title: Col leaf

description: MNAse digested DNA

data_processing:
read quality was checked with FastQC
Reads were mapped to TAIR10 genome with bowtie2.1.0
Nucleosome positions were obtained comparing the mapped bam files with danpos 2.1.3
nucleosomal information was further processed in R.
Genome_build: TAIR10
Supplementary_files_format_and_content: danpos_output_Col_vs_fas2G6.allPeaks.tsv contains position and coverage of nucleosomal dyads of wt and mutant and their related statistics

growth_protocol: Seeds were sown on x0.5 (MS) medium, stratified at 4C for 48 h, and allowed to germinate for 10 days in growth chambers under SD (8 h light, 100 μmoles m -2 s -1 , 22 °C) conditions. Plantlets were planted in soil and grown in growth chambers under the same conditions. For chromatin extraction, leaf number 6 was harvested after 38 days

extract_protocol:
Leaf material was cross-linked using 1% formaldehyde under vacuum for 15 min
To extract native chromatin, 100 mg of ground frozen leaf material was treated in Nuclei Extraction Buffer for 15 min at 4°C
The homogenate was filtered through 50 μm Nylon filter and pellets were collected by centrifugation for 10 min at 1500xg at 4°C.
Pellets were washed once in MNase buffer and were re-suspended in 100 μl of MNase buffer.
1.3 μl of RNase A was added to the suspension. This mixture was digested with Micrococcal Nuclease (MNase, New England BioLabs, Schwalbach, Germany, 0.2 U/μl) for 8 min in MNase Buffer.
The reaction was stopped with 10 mM EDTA. The supernatant after a centrifugation for 5 min at 1500x g at 4°C
was collected as supernatant 1. The pellet was re-suspended in S2 buffer and treated for 30 min on ice.
The suspension was centrifuged again for 5 min at 1500x g at 4°C.
After pooling supernatant 1 and 2, formaldehyde crosslinks were reversed by treatment at 65°C overnight with elevated salt concentration (1 M NaCl).
The mixture was treated with de-proteinization solution at 45°C for 3 hours. Nucleosome DNA was recovered as above.
Digested DNA was resolved on 1% agarose gels.
Gel slabs containing the DNA fraction 150 ± 50 bp were sliced and DNA was recovered
Sequencing libraries were constructed using an Ovation Ultralow Library System (Nugen, San Carlos, CA)

tag: ecotype background

tag: genotype/variation

value: wild type

value: stem


title: fas2 leaf

status: Public on Nov 13 2017

type: SRA

city: Alicante

first: Angel

last: Barco

address: Ramon y Cajal

department: Neuro Plasticity

country: Spain

institute: NeuroSciences Institute of Alicante CSIC

description: MNAse digested DNA

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: fas2 mutant_stem

tag: tissue


title: ChIP-seq_S10P of shControl cells

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

institute: Institut for Research in Biomedicine (IRB-Barcelona)

description:
dormant bone metastatic cell subline
Shctrl_only_S10P_ATCACG

data_processing:
Quality trimming and removal of artifacts with Trimmomatic version 0.33 and parameters adapters-all.fa:2:30:10 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:25
Alignment with BWA (version 0.7.5a-r405)21 with parameters -n 2 -l 20 and -k 1
Removal of duplicated reads with samtools version 1.3.1
Peak calling with MACS2 version 2.1.1.20160309 and parameters  -q 0.01 --broad -B --broad-cutoff 0.01 --nomodel --extsize 300
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files of the signal as generated by Macs2

organism: Homo sapiens

growth_protocol: cultured in standard conditions (37C, 5% CO2) in DMEM 4.5g l–1 D-glucose medium (GIBCO) supplemented with 10% fetal bovine serum (FBS), 50 U ml–1 penicillin, 50 µg ml–1 streptomycin and 5% glutamine;

extract_protocol:
DBM shCTRL and shMSK1 cells were trypsinised and crosslinked in 1% formaldehyde for 10 min at RT. rosslinking was quenched with 0.125 M glycine. Pelleted cells were lysed in 1 ml ChIP buffer (150 mM NaCl, 10 mM Tris-HCl, 5 mM EDTA, 1% SDS, 0.5 mM DTT and 1% Triton X-100) and sonicated for 20 min in a Bioruptor Pico (Diagenode).
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following manufacturer's instruction. Antibodies used for ChIP were: H3S10p (Abcam ab5176), H3S28p (Sigma-Aldrich H9908)

tag: cell line

value: Breast cancer cell line


title: mc2155(StarStuff)

city: Pittsburgh

first: Rebekah

middle: M

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned using bowtie2 version 2.2.6
Reads that did not uniquely align to reference genome were removed with sed command line utility using the "XS:I" flag in the bowtie alignment output
SAM converted to BAM using samtools version 1.2
BAM converted to BED using bedtools version 2.25.0
Expression levels were computerd as reads mapped per base pair per strand using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: NC_001900.1 (Mycobacterium phage D29)
Genome_build: KX897981.1 (Mycobacterium phage StarStuff)
Genome_build: NC_001335.1 (Mycobacterium phage L5)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

molecule: total RNA

organism: Mycobacterium phage StarStuff

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen), rRNA was depleated using RiboZero (Illumina)
Illumina TruSeq Stranded mRNA sample prep kit

tag: time

value: lysogen

tag: host

value: Mycobacterium smegmatis


title: Jan25_Chip170_Cell_23

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Ly6G- Cd11b+CD115+Ly6CHi

data_processing:
FASTQ sequence files were aligned to the mouse genome version 9 (mm9) using RSEM.
Single-cell were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using an empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of TPM RSEM expression values

organism: Mus musculus

source_name: bone marrow (femurs and tibias)

extract_protocol:
Cells were harvested from bone marrow.  Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS. Ly6Chi monocytes (CD11b+ Ly6G– CD115+ F4/80– Ly6Chi cells) were isolated from the bone marrow of wild-type and Gfi1-Tomato IRF8-GFP mice by FACS sorting on BD FACSAria II with a 100μm nozzle.
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system. Single-cell libraries were subjected to paired-end 75 bp RNA-sequencing on a HiSeq 2500 (Illumina Inc.). 96 scRNA-seq libraries were sequenced per HiSeq 2500 gel (~300 million bp per gel).

tag: genotype

value: Wild-type

tag: differentiation

value: In vitro

tag: strain

tag: cell type

value: Ly6G- Cd11b+CD115+Ly6CHi


title: WT_rep1

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.32) tool: (1) removing the reads with adaptor contamination; (2) filtering the low-quality reads with ambiguous sequences ‘N’; (3) removing the low-quality bases (quality score < Q30).
All downstream analyses were based on clean, high quality data. De novo assembly of the high quality reads was performed using Trinity, which is composed of three independent software modules: Inchworm, Chrysalis and Butterfly. By Inchworm, RNA-seq data was assembled into unique sequences through establishing a k-mer graph (K = 25). By Chrysalis, the contigs generated in the previous step were clustered, and a de Bruijn graph was constructed for each cluster. Subsequently, by Butterfly, these Bruijn graphs were processed in parallel and the paths were traced according to reads and pairs of reads within graphs to obtain full-length transcripts for alternative splicing isoforms and distinguish transcripts of paralogous genes. Finally, the distributed situation of length of result sequences was counted and analyzed using RSEM method. A Pearson’s correlation analysis was performed to obtain the transcript-level R2 between biological replicates.
For count-based differential expression testing between WT, UV-715 and EMS-25 cells, edgeR was used. We used min_rowSum_counts of 10, stringent q-value < 0.01 (false discovery rate, FDR) and the absolute value of | log2 fold change| ≥ 1 as the threshold to judge the significant differences in gene expression between WT and mutant cells.
Genome_build: De novo assembly
Supplementary_files_format_and_content: matrix text file (transcript count values of rsem output across samples)

organism: Chlorella vulgaris

source_name: WT

growth_protocol: Chlorella vulgaris (SAG 211-12) was obtained from the collection of algal cultures at the University of Göttingen, Germany. The inoculum was grown in Bold’s Basal medium consisting of (per liter): 0.25 g NaNO3, 0.075 g MgSO4.7H2O, 0.075 g K2HPO4, 0.175 g KH2PO4, 0.025 g NaCl, 0.025 g CaCl2.2H2O, 8.82 mg ZnSO4.7H2O, 0.44 mg MnCl2.4H2O, 0.71 mg MoO3, 1.57 mg CuSO4.5H2O, 0.49 mg CoCl2.6H2O, 11.42 mg H3BO3, 50 mg EDTA, 31 mg KOH, 4.98 mg feSO4.7H2O. Cultures were maintained at 25◦C under continuous illumination by four fluorescent lamps.

extract_protocol:
Total RNA was extracted from 14-days old stationary phase reached (OD680=5) 5 ml cell culture using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. Briefly, after quality and quantity measurement using 2100 BioAnalyzer (Agilent, USA), it was treated with RNase-free DNase I (Thermo Scientific, USA) at a concentration of 1 U/µg to remove residual genomic DNA. Then, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions.
mRNAs were purified from the 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer. Afterthat, the cleaved short RNA fragments were used for first-strand cDNA synthesis using first strand synthesis mix, and the second strand was synthesized using second strand marking master mix. The double strand cDNAs were purified with AMPure XP beads (Beckman Coulter, USA) and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. 75x2 paired-end sequencing of three cDNA libraries (WT, UV-715 and EMS-25) with two biological replicates were performed using the Illumina MiSeq sequencing platform (Illumina, USA). All sequence data are PE 2x75 bp.  Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format.

treatment_protocol: 250 µl culture of C. vulgaris with the cell count of   4×10e8 cells/ml was spread on solid Bold’s basal media and then exposed to UV irradiation (254 nm) with an intensity of 2.9 ×10-2 W/cm2 for 0.5 to 10 minutes at a distance of 15 cm. UVX Digital Radiometer (UVP, USA) was used to measure the UV-light intensity. The UV-irradiated plates were kept in dark for 24 h to prevent light-induced repair. The plates were then maintained under normal light for 2 weeks. Single colonies appearing on plates were selected and transferred individually into 2 ml Bold’s basal medium. After 10 days of culturing, the cell densities were determined by measuring OD at 680 nm.


title: Input DNA from shControl cells

description:
dormant bone metastatic cell subline
Shtrl_only_Input_GATCAG


title: ChIP-seq_S28P of shControl cells

description:
dormant bone metastatic cell subline
Shctrl_only_S28P_ACAGTG


title: Mycobacerium smegmatis infected with mycobacteriophage D29 for 30min

organism: Fromanvirus D29

value: 30min post infection


title: ChIP-seq_S28P of shMSK1 cells

description:
dormant bone metastatic cell subline
MSK1_only_S28P_CAGATC


title: ChIP-seq_S10P of shMSK1 cells

description:
dormant bone metastatic cell subline
MSK1_only_S10P_TTAGGC


title: Namalwa RNA-seq rep 1

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

data_processing:
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
The number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to the Integrative Genomics Viewer (www.broadinstitute.org/igv)
Genome_build: hg19, EBV NC_007605.1
Supplementary_files_format_and_content: wig files

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: Namalwa cells

extract_protocol:
We isolated RNA from 5 × 10^6 log phase cells homogenized with a QIAshredder spin column (Qiagen). Total RNA was purified by silica-based membrane affinity as packaged in the RNeasy Mini Kit (Qiagen). Preparations included the optional DNAse treatment step. Single primer isothermal linear amplification to cDNA was achieved using the Ovation RNA-Seq System V2 (NuGEN) and 20 ng of RNA. 3 μg of cDNA was then sheared in a 40 μL volume using a Covaris S2 Focused-ultrasonicator.
We prepared deep sequencing libraries by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).

value: Namalwa cells


title: WT_rep2


title: Input DNA from shMSK1 cells

description:
dormant bone metastatic cell subline
MSK1_only_Input_GGCTAC


title: K562_pD transient HiC

data_processing:
library strategy: HiC-seq
General HiC processing: Paired reads were aligned to combined human/viral reference genomes with HiCUP version 0.5.0 using default parameters (Wingett et al., 2015) to generate a set of interactions. We used the human hg19 sequence merged with the EBV NC_007605.1, KSHV NC_009333.1, HPV16 NC_001526.2, or HPV31 J04353.1 sequence. Only alignments with mapq scores equal to or greater than 30 were retained.
Chromosome-resolution heatmaps of interactions were determined from the HiCUP-filtered interchromosomal Hi-C interactions in sam format. Expected interactions were calculated using the following equation for each chromosome pair, where chrA represents the number of single end interchromosomal reads containing chrA, chrB represents the number of single end interchromosomal reads containing chrB, totalPairs represents the total number of interchromosomal paired end reads, and all represents the total number of interchromosomal single end reads, which is equal to 2 x totalPairs: (((chrA/all)*(chrB/(all-chrA)))+((chrB/all)*(chrA/(all-chrB)))) * total_pairs.
Lamin association analysis: The set of lamin interacting domains from Tig3 cells (Guelen et al., 2008) was downloaded from the UCSC genome browser (Kent et al., 2002). Hi-C interactions identified by HiCUP were processed into a format readable by the HiTC package (Servant, 2015) using 1 Mb bins for the human genome and 1 kb bins for the viral genome. We performed further analyses on these interaction matrices in R (R Core Team, 2016). First a full interaction matrix for all autosomes was constructed. Next, for each bin, the mean of interaction counts with LAD bins was calculated as was the mean of interaction counts with non-LAD bins. Correlations were then performed across all autosomal bins with the LAD mean vector and the non-LAD mean vector. A logistic regression was performed on the LAD and non-LAD correlation values estimate the probability with which each genome region would interact with lamin. Next, we calculated the probability that each viral bin interacted with the lamin by applying the logistic regression model of the autosomal LAD correlations to the viral interaction data.
Genome_build: human hg19 sequence merged with the EBV NC_007605.1, KSHV NC_009333.1, HPV16 NC_001526.2, or HPV31 J04353.1 sequence
Supplementary_files_format_and_content: Chromsome-resolution heatmap generation results in two plain text files *interchrom_raw_counts_label.txt and *obs_exp_log2_label.txt. The *interchrom_raw_counts_label.txt contains a labeled 26 x 26 matrix for the raw counts of interchromosomal interactions between whole chromosomes. The *obs_exp_log2_label.txt file contains the same labeled 26 x 26 matrix, with raw interchromosomal counts normalized as described above.
Supplementary_files_format_and_content: Lamin association analysis results in plain text files ending in *allCounts.txt, which contains three columns, the first two are individual genomic bins and the third column is the number of interactions between those two bins.

