title: JJC1392_M9_BR2

city: Edinburgh

first: David

last: Leach

address: KIng's Building

institute: University of Edinburgh

data_processing:
files in fastq format were converted to fasta format - Example: fastq_to_fasta -i [FILE_NAME].sanfastq -o [FILE_NAME].fasta
reads were mapped to the E. coli K12 MG1655 (NC000913.3) genome using Novoalign version 2.07  (www.novocraft.com) - Example: (novoalign -f [FILE_NAME].fasta -d NC000913.3.nix -r Random > [FILE_NAME].novo)
pyCRAC software (http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html) was used to convert the novo file into a GTF file and hit tables - Example:  pyReadCounters.py -f [FILE_NAME].novo --gtf=Ecoli_K12.gtf --ignorestrand
bedtools version 2.26.0 (http://bedtools.readthedocs.io/en/latest/) were used to generate bedgraph files that were viewed in IGB version 9.0.0 (bioviz.org/igb) - Example: bedtools genomecov -bg -i [FILE_NAME]_count_output_reads.gtf -g chromosome.txt > [FILE_NAME].bedgraph
Genome_build: Escherichia coli K12 MG1655 NC000913.3
Supplementary_files_format_and_content: bedgraph files including count data for the whole genome

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in either M9 minimal medium supplemented with 0.4% glucose, 5 μM, CaCl2 and 1 mM MgSO4 or LB medium supplemented with 0.5% glucose at 37 °C to an OD600nm of 0.2-0.25

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

tag: growth medium

tag: chip antibody

value: anti-RecA antibody (Abcam, ab63797)


title: SORT-Seq; 2h-collagenase-treated; library4

status: Public on Sep 28 2017

type: SRA

city: Utrecht

first: Susanne C

middle: van den

last: Brink

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e2h-pl3-lib4-Diss2h_AHVCTTBGXX_S19

library_source: transcriptomic

data_processing:
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using bwa (version 0.6.2-r126) with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel-specific barcode information (first 8 bases) followed by a UMI-sequence (4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data) and a polyT-stretch. Reads 1 were thus used to extract the cell-barcode sequences (see “Cel-seq_barcodes_96.csv” file for sequences used for unstained satellite cell data and see "Cel-seq_barcodes_384" for MitoTracker stained satellite cells and zebrafish data) and UMIs; see Supplementary Methods for details.
After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (see Supplementary Methods section for details). Note that processed files for satellite cell data here still contain ERCC Spike-in molecules, bulk samples (bulk samples are only included in CEL-Seq experiments; see “BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library) and mitochondrial reads (only for MitoTracker stained satellite cells).
Genome_build: mus musculus: mm10; danio rerio: Zv9 (Ensembl release 74); both were extended with spike-ins (see "ERCC92.fa")
Supplementary_files_format_and_content: *.coutt.csv, *TranscriptCounts.tsv and *count_table.csv: tab-separated data files listing how many reads of which transcripts were detected in all sequenced cells (after UMI-correction). Column names refer to cells sequenced in this library (numbers refer the the CEL-Seq primer barcode used for that cell). The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike-in molecules, bulk samples (bulk samples are only included in CEL-Seq experiments; see “BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library) and mitochondrial reads (only for MitoTracker stained satellite cells).

molecule: total RNA

organism: Mus musculus

source_name: Satellite cells from Tibialis Anterior muscle

extract_protocol:
Cells were sorted into Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius, after which SORT-Seq (Muraro et al., 2016, with minor modifications as desribed in Supplementary Methods of van den Brink et al., 2017) was applied.
As in SORT-Seq protocol (Muraro et al., 2016), with minor modifications as desribed in Supplementary Methods of van den Brink et al., 2017.

tag: tissue

tag: strain

tag: gender

value: male


title: 48 hpf hace1 MO-injected sample A

status: Public on Sep 29 2017

city: Ottawa

first: Sergey

middle: V

last: Prykhozhij

state: Ontario

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

data_processing:
Torrent_Suite 4.2.1 used for basecalling
Trimming with Cutadapt v1.2.1
Second pass trimming with home-made script in order to remove reads shorter than 17bp and larger than 300bp and Q<20
2 steps alignement for RNA with tophat v2.0.6 and bowtie2 v2.0.2
Quantification and normalization with StrandNGS Version 2.1 with the following settings
Strand specific reads: false
Consider partial reads: true
Max EM Iterations: 1000
Convergence criterion for EM: 0.0010
Normalization Type = DeSeq
Threshold for normalization = 1
Baseline type =  median of all samples
Genome_build: Danio_rerio_Zv9-78 Transcripts (2015.01.22)
Supplementary_files_format_and_content: tab-delimited text files include normalised values or raw counts for each sample

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish housing, breeding conditions, and developmental staging of larvae, were performed according to Westerfield (Westerfield, 2000).  Use of zebrafish in this study was approved by the Dalhousie University Committee on Laboratory Animals (Protocol 15-123).  All zebrafish embryos were maintained in E3 embryo medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in 10 cm Petri dishes at 28oC.

extract_protocol:
TRIzol Reagent RNA Extraction protocol (Ambion RNA Life technologies) was used to extract RNA from pooled samples of hace1 or control morphants (n=6 per group).  Approximately 100 embryos per sample were used.  Tubingen wild type strain (TU) fish were previously injected with either hace1 MO or control MO using the injection protocol noted above.  RNA samples were quantified using the NanoDrop Spectrophotometer ND-1000 (Thermo Fisher Scientific, Wilmington, DE).  RNA yields for this experiment were lower than the 100µg of RNA needed for RNA sequencing, so 3 samples were pooled into one, for a final n=2 for each of the hace1 MO and control MO groups.
Barcoded cDNA libraries were prepared using RNA-Seq Version 2 kit from Life Technologies following their recommended protocol. Library preparations were assayed for both quality control and quantity using Experion DNA 1K chip (Life Technologies) and diluted to 16 pM concentration. Samples were sequenced using a Proton Sequencer from Life Technologies on a PI chip following the manufacturer recommended protocol. Each chip was loaded with 2 samples.

