title: siCOPS2 C

city: Boston

first: Dr. Kathryn

last: Swoboda

state: MA

address: 165 Cambridge Street

department: Neurology

institute: Massachusetts General Hospital

hyb_protocol: Done by Thermo Fisher Scientific facility services (SantaClara, CA, USA): Using GeneChip hybridization oven 645 and GeneChip Hybridization, Wash, and Strain kit (Cat#: 900720)

scan_protocol: Done by Thermo Fisher Scientific facility services (SantaClara, CA, USA): Scanning of GeneChips were done on the GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the R packages Limma and Oligo through bioconductor, RMA values uploaded in data file

source_name: Human myotubes post differentiation

label_protocol: Done by Thermo Fisher Scientific facility services (SantaClara, CA, USA): WT terminal labeling Kit (902927)

growth_protocol: Cells were differentiation from myoblasts by using 2% horse serum in DMEM. Cells were treated with siRNA after a myotube phenotype was reached

extract_protocol: RNA was extracted using Rneasy plus inversal kit (Qiagen)

treatment_protocol: siRNA was introduced to human myotubes by using lipofectamine RNAiMax

value: mature myotubes


title: hiPSCs_THz_rep1

status: Public on Jun 02 2020

type: SRA

city: Kyoto

first: Ken-ichiro

last: Kamei

state: Kyoto

address: Yoshida-Ushinomiya-cho, Sakyo-ku

department: iCeMS

country: Japan

institute: Kyoto University

description:
THz_rep1
RNA obtained from 585A1 hiPSCs under mTeSR-1 self-renewal condition treated with THz light, replicate 1

library_source: transcriptomic

data_processing:
Base-calling and demultiplexing were performed with EPI2ME software (Oxford NANOPORE Technologies).
Failed reads were discarded and Fast5 files were converted into FASTQ and FASTA files using EPI2ME software.
Generated FASTQ files were loaded to BioJupies for alignment with human genomes and annotation.
the counts were analysed using TCC in R Bioconducter. Briefly, the counted data set was introduced into the TCC-GUI package.
Genome_build: human_matrix.h5 v2
Supplementary_files_format_and_content: Gene counts were normalized using TMM (Trimmed mean of M values) methods in the edgeR package with the parameters: Number of Iterations = 3; FDR < 0.1; Elimination of Potential DEGs = 0.05.

molecule: total RNA

organism: Homo sapiens

source_name: 585A1 hiPSCs

growth_protocol: 585A1 hiPSCs were maintained in mTeSR-1-defined medium (Stem Cell Technologies).

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
To prepare the cDNA library, 10 ng of total RNA was diluted with 9 µL of RNase free water, then mixed with VN primer (Oxford NANOPORE Technologies, UK), 1 µL of 10 mM dNTPs (New England Biolabs Inc. Ipswich, Massachusetts, USA), and incubated at 65˚C for 5 min as the RNA solution. Separately, 4 µL of 5x RT Buffer (Thermo Fisher Scientific), 1 µL of RNaseOUT (Thermo Fisher Scientific), 1 µL of Nuclease-free water and 2 µL of Strand-Switching Primer (Oxford NANOPORE Technologies) was mixed as the strand-switching buffer. The two solutions were mixed at 42˚C for 2 min; then, 1 µL of Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) was added, incubated at 42˚C for 90 min, 85˚C for 5 min, and stored at 4˚C until use as the cDNA library.

treatment_protocol: 0.5 MV/cm of THz light was irradiated to hiPSCs.