source_name: K562_pD transient HiC

growth_protocol: EBV-positive Daudi, KemIII, RaeI, and Raji cells were maintained under standard conditions (Phan et al., 2016). K562 (C. B. Lozzio and B. B. Lozzio, 1975), EBV- and KSHV-positive BC-1 (Cesarman et al., 1995) and EBV-positive Namalwa (Klein et al., 1972) cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) fetal bovine serum (Invitrogen) in 5% CO2 at 37 °C.  EBV-positive Akata-Zta cells (Ramasubramanyan et al., 2015) were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech). The HPV16-positive 20863 (Jeon et al., 1995) and HPV31-positive 9E (De Geest et al., 1993) keratinocyte cell lines were grown in F-medium, 3:1 (v/v) F-12-DMEM, 5% fetal bovine serum, 400 ng/ml hydrocortisone, 5 µg/ml insulin, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 100 U/ml penicillin, and 100 µg/ml streptomycin, in the presence of irradiated 3T3-J2 feeder cells, as described previously (Chapman et al., 2014). Irradiated feeder cells were removed by versene treatment before the cells were harvested.

extract_protocol:
In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI as described (Rao et al., 2014) with slight modifications. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0 and transferred to new tubes.
Sequencing libraries were created from bound DNA using the Ovation Ultralow Library System V2 kit (NuGEN) with one modification. After adapter ligation, because DNA is still attached to the beads, water instead of SPRI beads was added to the reaction. DNA bound to the beads was purified with a magnet, washed, and the beads were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0. After library amplification, SPRI beads were added as directed to purify the amplified DNA.

treatment_protocol: All cells except Akata-Zta were untreated. 5 million cells per experiment were fixed for in situ Hi-C as previously described (Rao et al., 2014). Akata-Zta cells were pretreated with 200 μM acyclovir for 1 hour before reactivation of the lytic cycle with 500 ng/mL doxycycline. After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotech). 5 million cells each of LGNFR+ and LGNFR- were fixed for in situ Hi-C as previously described (Rao et al. 2014)

value: K562 cells + pD plasmid


title: K562_pDdE transient HiC

source_name: K562_pDdE transient HiC

value: K562 cells + pDdE plasmid


title: Akata-Tet Z, LGNFR- HiC rep 5

source_name: Akata-Tet Z, LGNFR- HiC

value: Akata-Tet Z cells


title: EBNA1 ChIP-seq

data_processing:
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
Peaks were visualized after normalization to the background baseline
Formatted for uploading to the Integrative Genomics Viewer (www.broadinstitute.org/igv)
Genome_build: hg19, EBV NC_007605.1
Supplementary_files_format_and_content: wig files

extract_protocol:
BZLF1 and EBNA1 ChIPs were performed as previously described (Keck et al., submitted) using 3 µg of the anti-BZLF1 antibody BZ1 (Santa Cruz, sc-53904, lot 2313) and 3 µg of the anti-EBNA1 antibody 0211 (Santa Cruz, sc-57719, lot K2013).
We prepared deep sequencing libraries by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).

tag: chip antibody


title: Akata-Tet Z, LGNFR+ HiC rep 5

source_name: Akata-Tet Z, LGNFR+ HiC


title: EMS_rep2

source_name: EMS

value: EMS mutant (EMS-25)


title: Untreated Kupffer (first replicate)

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

data_processing:
Basecalling was performed with a pipeline, using HiSeq Control Software 2.2.58, RTA 1.18.64.0 and CASAVA-1.8.2
After quality assessment of the corresponding FASTQ files with FastQC v0.11.5 (1), adaptor sequences were trimmed from the reads.
Additionally, 10 bases were trimmed from the 5-prime end and 5 bases from the 3-prime end of each read.
Trimmed reads shorter than 50 nucleotides were discarded.
Low-quality sequences (Phred quality score < 30) were also removed.
These quality enhancement steps were performed using TrimGalore v0.4.1 (2).
The reads were subsequently aligned to the mm10 reference genome sequence using HISAT2 v2.0.5 (3) with default parameters.
In the quantification step, reads were counted with HTSeq v0.6.1p1 (4).
Finally fold changes and their corresponding p-values were computed for each condition using DESeq2 v1.10.1 (5).
Genome_build: mm10
Supplementary_files_format_and_content: Excel File for each condition containing FKPKM values, FoldChanges, Pvalues and Various annotations.
Supplementary_files_format_and_content: Tab delmited file for the pair (treated MOMF vs. Treated Kupffer Cells, containing fold changed andy very precise p-values as computed by the deseq package for the volcano plot.

source_name: Kupffer cells

growth_protocol: 8 week old C57BL6/J mice were used for the experiments

extract_protocol:
Hepatic macrophages were isolated from MCD-treated mice and sorted by fluorescent activated cell sorting using an Aria-II (BD Biosciences). Total RNA of MoMF and Kupffer cells was isolated directly afterwards by using PeqGold (VWR Technologies).
Illumina TruSeq stranded mRNA kit, Library dilution at 10nM

treatment_protocol: treatment with methionine and choline deficient (MCD) diet started at week 8 for 4 weeks

tag: library type

tag: treatment

value: untreated

tag: target population

value: KC


title: K562_pD stable HiC rep 2

source_name: K562_pD stable HiC


title: Akata-Tet Z, LGNFR+ HiC rep 4


title: Healthy2-Organoid [WES]

city: Cambridge

first: Charles

middle: Richard

last: Bradshaw

address: Tennis Court Road

country: United Kingdom

institute: Gurdon Institute

description: Sample 61

data_processing:
Library strategy: WES
RNAseq
Removed low quality reads (<Q20) and trimmed low quality bases (<Q20)
Mapped to hg19 using TopHat
Counts generated and DE performed using edgeR
Genome_build: hg19
WES
Reads were aligned to the UCSC hg38 genome using Bowtie2 (v2.2.6)
Reads were preprocessed for variant calling by marking duplicates with Picard
Indel realignment with the GATK toolkit
SNPs and Indels were called with Varscan (v.2.3) from SAMtools (v1.3.1) mpileup files
Genome_build: hg38

source_name: Human liver organoid

growth_protocol: Tumoroid cultures were grown from single isolated cells and cultured as described in Material and Methods

extract_protocol:
Total DNA extracted using DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions.
Exome, SeqCap EZ Library SR (human)

value: Human liver tumoral cell

tag: passages

tag: gender

value: F


title: Akata-Tet Z, LGNFR- HiC rep 3


title: Akata-Tet Z, LGNFR+ HiC rep 3


title: Healthy1-Organoid [WES]

description: Sample 60

value: M


title: Akata-Tet Z, LGNFR- HiC rep 2


title: Akata-Tet Z, LGNFR+ HiC rep 2


title: BZLF1 ChIP-seq

value: anti-BZLF1 antibody BZ1 (Santa Cruz, sc-53904, lot 2313)


title: Healthy1-Tissue [WES]

description: Sample 59

source_name: Human liver tissue


title: CC3-Organoid-early [WES]

description: Sample 57, tumouroids expanded for short period

data_processing:
Library strategy: WES
RNAseq
Removed low quality reads (<Q20) and trimmed low quality bases (<Q20)
Mapped to hg19 using TopHat
Counts generated and DE performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Counts
WES
Reads were aligned to the UCSC hg38 genome using Bowtie2 (v2.2.6)
Reads were preprocessed for variant calling by marking duplicates with Picard
Indel realignment with the GATK toolkit
SNPs and Indels were called with Varscan (v.2.3) from SAMtools (v1.3.1) mpileup files
Genome_build: hg38
Supplementary_files_format_and_content: Variant Calls


title: CC2-Organoid-late [WES]

description: Sample 56, tumouroids expanded for extended period


title: CC2-Organoid-early [WES]

description: Sample 55, tumouroids expanded for short period


title: Akata-Tet Z, LGNFR- HiC rep 1


title: Namalwa HiC rep 2

source_name: Namalwa HiC


title: CC3-Organoid [RNA-Seq]

description: Sample 35

data_processing:
RNAseq
Removed low quality reads (<Q20) and trimmed low quality bases (<Q20)
Mapped to hg19 using TopHat
Counts generated and DE performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Counts
WES
Reads were aligned to the UCSC hg38 genome using Bowtie2 (v2.2.6)
Reads were preprocessed for variant calling by marking duplicates with Picard
Indel realignment with the GATK toolkit
SNPs and Indels were called with Varscan (v.2.3) from SAMtools (v1.3.1) mpileup files
Genome_build: hg38
Supplementary_files_format_and_content: Variant Calls

source_name: Human liver tumoroid

growth_protocol: Organoid and tumoroid cultures were grown from single isolated cells and cultured as described in Material and Methods.

extract_protocol:
Total RNA extracted using RNeasy mini kit (Qiagen)
Smartseq2 method (doi:10.1038/nprot.2014.006)


title: CC2-Organoid [RNA-Seq]

description: Sample 34


title: Namalwa HiC rep 1


title: Akata-Tet Z, LGNFR- HiC rep 4


title: CC1-Organoid-late [WES]

description: Sample 54, tumouroids expanded for extended period


title: CC1-Organoid_b [RNA-Seq]

description: Samples 29/30, 31, 32, 33  are biological replicates


title: CC1-Organoid_a [RNA-Seq]


title: K562_pD stable HiC rep 1


title: Raji HiC rep 2

source_name: Raji HiC

value: Raji cells


title: CC1-Organoid_c [RNA-Seq]


title: CC1-Organoid-early [WES]

description: Sample 53, tumouroids expanded for short period


title: CC1-Organoid_2 [RNA-Seq]

description: Samples 29 and 30 are technical replicates


title: Raji HiC rep 1


title: CHC2-Organoid-late [WES]

description: Sample 52, tumouroids expanded for extended period


title: CC1-Organoid_1 [RNA-Seq]


title: CHC2-Organoid [RNA-Seq]

description: Sample 28


title: CC3-Organoid-late [WES]

description: Sample 58, tumouroids expanded for extended period


title: CHC2-Organoid-early [WES]

description: Sample 51, tumouroids expanded for short period


title: RaeI HiC rep 2

source_name: RaeI HiC

value: RaeI cells


title: Akata-Tet Z, LGNFR+ HiC rep 1


title: CHC1-Organoid_b [RNA-Seq]

description: Samples 24/25, 26 and 27 are biological replicates


title: RaeI HiC rep 1


title: CHC1-Organoid_2 [RNA-Seq]

description: Samples 24 and 25 are technical replicates


title: CHC1-Organoid_1 [RNA-Seq]


title: KemIII HiC rep 2

source_name: KemIII HiC

value: KemIII cells


title: HCC3-Organoid [RNA-Seq]

description: Sample 23


title: HCC1-Organoid_2 [RNA-Seq]

description: Samples 21 and 22 are technical replicates


title: CHC1-Organoid_a [RNA-Seq]


title: HCC3-Organoid-late [WES]

description: Sample 48, tumouroids expanded for extended period


title: CHC1-Organoid-late [WES]

description: Sample 50, tumouroids expanded for extended period


title: HCC1-Organoid_1 [RNA-Seq]


title: Healthy3-Organoid-DM [RNA-Seq]

description: Sample 20  is cultured in differentiation medium

value: Human liver progenitor


title: Healthy3-Organoid [RNA-Seq]

description: Sample 19


title: HCC3-Organoid-early [WES]

description: Sample 47, tumouroids expanded for short period


title: Daudi HiC rep 2

source_name: Daudi HiC

value: Daudi cells


title: Healthy2-Organoid-DM [RNA-Seq]

description: Sample 18 is cultured in differentiation medium


title: Daudi HiC rep 1


title: HCC1-Organoid-late [WES]

description: Sample 46, tumouroids expanded for extended period


title: Healthy2-Organoid [RNA-Seq]

description: Sample 17


title: Healthy1-Organoid_2 [RNA-Seq]

description: Samples 15 and 16 are technical replicates


title: 9E HiC rep 2

organism:
Homo sapiens
Human papillomavirus 16

source_name: 9E HiC

value: 9E cells


title: 9E HiC rep 1


title: HCC1-Organoid-early [WES]

description: Sample 45, tumouroids expanded for short period


title: Healthy1-Organoid_1 [RNA-Seq]


title: CC3-Tissue [WES]

description: Sample 44

value: Human liver biopsy


title: CC3-Tissue [RNA-Seq]

description: Sample 14


title: CC2-Tissue [RNA-Seq]

description: Sample 13


title: CC1-Tissue_2 [RNA-Seq]

description: Samples 11 and 12 are technical replicates


title: CC2-Tissue [WES]

description: Sample 43


title: KemIII HiC rep 1


title: CHC1-Organoid-early [WES]

description: Sample 49, tumouroids expanded for short period


title: NCTC11168_MHD18

city: Pullman

first: Michael

middle: E

last: Konkel

state: WA

institute: Washington State University

data_processing:
BaseCaller (Torrent Suite verision 5.0.4) was used for basecalling and demultiplexing
Reads were aligned to the approproate genome using bowtie2 version 2.2.5 using default options.
Reads mapping to each CDS were counted using featureCounts from the subread package, version 1.5.0 using the --largestOverlap option.
Genome_build: Genbank accession numbers for the sequences used for read mapping are as follows: C. jejuni strain 81-176  [chromosome sequence: (NC_008787), plasmid sequences: pTet (NC_008790) and pVir (NC_008770)]; C. jejuni strain F38011 (CP006851); C. jejuni strain NCTC 11168 (AL111168);
Supplementary_files_format_and_content: Tab delimited text file containing counts of mapped transcripts CDS for each strain.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

growth_protocol: C. jejuni were grown in 250 mL MH broth cultures with or without 0.05% sodium deoxycholate (w/v) in a microaerobic environment shaking at 220 rpm on an orbital shaker.