treatment_protocol: The hace1-HECT (5’-CCCTCGAACTGTTAGACAGAATAAA-3’) and standard control morpholinos (5’-CCTCTTACCTCAGTTACAATTTATA-3’) were purchased from Genetools LLC (Philomath, OR).  The hace1 morpholino splice site resides within the catalytically active HECT domain, upstream of the critical cysteine residue required for hace1 ubiquitin ligase function.  Knockdown of hace1 was verified by RT-PCR as described in Daugaard et al (Daugaard et al., 2013).

tag: morpholino

value: Tubingen

tag: Stage

value: 48 hpf


title: SORT-Seq MitoTracker stained; Repeat; plate 3

description: mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France

value: Satellite cells from Tibialis Anterior muscle

value: female


title: JJC1392_M9_BR1

country: United Kingdom

library_source: genomic

molecule: genomic DNA

organism: Escherichia coli


title: SORT-Seq; 1h-collagenase-treated; library4

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e1h-pl1-lib4-Diss1h_AHVCTTBGXX_S15


title: SORT-Seq; 1h-collagenase-treated; library3

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e1h-pl1-lib3-Diss1h_AHVCTTBGXX_S14


title: SORT-Seq; 2h-collagenase-treated; library1

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e2h-pl3-lib1-Diss2h_AHVCTTBGXX_S16


title: SORT-Seq; 1h-collagenase-treated; library2

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e1h-pl1-lib2-Diss1h_AHVCTTBGXX_S13


title: SORT-Seq; 1h-collagenase-treated; library1

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e1h-pl1-lib1-Diss1h_AHVCTTBGXX_S12


title: CEL-Seq; mouse d; library 1

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SVDB1D1_S13

extract_protocol:
Manual Trizol-extractions, after which we applied CEL-Seq (Hashimshony et al., 2012), with minor modifications as described in Supplementary Methods of van den Brink et al., 2017).
As in CEL-Seq protocol (Hashimshony et al., 2012), with minor modifications as described in Supplementary Methods of van den Brink et al., 2017.


title: CEL-Seq; mouse c; library 2

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SVDB1C4_S14


title: CEL-Seq; mouse b; library 4

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB1b4-H15CNBGXX_S5


title: CEL-Seq; mouse b; library 2

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB1b2-H15CNBGXX_S3


title: CEL-Seq; mouse b; library 1

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
Sat-H10N3BGXX_S5


title: CEL-Seq; mouse b; library 3

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB1b3-H15CNBGXX_S4


title: RQ LL36 rep1

city: Bielefeld

first: Martin

last: Lewinski

address: Universitätsstraße 25

department: RNA Biology and Molecular Physiology

country: Germany

institute: Bielefeld University

data_processing:
Library strategy: iCLIP
Raw iCLIP reads were subjected to 3´ adapter trimming and quality filtering using cutadapt version 1.9.1
reads with a minimal length of 15 nt and a quality score of 20 were kept
The trimmed and filtered reads were de-multiplexed using a python script
Identical reads including the same random barcode sequence were considered PCR duplicates and hence removed
The barcodes were trimmed from the remaining reads using barcodeRemoval from PIPE-CLIP
The reads were mapped to the Arabidopsis thaliana TAIR10 reference genome with STAR v2.5.2a using the additional transcript annotation file atRTD.gff from atRTD allowing up to three mismatches. Only reads mapping uniquely were kept.
Crosslink sites (-1 position of the reads) were assigned to separate transcript regions; namely 5'UTR, Exon (concatenated), Intron and 3'UTR
significant crosslink sites determined by FDR (<0.05) as described in König et al. 2010, region wise
significant site determination was repeated 1000 times. Sites appearing at least 95% of repeats were kept.
Sites ocurring in most biological replicates were kept. (at LL24 2 of 3; 7GFP  and GFP at LL36 4 of 5; RQ at LL36 2 of 2)
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph files generated, representing significant crosslink sites. Score equals number of reads determined at the given position
Supplementary_files_format_and_content: significant_crosslinks.tar.gz (crosslink sites which were present in most replicates )

organism: Arabidopsis thaliana

source_name: aerial tissue harvested at LL36

growth_protocol: Arabidopsis seeds from three genotypes (AtGRP7-GFP, AtGRP7-R49Q-GFP and GFP only) were surface-sterilized and sown on half-strength MS (Murashige-Skoog) (Duchefa) plates. Plants were grown in 12 h light/12 h dark cycles at 20 °C in Percival incubators (CLF laboratories) for 16 days followed by free run under continuous light (LL).

extract_protocol:
Seedlings on plates were subjected to irradiation with 254 nm UV light at a dose of 500 mJ/cm2 in a UVP CL-1000 UV crosslinker (on ice). Cell lysates from aerial tissue were prepared, precleared with sepharose beads and subjected to immunoprecipitation with GFP Trap beads (Chromotek) or mock precipitation with RFP Trap beads (Chromotek). On the beads, the precipitate was treated with DNase (Thermo Scientific). Subsequently, the RNAs were dephosphorylated and the L3 linker was ligated to the 3´ends using RNA ligase (NEB). 5′ termini were labeled using [γ-32P] ATP and polynucleotide kinase and the covalently linked RNA–protein complexes were separated on a 4-12 % NuPAGE Bis-Tris gel (Thermo Scientific), and electroblotted onto a nitrocellulose membrane. Upon autoradiography, the regions above the fusion protein were cut out and subjected to proteinase K treatment, leaving a polypeptide at the interaction site. Subsequently, RNA was isolated from the membrane using TriReagent.
RNA was reverse transcribed using primers containing a cleavable adapter region and individual barcode sequences. After NaOH treatment, the cDNA was purified on a 6% urea-polyacrylamide gel and fragments in the size range of approx. 70–85 nt (high, H), 85–120 nt (medium, M), and 120–200 nt (low, L), respectively, were eluted from the gel. The cDNAs were then circularized using CircLigase II (Epicentre) and an oligonucleotide (Cut-oligo) was annealed to generate a BamHI restriction site. Relineariztion via BamHI digestion results in adapters at both ends of the cDNA which then were PCR-amplified. After PCR optimization the three size fractions (H, M, L) are pooled with a ratio of 1:1:1, concentrations were assessed with Qubit dsDNA HS Assay Kit (Thermo Scientific).10 nM of the libraries were submitted to high throughput sequencing after multiplexing of multiple samples. Sequencing was carried out using an Illumina HiSeq2500 (Eurofins) with 50 nt single end or 100 nt single end reads.