tag: conditions

value: self-renewal condition

tag: treatment

value: THz


title: VeryYoung2: RNA6 MACS 3mo RNA

status: Public on Jun 01 2020

city: ANKARA

first: Ayca

last: Arslan Ergul

state: ÇANKAYA

address: Bilkent Üniversitesi UNAM

department: UNAM

country: Turkey

institute: Bilkent University

data_processing:
TopHat 2.1.1: Alignment of fragments to the reference genome
Cufflinks 2.2.1: Fragments per kilobase of transcript per million mapped reads were calculated using cufflinks
Cuffmerge (Cufflinks v. 2.2.1): transcripts were merged
CuffQuant (Cufflinks v. 2.2.1): transcripts were quantified
Cuffdiff (Cufflinks v. 2.2.1): Gene expression comparisons between groups
Genome_build: Genome Reference Consortium Zebrafish Build 10
Supplementary_files_format_and_content: .FPKM_TRACKING:Gene FPKMs. Tracks the summed FPKM of transcripts sharing each gene_id
Supplementary_files_format_and_content: .gtf: input assemblies merged
Supplementary_files_format_and_content: .cxb: cuffquant output
Supplementary_files_format_and_content: .DIFF: difference in gene expression. Differences in the total FPKM of transcripts sharing each gene_id are measured

organism: Danio rerio

source_name: 10 brains pooled

growth_protocol: Wild-type AB strain,  zebrafish were used. Animals were fed twice a day with dry food and three times a week with artemia and kept in standard conditions. After anesthesizing and decapitating the animals, brains were dissected and underwent a stem cell isolation procedure using MACS Miltenyi Biotec Neural Tissue Dissociation Kit(P). Isolated stem cells were seeded using L15 medium (supplemented with 1% P/S, 5%FBS, 20ng/ml EGF & FGF) onto the poly-D Lysin and Laminin coated culture plates (for ICC), 75cm2 Corning Cell Bind flasks (for RNA Seq.), or FalconTM Chambered Cell Culture Slides (for ICC) and were incubated at 28oC. Five to ten fish brains were pooled prior to the stem cell isolation procedure depending on the size of the culture area, in order to obtain a visible amount of stem cells in a culture.

extract_protocol:
After anesthesia and decapitation, whole fish brains were dissected under the stereo microscope. Total RNAs were isolated from the scraped stem cell cultures, each containing 10 fish brain isolates, using Qiagen's RNeasy Mini Kit according to the manufacturer’s instructions. The isolation protocol was followed by DNase treatment with Ambion TURBO DNA-free Kit from Thermo Fisher Scientific.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Brain progenitor cells

tag: age

value: 3 months old

tag: strain

value: AB


title: VeryYoung3: RNA7 MACS 3mo RNA


title: siCOPS2 B

type: RNA

country: USA

label: biotin

tag: cell type


title: siCOPS2 A


title: siScramble C

value: siScramble


title: siScramble A


title: Young3: RNA4 MACS Young RNA

source_name: 5 brains pooled

value: 5,5 months old


title: VeryYoung1: RNA5 MACS 3mo RNA


title: Old3: RNA3 MACS Old RNA

value: 30-31 months old


title: Young1: CellBind Young RNA Dnased

value: 8,5 months old


title: Irradiated melanocytes

city: Cleveland

first: Nikki

last: Harter

state: Ohio

address: 10900 Euclid Avenue

department: Biochemistry

institute: Case Western Reserve University

description: miRNA expression data from post-irradiated melanocytes

hyb_protocol: For hybridization, Affymetrix GeneChip Hybridization Wash and Stain Kit was used.

scan_protocol: Chips were scanned with Affymetrix GeneChip Scanner 3000 7G.

data_processing: The CEL files were imported into the Affymetrix Expression Console Software for analysis and the generation of CHP files.  CHP files were analyzed using the Affymetrix Transcriptome Analysis Consol (TAC) software.

label: Biotin

source_name: Primary melanocytes

label_protocol: 130 ng of total RNA was labeled by using Affymetrix's Flash Tag Biotin HS RNA Labeling Kit.

growth_protocol: Cultured primary melanocytes were made quiescent prior to the exposure of solar UVR (UVA+UVB)

extract_protocol: By 64 hr post-irradiation, exosomes from the irradiated or un-irradiated melanocytes were subjected to RNA extraction using the Total Exosome RNA and Protein Kit (Invitrogen).

treatment_protocol: A dose of irradiation was applied to quiescent melanocytes on day 1 and then again 24 hrs later.