extract_protocol:
Bacterial pellets were collected by centrifugation and snap frozen. RNA Extraction was done using the Ambion Ribopure Bacteria kit. rRNA was depleted with 3’ biotinylated oligonucleotides that were designed to hybridize with C. jejuni 16S and 23S rRNAs.
RNA Libraries were generated with the Ion Total RNA-Seq Kit v2

tag: culture time (hours)

tag: culture condition

value: Mueller-Hinton Broth + 0.05% Deoxycholate


title: CC1-Tissue_1 [RNA-Seq]


title: NCTC11168_MHD16


title: CC1-Tissue [WES]

description: Sample 42


title: CHC1-Tissue_2 [RNA-Seq]

description: Samples 8 and 9 are technical replicates


title: CHC1-Tissue_1 [RNA-Seq]


title: CHC2-Tissue [WES]

description: Sample 41


title: NCTC11168_MHD14


title: HCC3-Tissue [RNA-Seq]

description: Sample 7


title: NCTC11168_MH12

value: Mueller-Hinton Broth


title: HCC1-Tissue_1 [RNA-Seq]

description: Samples 5 and 6 are technical replicates


title: F38011_MHD20

organism: Campylobacter jejuni subsp. jejuni F38011


title: CHC1-Tissue [WES]

description: Sample 40


title: HCC1-Tissue_2 [RNA-Seq]


title: HCC3-Tissue [WES]

description: Sample 39


title: Healthy2-Tissue [RNA-Seq]

description: Sample 3


title: 20863 HiC rep 2

organism:
Homo sapiens
human papillomavirus 31

value: 20863 cells


title: Healthy1-Tissue_2 [RNA-Seq]

description: Sample 1 and 2 are technical replicates


title: 20863 HiC rep 1


title: Healthy3-Tissue [RNA-Seq]

description: Sample 4


title: F38011_MH20


title: F38011_MHD18


title: T3_INPUT_b

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Alignement: Bowtie2 v2.2.6.2
Peak Calling: MACS2 v2.1.0
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: Coverage file in bigwig format

source_name: Skeletal muscle stem cells (satellite cells)

growth_protocol: no

extract_protocol:
Genomic DNA was extracted after cell lysis and immunoprecipitated by Diagenode ChIP-seq grade antibodies using the Diagenode iDeal Histones ChIP-seq kit
Libraries were prepared with the NEBNext ultra 2 kit (NEB E7645L).
Library pools were separated on an agarose gel and DNA of a 100-280 bp size-range was selected for sequencing on an Illumina HiSEQ 4000 as paired-end 75-bp reads.

treatment_protocol: T0: muscles fixed with 0.5% paraformaldehyde (PFA), 1h, 4°C. T3: MuSCs fixed with 0.5% PFA, 30min on ice after FACS-isolation. T0 and T3 cells were additionally fixed with 1% formaldehyde for 10 minutes at RT prior to ChIP.

tag: fixation

tag: chip antibodies

value: input sample


title: F38011_MHD16


title: Healthy1-Tissue_1 [RNA-Seq]

description: Samples 1 and 2 are technical replicates


title: CHC2-Tissue [RNA-Seq]

description: Sample 10


title: BC-1 KSHV HiC 2 rep 2

organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8

source_name: BC-1 KSHV HiC 2

value: BC-1 cells


title: T0_INPUT_b


title: BC-1 KSHV HiC rep 1

source_name: BC-1 KSHV HiC


title: T3_INPUT_a


title: T0_INPUT_a


title: F38011_MH12


title: F38011_MHD14


title: T3_H3K27me3_b


title: r20

city: BIRMINGHAM

first: Elena

middle: I

last: Frolova

state: Alabama

address: 1720 2nd Ave South, BBRB373, Box 3

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Illumina BaseSpace was used for basecalling
Sequenced reads were trimmed of primer adapter contamination using TrimGalore version 0.4.4 with parameters --paired --trim1 --length 15 -q 30
Trimmed paired-end reads were then merged into one fastq file using zcat
The merged fastq file was then aligned to the veev reference genome using BWA version 0.7.15-r1140 with parameters -M
Aligned reads were sorted with Picard version 2.9.2 SortSam by coordinate and then duplicates were removed with Picard MarkDuplicates using default settings
Naïve Variant Caller (Galaxy version 0.0.2) called the variants and Variant Annotator (Galaxy version 1.2) counted the bases at each position
Genome_build: VEEV TC83
Genome_build: VEEV TC83 PP2
Supplementary_files_format_and_content: Mutli-tabbed Excel file containing the counts of bases at each position in the genome

organism: Venezuelan equine encephalitis virus

source_name: virion

growth_protocol: Vero cells were maintained at 37 C in alpha minimum essential medium supplemented with 10% fetal bovine serum and vitamins.

extract_protocol:
Viral genomic RNAs were isolated using ZR Viral RNA or Direct-zol RNA mini prep kit (Zymo Research)
Libraries were constructed using Agilent SureSelect Strand Specific mRNA library kit

value: PP2 clone of VEEV TC83

tag: passage


title: ATZ LGNFR+ DNA seq rep 5

source_name: ATZ LGNFR+ DNA-seq

growth_protocol: EBV-positive Akata-Zta cells (Ramasubramanyan et al., 2015) were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech).

extract_protocol:
DNA was isolated from 1 million cells each of LGNFR+ and LGNFR- using a Qiagen DNeasy Blood and Tissue kit.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).

treatment_protocol: Akata-Zta cells were pretreated with 200 μM acyclovir for 1 hour before reactivation of the lytic cycle with 500 ng/mL doxycycline. After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotech).

value: EBV-positive Akata-Zta cells

tag: pretreated with

value: 200 μM acyclovir for 1 hour

tag: sorted fraction

value: LGNFR+


title: r15


title: T3_H3K27me3_a


title: ATZ LGNFR- DNA seq rep 4

source_name: ATZ LGNFR- DNA-seq

value: LGNFR-


title: r10


title: ATZ LGNFR- DNA seq rep 5


title: HCC1-Tissue [WES]

description: Sample 38

value: M


title: T3_H3K27ac_b

value: Diagenode C15410196


title: T3_H3K27ac_a


title: ATZ LGNFR+ DNA seq rep 4


title: T3_no_PFA_Control_c

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
STAR version 2.5.0a [1], with default parameters, was used for alignment on the reference genome (GRCm38 from Ensembl database)
Genes were counted using featureCounts version 1.4.6-p3 [2] from Subreads package (parameters: -t gene -s 0 -O)
Count data were analyzed using R version 3.3.1 and the Bioconductor package DESeq2 version 1.12.3]. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed without applying the independent filtering algorithm.Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: GRCm38 from Ensembl database version 74
Supplementary_files_format_and_content: matrix of count from featurecounts

extract_protocol:
Total RNA was extracted from fixed MuSCs using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE, Ambion, AM1975. Modification: cells were incubated at 50°C for 1h in digestion buffer plus Proteases. No 80°C incubation was performed as recommended by the manufacturer as this deteriorated RNA quality.
Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input Mammalian following manufacturer’s instructions (Clontech, 635005). The quality of all libraries was assessed with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen).
Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: Cell fixed with 0.5% paraformaldehyde (PFA), 30m, 4°C

tag: muscle stem cells manipulation

value: Standard MuSCs isolation, no fixation.


title: r5


title: d20

value: VEEV TC-83

value: 1-3.2 uM of β-D-N(4)-hydroxycytidine


title: T3_H3K4me3_b


title: ATZ LGNFR- DNA seq rep 3


title: T3_no_PFA_Control_b


title: T3_no_PFA_Control_a


title: d15


title: ATZ LGNFR+ DNA seq rep 3


title: T3_H3K4me3_a


title: d10


title: T3_with_PFA_Control_c

value: Standard MuSCs isolation; post-isolation fixed MuSCs.


title: T3_with_PFA_Control_b


title: T0_H3K27me3_b


title: d5


title: ATZ LGNFR- DNA seq rep 2


title: T0_H3K27me3_a


title: T3_with_PFA_Control_a


title: ATZ LGNFR- DNA seq rep 1


title: ATZ LGNFR+ DNA seq rep 2


title: T0_H3K27ac_b


title: ATZ LGNFR+ DNA seq rep 1


title: Jan25_Chip320_Cell_53

description: Ly6G- Cd11b+CD115+Ly6CHi

source_name: bone marrow (femurs and tibias)

tag: genotype

value: Wild-type

tag: differentiation

value: In vitro

value: Ly6G- Cd11b+CD115+Ly6CHi


title: T0_H3K27ac_a

tag: strain


title: 81-176_MHD16

organism: Campylobacter jejuni subsp. jejuni 81-176

value: Mueller-Hinton Broth + 0.05% Deoxycholate


title: W20


title: 81-176_MHD18


title: W5


title: T0_H3K4me3_b


title: 81-176_MHD14


title: RaeI shEBNA1 HiC

source_name: RaeI shEBNA1 HiC

tag: cell type

value: RaeI cells


title: Namalwa RNA-seq rep 2

source_name: Namalwa cells

value: Namalwa cells


title: W10


title: T0_H3K4me3_a


title: W0


title: 9d-2_rep1

status: Public on Nov 12 2017

city: Shanghai

first: Jizhou

last: Yan

address: 999 Hucheng Ring Road,

department: Biology

country: China

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.8.4 software used for basecalling.
FASTX Toolkit 0.0.13 softwere used for filtering and trimming
bowtie2-2.2.5 sofrware used for alignment
MACS-1.4.2 software for peak-calling and R package DiffBind 1.16.3 for peak comparison
R package GenomicRanges 1.22.4 for annotation
Genome_build: danRer10 fasta file downloaded from UCSC and alignment reference built by bowtie2-2.2.5
Supplementary_files_format_and_content: bam files containing alignment results; tab-delimited text files containing information about every called peak, including chromosome, start postion, end postion, etc.

organism: Danio rerio

source_name: heart tissue

growth_protocol: Fish breeding. See reference for zebr4afish growth(Dai, Y. et al. Tissue Extract Fractions from Starfish Undergoing Regeneration Promote Wound Healing and Lower Jaw Blastema Regeneration of Zebrafish. Sci. Rep.2016, 6, 38693; doi: 10.1038/srep38693)

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. EZ-ChIP (Upstate), ChIP-IT high sensitivity (Active Motif)

treatment_protocol: Cardical ventricle tip was cut.See reference for zebrafish heart cut (Poss, et al. Heart regeneration in zebrafish Science, 2002,298:2188)

value: 9 days postamputation

tag: chip antibody

value: H3K9Ac (abcam, ab10812)

tag: FISH

value: 1 -1.5 year old


title: 0d-2_rep1

tag: treatment

value: uncut


title: 0d-1_rep1


title: 9d-1_rep1


title: spp1delta H3K4me2 ChIP-Seq

city: Boston

first: Luis

last: Soares

state: Massachusetts

address: 240 Longwood Ave, Building C1-207

department: BCMP

institute: Harvard Medical School

data_processing:
Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode.
Demultiplexed reads were aligned to S.cerevisiae genome, with bowtie1.1.1, reads with multiple alignments removed. S.pombe spiked-in samples were aligned first to S.pombe genome with bowtie1.1.1, S.pombe unaligned reads were aligned to S.cerevisiae genome, with reads with multiple alignments removed.
Genome_build: S.cerevisiae version R64-1-1, S.pombe version ASM294v2.31
Supplementary_files_format_and_content: bedgraph files were generated with macs2.0 callpeak function with extsize of 150, number of duplicates 1, normalized for SPMR

organism: Saccharomyces cerevisiae

source_name: exponential growing culture

growth_protocol: Cells were grown in indicated media at 25 C  to an OD of 0.500.

extract_protocol:
Cells were lysed in FA buffer 0.5% SDS using glass beads. Cross-linked extracted were sonicated using a Misonix 300 with cup horns, with 10s on/off pulses for a total sonication time of 20 min. Soluble chromatin was recovered by centrifugation and protein concentration quantified by Bradford assay. A total of 700 ug of chromatin was used per immunoprecipitation. Where S.pombe “spike-in” was used, 10 % S.pombe chromatin prepared similarly was added to the immunoprecipitation. The indicated antibody and 10 ul of Protein-G sepharose beads were added, followed by overnight incubation at 4 C. Beads were washed once with FA buffer, 0.1% SDS, 275 mM NaCl, once with FA buffer, 0.1% SDS, 500 mM NaCl, once with 10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na Deoxycholate, and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). Immunoprecipitated material was eluted with 50 mM Tris-HCl 7.5, 10 mM EDTA, 1% SDS by incubating at 65 C for 20 min. Beads were washed once with TE, and the supernatant added to eluted material. Recovered immunoprecipitate was de-crosslinked with 40 ug of Pronase 1 hour at 42 C and overnight at 65 C. Samples were treated with 5 ug RNAse A and phenol-chloroform/chloroform extracted followed by precipitation with LiCl, 40 ug Glycogen, and 100 % EtOH. Precipitated DNA was resuspended in appropriate volume of water and quantified using Qubit assay.
5 ng of immunoprecipitated DNA was used for ChIP-Seq library production. Immunoprecipitated DNA was end repaired using T4 DNA polymerase, T4 PNK and DNA Polymerase I, Large (Klenow) fragment. A single adenosine “tail” was added to the 3’ end of fragments using Klenow (3’ to 5’ exo minus) and  adapters containing inline multiplexing barcodes were added using T4 Quick DNA ligase. Adapter ligated DNA fragments between 200 and 500 bp were gel purified and PCR amplified with 16 cycles. Library quality was assessed using Agilent 2100 Bioanalyzer. Equal molarity of each library was mixed.

treatment_protocol: Cells were crosslinked with formaldehyde  to a final concentration of 1%. Cells were incubated for 20 min at room temperature and the reaction quenched for 5 minutes with 3M glycine. Cell pellets were recovered and washed with FA buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1mM EDTA,1% Triton X-100 and 0.1% Na Deoxycholate), 0.1% SDS.