treatment_protocol: Harvesting at timepoint LL24 and L36

tag: genotype

value: AtGRP7::AtGRP7 R49Q-GFP in grp7-1

tag: age

value: 18 days


title: SORT-Seq; 2h-collagenase-treated; library3

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e2h-pl3-lib3-Diss2h_AHVCTTBGXX_S18


title: RQ LL36 rep2


title: RQ LL24 rep1

source_name: aerial tissue harvested at LL24


title: RQ LL24 rep2


title: GFP LL36 rep3

value: AtGRP7::GFP in Col-0


title: GFP LL36 rep5


title: GFP LL36 rep4


title: RQ LL24 rep3


title: GFP LL36 rep1


title: GFP LL36 rep2


title: GFP LL24 rep3


title: GFP LL24 rep2


title: 7GFP LL36 rep2

value: AtGRP7::AtGRP7-GFP in grp7-1


title: 7GFP LL36 rep4


title: 7GFP LL36 rep5


title: 7GFP LL36 rep1


title: GFP LL24 rep1


title: 7GFP LL36 rep3


title: 7GFP LL24 rep3


title: SORT-Seq; 2h-collagenase-treated; library2

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e2h-pl3-lib2-Diss2h_AHVCTTBGXX_S17


title: CEL-Seq; mouse c; library 1

description:
mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SVDB1C1_S12


title: 7GFP LL24 rep1


title: 54yr_male_cell1988

city: Stanford

last: Enge

state: CA

address: James H. Clark Center, 318 Campus Drive,

department: Bioengineering

country: USA

institute: Stanford University

description: Single cell from human pancreas

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

organism: Homo sapiens

source_name: Pancreatic islet

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturer’s instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