tag: developmental stage

value: neonatal

value: Primary melanocytes

tag: rna fraction

value: exosome


title: Old2: RNA1 MACS Old RNA


title: Old1 : CellBind OLD RNA Dnased

value: 26-28 months old


title: siScramble B


title: Unirradiated melanocytes

description: miRNA expression data from non-irradiated melanocytes


title: LN-elongation zone-R1

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

country: China

institute: Henan Agricultural University

description: supply 0.04mM nitrogen (LN)

data_processing:
Raw reads were pre-processed to remove low quality regions and adapter sequences.
Clean reads from each sample were aligned to the maize reference genome (B73 RefGen_v3, http://www.maizegdb.org/assembly/) using TopHat2
Aligned reads from TopHat2 mapping were subjected to String Tie for DeNovo transcript assembly
The R package edgeR was used to identify the differentially expressed genes.The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples.
Genome_build: B73 RefGen_v3 (http://www.maizegdb.org/assembly/)
Supplementary_files_format_and_content: tab-delimited text files include tags,copy number and FPKM

organism: Zea mays

source_name: elongation zone of leaf sixth_0.04mM nitrogen

growth_protocol: maize inbred B73 grown in hydroculture.

extract_protocol:
The elongation zone of maize leaf 6 was harvested, flash frozen and stored at -80℃.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: maize inbred B73

value: the sixth Leaf

tag: tissue compartment

value: elongation zone


title: LN-elongation zone-R2

description: supply 0.04mM nitrogen (LN)


title: HN-elongation zone-R2

description: supply 4mM nitrogen (HN)

source_name: elongation zone of leaf sixth_4nM nitrogen


title: HN-elongation zone-R1

description: supply 4mM nitrogen (HN)


title: Young2: RNA2 MACS Young RNA


title: IAA_6h_Pol2_Hi-C_rep2 (with spike-in)

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

description: Pol2_IAA_6h_downsampled_55mi_allValidPairs_2nd.hic

library_source: genomic

data_processing:
Linker detection: The bridge linker sequences were trimmed using trimlinker from ChIA-PET2 software, paired-end reads containing at least one instance of the bridge-linker in either end are adapted for further processing.
Reads alignment: The resulting reads were aligned against the mm10 genome and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (special paramters: --very-sensitive-local --local)
Filtering: Discard read-pairs marked as multihits, PCR duplicates, low mapping quality (MAPQ < 20), self-ligated fragments and dangling-end; only the valid read pairs involving two different restriction fragments were used to build the contact matrices.
Matrix generation: For unbiased comparison, we randomly sampled equal numbers of long range (>20 kb) intra-chromosomal read pairs (n=75 million) from each sample, Hi-C contact matrices  with binned interactions (range from 5 kb to 100 kb) were generated.
Normalization: the raw Hi-C contact matrices were normalized using the iterative correction method with iced script to correct for systematic biases and the distance between restriction fragments as recently described.
Processed reads and downsampled allValidPairs were then inputted into the Juicebox pipeline (hicpro2juicebox.sh) to allow for visualization of the interaction matrix. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (.hic) were generated useing juicebox pre. hic files contain the HiC contact matrix at different resolution

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: The V6.5 mouse ES (mES) cell line was cultured with irradiated mouse embryonic fibroblasts in DMEM-KO containing 15% FBS, leukaemia inhibiting factor (LIF), L-glutamine, β-mercaptoethanol, non-essential amino acids and penicillin/ streptomycin at 37 ℃ with 5% CO2, and passage twice for experiments.

extract_protocol:
Hi-C was conducted as BAT Hi-C (Huang et al., 2019). After AluI digestion, proximal ligation was mediated with biotin labeled linker, then remove unligated linker with ExoI and ligated DNA was extracted with streptavidin beads.
Llibrary was constructed with Illumina Nextera DNA Sample Preparation Kit (FC-121-1030), sequencing adaptor was added with Tn5 transposase.

