute: Tel Aviv University

library_source: genomic

data_processing:
Perl scripts were used to convert all the Cs in the ‘forward’ reads and reference sequence to Ts, and all the Gs in the ‘reverse’ reads and reference sequence to As
Reads were aligned to the reference genome using Bowtie1
Perl scripts were used to recover the original sequence information and, for each C (on either strand), to count the number of times it was sequenced as a C or a T.
For each sequence context (CG, CHG, CHH),  the genomic averaged fractional methylation as well as fractional methylation within a 50 bp sliding window that were used in downstream analyses were calculated.
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents one citosine. Scores represent methylation level for each position, column 9 contains numbers of times each cytosine was sequenced as either C or T, as well as total reads coverage of the given citosine.
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents 50-bp window. Scores represent methylation level for each window, column 9 contains numbers of times cytosines within the given window were sequenced as either C or T, as well as total reads coverage of citosines within the window.

organism: Physcomitrium patens

source_name: protonema

growth_protocol: 7 day protonemata on BCDAT medium

extract_protocol:
Genomic DNA was isolated from protonema, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adaptors. Adaptor-ligated libraries were subjected to bisulfite conversion treatment using the Methylation-Gold kit (ZYMO) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR and gel purified (~350-400 bp size range) prior to quantification with a Bioanalyzer (Agilent).
DNA was extracted from approximately 500 mg tissue using NucleoSpin® Plant II Midi kit for Genomic DNA extraction from plant and fungi (Macherey-Nagel), according to recommended protocol

value: Grandsen

tag: age

value: 7 days

tag: genotype/variation

value: mutant rdr2 with RPS (repetitive petunia sequence) transgene)

tag: tissue/cell type

value: protonema


title: KLRG1-CD62L- T cells overexpressing with ctrl miR, rep 1

type: SRA

city: Bethesda

first: Luca

last: Gattinoni

state: MD

address: 10 Center Drive

department: Center for Cancer Research

country: USA

institute: National Cancer Institute

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using R package
log2-transformed RPKM
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed RPKM values for all samples

molecule: total RNA

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: Cells were collected 5 days fter transducing miR-155 or control miRNA

extract_protocol:
RNA was isolated with a miRNeasy Mini kit (Qiagen)
RNA concentration was determined with the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen) and RNA integrity was determined with Eukaryote Total RNA Nano Series II ChIP on a 2100 Bioanalyzer (Agilent). RNA-seq libraries were prepared from 4 μg of total RNA via the TruSeq RNA sample prep kit according to manufacturer’s protocol (Illumina). In brief, oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA synthesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors.
The resulting cDNA libraries were verified and quantified on Agilent Bioanalyzer and single-end 96 cycle RNA-seq was conducted with the GAIIx Genome Analyzer (Illumina).

treatment_protocol: CD8+ T cells were separated from non-CD8+ T cells with a MACS negative selection kit (Miltenyi Biotech) and were activated on plates coated with anti-CD3ε (2 μg/ml; BD Biosciences) and soluble anti-CD28 (1 μg/ml; BD Biosciences) in culture medium containing rhIL-2 (120 IU/ml; Chiron). Virus was 'spin-inoculated' at 2,000 g for 2 h at 32 °C onto plates coated with retronectin (Takara). CD8+ T cells activated for 24 h were transduced following standard protocol. Cells (3 × 105 to 2 x 106 cells) were adoptively transferred into hosts followed by infection with recombinant vaccinia virus expressing human gp100 (Virapur).

tag: strain

tag: tissue

value: Spleen

tag: origin

value: ex vivo

tag: overexpression

value: control miR


title: KLRG1-CD62L- T cells overexpressing with miR-155, rep 3


title: met

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated from protonema, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adaptors. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR and either gel purified (~300 bp band) or purified with the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
DNA was extracted from approximately 500 mg tissue using NucleoSpin® Plant II Midi kit for Genomic DNA extraction from plant and fungi (Macherey-Nagel), according to recommended protocol

value: met


title: KLRG1-CD62L- T cells overexpressing with miR-155, rep 1


title: KLRG1-CD62L- T cells overexpressing with miR-155, rep 2


title: KLRG1-CD62L- T cells overexpressing with ctrl miR, rep 2


title: KLRG1-CD62L- T cells overexpressing with ctrl miR, rep 3


title: dnmt3a/dnmt3b


title: dnmt3b


title: drm1/drm2


title: dnmt3a


title: cmt

value: cmt


title: drm2


title: drm1


title: Sample_G13-1

status: Public on Mar 09 2019

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

description: processed data file: FES_isoforms_FPKM.txt

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 mapped to hg19 RefSeq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FES_isoforms_FPKM.txt: Tab-delimited text file includes gene isoforms abundance normalized as FPKM.