value: alpha


title: 1yr_male_cell1981

description: Single cell from human pancreas

value: beta


title: 54yr_male_cell1992

description: Single cell from human pancreas


title: 1yr_male_cell1984

description: Single cell from human pancreas

value: acinar


title: 1yr_male_cell1983

description: Single cell from human pancreas


title: 54yr_male_cell1989

description: Single cell from human pancreas

value: unsure


title: 1yr_male_cell1979

description: Single cell from human pancreas

value: ductal


title: 1yr_male_cell1986

description: Single cell from human pancreas


title: 1yr_male_cell1980

description: Single cell from human pancreas

value: delta


title: 54yr_male_cell1991

description: Single cell from human pancreas


title: 1yr_male_cell1982

description: Single cell from human pancreas


title: 54yr_male_cell1990

description: Single cell from human pancreas


title: 54yr_male_cell1987

description: Single cell from human pancreas


title: 1yr_male_cell1985

description: Single cell from human pancreas


title: 7GFP LL24 rep2


title: 1yr_male_cell1970

description: Single cell from human pancreas


title: 1yr_male_cell1968

description: Single cell from human pancreas


title: 1yr_male_cell1967

description: Single cell from human pancreas


title: 1yr_male_cell1966

description: Single cell from human pancreas


title: 1yr_male_cell1975

description: Single cell from human pancreas


title: 1yr_male_cell1969

description: Single cell from human pancreas


title: 1yr_male_cell1978

description: Single cell from human pancreas


title: 1yr_male_cell1977

description: Single cell from human pancreas


title: 1yr_male_cell1974

description: Single cell from human pancreas


title: 1yr_male_cell1971

description: Single cell from human pancreas


title: 1yr_male_cell1973

description: Single cell from human pancreas


title: 1yr_male_cell1976

description: Single cell from human pancreas


title: 1yr_male_cell1972

description: Single cell from human pancreas


title: 1yr_male_cell1965

description: Single cell from human pancreas


title: 1yr_male_cell1964

description: Single cell from human pancreas


title: 1yr_male_cell1963

description: Single cell from human pancreas


title: 1yr_male_cell1958

description: Single cell from human pancreas


title: 1yr_male_cell1959

description: Single cell from human pancreas


title: 1yr_male_cell1962

description: Single cell from human pancreas


title: 1yr_male_cell1955

description: Single cell from human pancreas


title: 1yr_male_cell1951

description: Single cell from human pancreas


title: 1yr_male_cell1954

description: Single cell from human pancreas


title: 1yr_male_cell1956

description: Single cell from human pancreas


title: 1yr_male_cell1952

description: Single cell from human pancreas


title: 1yr_male_cell1957

description: Single cell from human pancreas


title: 1yr_male_cell1950

description: Single cell from human pancreas


title: 1yr_male_cell1960

description: Single cell from human pancreas


title: 1yr_male_cell1941

description: Single cell from human pancreas

value: mesenchymal


title: 1yr_male_cell1961

description: Single cell from human pancreas


title: 1yr_male_cell1940

description: Single cell from human pancreas


title: 1yr_male_cell1943

description: Single cell from human pancreas


title: 1yr_male_cell1953

description: Single cell from human pancreas


title: 1yr_male_cell1948

description: Single cell from human pancreas


title: 1yr_male_cell1949

description: Single cell from human pancreas


title: 1yr_male_cell1939

description: Single cell from human pancreas


title: 1yr_male_cell1935

description: Single cell from human pancreas


title: 1yr_male_cell1942

description: Single cell from human pancreas


title: 1yr_male_cell1945

description: Single cell from human pancreas


title: 1yr_male_cell1938

description: Single cell from human pancreas


title: 1yr_male_cell1947

description: Single cell from human pancreas


title: 1yr_male_cell1944

description: Single cell from human pancreas


title: 1yr_male_cell1936

description: Single cell from human pancreas


title: 1yr_male_cell1937

description: Single cell from human pancreas


title: 1yr_male_cell1934

description: Single cell from human pancreas


title: 1yr_male_cell1933

description: Single cell from human pancreas


title: 1yr_male_cell1946

description: Single cell from human pancreas


title: 1yr_male_cell1931

description: Single cell from human pancreas


title: 1yr_male_cell1932

description: Single cell from human pancreas


title: 1yr_male_cell1930

description: Single cell from human pancreas


title: 1yr_male_cell1928

description: Single cell from human pancreas


title: 1yr_male_cell1924

description: Single cell from human pancreas


title: 1yr_male_cell1927

description: Single cell from human pancreas


title: 1yr_male_cell1926

description: Single cell from human pancreas


title: 1yr_male_cell1920

description: Single cell from human pancreas


title: 1yr_male_cell1922

description: Single cell from human pancreas


title: 1yr_male_cell1929

description: Single cell from human pancreas


title: 1yr_male_cell1923

description: Single cell from human pancreas


title: 1yr_male_cell1919

description: Single cell from human pancreas


title: 1yr_male_cell1918

description: Single cell from human pancreas


title: 1yr_male_cell1916

description: Single cell from human pancreas


title: 1yr_male_cell1914

description: Single cell from human pancreas


title: 1yr_male_cell1915

description: Single cell from human pancreas


title: 1yr_male_cell1912

description: Single cell from human pancreas


title: 1yr_male_cell1917

description: Single cell from human pancreas


title: 1yr_male_cell1913

description: Single cell from human pancreas


title: 1yr_male_cell1909

description: Single cell from human pancreas


title: 1yr_male_cell1910

description: Single cell from human pancreas


title: 1yr_male_cell1906

description: Single cell from human pancreas


title: 1yr_male_cell1907

description: Single cell from human pancreas


title: 1yr_male_cell1905

description: Single cell from human pancreas


title: 1yr_male_cell1904

description: Single cell from human pancreas


title: 1yr_male_cell1925

description: Single cell from human pancreas


title: 1yr_male_cell1903

description: Single cell from human pancreas


title: 1yr_male_cell1899

description: Single cell from human pancreas


title: 1yr_male_cell1921

description: Single cell from human pancreas


title: 1yr_male_cell1900

description: Single cell from human pancreas


title: 1yr_male_cell1902

description: Single cell from human pancreas


title: 1yr_male_cell1897

description: Single cell from human pancreas


title: 1yr_male_cell1898

description: Single cell from human pancreas


title: 1yr_male_cell1911

description: Single cell from human pancreas


title: 1yr_male_cell1893

description: Single cell from human pancreas


title: 1yr_male_cell1892

description: Single cell from human pancreas


title: 1yr_male_cell1894

description: Single cell from human pancreas


title: 1yr_male_cell1891

description: Single cell from human pancreas


title: 1yr_male_cell1908

description: Single cell from human pancreas


title: 1yr_male_cell1887

description: Single cell from human pancreas


title: 1yr_male_cell1885

description: Single cell from human pancreas


title: 1yr_male_cell1888

description: Single cell from human pancreas


title: 1yr_male_cell1884

description: Single cell from human pancreas


title: 1yr_male_cell1886

description: Single cell from human pancreas


title: 1yr_male_cell1881

description: Single cell from human pancreas


title: 1yr_male_cell1880

description: Single cell from human pancreas


title: 1yr_male_cell1879

description: Single cell from human pancreas


title: 1yr_male_cell1901

description: Single cell from human pancreas


title: 1yr_male_cell1878

description: Single cell from human pancreas


title: 1yr_male_cell1896

description: Single cell from human pancreas


title: 1yr_male_cell1889

description: Single cell from human pancreas


title: 1yr_male_cell1890

description: Single cell from human pancreas


title: 1yr_male_cell1874

description: Single cell from human pancreas


title: 1yr_male_cell1876

description: Single cell from human pancreas


title: 1yr_male_cell1875

description: Single cell from human pancreas


title: 1yr_male_cell1872

description: Single cell from human pancreas


title: 1yr_male_cell1870

description: Single cell from human pancreas


title: 1yr_male_cell1883

description: Single cell from human pancreas


title: 1yr_male_cell1877

description: Single cell from human pancreas


title: 1yr_male_cell1864

description: Single cell from human pancreas


title: 1yr_male_cell1871

description: Single cell from human pancreas


title: 1yr_male_cell1863

description: Single cell from human pancreas


title: 1yr_male_cell1866

description: Single cell from human pancreas


title: 1yr_male_cell1862

description: Single cell from human pancreas


title: 1yr_male_cell1867

description: Single cell from human pancreas


title: 1yr_male_cell1882

description: Single cell from human pancreas


title: 1yr_male_cell1860

description: Single cell from human pancreas


title: 1yr_male_cell1869

description: Single cell from human pancreas


title: 1yr_male_cell1859

description: Single cell from human pancreas


title: 1yr_male_cell1861

description: Single cell from human pancreas


title: 1yr_male_cell1865

description: Single cell from human pancreas


title: 1yr_male_cell1858

description: Single cell from human pancreas


title: 1yr_male_cell1857

description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


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description: Single cell from human pancreas