tag: background

tag: strain name

tag: growth media

value: YPD

tag: sequence barcode

value: CACAGTTGG+T

tag: s.pombe spike-in

value: yes


title: 6d-2_rep1

value: 6 days postamputation


title: 6d-1_rep1


title: spp1delta input DNA

value: TATACCGT+T


title: spp1delta H3K4me3 ChIP-Seq

value: TAGCTAGTA+T


title: W15

value: VEEV TC-83


title: wt(SPP1) H3K4me2 ChIP-Seq

value: wt

value: ACAGTGCAC+T


title: wt(RPB1) SER5P ChIP-Seq

value: AATGCTGAC+T


title: wt(RPB1) SER2P ChIP-Seq

value: ATATAGGA+T


title: wt(RPB1) RPB3 ChIP-Seq

value: GTTGTCCCA+T


title: wt(RPB1) input DNA [replicate]

value: GACACTCTA+T


title: wt(RPB1) H3 ChIP-Seq

value: GCGTTTCGA+T


title: rpb1-N488D SER5P ChIP-Seq

value: AGTAGTGGC+T


title: rpb1-N488D RPB3 ChIP-Seq

value: GCAAGTAGA+T


title: rpb1-N488D H3 ChIP-Seq

value: GTGACTACA+T


title: rpb1-E1103G SER2P ChIP-Seq

value: YPD

value: CGCATTAA+T


title: rpb1-N488D SER2P ChIP-Seq

value: CCATACAC+T

value: yes


title: rpb1-E1103G RPB3 ChIP-Seq

value: TGATCCGA+T


title: rpb1-E1103G input DNA [replicate]

value: AGAACACC+T


title: 81-176_MH12

tag: culture time (hours)

tag: culture condition

value: Mueller-Hinton Broth


title: rpb1-E1103G SER5P ChIP-Seq

value: CTAGTCATG+T


title: rpb1-E1103G H3 ChIP-Seq

value: TGAGAGTG+T


title: wt(SET1) H3 ChIP-Seq

value: wt


title: wt(SPP1) H3K4me3 ChIP-Seq

value: CGAACTGTG+T


title: wt(SPP1) input DNA

value: TCGCGTAC+T


title: pset1delta500 RPB4 ChIP-Seq rep1

value: set1delta500 (plasmid)

value: SC

value: a-Rpb4 (NeoClone W0013)

value: GTCTACAT+T

value: yes*


title: pset1delta500 RPB3 ChIP-Seq rep2

value: a-Rpb3 (NeoClone W0012)

value: AACCGTGT+T


title: wt(pSET1) RPB4 ChIP-Seq rep2

value: SET1 (plasmid)

value: CGCATTAA+T


title: rpb1-N488D input DNA [replicate]

value: YPD

value: GAACGCTGA+T

value: yes


title: prpb4-set1delta500 RPB3  ChIP-Seq rep2

value: rpb4-set1delta500 (plasmid)

value: CTCTGTCT+T


title: wt(pSET1) RPB3 ChIP-Seq rep1


title: prpb4-set1delta500 RPB3 ChIP-Seq rep1

value: AGGTCAGT+T


title: pset1delta500 RPB4  ChIP-Seq rep2

value: GAGTTAAC+T


title: prpb4-set1delta500 H3 ChIP-Seq rep2

value: a-H3 (Abcam ab1791)

value: AGAACACC+T


title: prpb4-set1delta500 H3K4me1 ChIP-Seq rep2

value: SC

value: a-H3K4me1(Millipore 07-436)

value: CTAGTCATG+T


title: wt(pSET1) RPB3 ChIP-Seq rep2

value: yes*


title: prpb4-set1delta500 input DNA rep2

value: TGATCCGA+T


title: prpb4-set1delta500 H3K4me3 ChIP-Seq rep2

value: a-H3K4me3 (Millipore 07-473)

value: CGGACGTGG+T


title: prpb4-set1delta500 H3 ChIP-Seq rep1


title: prpb4-set1delta500 H3K4me2 ChIP-Seq rep2

value: a-H3K4me2 (Millipore 07-030)

value: TGAGAGTG+T


title: prpb4-set1delta500 RPB4 ChIP-Seq rep1

value: a-Rpb4 (NeoClone W0013)

value: GCAGCCTC+T


title: prpb4-set1delta500 H3K4me1 ChIP-Seq rep1

value: rpb4-set1delta500 (plasmid)

value: AGTAGTGGC+T

value: yes


title: prpb4-set1delta500 input DNA rep1

value: GCAAGTAGA+T


title: pset1delta500 RPB3 ChIP-Seq rep1

value: set1delta500 (plasmid)

value: a-Rpb3 (NeoClone W0012)

value: ATATAGGA+T


title: pset1delta500 H3K4me1 ChIP-Seq rep2

value: SC

value: a-H3K4me1(Millipore 07-436)

value: TTCTGATG+T


title: prpb4-set1delta500 H3K4me2 ChIP-Seq rep1

value: GTGACTACA+T


title: pset1delta500 input DNA rep2

value: CATTCCAAG+T


title: prpb4-set1delta500 H3K4me3 ChIP-Seq rep1

value: a-H3K4me3 (Millipore 07-473)

value: ATCCTATTC+T


title: pset1delta500 H3K4me3 ChIP-Seq rep2

value: GTGGGATA+T


title: pset1delta500 H3 ChIP-Seq rep2

value: a-H3 (Abcam ab1791)

value: CTAGATTCG+T


title: pset1delta500 H3K4me1 ChIP-Seq rep1

value: GGCAGACGA+T


title: pset1delta500 H3 ChIP-Seq rep1

value: TCCAGCCTC+T


title: prpb4-set1delta500 RPB4 ChIP-Seq rep2

value: rpb4-set1delta500 (plasmid)

value: a-Rpb4 (NeoClone W0013)

value: TCGCGTAC+T

value: yes*


title: pset1delta500 input DNA rep1

value: set1delta500 (plasmid)

value: ATCGCCAGC+T

value: yes


title: pset1delta500 H3K4me2 ChIP-Seq rep1

value: SC

value: a-H3K4me2 (Millipore 07-030)

value: ACAGTGCAC+T


title: pset1delta500 H3K4me3 ChIP-Seq rep1

value: a-H3K4me3 (Millipore 07-473)

value: TAGCTAGTA+T


title: wt(pSET1) H3 ChIP-Seq rep2

value: SET1 (plasmid)

value: TCATTAGG+T


title: wt(pSET1) input DNA rep2

value: TGACGCAT+T


title: wt(pSET1) H3K4me3 ChIP-Seq rep2

value: CGAACTGTG+T


title: wt(pSET1) H3K4me1 ChIP-Seq rep1

value: a-H3K4me1(Millipore 07-436)

value: AATGCTGAC+T


title: wt(pSET1) H3 ChIP-Seq rep1

value: a-H3 (Abcam ab1791)

value: GACACTCTA+T


title: wt(pSET1) H3K4me2 ChIP-Seq rep2

value: TATCTCCG+T


title: wt(pSET1) H3K4me1 ChIP-Seq rep2

value: CCGTCTGAG+T


title: pset1delta500 H3K4me2 ChIP-Seq rep2

value: set1delta500 (plasmid)

value: CACAGTTGG+T


title: wt(pSET1) H3K4me3 ChIP-Seq rep1

value: SC

value: ACGTAGCTC+T

value: yes


title: wt(pSET1) input DNA rep1

value: GTTGTCCCA+T


title: wt(pSET1) H3K4me2 ChIP-Seq rep1

value: a-H3K4me2 (Millipore 07-030)

value: GCGTTTCGA+T


title: rpb1-N488D input DNA

value: YPD

value: GGTCCTTGA+T


title: rpb1-N488D H3K4me2 ChIP-Seq


title: rpb1-E1103G H3K4me3 ChIP-Seq

value: a-H3K4me3 (Millipore 07-473)

value: TAGCTAGTA+T


title: rpb1-E1103G input DNA

value: TGCGGTTA+T


title: spt6-1004 input DNA

value: AACACCTAC+T


title: wt(RPB1) input DNA

value: wt

value: CTAGATTCG+T


title: spt6-1004 H3K4me2 ChIP-Seq

value: CTAGTCATG+T


title: wt(RPB1) H3K4me2 ChIP-Seq

value: TATCTCCG+T


title: rpb1-N488D H3K4me3 ChIP-Seq

value: CGAACTGTG+T


title: wt(RPB1) H3K4me3 ChIP-Seq

value: ATCGCCAGC+T


title: wt(SPT6) H3K4me3 ChIP-Seq

value: TGACGCAT+T


title: rpb1-E1103G H3K4me2 ChIP-Seq

value: CCGTCTGAG+T

value: yes


title: wt(SPT6) input DNA

value: TCCAGCCTC+T


title: wt(SPT6) H3K4me2 ChIP-Seq

value: a-H3K4me2 (Millipore 07-030)

value: GCGTTTCGA+T


title: set2delta H3K4me3 ChIP-Seq

value: YPD

value: TTGAGTGT+T

value: no


title: Stau_RIP_StauKO2

city: Seattle

first: Cindy

last: van Velthoven

address: 615 Westlake Ave N

institute: Allen Institute

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50)
Trimmed reads were mapped to mm10 with STAR (Dobin et al. 2013) (mismatch cutoff 4% of read length, no non-canonical junction alignments)
Exon-mapping reads were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014) (ignoring multi-mapping reads and reads overlapping multiple genes).
Count data was analyzed in edgeR (Robinson et al. 2010). Genes were filtered for those with at least 3 fragments in at least 3 samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file containing annotated counts

molecule: polyA RNA

source_name: Skeletal muscle stem cells

extract_protocol:
Rneasy micro kit
100pg RNA was reverse-transcribed with the SMARTseq v4 Ultra Low Input RNA kit for Sequencing (Clontech), which uses oligo(dT) priming and sheared with a Covaris S220. End repair, multiplexed adaptor ligation, and library amplification (13-15 cycles) were performed using the Ovation Ultralow Library System V2 1-96 (NuGEN). Libraries were sequenced (101 bp, paired-end) at the Stanford Functional Genomics Facility with a HiSeq 4000 (Illumina).

treatment_protocol: RNA IP was performed using 4x105 MuSCs from Wild-type or Staufen-/- mice. Cells were homogenized in 50 mM Tris, pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/mL Promega RNasin, 1 mg/mL heparin, and Sigma protease inhibitor mixture.Samples were centrifuged at 10,000g for 10 minutes. Rabbit-anti-Staufen1 (Bioss USA, bs-9877R)was added to the supernatant and the mixture was rotated for four hours at 4C, after which Protein G magnetic beads were added and the samples were rotated overnight at 4C. The following day, samples were placed in a magnet on ice and the pellets were washed three times for 5 min in high salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT) and taken up in 300 µl of Qiagen RLT buffer. Total RNA was prepared using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions.

value: Stau-/-

tag: tissue

value: Skeletal muscle stem cells


title: Stau_RIP_WT2

value: Stau+/+


title: Stau_RIP_StauKO1


title: set2delta input DNA

value: GGTCCTTGA+T


title: Stau_RIP_WT3


title: Stau_RIP_WT1


title: wt(SET2) H3K4me3 ChIP-Seq

value: wt

value: a-H3K4me3 (Millipore 07-473)

value: GTGGGATA+T


title: TU_sort ex vivo_3

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50)
Trimmed reads were mapped to mm10 with STAR (Dobin et al. 2013) (mismatch cutoff 4% of read length, no non-canonical junction alignments)
Exon-mapping reads were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014) (ignoring multi-mapping reads and reads overlapping multiple genes).
Count data was analyzed in edgeR (Robinson et al. 2010). Genes were filtered for those with at least 3 fragments in at least 3 samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file containing TMM-normalized FPKMs

source_name: TU_sort ex vivo

extract_protocol:
TriZol with Rneasy
500pg RNA was reverse-transcribed with the SMARTseq v4 Ultra Low Input RNA kit for Sequencing (Clontech), which uses oligo(dT) priming and sheared with a Covaris S220. End repair, multiplexed adaptor ligation, and library amplification (13-15 cycles) were performed using the Ovation Ultralow Library System V2 1-96 (NuGEN). Libraries were sequenced (101 bp, paired-end) at the Stanford Functional Genomics Facility with a HiSeq 4000 (Illumina).

treatment_protocol: To examine nascent transcripts in MuSCs in vivo, Pax7CreER/+: UPRTHA/+ mice were injected with 4tU every 12 hours for 4 days (TU_4d), every 12 hours for 1 day (TU_1d), or 6 hours (TU_6h  in vivo) prior to harvesting of hindlimb muscles. Total RNA from hindlimb muscle (Input_muscle) was extracted and 4tU labelled transcripts were pulled down. In vivo labeling of MuSCs was compated to labeling nascent transcripts during the isolation procedure of MuSCs. During the ~6hr isolation procedure 4tU was added to the samples. Total RNA was isolated from purified MuSCs (Input_MuSC) and 4tU labeled RNA was pulled down (TU_sort ex vivo). The effect of nascent transcription on global RNA levels was determined by treating MuSC during the isolation procedure with the transcription inhibitor α-amanitin (MuSC_aAM) or DMSO control (MuSC_ctrlAM).

tag: 4tu labeling

value: 4tU labeling during isolation of MuSCs (~6 hours)

tag: transcription inhibition

value: no α-amanitin treatment

tag: tissue/cell type

tag: molecule subtype

value: polyA-selected 4tU-tagged RNA


title: spt6-1004 H3K4me3 ChIP-Seq

tag: genotype

value: TGATCCGA+T

value: yes


title: TU_sort ex vivo_4


title: TU_sort ex vivo_1


title: TU_sort ex vivo_2


title: TU_6h in vivo_3

source_name: TU_6h in vivo

value: mice injected with 4tU 6 hours before sacrifice


title: TU_6h in vivo_2


title: Fix_Control_2

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50)
Trimmed reads were mapped to mm10 with STAR (Dobin et al. 2013) (mismatch cutoff 4% of read length, no non-canonical junction alignments)
Exon-mapping reads were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014) (ignoring multi-mapping reads and reads overlapping multiple genes).
Batch effects were corrected using RUVSeq (Risso et al., 2014)
Count data was analyzed in edgeR (Robinson et al. 2010). Genes were filtered for those with at least 3 fragments in at least 3 samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file containing TMM-normalized FPKMs

extract_protocol:
Rneasy FFPE kit
1ng RNA was reverse-transcribed with the SMARTseq v4 Ultra Low Input RNA kit for Sequencing (Clontech), which uses oligo(dT) priming and sheared with a Covaris S220. End repair, multiplexed adaptor ligation, and library amplification (13-15 cycles) were performed using the Ovation Ultralow Library System V2 1-96 (NuGEN). Libraries were sequenced (101 bp, paired-end) at the Stanford Functional Genomics Facility with a HiSeq 4000 (Illumina).