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Whole blood (2.5 mL) from cases and controls was drawn into a PAXgene Blood RNA Tube (Qiagen, Valencia, CA) to stabilize RNA prior to extraction and stored at -20C. Total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) and all samples were lyophilized in RNAstable reagent (Biomatrica, San Diego, CA) for shipment at room temperature and long-term storage.
The Ovation Human blood RNA-seq kit (Nugen, San Carlos, CA) was used to generate strand-specific RNA-seq libraries depleted for reads derived from rRNA (12S, 16S, 18S and 28S genes) and globin (HBA1, HBA2, HBB and HBD genes) according to the manufacturer's protocol. Briefly, 100ng RNA extract, as measured by Qubit RNA high sensitivity kit (Thermo Fisher, South San Francisco), were DNased and cDNA was prepared from extracted total RNA by reverse transcription using a mixture of random and poly(T) primers. Successive steps of end-repair, adaptor ligation, strand selection via nucleotide analog-targeted degradation, insert-dependent adaptor cleavage for targeted depletion of rRNA and globin reads, PCR amplification, and bead-based purification were then used to construct cDNA libraries for RNA-seq analysis.

value: Whole blood

tag: disease state

value: ME/CFS

tag: treatment

value: Cardiopulmonary exercise

tag: timepoint (day)

tag: individual identifier


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 11

city: Delft

first: Joana

middle: P

last: Goncalves

address: Van Mourik Broekmanweg 6

department: Intelligent Systems

country: Netherlands

institute: Delft University of Technology

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc11

data_processing:
Library strategy: TRIP
Basecalling and filtering was performed using standard Illumina software.
For Expression: Sequences of indices (10 bp in cell line, 8 bp in pool) and barcodes (16 bp in cell line, 18-bp in pool) were determined in each read using Bioconductor package ShortRead. For each replicate of the normalization reads (norm counts), only the barcodes with at least 100 counts were taken for the subsequent analysis. To eliminate aberrant barcodes arising from mutations during PCR and sequencing, the following algorithm was used. First, we sorted barcodes according to their counts. Then, for each barcode (starting from the most frequent one), we identified and removed all its mutant versions, defined as barcodes within a Hamming distance of 3. The remaining sequences were regarded as ‘genuine’ barcodes. The set of genuine barcodes was used as a reference to identify and count the barcodes in the expression (expr counts) and normalization reads (norm counts). The expr counts were normalized by dividing by corresponding norm counts to obtain the expression for each barcode.
For mapping: Sequences of indices (10 bp in the cell line, 8 bp in pool), barcodes (16 bp in cell line, 18 bp in pool) and associated genomic DNA were determined in each read using Bioconductor package ShortRead. The reads containing the ‘genuine barcodes’ from the corresponding cell line were retained. The genomic DNA sequences in the reads retained were aligned against mouse genome mm9 using Bowtie 2.0 with the following settings. -p 6 -f --sensitive -x mm9 –U To find the location of integration of a barcode i) At first the DpnII data was analyzed. If there are reads associated then the most frequent read should represent at least 60% of total reads whereas the representation of the second most frequent read should be less than 20%. ii). After getting the associated genomic region from DpnII data, the Sau3AI data was used to find if location found by DpnII data analysis could be confirmed. For this, there should be reads mapping within 1000 bp from the reads associated with this barcode in DpnII data. In addition, if found, a site was selected that was nearer to the actual site of integration (because Sau3AI also cuts other similar sites than GATC, so multiple closely spaced ligation points are possible for one barcode). It is important to note that because the sequencing was performed only from one side (the barcode side) so it is mostly not possible to detect the exact site of integration. In the end the length of the aligned read was either added (if the integration is on ‘-’ strand) or subtracted (if the integration is on ‘+’ strand) from the position of alignment to get a position, which is nearest to the actual site of integration.
For mutation profiling: We parsed the DNA reads obtained from Cas9-targeted TRIP cells in order to map barcodes and UIDs, and extract the sequences of interest containing the 20-nucleotide region targeted by Cas9. These were aligned against the wild-type sequence to identify and characterize Cas9-induced lesions. We used semi-global alignment with the following weights: match +2, mismatch -2, gap opening penalty -5, gap extension penalty -0.5, and initial score 30. For TRIP cell line experiments with sgRNA1, sgRNA2 and sgRNA3, respectively 96%, 95% and 91% of the reads could be parsed, whereas TRIP pools yielded between 86% and 89% of successfully parsed reads. Quality control and filtering of aberrant barcodes were further performed as described in previous work (Akhtar et al., Cell 2013; Akhtar et al., 2014). For the TRIP pool, we analyzed only barcodes with at least 30 reads in every experiment.
Genome_build: MGSCv37 (mm9)

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem (mES) cells EBRTcH3 expressing the tetracycline-controlled transactivator (tTA) from the endogenous ROSA26 promoter (EStTA) were cultured in 60% BRL cell-conditioned medium in the presence of 10% fetal calf serum (FCS), leukemia inhibitory factor, MEK inhibitor PD0325901, and GSK-3 inhibitor CHIR9902143. Culture dishes were coated with 0.15% gelatin and incubated at 37˚C for one hour before plating. We used two different TRIP barcoded plasmid libraries, comprising PiggyBac (PB) integrated reporter constructs with the enhanced green fluorescent protein gene (EGFP) as transcription unit. Each reporter unit comprised the following key elements: 5’LTR sequence, promoter, EGFP reporter gene, promoter index, reporter barcode, and 3’LTR sequence. The reporter expression unit contains the soluble neuropilin-1 (sNRP) polyadenylation signal. For the TRIP cell line, reporter transcription was driven by the phosphoglycerate kinase (PGK) promoter. For the TRIP pool, individual reporter constructs were paired with one of seven promoters, namely: CMV, cMyc, Hoxb1, Nanog, Oct4, p53 and PGK. These were used to investigate potential effects of promoters with different characteristics, such as promoter strength, exogeneity, housekeeping status, retinoic acid-inducibility, and TATA-less status. The TRIP libraries were transfected into separate pools of cultured EStTA cells, which were fluorescence-sorted to enrich for a desirable level of transfected DNA. Three weeks later, the sorted cells were subcultured to establish the TRIP cell line and pool. The cell line was expanded from a single cell containing 36 integrated reporters (IRs) with the mPGK promoter, while the TRIP pool was grown from approximately 500 cells containing an average of ~25 integrations per cell with heterogeneous promoters.