title: 44yr_female_cell1471

description: Single cell from human pancreas


title: 5yr_male_cell1492

description: Single cell from human pancreas


title: 44yr_female_cell1493

description: Single cell from human pancreas


title: 44yr_female_cell1469

description: Single cell from human pancreas


title: 44yr_female_cell1467

description: Single cell from human pancreas


title: 44yr_female_cell1466

description: Single cell from human pancreas


title: 44yr_female_cell1465

description: Single cell from human pancreas


title: 44yr_female_cell1463

description: Single cell from human pancreas


title: 5yr_male_cell1462

description: Single cell from human pancreas


title: 44yr_female_cell1468

description: Single cell from human pancreas


title: 44yr_female_cell1461

description: Single cell from human pancreas


title: 5yr_male_cell1460

description: Single cell from human pancreas


title: 44yr_female_cell1458

description: Single cell from human pancreas


title: 44yr_female_cell1459

description: Single cell from human pancreas


title: 5yr_male_cell1457

description: Single cell from human pancreas


title: 44yr_female_cell1456

description: Single cell from human pancreas


title: 44yr_female_cell1455

description: Single cell from human pancreas


title: 44yr_female_cell1454

description: Single cell from human pancreas


title: 44yr_female_cell1452

description: Single cell from human pancreas


title: 6yr_male_cell1451

description: Single cell from human pancreas


title: 44yr_female_cell1453

description: Single cell from human pancreas


title: 6yr_male_cell1449

description: Single cell from human pancreas


title: 6yr_male_cell1450

description: Single cell from human pancreas


title: 6yr_male_cell1447

description: Single cell from human pancreas


title: 6yr_male_cell1448

description: Single cell from human pancreas


title: 6yr_male_cell1446

description: Single cell from human pancreas


title: 6yr_male_cell1445

description: Single cell from human pancreas


title: 6yr_male_cell1444

description: Single cell from human pancreas


title: 6yr_male_cell1443

description: Single cell from human pancreas


title: 6yr_male_cell1442

description: Single cell from human pancreas


title: 44yr_female_cell1464

description: Single cell from human pancreas


title: 6yr_male_cell1441

description: Single cell from human pancreas


title: 6yr_male_cell1436

description: Single cell from human pancreas


title: 6yr_male_cell1437

description: Single cell from human pancreas


title: 6yr_male_cell1440

description: Single cell from human pancreas


title: 6yr_male_cell1439

description: Single cell from human pancreas


title: 6yr_male_cell1438

description: Single cell from human pancreas


title: 44yr_female_cell1514

description: Single cell from human pancreas


title: 6yr_male_cell1429

description: Single cell from human pancreas


title: 6yr_male_cell1427

description: Single cell from human pancreas


title: 6yr_male_cell1432

description: Single cell from human pancreas


title: 6yr_male_cell1431

description: Single cell from human pancreas


title: 6yr_male_cell1434

description: Single cell from human pancreas


title: 6yr_male_cell1430

description: Single cell from human pancreas


title: 6yr_male_cell1428

description: Single cell from human pancreas


title: 6yr_male_cell1421

description: Single cell from human pancreas


title: 6yr_male_cell1419

description: Single cell from human pancreas


title: 6yr_male_cell1420

description: Single cell from human pancreas


title: 6yr_male_cell1418

description: Single cell from human pancreas


title: 6yr_male_cell1417

description: Single cell from human pancreas


title: 6yr_male_cell1426

description: Single cell from human pancreas


title: 6yr_male_cell1416

description: Single cell from human pancreas


title: 6yr_male_cell1422

description: Single cell from human pancreas


title: 6yr_male_cell1435

description: Single cell from human pancreas


title: 6yr_male_cell1414

description: Single cell from human pancreas


title: 6yr_male_cell1415

description: Single cell from human pancreas


title: 6yr_male_cell1413

description: Single cell from human pancreas


title: 6yr_male_cell1412

description: Single cell from human pancreas


title: 6yr_male_cell1410

description: Single cell from human pancreas


title: 6yr_male_cell1411

description: Single cell from human pancreas


title: 6yr_male_cell1433

description: Single cell from human pancreas


title: 6yr_male_cell1409

description: Single cell from human pancreas


title: 6yr_male_cell1408

description: Single cell from human pancreas


title: 6yr_male_cell1425

description: Single cell from human pancreas


title: 6yr_male_cell1424

description: Single cell from human pancreas


title: 6yr_male_cell1423

description: Single cell from human pancreas


title: 6yr_male_cell1405

description: Single cell from human pancreas


title: 6yr_male_cell1403

description: Single cell from human pancreas


title: 6yr_male_cell1404

description: Single cell from human pancreas


title: 6yr_male_cell1399

description: Single cell from human pancreas


title: 6yr_male_cell1402

description: Single cell from human pancreas


title: 6yr_male_cell1400

description: Single cell from human pancreas


title: 6yr_male_cell1398

description: Single cell from human pancreas


title: 6yr_male_cell1397

description: Single cell from human pancreas


title: 6yr_male_cell1395

description: Single cell from human pancreas


title: 6yr_male_cell1394

description: Single cell from human pancreas


title: 6yr_male_cell1392

description: Single cell from human pancreas


title: 6yr_male_cell1396

description: Single cell from human pancreas


title: 6yr_male_cell1391

description: Single cell from human pancreas


title: 6yr_male_cell1393

description: Single cell from human pancreas


title: 6yr_male_cell1389

description: Single cell from human pancreas


title: 6yr_male_cell1390

description: Single cell from human pancreas


title: 6yr_male_cell1386

description: Single cell from human pancreas


title: 6yr_male_cell1385

description: Single cell from human pancreas


title: 6yr_male_cell1407

description: Single cell from human pancreas


title: 6yr_male_cell1383

description: Single cell from human pancreas


title: 6yr_male_cell1387

description: Single cell from human pancreas


title: 6yr_male_cell1382

description: Single cell from human pancreas


title: 6yr_male_cell1406

description: Single cell from human pancreas


title: 6yr_male_cell1388

description: Single cell from human pancreas


title: 6yr_male_cell1380

description: Single cell from human pancreas


title: 6yr_male_cell1378

description: Single cell from human pancreas


title: 6yr_male_cell1384

description: Single cell from human pancreas


title: 6yr_male_cell1379

description: Single cell from human pancreas


title: 6yr_male_cell1401

description: Single cell from human pancreas


title: 6yr_male_cell1377

description: Single cell from human pancreas


title: 6yr_male_cell1372

description: Single cell from human pancreas


title: 6yr_male_cell1376

description: Single cell from human pancreas


title: 6yr_male_cell1370

description: Single cell from human pancreas


title: 6yr_male_cell1369

description: Single cell from human pancreas


title: 6yr_male_cell1368

description: Single cell from human pancreas


title: 6yr_male_cell1366

description: Single cell from human pancreas