treatment_protocol: All degron mES cells were pre-treated with 1 μg/ml Doxycycline for 12 hours. Pol II degron mES was treated with or without 500 μM indole-3-acetic acid (IAA) for 6 hours, whereas Pol I and Pol III degron mES were treated for 24 hours with same concentration. For the time course of Pol II degron, IAA was added 1 hour and 6 hours respectively.

tag: cell line

value: mouse embryonic stem cells

value: Pol II degron 6h mES

tag: tag

value: restriction enzyme:AluI


title: IAA_6h_Pol2_Hi-C_rep1 (with spike-in)


title: Pol2_wt_RNAseq_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The resulting FASTQ reads were mapped to the mm10 reference genome using hisat2 (version 2.1.0)
Transcript abundance values were obtained from Salmon and gene-level count matrices were quantified by htseq-count
Differential expression testing was performed using DESeq2 bioconductor package (Love et al., 2014).
A threshold of  corrected p-value < 0.05 and log2(FC) > 1 was chosen to determine significantly changed gene expression after treatment.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw counts include DESeq2 annotated values of differentially expressed genes per sample in tab-delimited text format.

extract_protocol:
Retinas were removed, total RNA was isolated using TRIzol following manufacturer’s recommendations.
Sequencing libraries were generated by Novogene corporation with standard Illumina protocols.

value: mouse embryonic stem cells (mES)

tag: genotype/variation

value: Pol2 wild type


title: Pol2_wt_RNAseq_rep1


title: IAA_24h_Pol3_Hi-C_rep2

description: Pol3_IAA_24h_downsampled_75mi_allValidPairs.hic

value: Pol III degron 24h mES


title: Untreated_Pol2_Hi-C_rep1 (with spike-in)

description: Pol2_untreated_downsampled_55mi_allValidPairs_2nd.hic

value: Untreated mES


title: Untreated_Pol2_Hi-C_rep2 (with spike-in)


title: IAA_1h_Pol2_Hi-C_rep1 (with spike-in)

description: Pol2_IAA_1h_downsampled_55mi_allValidPairs_2nd.hic

value: Pol II degron 1h mES


title: IAA_1h_Pol2_Hi-C_rep2 (with spike-in)


title: IAA_24h_Pol3_Hi-C_rep1


title: Untreated_Pol3_Hi-C_rep2

description: Pol3_untreated_downsampled_75mi_allValidPairs.hic


title: neofascia from mesh A of patient CS_43

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: neofascia from mesh A of patient CS_43

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor package affy; background correction, normalization and probeset summary were performed with the rma command using default parameter settings.

source_name: bioreactor culture in presence of mesh A

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturer's protocols.

growth_protocol: Fibroblasts were generated by collagenase digestion for 16h in DMEM+10% fetal bovine serum (FBS)+1% Penicillin/Streptomycin (Pen/Strep) at 37°C, after sieving, life cells were precultured in DMEM+10% FBS+1%Pen/Strep; for bioreactor culture, 750,000 cells were embedded in 5ml collagen type 1 gel matrix, fed with 5ml DMEM+10% FBS+1%Pen/Strep and incubated for 14 days at 37°C.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) according to the manufactuer's instractions.

treatment_protocol: Bioreactor culture was performed in the presence of mesh A (Parietex) or mesh B (ULTRAPRO).

tag: patient

tag: environment

value: mesh A (Parietex)

tag: healer

value: bad

tag: rna integrity number [rin]


title: neofascia from mesh A of patient CS_15

description: neofascia from mesh A of patient CS_15

value: good


title: neofascia from native environment of patient CS_15

source_name: native tissue sample

value: native


title: IAA_6h_Pol2_Hi-C_rep2

description: Pol2_IAA_6h_downsampled_75mi_allValidPairs.hic


title: neofascia from mesh A of patient CS_10

description: neofascia from mesh A of patient CS_10


title: neofascia from mesh B of patient CS_15

description: neofascia from mesh B of patient CS_15

source_name: bioreactor culture in presence of mesh B

value: mesh B (ULTRAPRO)