extract_protocol:
After incubation of Cas9-sgRNA-transfected mES cells, DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen) and prepared for sequencing. We PCR amplified cell line DNA IR regions of 414bp surrounding the sgRNA target sites using 10µM of PB-cDNA-forward-1-BC primers, containing different index sequences for multiple reactions, and 10µM of PB-cDNA-Reverse-5 primer. The PCR product was sent for Illumina MiSeq. In TRIP pool experiments, we tagged amplicons using 16-bp Unique IDentifiers (UIDs) to be able to detect multiple readings of the same DNA molecules. We performed all Cas9 targeting assays in triplicate. Barcoded IR regions were PCR amplified using Phusion® High-Fidelity DNA Polymerase (NEB). We used Exonuclease-I (20 units) (Enzymatics) for cleavage of single stranded DNA. Purified sequences were sent for Illumina HiSeq. Replicates were assessed for consistency of IR mutation frequencies, and merged for subsequent analyses.
TRIP library construction and transfection were performed according to the TRIP protocol (Akhtar et al, Cell 2013; Akhtar et al, Nature Protocols 2014).

treatment_protocol: All oligonucleotides used in this study were purchased from Integrated DNA Technologies. We designed three sgRNAs targeting different regions within the EGFP reporter gene, using the CRISPR design tool http://crispr.mit.edu/. We considered three primary criteria. First, purposed sgRNA-targeting of a sequence within the EGFP gene body in close proximity to the barcode, enabling reliable amplification of both barcode and target site. Second, reliability according to the CRISPR design tool, with no or minimal reported off-target sites. Third, EGFP recognition in both sense and anti-sense orientation, to exclude orientation-dependent effects. In addition, we designed a 141-bp single-stranded oligodeoxyribonucleotide (ssODN) template for HDR-based knock-in in with sgRNA2. Our ssODN comprised a 21-bp sequence for knock-in with ~60-bp homology arms at each side. Following the recommendations in https://www.addgene.org/crispr/zhang/faq/, we avoided overlap between the ssODN homology arms and the barcode located downstream of the EGFP reporter gene. We also designed the junction of the homology arms <10bp from the Cas9 target site. Lastly, we designed the ssODN template with 58 and 62 nucleotide-long homology arms, in agreement with the recommended 50-80 range. Cloning and transfection of sgRNA-guided CRISPR/Cas9.  We used human codon-optimized SpCas9 and chimeric guide RNA expression plasmid pX330-U6-Chimeric_BB-CBh-hSpCas9 to complex Cas9 with different sgRNAs (1-3). In addition, we used mCherry as a fluorescent marker for visualization and sorting of Cas9-sgRNA transfected mES cells. All Cas9 targeting assays experiments were performed in triplicate. For cell line experiments, we co-transfected the Cas9-sgRNAs and mPB-L3-ERT2.TatRRR-mCherry plasmids. Ten million mES cells were first seeded on a 10-cm dish. Four hours later, the cells were transfected with 13.5µg of Cas9-sgRNA and 1.5µg of mPB-L3-ERT2.TatRRR-mCherry plasmids using 45µl of Lipofectamin 2000 (Invitrogen). For TRIP pool experiments, we cloned mCherry-expressing Cas9-sgRNA plasmids. We first digested the Cas9-sgRNA plasmids with 10 units NotI (Roche) and 10 units SbfI (NEB). We further PCR-amplified CMV-driven tatRRR-mCherry from mPB-L3-ERT2.TatRRR-mCherry using primers Fragment.FOR (10µM) and Fragment.REV (10µM). The digested Cas9-sgRNA plasmid and PCR-amplified tatRRR-mCherry fragment were then cloned using Gibson Assembly Master Mix (NEB). To avoid reduced transfection efficiency of mCherry-expressing Cas9-sgRNA plasmid and ssODN with Lipofectamin 2000, we followed the protocol from Nucleofector™ Kit for Mouse Embryonic Stem Cells (Lonza) instead. Five million mES cells per condition were trypsinized, spun down and resuspended in 90µl of Mouse ES Cell Nucleofector™ solution. They were thereafter transfected with a total of 6.25µg of DNA (3.75µg mCherry-expressing Cas9-sgRNA and 2.5µg ssODN) using the program A-024 of the Nucleofector™ Kit for Mouse Embryonic Stem Cells (Lonza). Transfected cells were resuspended in 500µl of pre-warmed culture medium and plated in gelatin-coated 10 cm dishes. Cells were sorted 24 hours after transfection. For disruption assays, we transfected five million mES cells with 8µg of mCherry-expressing Cas9-sgRNA. For editing, five million cells were transfected with 4µg of mCherry-expressing Cas9-sgRNA together with 1µg of designed ssODN containing the 21-bp sequence for knock-in with ~60-bp homology arms. We decided to use sgRNA2 in editing assays, given that the short distance between the region targeted by sgRNA and the IR barcode prevented the design of proper ssODN homology arms (Figure S8). Additionally, sgRNA2 was preferred over sgRNA1 due to its larger mutation efficiency. In all experiments, transfected mCherry-positive mES cells were sorted by flow cytometry (MoFlo), collected in conditioned media containing 20% FCS, and subsequently spun down plated in conditioned media containing 10% FCS. Finally, Cas9-sgRNA-transfected mES cells were expanded for five days before isolating genomic DNA.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: promoter construct

value: CMV / cMyc / Hoxb1 / Nanog / Oct4 / p53 / PGK

tag: guide rna


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 10

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc10


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 12

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc12


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, add. exp. 1, 12 UIDs

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_additionalHR1_3284_sgRNA2+ssODN_indels.txt
3284_crispr_HR_bc1