title: 6yr_male_cell1367

description: Single cell from human pancreas


title: 6yr_male_cell1365

description: Single cell from human pancreas


title: 6yr_male_cell1364

description: Single cell from human pancreas


title: 6yr_male_cell1373

description: Single cell from human pancreas


title: 6yr_male_cell1363

description: Single cell from human pancreas


title: 6yr_male_cell1362

description: Single cell from human pancreas


title: 6yr_male_cell1381

description: Single cell from human pancreas


title: 6yr_male_cell1358

description: Single cell from human pancreas


title: 6yr_male_cell1359

description: Single cell from human pancreas


title: 6yr_male_cell1361

description: Single cell from human pancreas


title: 6yr_male_cell1360

description: Single cell from human pancreas


title: 6yr_male_cell1371

description: Single cell from human pancreas


title: 6yr_male_cell1357

description: Single cell from human pancreas


title: 6yr_male_cell1355

description: Single cell from human pancreas


title: 6yr_male_cell1354

description: Single cell from human pancreas


title: 6yr_male_cell1351

description: Single cell from human pancreas


title: 6yr_male_cell1352

description: Single cell from human pancreas


title: 6yr_male_cell1350

description: Single cell from human pancreas


title: 6yr_male_cell1375

description: Single cell from human pancreas


title: 6yr_male_cell1374

description: Single cell from human pancreas


title: 6yr_male_cell1353

description: Single cell from human pancreas


title: 6yr_male_cell1347

description: Single cell from human pancreas


title: 6yr_male_cell1345

description: Single cell from human pancreas


title: 6yr_male_cell1349

description: Single cell from human pancreas


title: 6yr_male_cell1344

description: Single cell from human pancreas


title: 6yr_male_cell1342

description: Single cell from human pancreas


title: 6yr_male_cell1348

description: Single cell from human pancreas


title: 6yr_male_cell1343

description: Single cell from human pancreas


title: 6yr_male_cell1341

description: Single cell from human pancreas


title: 6yr_male_cell1339

description: Single cell from human pancreas


title: 6yr_male_cell1340

description: Single cell from human pancreas


title: 6yr_male_cell1337

description: Single cell from human pancreas


title: 6yr_male_cell1356

description: Single cell from human pancreas


title: 6yr_male_cell1336

description: Single cell from human pancreas


title: 6yr_male_cell1335

description: Single cell from human pancreas


title: 6yr_male_cell1338

description: Single cell from human pancreas


title: 6yr_male_cell1334

description: Single cell from human pancreas


title: 6yr_male_cell1333

description: Single cell from human pancreas


title: 6yr_male_cell1330

description: Single cell from human pancreas


title: 6yr_male_cell1346

description: Single cell from human pancreas


title: 6yr_male_cell1329

description: Single cell from human pancreas


title: 6yr_male_cell1331

description: Single cell from human pancreas


title: 6yr_male_cell1327

description: Single cell from human pancreas


title: 6yr_male_cell1323

description: Single cell from human pancreas


title: 6yr_male_cell1332

description: Single cell from human pancreas


title: 6yr_male_cell1324

description: Single cell from human pancreas


title: 6yr_male_cell1319

description: Single cell from human pancreas


title: 6yr_male_cell1326

description: Single cell from human pancreas


title: 6yr_male_cell1320

description: Single cell from human pancreas


title: 6yr_male_cell1321

description: Single cell from human pancreas


title: 6yr_male_cell1322

description: Single cell from human pancreas


title: 6yr_male_cell1317

description: Single cell from human pancreas


title: 6yr_male_cell1328

description: Single cell from human pancreas


title: 6yr_male_cell1315

description: Single cell from human pancreas


title: 6yr_male_cell1313

description: Single cell from human pancreas


title: 6yr_male_cell1318

description: Single cell from human pancreas


title: 6yr_male_cell1314

description: Single cell from human pancreas


title: 6yr_male_cell1325

description: Single cell from human pancreas


title: 6yr_male_cell1312

description: Single cell from human pancreas


title: 6yr_male_cell1316

description: Single cell from human pancreas


title: 6yr_male_cell1311

description: Single cell from human pancreas


title: HeLa cells, stranded RiboZero RNA-seq, EYFP overexpression

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
Stranded RNA-seq
processed data file: HSV1_antisensetranscripts.tsv
RiboZero RNA

data_processing:
Data was mapped onto the hg19 reference using Tophat2 (Kim et al. 2013).
Antisense transcripts were defined on the coverage tracks using a custom running sum algorithm, followed by extensive filtering.
Antisense transcripts were classified into divergent, convergent and intal, based on the location of the TSS in respect to the sense transcript.
Expression values for the different samples (columns X-X) are presented as log(2) transformed RPKM values of averages from biological replicates.
Expression values are shown for the stranded RNA-sequencing data provided here (columns X-X). In addition, published RNA-sequencing data was reanalyzed the same way (columns X-X, as indicated by first author name and GSM identifiers).
The following datasets were reanalyzed: HSV-1 infected HFF cells (Rutkowski et al. 2015, PMID: 25989971, GEO: GSE59717), RNA-sequencing from VZV keratinocytes (Jones et al. 2014, PMID: 24497829, SRA: E-MTAB-1717) and CMV infected fibroblast (Tirosh et al. 2015, PMID: 26599541, GEO: GSE69906), and NET-seq data from HeLa cells (Schlackow et al. 2017, PMID: 28017589, GEO: GSE81662)
Column names contain first author name, SRA identifiers for VZV data and GEO identifiers for all others. Several identifiers indicate that replicates were available and averaged.
Nearest FANTOM transcripts (Hon et al. 2017) are also provided.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text

source_name: HeLa cells

growth_protocol: WI38 fibroblasts were cultured in Minimal Essential Medium (MEM) supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin. HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM)  supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin.

extract_protocol:
TruSeq Stranded mRNA Library Prep Kit
Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo).

treatment_protocol: For RNA labeling, 4SU at a concentration of 500 µM was added one hour before harvesting. Cells were infected with Herpes simplex virus 1 as indicated.

tag: cell line

value: HeLa

tag: 4su treatment

tag: hsv-1 infection

value: Uninfected

tag: rna isolation

value: total RNA

tag: adapter sequence

value: GATCGGAAGAGCACACGT

tag: barcode

value: CGATGTA


title: shScr rep4

city: Boston

first: Jingwei

last: Cheng

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were mapped or aligned to the reference organism using STAR software.
Genome_build: hg19
Supplementary_files_format_and_content: format: txt and csv files. Content: count-based differential expression

source_name: Merkel cell carcinoma cell line

growth_protocol: MKL-1 cells grow as suspension clumps in RPMI medium supplemented with 10% FBS, Penicillin-Streptomycin, and glutamax

extract_protocol: Total RNA was purified from MKL-1 cells using RNeasy plus mini kit (Qiagen).