treatment_protocol: To examine the global transcriptome of MuSCs in vivo, mice were perfused with 1% paraformaldehyde prior to isolation of MuSCs (Fix). Total RNA was isolated from fixed and unfixed purified MuSCs using the RNeasy FFPE kit.

value: no 4tU labeling

tag: in vivo fixation

value: no fixation, FACS isolation of MuSCs


title: jhd2delta H3K4me3 ChIP-Seq

value: YPD

tag: chip antibody

value: ACGTAGCTC+T


title: Fix_Control_3


title: jhd2delta H3K4me2 ChIP-Seq

value: a-H3K4me2 (Millipore 07-030)

value: GACACTCTA+T


title: TU_4d_4

value: mice injected with 4tU every 12 hours for 4 days before sacrifice

value: Skeletal muscle stem cells


title: TU_4d_3


title: jhd2delta input DNA

value: CCTTTACAG+T


title: TU_4d_2


title: set2delta H3K4me2 ChIP-Seq

value: ACTAACTGC+T

value: no


title: TU_6h in vivo_1


title: Fix_Control_1


title: wt(SET2) H3K4me2 ChIP-Seq

value: wt

value: AATGCTGAC+T


title: wt(JHD2) H3K4me3 ChIP-Seq

value: a-H3K4me3 (Millipore 07-473)

value: GTTGTCCCA+T


title: wt(JHD2) H3K4me2 ChIP-Seq

value: CGGACGTGG+T

value: yes


title: TU_4d_1

value: no α-amanitin treatment

value: polyA-selected 4tU-tagged RNA


title: TU_1d_3

value: mice injected with 4tU every 12 hours for 1 day before sacrifice


title: TU_1d_4


title: Fix_4

value: no 4tU labeling

value: mouse perfused with 1% paraformaldehyde, followed by FACS isolation of MuSCs


title: TU_6h in vivo_4

value: mice injected with 4tU 6 hours before sacrifice


title: wt(SET2) input DNA

value: YPD


title: MuSC_ctrlAM_4

value: Skeletal muscle stem cells

value: polyA-selected RNA


title: wt(JHD2) input DNA

value: TCATTAGG+T


title: Fix_3


title: TU_1d_1


title: MuSC_ctrlAM_3


title: MuSC_ctrlAM_1


title: set1delta700 H3K4me1 ChIP-Seq

value: a-H3K4me1(Millipore 07-436)

value: ACGTAGCTC+T


title: set1delta700 H3K4me2 ChIP-Seq

value: a-H3K4me2 (Millipore 07-030)

value: GGCAGACGA+T


title: set1delta700 H3K4me3 ChIP-Seq

value: a-H3K4me3 (Millipore 07-473)

value: TATCTCCG+T


title: MuSC_aAM_3

value: α-amanitin treatment during isolation of MuSCs


title: MuSC_aAM_4


title: MuSC_aAM_1


title: Input_muscle_4

value: no α-amanitin treatment

value: Hindlimb muscle


title: set1delta700 input DNA

value: TTGAGTGT+T

value: yes


title: Input_muscle_3

value: no 4tU labeling


title: Fix_5

value: mouse perfused with 1% paraformaldehyde, followed by FACS isolation of MuSCs


title: TU_1d_2

value: mice injected with 4tU every 12 hours for 1 day before sacrifice

value: polyA-selected 4tU-tagged RNA


title: Input_muscle_2

value: polyA-selected RNA


title: wt(SET1) H3K4me1 ChIP-Seq

value: wt

value: YPD

value: GTTGTCCCA+T


title: Input_MuSC_2

value: Skeletal muscle stem cells


title: Input_MuSC_3


title: Input_muscle_1


title: Input_MuSC_1


title: MuSC_ctrlAM_2


title: Fix_1


title: Maf_flox_Foxp3yfpcre_rep2

status: Public on Nov 11 2017

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

data_processing:
Aligned to mouse genome using Tophat 2.1.1 with parameters “--library-type fr-firststrand--no-novel-juncs -G”
Count reads in features from mm10 genome annotation using htseq-count 0.6.1 with options “-s yes -m union”
Read counts were filtered to remove lowly-expressed genes (with less than 1 count per million reads in 2 or more samples), normalized to library size, and statistical analysis performed using edgeR ver 3.14 with Fisher's Exact Test.
Genome_build: mm10
Supplementary_files_format_and_content: Matrices of raw and filtered / normalized read counts output from edgeR.

growth_protocol: Animals were housed under specific pathogen-free conditions that excluded Helicobacter hepaticus.

extract_protocol:
~40,000 cPeyer's patch effector Tregs were isolated from mice and sort purified by FACS. RNA was isolated and purified from sorted cells using a hybrid protocol employing Trizol for collection and the Qiagen RNeasy Micro Kit per manufactuer's directions.
Libraries were constructed from RNA using the Clontech Ultra-Low Input mRNA Seq Kit.

tag: strain background

value: C57BL/6 (N5 backcross)

tag: age

value: 13 weeks

tag: genotype/variation

tag: cell type

value: CD4+FoxP3+CD62L- regulatory T cells from Peyer's patches

tag: replicate

value: rep 2


title: Maf_wt_Foxp3yfpcre_rep2

value: wild type; Maf+/+FoxP3-YFP-cre

value: rep 1


title: Maf_flox_Foxp3yfpcre_rep1


title: wt(SET1) input DNA

tag: background

tag: strain name

tag: growth media

tag: sequence barcode

value: TCGCGTAC+T


title: Maf_wt_Foxp3yfpcre_rep1


title: MuSC_aAM_2

value: α-amanitin treatment during isolation of MuSCs


title: E15.25_Bud2_Trunk_Plate1_94

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

source_name: Pancreas

extract_protocol:
Pancreatic cells were isolated from pancreata of E13.25 embryos.
The cells were stained with antibodies to separate individual populations by FACS.
Single-cell sorting was done using a FACS Influx5 (BD Biosciences) using unstained cells and single-stained cells are gate-settng controls.
Cells were sorted directly into individual wells of a 96-well PCR plate containing lysis buffer.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: strain

value: Embryonic pancreaatic cell


title: E15.25_Bud2_Trunk_Plate1_96


title: E15.25_Bud2_Trunk_Plate1_91


title: E15.25_Bud2_Trunk_Plate1_92


title: E15.25_Bud2_Trunk_Plate1_88


title: E15.25_Bud2_Trunk_Plate1_90


title: E15.25_Bud2_Trunk_Plate1_95


title: E15.25_Bud2_Trunk_Plate1_93


title: E15.25_Bud2_Trunk_Plate1_87


title: E15.25_Bud2_Trunk_Plate1_89


title: E15.25_Bud2_Trunk_Plate1_86


title: E15.25_Bud2_Trunk_Plate1_85


title: Input_MuSC_4

tag: 4tu labeling

value: no 4tU labeling

value: no α-amanitin treatment


title: wt(SET1) H3K4me2 ChIP-Seq

value: a-H3K4me2 (Millipore 07-030)

value: ACAGTGCAC+T

tag: s.pombe spike-in

value: yes


title: E15.25_Bud2_Trunk_Plate1_84


title: E15.25_Bud2_Trunk_Plate1_83


title: E15.25_Bud2_Trunk_Plate1_80


title: E15.25_Bud2_Trunk_Plate1_82


title: E15.25_Bud2_Trunk_Plate1_79


title: E15.25_Bud2_Trunk_Plate1_76


title: E15.25_Bud2_Trunk_Plate1_75


title: E15.25_Bud2_Trunk_Plate1_77


title: E15.25_Bud2_Trunk_Plate1_73


title: E15.25_Bud2_Trunk_Plate1_78


title: E15.25_Bud2_Trunk_Plate1_74


title: E15.25_Bud2_Trunk_Plate1_72


title: E15.25_Bud2_Trunk_Plate1_71


title: E15.25_Bud2_Trunk_Plate1_65


title: E15.25_Bud2_Trunk_Plate1_66


title: E15.25_Bud2_Trunk_Plate1_69


title: E15.25_Bud2_Trunk_Plate1_64


title: E15.25_Bud2_Trunk_Plate1_63


title: E15.25_Bud2_Trunk_Plate1_62


title: E15.25_Bud2_Trunk_Plate1_81


title: E15.25_Bud2_Trunk_Plate1_60


title: E15.25_Bud2_Trunk_Plate1_58


title: E15.25_Bud2_Trunk_Plate1_57


title: wt(SET1) H3K4me3 ChIP-Seq

value: wt

value: YPD

value: a-H3K4me3 (Millipore 07-473)

value: CGAACTGTG+T


title: E15.25_Bud2_Trunk_Plate1_56


title: E15.25_Bud2_Trunk_Plate1_52


title: E15.25_Bud2_Trunk_Plate1_50


title: E15.25_Bud2_Trunk_Plate1_54


title: E15.25_Bud2_Trunk_Plate1_59


title: E15.25_Bud2_Trunk_Plate1_53


title: E15.25_Bud2_Trunk_Plate1_51


title: E15.25_Bud2_Trunk_Plate1_49


title: E15.25_Bud2_Trunk_Plate1_46


title: E15.25_Bud2_Trunk_Plate1_45


title: E15.25_Bud2_Trunk_Plate1_68


title: E15.25_Bud2_Trunk_Plate1_48


title: E15.25_Bud2_Trunk_Plate1_70


title: E15.25_Bud2_Trunk_Plate1_47


title: E15.25_Bud2_Trunk_Plate1_61


title: E15.25_Bud2_Trunk_Plate1_43


title: E15.25_Bud2_Trunk_Plate1_41


title: E15.25_Bud2_Trunk_Plate1_40


title: E15.25_Bud2_Trunk_Plate1_42


title: E15.25_Bud2_Trunk_Plate1_38


title: E15.25_Bud2_Trunk_Plate1_35


title: E15.25_Bud2_Trunk_Plate1_33


title: E15.25_Bud2_Trunk_Plate1_44


title: E15.25_Bud2_Trunk_Plate1_39


title: E15.25_Bud2_Trunk_Plate1_37


title: E15.25_Bud2_Trunk_Plate1_36


title: E15.25_Bud2_Trunk_Plate1_67


title: E15.25_Bud2_Trunk_Plate1_31


title: E15.25_Bud2_Trunk_Plate1_28


title: E15.25_Bud2_Trunk_Plate1_30


title: E15.25_Bud2_Trunk_Plate1_27


title: E15.25_Bud2_Trunk_Plate1_55


title: E15.25_Bud2_Trunk_Plate1_18


title: E15.25_Bud2_Trunk_Plate1_20


title: E15.25_Bud2_Trunk_Plate1_24


title: E15.25_Bud2_Trunk_Plate1_25


title: E15.25_Bud2_Trunk_Plate1_15


title: E15.25_Bud2_Trunk_Plate1_22


title: E15.25_Bud2_Trunk_Plate1_26


title: E15.25_Bud2_Trunk_Plate1_23


title: E15.25_Bud2_Trunk_Plate1_13


title: E15.25_Bud2_Trunk_Plate1_21


title: E15.25_Bud2_Trunk_Plate1_14


title: E15.25_Bud2_Trunk_Plate1_16


title: E15.25_Bud2_Trunk_Plate1_19


title: E15.25_Bud2_Trunk_Plate1_17


title: E15.25_Bud2_Trunk_Plate1_12


title: E15.25_Bud2_Trunk_Plate1_6


title: E15.25_Bud2_Trunk_Plate1_7


title: E15.25_Bud2_Trunk_Plate1_34


title: E15.25_Bud2_Trunk_Plate1_29


title: E15.25_Bud2_Trunk_Plate1_9


title: E15.25_Bud2_Trunk_Plate1_11


title: E15.25_Bud2_Trunk_Plate1_10


title: E15.25_Bud2_Trunk_Plate1_8


title: E15.25_Bud2_Trunk_Plate1_32


title: E15.25_Bud2_Trunk_Plate1_2


title: E15.25_Bud2_Trunk_Plate1_3


title: E15.25_Bud2_Trunk_Plate1_5


title: E15.25_Bud2_Trunk_Plate1_1


title: E15.25_Bud2_Tip_Plate1_95


title: E15.25_Bud2_Tip_Plate1_96


title: E15.25_Bud2_Tip_Plate1_93


title: E15.25_Bud2_Tip_Plate1_94


title: E15.25_Bud2_Tip_Plate1_91


title: E15.25_Bud2_Trunk_Plate1_4


title: E15.25_Bud2_Tip_Plate1_92


title: E15.25_Bud2_Tip_Plate1_88


title: E15.25_Bud2_Tip_Plate1_86


title: E15.25_Bud2_Tip_Plate1_83


title: E15.25_Bud2_Tip_Plate1_82


title: E15.25_Bud2_Tip_Plate1_80


title: E15.25_Bud2_Tip_Plate1_81


title: E15.25_Bud2_Tip_Plate1_78


title: E15.25_Bud2_Tip_Plate1_77


title: E15.25_Bud2_Tip_Plate1_85


title: E15.25_Bud2_Tip_Plate1_79


title: E15.25_Bud2_Tip_Plate1_76


title: E15.25_Bud2_Tip_Plate1_75


title: E15.25_Bud2_Tip_Plate1_73


title: E15.25_Bud2_Tip_Plate1_70


title: E15.25_Bud2_Tip_Plate1_72


title: E15.25_Bud2_Tip_Plate1_71


title: E15.25_Bud2_Tip_Plate1_69


title: E15.25_Bud2_Tip_Plate1_89


title: E15.25_Bud2_Tip_Plate1_65


title: E15.25_Bud2_Tip_Plate1_64


title: E15.25_Bud2_Tip_Plate1_66


title: E15.25_Bud2_Tip_Plate1_87


title: E15.25_Bud2_Tip_Plate1_68


title: E15.25_Bud2_Tip_Plate1_63


title: E15.25_Bud2_Tip_Plate1_67


title: E15.25_Bud2_Tip_Plate1_90


title: E15.25_Bud2_Tip_Plate1_59


title: E15.25_Bud2_Tip_Plate1_58


title: E15.25_Bud2_Tip_Plate1_61


title: E15.25_Bud2_Tip_Plate1_57


title: E15.25_Bud2_Tip_Plate1_56


title: E15.25_Bud2_Tip_Plate1_55


title: E15.25_Bud2_Tip_Plate1_53


title: E15.25_Bud2_Tip_Plate1_54


title: E15.25_Bud2_Tip_Plate1_50


title: E15.25_Bud2_Tip_Plate1_52


title: wt(pSET1) RPB4 ChIP-Seq rep1

value: SET1 (plasmid)