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 9

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc9


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 7

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc7


title: IRF8_negative_LMPP_exp2

type: RNA

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3 um.

data_processing: Data are extracted with Agilent Feature Extraction Software and normalized.

source_name: IRF8 negative LMPP

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturers' instructions.

treatment_protocol: Hematopoietic progenitor cells were isolated by cell sorting.

value: Bone marrow

value: lymphoid-primed multipotent progenitor (LMPP)

tag: isolation methods

value: MACS sorting followed by FACS sorting

tag: surface markers


title: IRF8_positive_LMPP_exp1

source_name: IRF8 positive LMPP


title: IRF8_positive_LMPP_exp2


title: IRF8_negative_LMPP_exp1


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 6

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc6


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 5

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc5


title: WT

value: Grandsen

tag: age

value: WT


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 4

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc4


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 3

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc3


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 2

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc2


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 1

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc1


title: Multi-promoter TRIP pool sgRNA3 mutation profiling reads, UID 8

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3297___sgRNA3_indels.txt
3297_eGFP3_NHEJ_bc8


title: Multi-promoter TRIP pool expression reads, repl 2

description:
Expression (cDNA) reads for expression quantification of multi-promoter TRIP reporters in GEMP-O pool.
processed data file: multiTRIP_GEMP-O_3109_mapping_normalization_expression_counts.txt
3109_GEMP-0-1-exp-140904_S1_L001_R1_001_cDNA2

molecule: polyA RNA


title: Multi-promoter TRIP pool normalization reads, repl 2, PCR 1

description:
Normalization (DNA) reads for expression quantification of multi-promoter TRIP reporters in GEMP-O pool.
processed data file: multiTRIP_GEMP-O_3109_mapping_normalization_expression_counts.txt
3109_GEMP-0-1-exp-140904_S1_L001_R1_001_gDNA2_1


title: mPGK-driven TRIP cell line sgRNA2 mutation profiling reads

description:
DNA reads for mutation profiling in cell line EStTA-PB-18 containing 36 TRIP mPGK-driven reporters
processed data file: crisprTRIP_EStTA-PB-B-18_2794_sgRNA2_indels.txt
2794_crisprTRIP_EStTA-PB-B-18_gRNA2

value: PGK


title: Multi-promoter TRIP pool normalization reads, repl 1, PCR 2

description:
Normalization (DNA) reads for expression quantification of multi-promoter TRIP reporters in GEMP-O pool.
processed data file: multiTRIP_GEMP-O_3109_mapping_normalization_expression_counts.txt
3109_GEMP-0-1-exp-140904_S1_L001_R1_001_gDNA1_2


title: Multi-promoter TRIP pool normalization reads, repl 2, PCR 2

description:
Normalization (DNA) reads for expression quantification of multi-promoter TRIP reporters in GEMP-O pool.
processed data file: multiTRIP_GEMP-O_3109_mapping_normalization_expression_counts.txt
3109_GEMP-0-1-exp-140904_S1_L001_R1_001_gDNA2_2


title: mPGK-driven TRIP cell line sgRNA1 mutation profiling reads

description:
DNA reads for mutation profiling in cell line EStTA-PB-18 containing 36 TRIP mPGK-driven reporters.
processed data file: crisprTRIP_EStTA-PB-B-18_2794_sgRNA1_indels.txt
2794_crisprTRIP_EStTA-PB-B-18_gRNA1


title: Multi-promoter TRIP pool normalization reads, repl 1, PCR 1

description:
Normalization (DNA) reads for expression quantification of multi-promoter TRIP reporters in GEMP-O pool.
processed data file: multiTRIP_GEMP-O_3109_mapping_normalization_expression_counts.txt
3109_GEMP-0-1-exp-140904_S1_L001_R1_001_gDNA1_1


title: mPGK-driven TRIP cell line sgRNA3 mutation profiling reads

description:
DNA reads for mutation profiling in cell line EStTA-PB-18 containing 36 TRIP mPGK-driven reporters
processed data file: crisprTRIP_EStTA-PB-B-18_2605_sgRNA3_indels.txt
2605_crisprTRIP_EStTA-PB-B-18_gRNA3_120bp


title: Zfhx3-CKO rep3

city: Shanghai

first: zhuangzhi

last: zhang

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using Hisat2（version:2.0.4).
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
edgeR was used to find the differential expression genes
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: lateral ganglionic eminence

growth_protocol: LGE from E16.5 control mice and Zfhx3 mutant mice were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC

extract_protocol:
the lateral ganglionic emnience were removed, flash frozen in liquid nitrogen, and 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

treatment_protocol: Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: lateral ganglionic eminence

value: embryonic 16.5

tag: genotype

value: Dlx5/6-Cre; Zfhx3F/F (Zfhx3-CKO)


title: Zfhx3-CKO rep2


title: Zfhx3-CKO rep1


title: Control rep1

description: control

value: Dlx5/6-Cre (Control)


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, add. exp. 2, 12 UIDs

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_additionalHR2_3593_1_sgRNA2+ssODN_indels.txt
3593_1_bc1


title: Control rep3

description: control


title: Control rep2

description: control


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 12

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc12


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 11

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc11


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 10

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc10


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, add. exp. 4, 12 UIDs

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_additionalHR3_3593_3_sgRNA2+ssODN_8uM_indels.txt
3593_3_bc1

value: sgRNA2+ssODN (8uM)