treatment_protocol: Cells were treated with doxycycline for 5 days to induce expression of EP400 shRNA -2 and -3. Cells were treated with doxycycline for 2 days to induce expression of MYCL shRNA

value: Merkel cell carcinoma cell line

value: MKL-1 line with Dox inducible scramble shRNA

tag: mcpyv

value: positive

tag: dox treatment


title: HeLa cells, stranded RiboZero RNA-seq, EYFP-ICP4 overexpression

value: CAGATCA


title: shEP400-3 rep3

value: MKL-1 line with Dox inducible EP400 shRNA #3


title: shMYCL rep2

value: MKL-1 line with Dox inducible MYCL shRNA


title: shMYCL rep1


title: shMYCL rep3


title: shEP400-3 rep2


title: shScr rep5


title: shEP400-2 rep2

value: MKL-1 line with Dox inducible EP400 shRNA #2


title: shEP400-3 rep1


title: shEP400-2 rep1


title: shScr rep3


title: shScr rep2


title: shScr rep1


title: shScr rep6


title: 22yr_male_cell2544

description: Single cell from human pancreas

value: male

value: alpha


title: 22yr_male_cell2542

description: Single cell from human pancreas


title: 22yr_male_cell2543

description: Single cell from human pancreas


title: 22yr_male_cell2537

description: Single cell from human pancreas


title: 22yr_male_cell2535

description: Single cell from human pancreas

value: beta


title: 22yr_male_cell2539

description: Single cell from human pancreas


title: 22yr_male_cell2538

description: Single cell from human pancreas


title: 22yr_male_cell2540

description: Single cell from human pancreas

value: unsure


title: 22yr_male_cell2534

description: Single cell from human pancreas


title: 22yr_male_cell2533

description: Single cell from human pancreas


title: 22yr_male_cell2531

description: Single cell from human pancreas


title: 22yr_male_cell2532

description: Single cell from human pancreas


title: 22yr_male_cell2536

description: Single cell from human pancreas


title: shEP400-2 rep3


title: 22yr_male_cell2530

description: Single cell from human pancreas


title: 22yr_male_cell2527

description: Single cell from human pancreas


title: 22yr_male_cell2526

description: Single cell from human pancreas


title: 22yr_male_cell2529

description: Single cell from human pancreas

value: ductal


title: 22yr_male_cell2523

description: Single cell from human pancreas


title: 22yr_male_cell2524

description: Single cell from human pancreas


title: 22yr_male_cell2525

description: Single cell from human pancreas


title: 22yr_male_cell2522

description: Single cell from human pancreas


title: 22yr_male_cell2521

description: Single cell from human pancreas


title: 22yr_male_cell2520

description: Single cell from human pancreas

value: delta


title: 22yr_male_cell2518

description: Single cell from human pancreas


title: 22yr_male_cell2519

description: Single cell from human pancreas


title: 22yr_male_cell2541

description: Single cell from human pancreas


title: 22yr_male_cell2517

description: Single cell from human pancreas


title: 22yr_male_cell2515

description: Single cell from human pancreas


title: 22yr_male_cell2516

description: Single cell from human pancreas


title: 22yr_male_cell2511

description: Single cell from human pancreas


title: 22yr_male_cell2510

description: Single cell from human pancreas


title: 22yr_male_cell2528

description: Single cell from human pancreas


title: 22yr_male_cell2512

description: Single cell from human pancreas


title: 22yr_male_cell2509

description: Single cell from human pancreas


title: 22yr_male_cell2508

description: Single cell from human pancreas


title: 22yr_male_cell2513

description: Single cell from human pancreas


title: 22yr_male_cell2507

description: Single cell from human pancreas

value: acinar


title: 22yr_male_cell2514

description: Single cell from human pancreas


title: 22yr_male_cell2502

description: Single cell from human pancreas


title: 22yr_male_cell2504

description: Single cell from human pancreas


title: 22yr_male_cell2505

description: Single cell from human pancreas


title: 22yr_male_cell2500

description: Single cell from human pancreas


title: 22yr_male_cell2499

description: Single cell from human pancreas


title: 22yr_male_cell2498

description: Single cell from human pancreas


title: 22yr_male_cell2497

description: Single cell from human pancreas


title: 22yr_male_cell2495

description: Single cell from human pancreas


title: 22yr_male_cell2496

description: Single cell from human pancreas


title: 22yr_male_cell2494

description: Single cell from human pancreas


title: 22yr_male_cell2492

description: Single cell from human pancreas


title: 22yr_male_cell2490

description: Single cell from human pancreas


title: 22yr_male_cell2491

description: Single cell from human pancreas


title: 22yr_male_cell2489

description: Single cell from human pancreas


title: 22yr_male_cell2488

description: Single cell from human pancreas


title: 22yr_male_cell2503

description: Single cell from human pancreas


title: 22yr_male_cell2506

description: Single cell from human pancreas


title: 22yr_male_cell2481

description: Single cell from human pancreas


title: 22yr_male_cell2485

description: Single cell from human pancreas


title: 22yr_male_cell2482

description: Single cell from human pancreas


title: 22yr_male_cell2480

description: Single cell from human pancreas


title: 22yr_male_cell2477

description: Single cell from human pancreas


title: 22yr_male_cell2475

description: Single cell from human pancreas


title: 22yr_male_cell2474

description: Single cell from human pancreas


title: 22yr_male_cell2501

description: Single cell from human pancreas


title: 22yr_male_cell2476

description: Single cell from human pancreas


title: 22yr_male_cell2470

description: Single cell from human pancreas


title: 22yr_male_cell2473

description: Single cell from human pancreas


title: 22yr_male_cell2467

description: Single cell from human pancreas


title: 22yr_male_cell2469

description: Single cell from human pancreas


title: 22yr_male_cell2468

description: Single cell from human pancreas


title: 22yr_male_cell2466

description: Single cell from human pancreas


title: 22yr_male_cell2464

description: Single cell from human pancreas


title: 22yr_male_cell2487

description: Single cell from human pancreas


title: 22yr_male_cell2471

description: Single cell from human pancreas


title: 22yr_male_cell2483

description: Single cell from human pancreas


title: 22yr_male_cell2462

description: Single cell from human pancreas


title: 22yr_male_cell2493

description: Single cell from human pancreas


title: 22yr_male_cell2484

description: Single cell from human pancreas