title: neofascia from native environment of patient CS_43


title: neofascia from native environment of patient CS_12


title: neofascia from mesh A of patient CS_26

description: neofascia from mesh A of patient CS_26


title: neofascia from mesh B of patient CS_43

description: neofascia from mesh B of patient CS_43


title: neofascia from mesh B of patient CS_26

description: neofascia from mesh B of patient CS_26


title: neofascia from mesh A of patient CS_7

description: neofascia from mesh A of patient CS_7


title: neofascia from native environment of patient CS_26


title: neofascia from native environment of patient CS_10


title: neofascia from mesh A of patient CS_12

description: neofascia from mesh A of patient CS_12


title: neofascia from mesh B of patient CS_7

description: neofascia from mesh B of patient CS_7


title: Untreated_Pol3_Hi-C_rep1


title: neofascia from mesh B of patient CS_10

description: neofascia from mesh B of patient CS_10


title: IAA_6h_Pol2_Hi-C_rep1


title: Untreated_Pol2_Hi-C_rep2

description: Pol2_untreated_downsampled_75mi_allValidPairs.hic


title: Untreated_Pol1_Hi-C_rep2

description: Pol1_untreated_downsampled_75mi_allValidPairs.hic


title: Untreated_Pol1_Hi-C_rep1


title: neofascia from native environment of patient CS_7


title: IAA_24h_Pol1_Hi-C_rep1

description: Pol1_IAA_24h_downsampled_75mi_allValidPairs.hic

value: Pol I degron 24h mES


title: IAA_6h_Ocean-C_rep1

description: Pol2_IAA_6h_OceanC_downsampled_75mi_allValidPairs.hic

data_processing:
Library strategy: Ocean-C
Linker detection: The bridge linker sequences were trimmed using trimlinker from ChIA-PET2 software, paired-end reads containing at least one instance of the bridge-linker in either end are adapted for further processing.
Reads alignment: The resulting reads were aligned against the mm10 genome and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (special paramters: --very-sensitive-local --local)
Filtering: Discard read-pairs marked as multihits, PCR duplicates, low mapping quality (MAPQ < 20), self-ligated fragments and dangling-end; only the valid read pairs involving two different restriction fragments were used to build the contact matrices.
Matrix generation: For unbiased comparison, we randomly sampled equal numbers of long range (>20 kb) intra-chromosomal read pairs from each sample, Ocean-C contact matrices  with binned interactions (range from 5 kb to 100 kb) were generated.
Normalization: the raw Ocean-C contact matrices were normalized using the iterative correction method with iced script to correct for systematic biases and the distance between restriction fragments as recently described.
Processed reads and downsampled allValidPairs were then inputted into the Juicebox pipeline (hicpro2juicebox.sh) to allow for visualization of the interaction matrix.  File can be loaded onto Juicebox to view either raw or normalized interaction matrices
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (.hic) were generated useing juicebox pre. hic files contain the Ocean-C contact matrix at different resolution

extract_protocol:
OCEAN-C was modified based on (Li et al., 2018) version. Cells harvest, lysis, endonuclease digestion, bridge linker mediated proximal ligation were the same as Hi-C described.
After biotinylated DNA pull down with streptavidin beads, library was completed and sequenced as HiChIP described.

treatment_protocol: All degron mES cells were pre-treated with 1 μg/ml Doxycycline for 12 hours. Pol II degron mES was treated with or without 500 μM indole-3-acetic acid (IAA) for 6 hours.