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, add. exp. 3, 12 UIDs

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_additionalHR3_3593_4_sgRNA2+ssODN_1uM_indels.txt
3593_4_bc1

value: sgRNA2+ssODN (1uM)


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 7

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc7


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 8

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc8


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 9

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc9


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 3

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc3


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 4

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc4


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 5

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc5


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 6

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc6


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 11

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc11


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 9

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc9


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 12

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc12


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 1

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc1


title: macaque16_control

city: Davis

first: Samuel

middle: Taler

last: Westreich

address: 1 Shields Ave

department: Genome Center

institute: University of California, Davis

data_processing:
Paired-end alignment with PEAR software
Cleanup & low-quality sequence removal with Trimmomatic
Removal of ribosomal sequences with SortMeRNA
Annotation with DIAMOND against RefSeq Bacteria database (release 102, 22 December 2015)
Aggregation by genus with SAMSA2 pipeline script
Normalization with R and DESeq2 package
Supplementary_files_format_and_content: Processed data files contain annotation results against RefSeq bacterial complete database for either best organism match (top 1) or best function match (top 1) per read.  Results are normalized across all samples, done using the DESeq package.

organism: Macaca mulatta

source_name: feces

extract_protocol:
Total RNA was extracted using Qiagen's RNeasy Micro kit, with RNA concentration and integrity verified by BioAnalyzer
Ribodepletion was performed using Illumina Ribo-Zero Gold (Epidemiology) kit, then cDNA libraries were prepared for PE100 sequencing

treatment_protocol: feces were frozen at -80 degrees Celsius and preserved in RNAlater

tag: diagnosis

value: control

tag: ribodepletion

value: ribodepleted


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 7

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc7


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 10

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc10


title: Multi-promoter TRIP pool sgRNA2 mutation profiling reads, UID 2

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_5_sgRNA2_indels.txt
3593_5_bc2


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 8

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc8


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 5

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc5


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 4

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc4


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 6

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc6


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 3

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc3


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 2

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc2


title: SAN-adult-1

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

description: processed data file: VENUS_vs_KATUSHKA_adult_RNA-seq_mm10.xlsx

data_processing:
Reads were mapped to mm10 or hg19 build of the mouse and human transcriptome, respectively, using STAR (Dobin et al. 2013).
Reads generated with SOLID sequencing were converted to fastqsanger with FASTQ Groomer and and aligned with TopHat using default settings
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Excel files with normalized (DESeq2) count data per gene & differential expression analysis: VENUS_vs_KATUSHKA_E17.5_sorted_counts_mm10.xlsx; VENUS_vs_KATUSHKA_adult_RNA-seq_mm10.xlsx; SAN_vs_RA_counts_hg19.xlsx

source_name: SAN tissue

growth_protocol: Human + adult and fetal mouse E17.5 SAN and working myocardium tissue was obtained in strict accordance with the Academic Medical Center Amsterdam and the Aix Marseille University

extract_protocol:
RNA from isolated SANs and chamber myocardial cells was obtained using the Nucleospin RNA XS isolation kit (Bioke, MN 740902.50), according to manufacturer’s protocol. The quality of total RNA was assessed by micro-electrophoresis on acrylamide gel (Agilent 2100 Bioanalyser, Agilen).
RNA template was processed with the Ovation V2 RNA-seq system (Nugen, 7102-32), according to manufacturer’s protocol. Libraries were generated using the Ovation Ultra-low system V2 1-96 (Nugen, 0344NB-A01). Amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter).

tag: tissue

value: sinoatrial node

tag: developmental tissue

value: Adult

tag: cell population

value: dissected using VENUS fluorescence as guide


title: Multi-promoter TRIP pool sgRNA2 with ssODN mutation profiling reads, UID 1

description:
DNA reads for mutation profiling in GEMP-O pool with thousands of multi-promoter TRIP reporters integrated across cells.
processed data file: crisprTRIP_multiTRIP-GEMP-O_3593_2_sgRNA2+ssODN_indels.txt
3593_2_bc1

value: embryonic stem cells

value: CMV / cMyc / Hoxb1 / Nanog / Oct4 / p53 / PGK


title: RA-adult-1

source_name: Right atrial tissue

value: Right atrial tissue

value: dissected using KAT fluorescence as guide


title: Whole_heart_E17.5_Katushka3

description: processed data file: VENUS_vs_KATUSHKA_E17.5_sorted_counts_mm10.xlsx

source_name: KATUSHKA+ working myocardial tissue

value: KATUSHKA+ working myocardial tissue

value: FACS on Nppb-KAT


title: Whole_heart_E17.5_Katushka2


title: Whole_heart_E17.5_Katushka1


title: SAN_E17.5_Venus2

source_name: VENUS+ SAN tissue

value: VENUS+ sinoatrial node

value: FACS on Tbx3-VENUS


title: SAN_E17.5_Venus3


title: SAN_E17.5_Venus1


title: DamWT-Tcf7l2 batch 2

city: Darlinghurst

first: Tomasz

last: Szczesnik

state: NSW

address: 405 Liverpool St

country: Australia

institute: Victor Chang Cardiac Research Institute

data_processing:
Library strategy: DamID-seq
Genomic alignment: bwa mem (version 0.7.15)
Remove reads not originating from a possible methylation site (GATC).
Sum all reads to give a count per GATC.
Genome_build: mm10
Supplementary_files_format_and_content: .bedgraph contains the read count at each GATC.

source_name: embryonic stem cell culture

growth_protocol: Mouse embryonic stem cells cultured in the usual way: gelatinised plates, mES + 2I (XV, UO126), split every 3 days.