value: SC

value: a-Rpb4 (NeoClone W0013)

value: CCATACAC+T

value: yes*


title: E15.25_Bud2_Tip_Plate1_49


title: E15.25_Bud2_Tip_Plate1_48


title: E15.25_Bud2_Tip_Plate1_47


title: E15.25_Bud2_Tip_Plate1_46


title: E15.25_Bud2_Tip_Plate1_45


title: E15.25_Bud2_Tip_Plate1_44


title: E15.25_Bud2_Tip_Plate1_41


title: E15.25_Bud2_Tip_Plate1_38


title: E15.25_Bud2_Tip_Plate1_42


title: E15.25_Bud2_Tip_Plate1_60


title: E15.25_Bud2_Tip_Plate1_40


title: E15.25_Bud2_Tip_Plate1_39


title: E15.25_Bud2_Tip_Plate1_37


title: E15.25_Bud2_Tip_Plate1_74


title: E15.25_Bud2_Tip_Plate1_36


title: E15.25_Bud2_Tip_Plate1_35


title: E15.25_Bud2_Tip_Plate1_62


title: E15.25_Bud2_Tip_Plate1_32


title: E15.25_Bud2_Tip_Plate1_84


title: E15.25_Bud2_Tip_Plate1_30


title: E15.25_Bud2_Tip_Plate1_34


title: E15.25_Bud2_Tip_Plate1_26


title: E15.25_Bud2_Tip_Plate1_31


title: E15.25_Bud2_Tip_Plate1_27


title: E15.25_Bud2_Tip_Plate1_25


title: E15.25_Bud2_Tip_Plate1_21


title: E15.25_Bud2_Tip_Plate1_22


title: E15.25_Bud2_Tip_Plate1_24


title: E15.25_Bud2_Tip_Plate1_23


title: E15.25_Bud2_Tip_Plate1_43


title: E15.25_Bud2_Tip_Plate1_20


title: E15.25_Bud2_Tip_Plate1_19


title: E15.25_Bud2_Tip_Plate1_17


title: E15.25_Bud2_Tip_Plate1_15


title: E15.25_Bud2_Tip_Plate1_18


title: E15.25_Bud2_Tip_Plate1_14


title: E15.25_Bud2_Tip_Plate1_33


title: E15.25_Bud2_Tip_Plate1_12


title: E15.25_Bud2_Tip_Plate1_13


title: E15.25_Bud2_Tip_Plate1_11


title: E15.25_Bud2_Tip_Plate1_16


title: E15.25_Bud2_Tip_Plate1_29


title: E15.25_Bud2_Tip_Plate1_5


title: E15.25_Bud2_Tip_Plate1_4


title: E15.25_Bud2_Tip_Plate1_7


title: E15.25_Bud2_Tip_Plate1_10


title: E15.25_Bud2_Tip_Plate1_3


title: E15.25_Bud2_Tip_Plate1_28


title: E15.25_Bud2_Tip_Plate1_8


title: E15.25_Bud2_Tip_Plate1_2


title: E15.25_Bud2_Tip_Plate1_1


title: E15.25_Bud1_Tip_Plate1_94


title: E15.25_Bud1_Tip_Plate1_93


title: E15.25_Bud1_Tip_Plate1_92


title: E15.25_Bud1_Tip_Plate1_91


title: E15.25_Bud1_Tip_Plate1_89


title: E15.25_Bud1_Tip_Plate1_88


title: E15.25_Bud1_Tip_Plate1_90


title: E15.25_Bud1_Tip_Plate1_82


title: E15.25_Bud1_Tip_Plate1_83


title: E15.25_Bud2_Tip_Plate1_9


title: E15.25_Bud1_Tip_Plate1_84


title: E15.25_Bud1_Tip_Plate1_86


title: E15.25_Bud1_Tip_Plate1_85


title: E15.25_Bud1_Tip_Plate1_87


title: E15.25_Bud1_Tip_Plate1_81


title: E15.25_Bud1_Tip_Plate1_80


title: E15.25_Bud1_Tip_Plate1_78


title: E15.25_Bud1_Tip_Plate1_79


title: E15.25_Bud1_Tip_Plate1_74


title: E15.25_Bud1_Tip_Plate1_73


title: E15.25_Bud1_Tip_Plate1_76


title: E15.25_Bud1_Tip_Plate1_75


title: E15.25_Bud1_Tip_Plate1_96


title: E15.25_Bud1_Tip_Plate1_72


title: E15.25_Bud1_Tip_Plate1_71


title: E15.25_Bud1_Tip_Plate1_70


title: E15.25_Bud2_Tip_Plate1_51


title: E15.25_Bud1_Tip_Plate1_95


title: E15.25_Bud1_Tip_Plate1_68


title: E15.25_Bud1_Tip_Plate1_69


title: E15.25_Bud1_Tip_Plate1_67


title: E15.25_Bud1_Tip_Plate1_66


title: E15.25_Bud1_Tip_Plate1_65


title: E15.25_Bud1_Tip_Plate1_63


title: E15.25_Bud1_Tip_Plate1_64


title: E15.25_Bud1_Tip_Plate1_61


title: E15.25_Bud1_Tip_Plate1_62


title: E15.25_Bud1_Tip_Plate1_58


title: E15.25_Bud1_Tip_Plate1_60


title: E15.25_Bud1_Tip_Plate1_55


title: E15.25_Bud1_Tip_Plate1_57


title: E15.25_Bud1_Tip_Plate1_59


title: E15.25_Bud1_Tip_Plate1_56


title: E15.25_Bud1_Tip_Plate1_54


title: E15.25_Bud1_Tip_Plate1_53


title: E15.25_Bud1_Tip_Plate1_51


title: E15.25_Bud1_Tip_Plate1_52


title: E15.25_Bud1_Tip_Plate1_50


title: E15.25_Bud1_Tip_Plate1_49


title: E15.25_Bud1_Tip_Plate1_46


title: E15.25_Bud2_Tip_Plate1_6


title: E15.25_Bud1_Tip_Plate1_48


title: E15.25_Bud1_Tip_Plate1_47


title: E15.25_Bud1_Tip_Plate1_45


title: E15.25_Bud1_Tip_Plate1_77


title: E15.25_Bud1_Tip_Plate1_44


title: E15.25_Bud1_Tip_Plate1_38


title: E15.25_Bud1_Tip_Plate1_43


title: E15.25_Bud1_Tip_Plate1_42


title: E15.25_Bud1_Tip_Plate1_41


title: E15.25_Bud1_Tip_Plate1_37


title: E15.25_Bud1_Tip_Plate1_36


title: E15.25_Bud1_Tip_Plate1_33


title: E15.25_Bud1_Tip_Plate1_34


title: E15.25_Bud1_Tip_Plate1_35


title: E15.25_Bud1_Tip_Plate1_30


title: E15.25_Bud1_Tip_Plate1_32


title: E15.25_Bud1_Tip_Plate1_31


title: E15.25_Bud1_Tip_Plate1_25


title: E15.25_Bud1_Tip_Plate1_29


title: E15.25_Bud1_Tip_Plate1_28


title: E15.25_Bud1_Tip_Plate1_22


title: E15.25_Bud1_Tip_Plate1_26


title: E15.25_Bud1_Tip_Plate1_23


title: E15.25_Bud1_Tip_Plate1_24


title: E15.25_Bud1_Tip_Plate1_17


title: E15.25_Bud1_Tip_Plate1_19


title: E15.25_Bud1_Tip_Plate1_20


title: E15.25_Bud1_Tip_Plate1_14


title: E15.25_Bud1_Tip_Plate1_40


title: E15.25_Bud1_Tip_Plate1_15


title: E15.25_Bud1_Tip_Plate1_39


title: E15.25_Bud1_Tip_Plate1_16


title: E15.25_Bud1_Tip_Plate1_13


title: E15.25_Bud1_Tip_Plate1_12


title: E15.25_Bud1_Tip_Plate1_11


title: E15.25_Bud1_Tip_Plate1_10


title: E15.25_Bud1_Tip_Plate1_9


title: E15.25_Bud1_Tip_Plate1_7


title: E15.25_Bud1_Tip_Plate1_27


title: E15.25_Bud1_Tip_Plate1_6


title: E15.25_Bud1_Tip_Plate1_4


title: E15.25_Bud1_Tip_Plate1_2


title: E15.25_Bud1_Tip_Plate1_1


title: E13.25_Mouse_2_pancreas_4_094

extract_protocol:
Pancreatic cells were isolated from pancreata of E13.25 embryos.
The cells were stained with antibodies to separate individual populations by FACS.
Single-cell sorting was done using a FACS Influx5 (BD Biosciences) using unstained cells and single-stained cells are gate-setting controls.
Cells were sorted directly into individual wells of a 96-well PCR plate containing lysis buffer.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