title: 22yr_male_cell2478

description: Single cell from human pancreas


title: 22yr_male_cell2457

description: Single cell from human pancreas


title: 22yr_male_cell2463

description: Single cell from human pancreas


title: 22yr_male_cell2461

description: Single cell from human pancreas


title: 22yr_male_cell2458

description: Single cell from human pancreas


title: 22yr_male_cell2460

description: Single cell from human pancreas


title: 22yr_male_cell2465

description: Single cell from human pancreas


title: 22yr_male_cell2456

description: Single cell from human pancreas


title: 22yr_male_cell2472

description: Single cell from human pancreas


title: 22yr_male_cell2455

description: Single cell from human pancreas


title: 22yr_male_cell2451

description: Single cell from human pancreas


title: 22yr_male_cell2454

description: Single cell from human pancreas


title: 22yr_male_cell2453

description: Single cell from human pancreas


title: 22yr_male_cell2452

description: Single cell from human pancreas


title: 22yr_male_cell2449

description: Single cell from human pancreas


title: 22yr_male_cell2486

description: Single cell from human pancreas


title: 22yr_male_cell2447

description: Single cell from human pancreas


title: 22yr_male_cell2446

description: Single cell from human pancreas


title: 22yr_male_cell2448

description: Single cell from human pancreas


title: 22yr_male_cell2443

description: Single cell from human pancreas


title: 22yr_male_cell2445

description: Single cell from human pancreas


title: 22yr_male_cell2442

description: Single cell from human pancreas


title: 22yr_male_cell2441

description: Single cell from human pancreas


title: 22yr_male_cell2459

description: Single cell from human pancreas


title: 22yr_male_cell2439

description: Single cell from human pancreas


title: 22yr_male_cell2438

description: Single cell from human pancreas


title: 22yr_male_cell2435

description: Single cell from human pancreas


title: 22yr_male_cell2436

description: Single cell from human pancreas


title: 22yr_male_cell2433

description: Single cell from human pancreas


title: 22yr_male_cell2434

description: Single cell from human pancreas

value: mesenchymal


title: 22yr_male_cell2432

description: Single cell from human pancreas


title: 22yr_male_cell2437

description: Single cell from human pancreas


title: 22yr_male_cell2479

description: Single cell from human pancreas


title: 22yr_male_cell2431

description: Single cell from human pancreas


title: 22yr_male_cell2428

description: Single cell from human pancreas


title: 22yr_male_cell2427

description: Single cell from human pancreas


title: 22yr_male_cell2429

description: Single cell from human pancreas


title: 22yr_male_cell2450

description: Single cell from human pancreas


title: 22yr_male_cell2425

description: Single cell from human pancreas


title: 22yr_male_cell2430

description: Single cell from human pancreas


title: 22yr_male_cell2424

description: Single cell from human pancreas


title: 22yr_male_cell2444

description: Single cell from human pancreas


title: 22yr_male_cell2422

description: Single cell from human pancreas


title: 22yr_male_cell2421

description: Single cell from human pancreas


title: 22yr_male_cell2419

description: Single cell from human pancreas


title: 22yr_male_cell2420

description: Single cell from human pancreas


title: 22yr_male_cell2418

description: Single cell from human pancreas


title: 22yr_male_cell2440

description: Single cell from human pancreas


title: 22yr_male_cell2414

description: Single cell from human pancreas


title: 22yr_male_cell2413

description: Single cell from human pancreas


title: 22yr_male_cell2415

description: Single cell from human pancreas


title: 22yr_male_cell2412

description: Single cell from human pancreas


title: 22yr_male_cell2410

description: Single cell from human pancreas


title: 22yr_male_cell2411

description: Single cell from human pancreas


title: 22yr_male_cell2408

description: Single cell from human pancreas


title: 22yr_male_cell2405

description: Single cell from human pancreas


title: 22yr_male_cell2407

description: Single cell from human pancreas


title: 22yr_male_cell2409

description: Single cell from human pancreas


title: 22yr_male_cell2426

description: Single cell from human pancreas


title: 22yr_male_cell2403

description: Single cell from human pancreas


title: 22yr_male_cell2401

description: Single cell from human pancreas


title: 22yr_male_cell2404

description: Single cell from human pancreas


title: 22yr_male_cell2400

description: Single cell from human pancreas


title: 22yr_male_cell2402

description: Single cell from human pancreas


title: 22yr_male_cell2398

description: Single cell from human pancreas


title: 22yr_male_cell2399

description: Single cell from human pancreas


title: 22yr_male_cell2397

description: Single cell from human pancreas


title: 22yr_male_cell2396

description: Single cell from human pancreas


title: 22yr_male_cell2417

description: Single cell from human pancreas


title: 22yr_male_cell2394

description: Single cell from human pancreas


title: 22yr_male_cell2395

description: Single cell from human pancreas


title: 22yr_male_cell2416

description: Single cell from human pancreas


title: 22yr_male_cell2390

description: Single cell from human pancreas


title: 22yr_male_cell2393

description: Single cell from human pancreas


title: 22yr_male_cell2406

description: Single cell from human pancreas


title: 22yr_male_cell2387

description: Single cell from human pancreas


title: 22yr_male_cell2388

description: Single cell from human pancreas


title: 22yr_male_cell2389

description: Single cell from human pancreas


title: 22yr_male_cell2391

description: Single cell from human pancreas


title: 22yr_male_cell2386

description: Single cell from human pancreas


title: 22yr_male_cell2385

description: Single cell from human pancreas


title: 22yr_male_cell2382

description: Single cell from human pancreas


title: 22yr_male_cell2383

description: Single cell from human pancreas


title: 22yr_male_cell2384

description: Single cell from human pancreas


title: 22yr_male_cell2381

description: Single cell from human pancreas


title: 22yr_male_cell2423

description: Single cell from human pancreas


title: 22yr_male_cell2378

description: Single cell from human pancreas


title: 22yr_male_cell2380

description: Single cell from human pancreas


title: 22yr_male_cell2379

description: Single cell from human pancreas


title: 22yr_male_cell2374

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