extract_protocol:
Purlink genomic DNA extraction kit (Invitrogen #K182001).
DamID-seq. Overnight DpnI digestion produces blunt ends, onto with an illumina PE1 sequencing adapter is ligated overnight with T4 ligase. This is followed by Nextera library construction with the following differences: only the i7 adapter is used, 4 extra cycles are used for amplification, and a higher AMPure bead concentration (1.6x) is used.

treatment_protocol: Treated with doxycycline for the specified number of hours immediately prior to DNA extraction.

value: embryonic stem cell culture

tag: strain

tag: dox treatment (hours)

tag: measure

value: adenine (GATC) methylation


title: DamN126A-Tcf7l2 batch 2


title: DamR95A-Tcf7l2 batch 2


title: Uninduced batch 2


title: Tw2-DM_K27me3_1

city: Dallas

first: Stephen

last: Li

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the GRCh38/mm10 genome assembly using default parameters in BWA v0.7.12,
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 and Sambamba version 0.6.6.
For E-box motif analysis,relaxed peaks were called using MACS version 2.1.0 with a p-value of 1x10-2 for H3K27ac and H3K27me3 and SPP version 1.4  with an IDR = 0.01 for each other sample
For PCA, differential peak analysis, peaks were called using HOMER version 4.7. For MyoD, Twist peaks were called using findpeaks command with with '-sytle factor' and FDR set to 1e-7. For histone marker ChIP-Seq data, peaks were called by findpeaks command with parameter ‘–style histone’ and other parameters set as default.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: HOMER peak files

source_name: Twist2+ Cells

growth_protocol: Twist2+ cells were isolated from hind limb of Twist2-CreERT2;tdTO mice treated with 3 doses of Tamoxifen via FACS sorting. Cells were cultured on matrigel in Ham's F10, 20% FBS,  0.2%% Primocin, and 5 ng/ml of basic fibroblast growth factor prior to infection.

extract_protocol: Cross-linked and fragment genomic DNA was extracted using the ChIP-IT Highsensitivity Kit from Active Motif

treatment_protocol: Twist2+ cells were retrovirally infected with either 3xTy1-Twist2 or GFP

value: Primary myoblast

tag: culture media

value: Growth Media

tag: mouse genotype

value: Twist2-CreERT2; tdTO


title: Tw2-DM_K27me3_2

tag: cell type


title: Tw2-GM_K27me3_2


title: Tw2_DM_Input


title: Tw2-DM_K27ac_2


title: Tw2_DM_Ty1_19


title: Tw2-GM_K27ac_2


title: Tw2-DM_K27ac_1


title: Multi-promoter TRIP pool expression reads, repl 1

description:
Expression (cDNA) reads for expression quantification of multi-promoter TRIP reporters in GEMP-O pool.
processed data file: multiTRIP_GEMP-O_3109_mapping_normalization_expression_counts.txt
3109_GEMP-0-1-exp-140904_S1_L001_R1_001_cDNA1

tag: cell line

tag: promoter construct


title: Tw2_DM_Ty1_20


title: Tw2_GM_MyoD_7


title: Tw2_GM_MyoD_8


title: Tw2_DM_MyoD_17


title: Tw2-GM_K27ac_1


title: Tw2_GM_Ty1_9


title: GFP-DM_K27me3_2


title: Tw2_GM_Ty1_10


title: Tw2_GM_Input_6


title: Tw2-GM_K27me3_1


title: GFP-DM_K27me3_1


title: GFP-DM_K27ac_1


title: GFP-DM_K27ac_2


title: GFP_DM_MyoD_13


title: GFP_DM_MyoD_12


title: GFP_DM_Ty1_15


title: Tw2_DM_MyoD_18


title: GFP_DM_Input


title: GFP-GM_K27me3_2


title: GFP_GM_Ty1_4


title: GFP_GM_MyoD_2


title: GFP_GM_MyoD_3


title: GFP_GM_Input_1


title: GFP-GM_K27ac_1


title: EXP2_COL15_ROW32

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Files were demultiplexed using Perl script mRNASeqHT_demultiplex.pl provided by Fluidigm
Demultiplexed FASTQ files were polyA trimmed using cutadapt (v 1.11)
polyA trimmed reads were aligned to the mouse genome using the STAR aligner (2.4.2a) allowing 2 mismatches and otherwise default parameters; if applicable, reads unmapped to the mouse genome were mapped to an ERCC spike-in reference using the BWA aligner (0.7.17-r1188) allowing 2 mismatches.
gene counting with featureCounts (1.5.1) counting multimappers fractionally
Genome_build: mm10

source_name: single-cell suspension from whole glomerulus, kidney

extract_protocol:
Glomerular cells were isolated by perfusing mice with PBS, followed by Dynabead solution and then 2 ml bead solution with enzymatic digestion buffer containing collagenase type II 300U/ml, Pronase E (1mg/ml) and DNase I (50μg/ml). Kidneys were then removed, decapsulated, minced into 1 mm3 pieces, and digested in 3 ml digestion buffer at 37°C for 15 minutes on a rotator (100 rpm). Digested tissue was then passed through a 100 μm cell strainer and collected by centrifugation. The pellet was resuspended in 2 ml of Hank's buffered salt solution and glomeruli were washed three times and collected using a magnet. Separated glomeruli were resuspended in 2 ml digestion buffer and incubated at 37°C for an additional 40 minutes rotating on a thermomixer. During the digestion period, the solution was vortexed every 10 minutes and sheared with a 27G needle every 15 minutes. The solution was then put on magnetic particle concentrator, and supernatants were pooled. The suspension was sieved through a 40 μm cell strainer and centrifuged at 1,500rpm for 5 minutes at 4°C.
RNA libraries were prepared for sequencing using version 2 of the Fluidigm C1 800-cell IFC protocol