value: Embryonic pancreatic cell


title: E15.25_Bud1_Tip_Plate1_18


title: E15.25_Bud1_Tip_Plate1_21


title: E13.25_Mouse_2_pancreas_4_095


title: E13.25_Mouse_2_pancreas_4_092


title: E13.25_Mouse_2_pancreas_4_096


title: E13.25_Mouse_2_pancreas_4_093


title: E13.25_Mouse_2_pancreas_4_091


title: E13.25_Mouse_2_pancreas_4_090


title: E13.25_Mouse_2_pancreas_4_089


title: E13.25_Mouse_2_pancreas_4_088


title: E13.25_Mouse_2_pancreas_4_081


title: E13.25_Mouse_2_pancreas_4_086


title: E13.25_Mouse_2_pancreas_4_083


title: E13.25_Mouse_2_pancreas_4_084


title: E13.25_Mouse_2_pancreas_4_085


title: E15.25_Bud1_Tip_Plate1_8


title: E13.25_Mouse_2_pancreas_4_079


title: E13.25_Mouse_2_pancreas_4_082


title: E13.25_Mouse_2_pancreas_4_080


title: E13.25_Mouse_2_pancreas_4_078


title: E15.25_Bud1_Tip_Plate1_5


title: E13.25_Mouse_2_pancreas_4_077


title: E13.25_Mouse_2_pancreas_4_075


title: E15.25_Bud1_Tip_Plate1_3


title: E13.25_Mouse_2_pancreas_4_073


title: E13.25_Mouse_2_pancreas_4_074


title: E13.25_Mouse_2_pancreas_4_076


title: E13.25_Mouse_2_pancreas_4_069


title: E13.25_Mouse_2_pancreas_4_072


title: E13.25_Mouse_2_pancreas_4_070


title: E13.25_Mouse_2_pancreas_4_068


title: E13.25_Mouse_2_pancreas_4_067


title: E13.25_Mouse_2_pancreas_4_066


title: E13.25_Mouse_2_pancreas_4_087


title: E13.25_Mouse_2_pancreas_4_071


title: E13.25_Mouse_2_pancreas_4_065


title: E13.25_Mouse_2_pancreas_4_060


title: E13.25_Mouse_2_pancreas_4_058


title: E13.25_Mouse_2_pancreas_4_059


title: E13.25_Mouse_2_pancreas_4_062


title: E13.25_Mouse_2_pancreas_4_055


title: E13.25_Mouse_2_pancreas_4_061


title: E13.25_Mouse_2_pancreas_4_063


title: E13.25_Mouse_2_pancreas_4_054


title: E13.25_Mouse_2_pancreas_4_050


title: E13.25_Mouse_2_pancreas_4_051


title: E13.25_Mouse_2_pancreas_4_053


title: E13.25_Mouse_2_pancreas_4_047


title: E13.25_Mouse_2_pancreas_4_052


title: E13.25_Mouse_2_pancreas_4_057


title: E13.25_Mouse_2_pancreas_4_046


title: E13.25_Mouse_2_pancreas_4_045


title: E13.25_Mouse_2_pancreas_4_044


title: E13.25_Mouse_2_pancreas_4_040


title: E13.25_Mouse_2_pancreas_4_043


title: E13.25_Mouse_2_pancreas_4_041


title: E13.25_Mouse_2_pancreas_4_064


title: E13.25_Mouse_2_pancreas_4_039


title: E13.25_Mouse_2_pancreas_4_037


title: E13.25_Mouse_2_pancreas_4_038


title: E13.25_Mouse_2_pancreas_4_036


title: E13.25_Mouse_2_pancreas_4_056


title: E13.25_Mouse_2_pancreas_4_032


title: E13.25_Mouse_2_pancreas_4_034


title: E13.25_Mouse_2_pancreas_4_031


title: E13.25_Mouse_2_pancreas_4_048


title: E13.25_Mouse_2_pancreas_4_029


title: E13.25_Mouse_2_pancreas_4_024


title: E13.25_Mouse_2_pancreas_4_030


title: E13.25_Mouse_2_pancreas_4_026


title: E13.25_Mouse_2_pancreas_4_028


title: E13.25_Mouse_2_pancreas_4_049


title: E13.25_Mouse_2_pancreas_4_025


title: E13.25_Mouse_2_pancreas_4_021


title: E13.25_Mouse_2_pancreas_4_023


title: E13.25_Mouse_2_pancreas_4_022


title: E13.25_Mouse_2_pancreas_4_020


title: E13.25_Mouse_2_pancreas_4_018


title: E13.25_Mouse_2_pancreas_4_027


title: E13.25_Mouse_2_pancreas_4_015


title: E13.25_Mouse_2_pancreas_4_035


title: E13.25_Mouse_2_pancreas_4_017


title: E13.25_Mouse_2_pancreas_4_014


title: E13.25_Mouse_2_pancreas_4_016


title: E13.25_Mouse_2_pancreas_4_013


title: E13.25_Mouse_2_pancreas_4_012


title: E13.25_Mouse_2_pancreas_4_011


title: E13.25_Mouse_2_pancreas_4_033


title: E13.25_Mouse_2_pancreas_4_010


title: E13.25_Mouse_2_pancreas_4_009


title: E13.25_Mouse_2_pancreas_4_008


title: E13.25_Mouse_2_pancreas_4_006


title: E13.25_Mouse_2_pancreas_4_005


title: E13.25_Mouse_2_pancreas_4_004


title: E13.25_Mouse_2_pancreas_4_007


title: E13.25_Mouse_2_pancreas_4_002


title: E13.25_Mouse_2_pancreas_4_003


title: E13.25_Mouse_2_pancreas_4_001


title: E13.25_Mouse_pancreas_3_096


title: E13.25_Mouse_2_pancreas_4_019


title: E13.25_Mouse_pancreas_3_094


title: E13.25_Mouse_pancreas_3_093


title: E13.25_Mouse_pancreas_3_091


title: E13.25_Mouse_pancreas_3_092


title: E13.25_Mouse_pancreas_3_095


title: E13.25_Mouse_pancreas_3_089


title: E13.25_Mouse_pancreas_3_090


title: E13.25_Mouse_pancreas_3_087


title: E13.25_Mouse_pancreas_3_086


title: E13.25_Mouse_pancreas_3_085


title: E13.25_Mouse_pancreas_3_083


title: E13.25_Mouse_pancreas_3_084


title: E13.25_Mouse_pancreas_3_081


title: E13.25_Mouse_pancreas_3_080


title: E13.25_Mouse_pancreas_3_082


title: E13.25_Mouse_pancreas_3_079


title: E13.25_Mouse_pancreas_3_078


title: E13.25_Mouse_pancreas_3_076


title: E13.25_Mouse_pancreas_3_074


title: E13.25_Mouse_pancreas_3_077


title: E13.25_Mouse_pancreas_3_073


title: E13.25_Mouse_pancreas_3_071


title: E13.25_Mouse_pancreas_3_068


title: E13.25_Mouse_pancreas_3_069


title: E13.25_Mouse_pancreas_3_070


title: E13.25_Mouse_2_pancreas_4_042


title: E13.25_Mouse_pancreas_3_088


title: E13.25_Mouse_pancreas_3_065


title: E13.25_Mouse_pancreas_3_063


title: E13.25_Mouse_pancreas_3_064


title: E13.25_Mouse_pancreas_3_067


title: E13.25_Mouse_pancreas_3_061


title: E13.25_Mouse_pancreas_3_062


title: E13.25_Mouse_pancreas_3_057


title: E13.25_Mouse_pancreas_3_058


title: E13.25_Mouse_pancreas_3_055


title: E13.25_Mouse_pancreas_3_060


title: E13.25_Mouse_pancreas_3_056


title: E13.25_Mouse_pancreas_3_054


title: E13.25_Mouse_pancreas_3_059


title: E13.25_Mouse_pancreas_3_052


title: E13.25_Mouse_pancreas_3_051


title: E13.25_Mouse_pancreas_3_075


title: E13.25_Mouse_pancreas_3_072


title: E13.25_Mouse_pancreas_3_050


title: E13.25_Mouse_pancreas_3_047


title: E13.25_Mouse_pancreas_3_049


title: E13.25_Mouse_pancreas_3_066


title: E13.25_Mouse_pancreas_3_046


title: E13.25_Mouse_pancreas_3_043


title: E13.25_Mouse_pancreas_3_045


title: E13.25_Mouse_pancreas_3_044


title: E13.25_Mouse_pancreas_3_048


title: E13.25_Mouse_pancreas_3_042


title: E13.25_Mouse_pancreas_3_040


title: E13.25_Mouse_pancreas_3_037


title: E13.25_Mouse_pancreas_3_039


title: E13.25_Mouse_pancreas_3_038


title: E13.25_Mouse_pancreas_3_035


title: E13.25_Mouse_pancreas_3_036


title: E13.25_Mouse_pancreas_3_034


title: E13.25_Mouse_pancreas_3_032


title: E13.25_Mouse_pancreas_3_053


title: E13.25_Mouse_pancreas_3_031


title: E13.25_Mouse_pancreas_3_033


title: E13.25_Mouse_pancreas_3_029


title: E13.25_Mouse_pancreas_3_030


title: E13.25_Mouse_pancreas_3_027


title: E13.25_Mouse_pancreas_3_024


title: E13.25_Mouse_pancreas_3_028


title: E13.25_Mouse_pancreas_3_023


title: E13.25_Mouse_pancreas_3_025


title: E13.25_Mouse_pancreas_3_022


title: E13.25_Mouse_pancreas_3_041


title: E13.25_Mouse_pancreas_3_020


title: E13.25_Mouse_pancreas_3_019


title: E13.25_Mouse_pancreas_3_021


title: E13.25_Mouse_pancreas_3_017


title: E13.25_Mouse_pancreas_3_015


title: E13.25_Mouse_pancreas_3_016


title: E13.25_Mouse_pancreas_3_012


title: E13.25_Mouse_pancreas_3_009


title: E13.25_Mouse_pancreas_3_011


title: E13.25_Mouse_pancreas_3_014


title: E13.25_Mouse_pancreas_3_010


title: E13.25_Mouse_pancreas_3_007


title: E13.25_Mouse_pancreas_3_006


title: E13.25_Mouse_pancreas_3_005


title: E13.25_Mouse_pancreas_3_008


title: E13.25_Mouse_pancreas_3_003


title: E13.25_Mouse_pancreas_3_004


title: E13.25_Mouse_pancreas_3_001


title: E13.25_Mouse_pancreas_2_096


title: E13.25_Mouse_pancreas_3_026


title: E13.25_Mouse_pancreas_2_095


title: E13.25_Mouse_pancreas_2_094


title: E13.25_Mouse_pancreas_2_093


title: E13.25_Mouse_pancreas_2_092


title: E13.25_Mouse_pancreas_2_091


title: E13.25_Mouse_pancreas_2_088


title: E13.25_Mouse_pancreas_2_089


title: E13.25_Mouse_pancreas_3_018


title: E13.25_Mouse_pancreas_2_087


title: E13.25_Mouse_pancreas_2_086


title: E13.25_Mouse_pancreas_3_013


title: E13.25_Mouse_pancreas_2_085


title: E13.25_Mouse_pancreas_2_083


title: E13.25_Mouse_pancreas_2_084


title: E13.25_Mouse_pancreas_3_002


title: E13.25_Mouse_pancreas_2_082


title: E13.25_Mouse_pancreas_2_081


title: E13.25_Mouse_pancreas_2_079


title: E13.25_Mouse_pancreas_2_076


title: E13.25_Mouse_pancreas_2_078


title: E13.25_Mouse_pancreas_2_077


title: E13.25_Mouse_pancreas_2_073


title: E13.25_Mouse_pancreas_2_071


title: E13.25_Mouse_pancreas_2_074


title: E13.25_Mouse_pancreas_2_075


title: E13.25_Mouse_pancreas_2_080


title: E13.25_Mouse_pancreas_2_068


title: E13.25_Mouse_pancreas_2_072


title: E13.25_Mouse_pancreas_2_090


title: E13.25_Mouse_pancreas_2_067


title: E13.25_Mouse_pancreas_2_066


title: E13.25_Mouse_pancreas_2_065


title: E13.25_Mouse_pancreas_2_063


title: E13.25_Mouse_pancreas_2_061


title: E13.25_Mouse_pancreas_2_062


title: E13.25_Mouse_pancreas_2_059


title: E13.25_Mouse_pancreas_2_058


title: E13.25_Mouse_pancreas_2_057


title: E13.25_Mouse_pancreas_2_056


title: E13.25_Mouse_pancreas_2_060


title: E13.25_Mouse_pancreas_2_064


title: E13.25_Mouse_pancreas_2_053


title: E13.25_Mouse_pancreas_2_054


title: E13.25_Mouse_pancreas_2_050


title: E13.25_Mouse_pancreas_2_048


title: E13.25_Mouse_pancreas_2_049


title: E13.25_Mouse_pancreas_2_070


title: E13.25_Mouse_pancreas_2_051


title: E13.25_Mouse_pancreas_2_047


title: E13.25_Mouse_pancreas_2_069


title: E13.25_Mouse_pancreas_2_052


title: E13.25_Mouse_pancreas_2_044


title: E13.25_Mouse_pancreas_2_045


title: E13.25_Mouse_pancreas_2_046


title: E13.25_Mouse_pancreas_2_042


title: E13.25_Mouse_pancreas_2_039


title: E13.25_Mouse_pancreas_2_040


title: E13.25_Mouse_pancreas_2_041


title: E13.25_Mouse_pancreas_2_038


title: E13.25_Mouse_pancreas_2_035


title: E13.25_Mouse_pancreas_2_037


title: E13.25_Mouse_pancreas_2_036


title: E13.25_Mouse_pancreas_2_055


title: E13.25_Mouse_pancreas_2_034


title: E13.25_Mouse_pancreas_2_032


title: E13.25_Mouse_pancreas_2_033


title: E13.25_Mouse_pancreas_2_031


title: E13.25_Mouse_pancreas_2_030


title: E13.25_Mouse_pancreas_2_028


title: E13.25_Mouse_pancreas_2_029


title: E13.25_Mouse_pancreas_2_043


title: E13.25_Mouse_pancreas_2_027


title: E13.25_Mouse_pancreas_2_026


title: E13.25_Mouse_pancreas_2_022


title: E13.25_Mouse_pancreas_2_025


title: E13.25_Mouse_pancreas_2_023


title: E13.25_Mouse_pancreas_2_019


title: E13.25_Mouse_pancreas_2_017


title: E13.25_Mouse_pancreas_2_018


title: E13.25_Mouse_pancreas_2_011


title: E13.25_Mouse_pancreas_2_015


title: E13.25_Mouse_pancreas_2_013


title: E13.25_Mouse_pancreas_2_021


title: E13.25_Mouse_pancreas_2_010


title: E13.25_Mouse_pancreas_2_024


title: E13.25_Mouse_pancreas_2_020


title: E13.25_Mouse_pancreas_2_008


title: E13.25_Mouse_pancreas_2_009


title: E13.25_Mouse_pancreas_2_005


title: E13.25_Mouse_pancreas_2_006


title: E13.25_Mouse_pancreas_2_014


title: E13.25_Mouse_pancreas_2_001


title: E13.25_Mouse_pancreas_2_004


title: E13.25_Mouse_pancreas_2_003


title: E13.25_Mouse_pancreas_2_002


title: E13.25_Mouse_Pancreas_1_095


title: E13.25_Mouse_pancreas_2_012


title: E13.25_Mouse_pancreas_2_016


title: E13.25_Mouse_Pancreas_1_094


title: E13.25_Mouse_Pancreas_1_093


title: E13.25_Mouse_Pancreas_1_091


title: E13.25_Mouse_Pancreas_1_096


title: E13.25_Mouse_Pancreas_1_092


title: E13.25_Mouse_Pancreas_1_087


title: E13.25_Mouse_Pancreas_1_090


title: E13.25_Mouse_Pancreas_1_086