tag: restriction enzyme

value: AluI


title: Untreated_Ocean-C_rep2

description: Pol2_untreated_OceanC_downsampled_75mi_allValidPairs.hic

tag: treatment


title: Untreated_Ocean-C_rep1


title: IAA_6h_Ocean-C_rep2


title: IAA_6h_H3K27Ac_HiChIP_rep1

description: Pol2_IAA_6h_H3K27Ac_HiChIP_downsampled_75mi_allValidPairs.hic

data_processing:
Library strategy: HiChIP
Linker detection: The bridge linker sequences were trimmed using trimlinker from ChIA-PET2 software, paired-end reads containing at least one instance of the bridge-linker in either end are adapted for further processing.
Reads alignment: The resulting reads were aligned against the mm10 genome and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (special paramters: --very-sensitive-local --local)
Filtering: Discard read-pairs marked as multihits, PCR duplicates, low mapping quality (MAPQ < 20), self-ligated fragments and dangling-end; only the valid read pairs involving two different restriction fragments were used to build the contact matrices.
Matrix generation: For unbiased comparison, we randomly sampled equal numbers of long range (>20 kb) intra-chromosomal read pairs  from each sample, HiChiP contact matrices  with binned interactions (range from 5 kb to 100 kb) were generated.
Normalization: the raw HiChiP contact matrices were normalized using the iterative correction method with iced script to correct for systematic biases and the distance between restriction fragments as recently described.
Processed reads and downsampled allValidPairs were then inputted into the Juicebox pipeline (hicpro2juicebox.sh) to allow for visualization of the interaction matrix.  File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (.hic) were generated useing juicebox pre. hic files contain the HiChIP contact matrix at different resolution.

extract_protocol:
HiChIP was modified based on (Mumbach et al., 2016) version,after AluI digestion and Biotinyled linker mediated proximal ligation, ligated DNA was extracted with specific antibody and streptavidin beads sequentially.
Library was constructed with NEB library prep kit (E7645). Breifly, DNA was end reparied and dATP tailing followed by Truseq sequencing adaptor linking.

tag: chip antibody


title: IAA_6h_H3K27Ac_HiChIP_rep2


title: Untreated_H3K27Ac_HiChIP_rep1

description: Pol2_untreated_H3K27Ac_HiChIP_downsampled_75mi_allValidPairs.hic


title: Pol2_IAA_6h_RNAseq_rep2

extract_protocol:
Total RNA was isolated using TRIzol following manufacturer’s recommendations.
Sequencing libraries were generated by Novogene corporation with standard Illumina protocols.

treatment_protocol: All degron mES cells were pre-treated with 1 g/ml Doxycycline for 12 hours. Pol II degron mES was treated with or without 500 M indole-3-acetic acid (IAA) for 6 hours, whereas Pol I and Pol III degron mES were treated for 24 hours with same concentration. For the time course of Pol II degron, IAA was added 1 hour and 6 hours respectively.


title: Pol2_IAA_6h_RNAseq_rep1


title: IAA_24h_Pol1_Hi-C_rep2


title: Pol2_untreated_RNAseq_rep1


title: Untreated_Pol2_Hi-C_rep1


title: Pol2_untreated_RNAseq_rep2


title: Smc1_ChIP_pol2_untreated_rep2

data_processing:
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
Raw fastq reads were trimmed by trim_galore, followed by mapping to the mouse reference genome mm10 using bowtie2 (version 2.3.2)  with the default parameters: ‘best –k 1 –m 1 and –l 18’.
Unmapped reads, low quality mapped reads and PCR duplicates were discarded. Only uniquely mapped were retained for downstream analysis.
Peaks were called against input control using the MACS2 function callpeak on each replicate with options ‘-g mm -q 0.0001 --nomodel --extsize 200’ and p-value threshold of 10-5 to ensure high confidence. Common peaks between the replicates were used for downstream analysis.
The ChIP reads at each genomic position were normalized and converted to bigwig format using bamCoverage from deeptools toolkit (version 3.13).
For subsequent meta-gene analysis and browser visualization, replicates for each biological condition were merged into one bigwig track file.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig (10 bp resolution with reads extended by 200bp) files of ChIP-seq data were generated using deepTools v3.13 with library size normalized to equal.

extract_protocol:
Lysates were clarified from MNase digested and sonicated nuclei and protein-DNA complexes were isolated with specific antibody.
ChIP DNA were used to construct Illumina sequencing libraries using TELP method from (Peng et al., 2015).