tag: treatment

value: Control

tag: cell count

value: >2 or debris

value: Postnatal week 10


title: EXP2_COL17_ROW31

tag: age


title: EXP2_COL15_ROW23

tag: genotype


title: EXP2_COL18_ROW23


title: EXP2_COL17_ROW11


title: EXP2_COL15_ROW29


title: EXP2_COL18_ROW40


title: EXP2_COL19_ROW11


title: EXP2_COL18_ROW30


title: EXP2_COL12_ROW03


title: EXP2_COL13_ROW20


title: EXP2_COL11_ROW19


title: EXP2_COL10_ROW28

value: Diabetes


title: EXP2_COL10_ROW12


title: EXP2_COL13_ROW25


title: EXP2_COL12_ROW19


title: EXP2_COL09_ROW35


title: GFP-GM_K27me3_1


title: EXP2_COL10_ROW27


title: EXP2_COL08_ROW16


title: EXP2_COL08_ROW24


title: EXP2_COL09_ROW24


title: EXP2_COL08_ROW17


title: EXP2_COL12_ROW24


title: EXP2_COL08_ROW08


title: EXP2_COL08_ROW05


title: EXP2_COL08_ROW03


title: EXP2_COL06_ROW40


title: EXP2_COL08_ROW09


title: EXP2_COL07_ROW18


title: EXP2_COL06_ROW27


title: EXP2_COL01_ROW11


title: EXP2_COL04_ROW37


title: EXP1_COL18_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL02_ROW03


title: EXP2_COL05_ROW16


title: EXP1_COL05_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL04_ROW40


title: EXP1_COL05_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL20_ROW36


title: EXP1_COL01_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL07_ROW34


title: EXP2_COL06_ROW30


title: EXP2_COL06_ROW29


title: EXP2_COL02_ROW24


title: EXP2_COL04_ROW29


title: EXP2_COL05_ROW07


title: EXP2_COL06_ROW03


title: EXP2_COL06_ROW36


title: EXP2_COL06_ROW24


title: EXP2_COL02_ROW22


title: EXP2_COL18_ROW38


title: EXP2_COL14_ROW06


title: EXP1_COL14_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL19_ROW21


title: EXP2_COL20_ROW38


title: EXP2_COL17_ROW03


title: EXP2_COL16_ROW26


title: EXP2_COL15_ROW39


title: EXP2_COL15_ROW38


title: EXP2_COL14_ROW29


title: EXP2_COL12_ROW38


title: EXP2_COL18_ROW15


title: EXP2_COL14_ROW27


title: EXP2_COL14_ROW37


title: EXP2_COL09_ROW03


title: EXP2_COL20_ROW32


title: EXP2_COL04_ROW09


title: EXP2_COL03_ROW24


title: EXP2_COL02_ROW32


title: EXP2_COL03_ROW16


title: EXP2_COL01_ROW06


title: EXP2_COL02_ROW10


title: EXP2_COL02_ROW30


title: EXP1_COL11_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL01_ROW18


title: EXP2_COL19_ROW16


title: EXP2_COL20_ROW08


title: EXP2_COL20_ROW27


title: EXP2_COL20_ROW34


title: EXP2_COL20_ROW06


title: EXP2_COL19_ROW13


title: EXP2_COL19_ROW23


title: EXP2_COL15_ROW33


title: EXP2_COL17_ROW27


title: EXP2_COL17_ROW35


title: EXP2_COL17_ROW23


title: EXP2_COL18_ROW06


title: EXP2_COL17_ROW18


title: EXP2_COL17_ROW17


title: EXP2_COL18_ROW08


title: EXP2_COL17_ROW29


title: GFP-GM_K27ac_2


title: EXP2_COL17_ROW15


title: EXP2_COL03_ROW02


title: EXP2_COL17_ROW04


title: EXP2_COL16_ROW13


title: EXP2_COL16_ROW29


title: EXP2_COL16_ROW36


title: EXP2_COL16_ROW07


title: EXP2_COL15_ROW18


title: EXP2_COL15_ROW31


title: EXP2_COL19_ROW19


title: EXP2_COL15_ROW02


title: EXP2_COL13_ROW38


title: EXP2_COL14_ROW19


title: EXP2_COL13_ROW36


title: EXP2_COL19_ROW18


title: EXP2_COL15_ROW17


title: EXP2_COL13_ROW35


title: EXP2_COL12_ROW05


title: EXP2_COL11_ROW33


title: EXP2_COL11_ROW29


title: EXP2_COL11_ROW38


title: EXP2_COL11_ROW39


title: EXP2_COL11_ROW18


title: EXP2_COL12_ROW37


title: EXP2_COL09_ROW37


title: EXP2_COL09_ROW01


title: EXP2_COL08_ROW35


title: EXP2_COL07_ROW23


title: EXP2_COL07_ROW22


title: EXP2_COL07_ROW21


title: EXP2_COL06_ROW11


title: EXP2_COL04_ROW04


title: EXP2_COL05_ROW27


title: EXP2_COL05_ROW33


title: EXP2_COL05_ROW38


title: EXP2_COL06_ROW04


title: EXP2_COL03_ROW06


title: EXP2_COL12_ROW01


title: EXP2_COL02_ROW40


title: EXP2_COL02_ROW39


title: EXP2_COL11_ROW13


title: EXP2_COL02_ROW14


title: EXP2_COL09_ROW32


title: EXP2_COL09_ROW26


title: EXP2_COL01_ROW39


title: EXP2_COL09_ROW25


title: EXP2_COL01_ROW22


title: EXP1_COL20_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL20_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL01_ROW30


title: EXP1_COL20_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL06_ROW34


title: EXP1_COL15_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
exp1_spike_counts.txt