title: E13.25_Mouse_Pancreas_1_088


title: E13.25_Mouse_pancreas_2_007


title: E13.25_Mouse_Pancreas_1_085


title: E13.25_Mouse_Pancreas_1_083


title: E13.25_Mouse_Pancreas_1_082


title: E13.25_Mouse_Pancreas_1_080


title: E13.25_Mouse_Pancreas_1_081


title: E13.25_Mouse_Pancreas_1_079


title: E13.25_Mouse_Pancreas_1_077


title: E13.25_Mouse_Pancreas_1_078


title: E13.25_Mouse_Pancreas_1_076


title: E13.25_Mouse_Pancreas_1_075


title: E13.25_Mouse_Pancreas_1_072


title: E13.25_Mouse_Pancreas_1_069


title: E13.25_Mouse_Pancreas_1_068


title: E13.25_Mouse_Pancreas_1_071


title: E13.25_Mouse_Pancreas_1_089


title: E13.25_Mouse_Pancreas_1_065


title: E13.25_Mouse_Pancreas_1_064


title: E13.25_Mouse_Pancreas_1_066


title: E13.25_Mouse_Pancreas_1_062


title: E13.25_Mouse_Pancreas_1_063


title: E13.25_Mouse_Pancreas_1_061


title: E13.25_Mouse_Pancreas_1_060


title: E13.25_Mouse_Pancreas_1_058


title: E13.25_Mouse_Pancreas_1_084


title: E13.25_Mouse_Pancreas_1_057


title: E13.25_Mouse_Pancreas_1_055


title: E13.25_Mouse_Pancreas_1_053


title: E13.25_Mouse_Pancreas_1_056


title: E13.25_Mouse_Pancreas_1_074


title: E13.25_Mouse_Pancreas_1_051


title: E13.25_Mouse_Pancreas_1_050


title: E13.25_Mouse_Pancreas_1_067


title: E13.25_Mouse_Pancreas_1_073


title: E13.25_Mouse_Pancreas_1_070


title: E13.25_Mouse_Pancreas_1_047


title: E13.25_Mouse_Pancreas_1_048


title: E13.25_Mouse_Pancreas_1_054


title: E13.25_Mouse_Pancreas_1_046


title: E13.25_Mouse_Pancreas_1_043


title: E13.25_Mouse_Pancreas_1_045


title: E13.25_Mouse_Pancreas_1_042


title: E13.25_Mouse_Pancreas_1_041


title: E13.25_Mouse_Pancreas_1_040


title: E13.25_Mouse_Pancreas_1_044


title: E13.25_Mouse_Pancreas_1_038


title: E13.25_Mouse_Pancreas_1_037


title: E13.25_Mouse_Pancreas_1_059


title: E13.25_Mouse_Pancreas_1_036


title: E13.25_Mouse_Pancreas_1_039


title: E13.25_Mouse_Pancreas_1_035


title: E13.25_Mouse_Pancreas_1_052


title: E13.25_Mouse_Pancreas_1_032


title: E13.25_Mouse_Pancreas_1_033


title: E13.25_Mouse_Pancreas_1_034


title: E13.25_Mouse_Pancreas_1_030


title: E13.25_Mouse_Pancreas_1_029


title: E13.25_Mouse_Pancreas_1_028


title: E13.25_Mouse_Pancreas_1_031


title: E13.25_Mouse_Pancreas_1_026


title: E13.25_Mouse_Pancreas_1_024


title: E13.25_Mouse_Pancreas_1_025


title: E13.25_Mouse_Pancreas_1_023


title: E13.25_Mouse_Pancreas_1_020


title: E13.25_Mouse_Pancreas_1_022


title: E13.25_Mouse_Pancreas_1_021


title: E13.25_Mouse_Pancreas_1_019


title: E13.25_Mouse_Pancreas_1_016


title: E13.25_Mouse_Pancreas_1_017


title: E13.25_Mouse_Pancreas_1_015


title: E13.25_Mouse_Pancreas_1_014


title: E13.25_Mouse_Pancreas_1_011


title: E13.25_Mouse_Pancreas_1_012


title: E13.25_Mouse_Pancreas_1_010


title: E13.25_Mouse_Pancreas_1_008


title: E13.25_Mouse_Pancreas_1_013


title: E13.25_Mouse_Pancreas_1_006


title: E13.25_Mouse_Pancreas_1_005


title: E13.25_Mouse_Pancreas_1_003


title: E13.25_Mouse_Pancreas_1_027


title: E13.25_Mouse_Pancreas_1_002


title: E13.25_Mouse_Pancreas_1_049


title: E13.25_Mouse_Pancreas_1_004


title: E13.25_Mouse_Pancreas_1_001


title: P6_H12_empty

data_processing:
RNA-seq reads were aligned to hg19 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19
Supplementary_files_format_and_content: HT-Seq counts (.txt)

source_name: cord blood

growth_protocol: Fresh cord blood from normal donors were obtained with informed consent. They were processed within 16-34h after collection. Mononuclear cells were isolated and CD34+ fraction was separated as described{Quek et al, Journal of Experimental Medicine 2016}.

extract_protocol:
Single cells were deposited in individual wells of 96 well plates, directly lysed according to the SmartSeq2 protocol and stored at -80C. No extraction protocol was performed
Single cell libraries for RNAseq were prepared using SmartSeq2 protocol (Picelli et al., Nature Protocols 2014) and the Illumina Nextera XT Index Kit (96 indexes, 384 samples, FC-131-1002) for cDNA tagmentation and indexing. ERCC RNA Spike-In Mix (Ambion, 4456740) are included.

treatment_protocol: Fresh Cord Blood cells were obtained and processed with ficoll to obtain mononuclear cells. CD34+ cells were purified using CD34 Microbead Kit and MACS  separation columns

value: Cord blood CD34+ haemopoietic stem and progenitor cells

tag: cell populations

tag: immunophenotype


title: P5_H12_empty


title: E13.25_Mouse_Pancreas_1_018


title: P3_H12_empty


title: P4_H12_empty


title: P6_F8_MLP

value: MLP


title: P6_H5_MLP


title: P6_G6_MLP


title: P6_G5_MLP


title: P6_G7_MLP


title: E13.25_Mouse_Pancreas_1_007


title: E13.25_Mouse_Pancreas_1_009


title: P6_F5_MLP


title: P6_F6_MLP


title: P6_E7_MLP


title: P6_F7_MLP


title: P2_H12_empty


title: P6_D8_MLP


title: P6_D6_MLP


title: P6_D5_MLP


title: P6_D7_MLP


title: P6_C8_MLP


title: P6_C6_MLP


title: P6_E5_MLP


title: P6_E6_MLP


title: P6_C5_MLP


title: P6_B7_MLP


title: P6_B5_MLP


title: P6_B6_MLP


title: P6_G8_MLP


title: P6_A7_MLP


title: P6_A8_MLP


title: P6_B8_MLP


title: P6_E8_MLP


title: P5_H7_MLP


title: P6_A5_MLP


title: P6_A6_MLP


title: P5_H8_MLP


title: P5_H6_MLP


title: P5_G8_MLP


title: P5_H5_MLP


title: P5_G5_MLP


title: P5_F8_MLP


title: P5_G7_MLP


title: P6_C7_MLP


title: P5_E8_MLP


title: P5_F6_MLP


title: P5_F7_MLP


title: P5_E5_MLP


title: P5_D8_MLP


title: P5_E6_MLP


title: P5_D7_MLP


title: P5_D5_MLP


title: P5_D6_MLP


title: P5_C8_MLP


title: P5_C7_MLP


title: P5_C6_MLP


title: P5_B8_MLP


title: P5_B7_MLP


title: P5_B6_MLP


title: P5_B5_MLP


title: P5_A8_MLP


title: P5_G6_MLP


title: P5_A6_MLP


title: P4_H8_MLP


title: P4_H6_MLP


title: P4_F6_MLP


title: P4_G8_MLP


title: P4_G6_MLP


title: P4_E6_MLP


title: P5_A7_MLP


title: P4_E5_MLP


title: P4_F5_MLP


title: P4_G5_MLP


title: P4_D6_MLP


title: P4_C8_MLP


title: P4_H5_MLP


title: P4_C7_MLP


title: P4_D8_MLP


title: P4_D5_MLP


title: P4_C5_MLP


title: P4_C6_MLP


title: P4_B8_MLP


title: P4_B6_MLP


title: P4_B7_MLP


title: P5_C5_MLP


title: P4_A8_MLP


title: P4_A7_MLP


title: P4_A5_MLP


title: P4_B5_MLP


title: P3_H8_MLP


title: P4_F8_MLP


title: P3_H6_MLP


title: P3_H7_MLP


title: P3_G5_MLP


title: P3_G8_MLP


title: P3_F8_MLP


title: P3_F7_MLP


title: P3_G7_MLP


title: P3_F6_MLP


title: P3_F5_MLP


title: P3_C8_MLP


title: P3_E7_MLP


title: P3_E6_MLP


title: P3_D7_MLP


title: P4_A6_MLP


title: P3_D8_MLP


title: P3_C5_MLP


title: P3_G6_MLP


title: P3_B6_MLP


title: P3_E8_MLP


title: P3_C6_MLP


title: P3_C7_MLP


title: P3_D6_MLP


title: P3_A7_MLP


title: P3_H5_MLP


title: P3_B7_MLP


title: P3_B5_MLP


title: P3_D5_MLP


title: P3_A8_MLP


title: P3_A5_MLP


title: P2_H7_MLP


title: P3_A6_MLP


title: P3_E5_MLP


title: P2_H8_MLP


title: P2_H5_MLP


title: P2_G7_MLP


title: P2_G8_MLP


title: P3_B8_MLP


title: P2_F7_MLP


title: P2_F5_MLP


title: P2_F8_MLP


title: P2_E8_MLP


title: P2_G5_MLP


title: P2_F6_MLP


title: P2_E6_MLP


title: P2_E5_MLP


title: P2_D7_MLP


title: P2_D5_MLP


title: P2_D8_MLP


title: P2_D6_MLP


title: P2_C7_MLP


title: P2_C8_MLP


title: P2_C6_MLP


title: P2_H6_MLP


title: P2_B7_MLP


title: P2_B6_MLP


title: P2_C5_MLP


title: P2_A7_MLP


title: P2_A6_MLP


title: P2_A5_MLP


title: P2_B5_MLP


title: P6_G3_LMPP

value: LMPP


title: P2_B8_MLP


title: P6_G2_LMPP


title: P6_G1_LMPP


title: P2_G6_MLP


title: P6_F3_LMPP


title: P6_E1_LMPP


title: P6_F1_LMPP


title: P6_E2_LMPP


title: P6_E3_LMPP


title: P6_E4_LMPP


title: P6_F4_LMPP


title: P6_D4_LMPP


title: P6_D1_LMPP


title: P6_C4_LMPP


title: P6_C1_LMPP


title: P6_C3_LMPP


title: P6_D3_LMPP


title: P6_G4_LMPP


title: P6_D2_LMPP


title: P2_A8_MLP


title: P6_B4_LMPP


title: P6_B3_LMPP


title: P6_B2_LMPP


title: P6_C2_LMPP


title: P6_B1_LMPP


title: P6_A3_LMPP


title: P6_A2_LMPP


title: P6_A4_LMPP


title: P6_A1_LMPP


title: P5_H3_LMPP


title: P5_H4_LMPP


title: P6_F2_LMPP


title: P5_H2_LMPP


title: P5_G4_LMPP


title: P5_G3_LMPP


title: P5_F2_LMPP


title: P5_F1_LMPP


title: P5_F3_LMPP


title: P5_H1_LMPP


title: P5_F4_LMPP


title: P5_E3_LMPP


title: P5_E2_LMPP


title: P5_E1_LMPP


title: P5_D4_LMPP


title: P5_C4_LMPP


title: P5_D2_LMPP


title: P5_D1_LMPP


title: P5_B4_LMPP


title: P5_C1_LMPP


title: P5_C2_LMPP


title: P5_B3_LMPP


title: P5_C3_LMPP


title: P5_A3_LMPP


title: P5_A2_LMPP


title: P4_H3_LMPP


title: P5_B2_LMPP


title: P4_H2_LMPP


title: P4_G2_LMPP


title: P4_H1_LMPP


title: P4_G1_LMPP


title: P4_F4_LMPP


title: P5_E4_LMPP


title: P4_F2_LMPP


title: P4_E2_LMPP


title: P4_F3_LMPP


title: P4_E1_LMPP


title: P4_D2_LMPP


title: P4_F1_LMPP


title: P4_D3_LMPP


title: P5_D3_LMPP


title: P4_D1_LMPP


title: P4_C1_LMPP


title: P4_B4_LMPP


title: P4_C3_LMPP


title: P5_B1_LMPP


title: P4_B3_LMPP


title: P4_B1_LMPP


title: P4_B2_LMPP


title: P4_A3_LMPP


title: P4_A4_LMPP


title: P4_A2_LMPP


title: P4_C2_LMPP


title: P4_A1_LMPP


title: P3_D4_LMPP


title: P3_D1_LMPP


title: P3_C4_LMPP


title: P3_C3_LMPP


title: P3_C2_LMPP


title: P3_C1_LMPP


title: P3_D3_LMPP


title: P3_B3_LMPP


title: P3_B4_LMPP


title: P3_B2_LMPP


title: P3_A4_LMPP


title: P3_B1_LMPP


title: P3_A3_LMPP


title: P3_A1_LMPP


title: P2_H4_LMPP


title: P2_H1_LMPP


title: P2_G3_LMPP


title: P2_H2_LMPP


title: P2_G4_LMPP


title: P2_G1_LMPP


title: P2_G2_LMPP


title: P2_F3_LMPP


title: P2_F2_LMPP


title: P3_D2_LMPP


title: P2_F1_LMPP


title: P2_E4_LMPP


title: P2_E2_LMPP


title: P2_D4_LMPP


title: P2_D2_LMPP


title: P2_D3_LMPP


title: P2_D1_LMPP


title: P2_C3_LMPP


title: P3_A2_LMPP


title: P2_C1_LMPP


title: P2_C4_LMPP


title: P2_B4_LMPP


title: P2_B3_LMPP


title: P2_C2_LMPP


title: P2_A4_LMPP


title: P2_F4_LMPP


title: P2_H3_LMPP


title: P2_A1_LMPP


title: P6_G9_GMP

value: GMP


title: P2_A2_LMPP


title: P2_E3_LMPP


title: P6_G12_GMP


title: P6_F9_GMP


title: P6_G10_GMP


title: P6_G11_GMP


title: P6_F11_GMP


title: P6_F10_GMP


title: P6_E9_GMP


title: P2_E1_LMPP


title: P6_E11_GMP


title: P6_E10_GMP


title: P6_E12_GMP


title: P6_D12_GMP


title: P6_D9_GMP


title: P2_B2_LMPP


title: P6_D10_GMP


title: P2_B1_LMPP


title: P6_C9_GMP


title: P6_C12_GMP


title: P6_C11_GMP


title: P6_B9_GMP


title: P6_C10_GMP


title: P6_B12_GMP


title: P6_B11_GMP


title: P6_B10_GMP


title: P6_F12_GMP


title: P5_H10_GMP


title: P5_H11_GMP


title: P5_H9_GMP


title: P5_G12_GMP


title: P5_G9_GMP


title: P5_G11_GMP


title: P6_A9_GMP


title: P6_A12_GMP


title: P5_G10_GMP


title: P6_A10_GMP


title: P5_F9_GMP


title: P6_D11_GMP


title: P5_E12_GMP


title: P5_F10_GMP


title: P5_F11_GMP


title: P5_E9_GMP


title: P5_E10_GMP


title: P5_E11_GMP


title: P5_F12_GMP


title: P5_D12_GMP


title: P5_D9_GMP


title: P5_D11_GMP


title: P5_D10_GMP


title: P5_C11_GMP


title: P5_C9_GMP


title: P5_B9_GMP


title: P5_B12_GMP


title: P5_C10_GMP


title: P6_A11_GMP


title: P5_B10_GMP


title: P5_A12_GMP


title: P5_B11_GMP


title: P5_A10_GMP


title: P4_H9_GMP


title: P5_A9_GMP


title: P4_H11_GMP


title: P4_G9_GMP


title: P4_G12_GMP


title: P4_F11_GMP


title: P4_E11_GMP


title: P4_F9_GMP


title: P4_E12_GMP


title: P5_C12_GMP


title: P4_D12_GMP


title: P4_E10_GMP