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description:
exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
exp1_spike_counts.txt


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title: EXP1_COL20_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


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exp1_counts.txt
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exp1_counts.txt
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exp1_counts.txt
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exp1_counts.txt
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exp1_counts.txt
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exp1_counts.txt
exp1_spike_counts.txt


title: Balb_c_4T1_5_34

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.4.2; parameters : --phred33 --length 36 --clip_R1 9).
Mapping using STAR (v 2.5.2a; parameters: --runMode alignReads --genomeLoad LoadAndExit) to a combined human (GRCh38) and mouse (GRCm38) genome reference
The gene-level expression counts computed with featureCounts (v1.5.1) using the gene annotations obtained from RefSeq (release 70).
To normalize gene counts for cell-specific biases, we used size factors computed utilizing the deconvolution strategy developed by Lun et al. (2016) implemented in the scran (v1.6.5) package available on R/Bioconductor
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing the gene counts as obtained from featureCounts; processed_normalized_matrix_hs.txt.gz and processed_normalized_matrix_mm.txt.gz contain normalized counts for human and mouse, respectively, using the method implemented in scran R/bioconductor package; sce_hs.rds.gz and sce_mm.rds.gz are R Data Format files containing a SingleCellExperiment class object for human and mouse, respectively.

source_name: CTC

extract_protocol:
Individual cells from CTC-WBC-clusters were mechanically separated with gentle micromanipulation (CellCelector, ALS). AF488/FITC-positive (or GFP-positive) and BV605-negative CTCs or AF488/FITC-negative and BV605-positive WBCs were immediately transferred into individual tubes (#321-032-501, Axygen) containing 2.5 μl RLT Plus lysis buffer (#1053393, Qiagen) and 1U/μl SUPERase In RNase Inhibitor (#AM2694, Invitrogen). Samples were immediately frozen on dry ice and kept at -80°C until further processing
Libraries were prepared with Smart -Seq2 protocol

tag: origin

value: mouse

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

value: CTC-single-WBC

value: CTC

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type

tag: donor

value: Balb


title: PyMT__CTC_B17

value: transgenic

value: CTC-cluster

tag: cell type

value: PyMT


title: EXP1_COL20_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: strain


title: Balb_c_4T1_CTC_H16

value: xenograft

value: CTC-single


title: PyMT_CTC_B18

value: CTC-cluster-WBC


title: EXP1_COL20_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: treatment


title: EXP1_COL20_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: cell count


title: EXP1_COL20_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: age


title: EXP1_COL20_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: genotype


title: EXP1_COL20_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL20_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL20_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL20_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL19_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL18_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL17_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP2_COL02_ROW11


title: EXP1_COL15_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL16_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL15_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL14_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL13_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL12_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL11_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL10_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL09_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL08_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL07_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL06_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: homeostatic_MuSCs_rep2

city: Bethsda

first: Vittorio

last: Sartorelli

address: 50 South Dr.

department: NIAMS

institute: NIH

description: Skeletal muscle stem cells (MuSCs) were sorted following described methods (Liu et al., 2015).

data_processing:
*R1_001.fastq.gz: contain cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98 bp RNA sequence.
*I1_001.fastq.gz: contains the 8 bp sample index.
scRNA-seq reads were processed with CellRanger ver. 2.2.0 and bcl2fastq/2.17.1 to generate fastq files with default parameters.
For clustering, filtering, variable gene selection, dimensionality reduction are performed using the Seurat ver.2.3.4
The trajectory analysis of scRNA(single cell RNA) was performed using Monocle v.2.8.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include barcodes,gene names, and UMI counts  for each Sample.

source_name: muscle

extract_protocol:
Samples were processed with 10X Genomics 3' library kit v2.2
3' single cells RNA library from 10X Genomics

tag: tissue

value: muscle

value: FACS Isolated Muscle satellite cells


title: inj_60h_MuSCs_rep1

description: Skeletal muscle stem cells (MuSCs) were isolated from TE-EDL muscles  60h post-injury (Notexin 2uM)

value: Post injury (60h) FACS Isolated Muscle satellite cells


title: inj_60h_MuSCs_rep2


title: Primary_MB

description: Primary myoblasts derived from the hindlimbs of three-month old C56BL/6J wild-type mice were cultured for four passages in HAM’s F10 (Invitrogen) supplemented with 2.5ng/ul of bFGF (Invitrogen), 10% horse serum (Invitrogen), and penicillin and streptomycin

value: FACS Isolated Muscle satellite cells cultured for 4-5 passages on collagen coated plates


title: homeostatic_MuSCs_rep1


title: EXP1_COL03_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Control


title: total_muscle_wt_rep2

description: Hindlimb muscles from three-month old C56BL/6J wild-type mice were dissociated into single cells by enzymatic digestion and live cells were isolated by Fluorescence-Activated Cell Sorting (FACS)

value: total muscle


title: RA-adult-2

value: Right atrial tissue

tag: developmental tissue

value: Adult

tag: cell population

value: dissected using KAT fluorescence as guide


title: total_muscle_wt_rep1


title: EXP1_COL03_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Postnatal week 10


title: EXP1_COL03_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: SAN-adult-2

value: sinoatrial node

value: dissected using VENUS fluorescence as guide