value: Pol II untreated mES


title: Smc1_ChIP_pol2_IAA_6h_rep2


title: Smc1_ChIP_pol2_IAA_1h_rep2


title: Smc1_ChIP_pol2_untreated_rep1


title: Smc1_ChIP_pol2_IAA_1h_rep1


title: WT_Pol3_ChIP_B2T4

value: WT untreated mES


title: WT_Pol3_ChIP_B2T3

value: mouse embryonic stem cells


title: WT_Pol3_ChIP_B2T2


title: WT_Pol3_ChIP_B1T2


title: WT_Pol3_ChIP_B2T1


title: WT_Pol2_ChIP_B2T2


title: WT_Pol3_ChIP_B1T1


title: WT_Pol1_ChIP_B2T2


title: WT_Pol2_ChIP_B1T2


title: WT_Pol2_ChIP_B1T1


title: Untreated_H3K27Ac_HiChIP_rep2


title: WT_Pol2_ChIP_B2T1


title: WT_Pol1_ChIP_B1T1


title: WT_Input_rep2


title: Smc1_ChIP_pol2_IAA_6h_rep1

value: Pol II degron 6h mES


title: WT_Input_rep1


title: GFP_Pol2_ChIP_rep2

value: GFP tagged mES


title: GFP_Pol3_ChIP_rep2


title: GFP_Pol2_ChIP_rep1


title: input_ChIP_pol2_untreated


title: GFP_Pol3_ChIP_rep1


title: GFP_Pol1_ChIP_rep2


title: Pol2_IAA_6h_ATAC_rep2

data_processing:
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
Raw fastq reads were trimmed by trim_galore, followed by mapping to the mouse reference genome mm10 using bowtie2 (version 2.3.2)  with the default parameters: ‘best –k 1 –m 1 and –l 18’.
Unmapped reads, low quality mapped reads and PCR duplicates were discarded. Only uniquely mapped were retained for downstream analysis. Additionally, reads mapping to the mitochondrial genome (chrM) were removed.
Processed data files contain bigwig coverage tracks were computed with reads per kilobase of transcript per million mapped reads (RPKM) using bamCoverage at 10 bp resolution.
Peaks were called using the MACS2 function callpeak on each replicate individually as ChIP-seq and parameters "-g mm -q 0.0001 --nomodel --extsize 200".
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files of ATAC-seq data were generated using deepTools v3.13 with library size normalized to equal.

extract_protocol:
ATAC-seq were performed according to the protocol from (Corces M.R et al., 2017).
50,000 viable cells were used for library preparation using Nextera™ DNA Sample Prep Kit, PCR amplified libraries were extracted with Megen gel purification kit (Megen # D2111-03) without size selection.


title: Pol2_IAA_6h_ATAC_rep1


title: Pol2_IAA_1h_ATAC_rep2


title: Pol2_IAA_6h_Dhx9_4C_rep2

data_processing:
Library strategy: 4C-seq
Linker detection: The paired-end reads were demultiplexed with fastq-multx (Version: 1.3.1), enzyme site was trimmed using trimlinker form ChIA-PET2 software, read pairs containing at least one enzyme site and bait sequences were selected.
Reads alignment: The selected reads were mapped to the mm10 genome with bowtie2 using the parameter “--very-sensitive-local -L 30 --score-min G,20,8”.
Filtering: Discard read-pairs marked as multihits, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, dangling-end and PCR artefacts.
Normalization: Final bam files were converted into wig file with pyicos, and then the wig files were performed quantile normalization with DANPOS2
The distributions of normalized contact intensities were put into bigwig files for visualization using the UCSC genome browser mm10.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files were generated using wigToBigWig, which the total tags are normalized to equal.

extract_protocol:
We modified 4C-seq protocol based on 3C-HTGTS version (Jain et al., 2018). Briefly, After Nla III digestion and proximal ligation, target DNA was extracted with biotinyled bait primer.
Library are constructed via two rounds of PCR with truseq adaptor.

treatment_protocol: All degron mES cells were pre-treated with 1 μg/ml Doxycycline for 12 hours. For the time course of Pol II degron, IAA was treated with or without 500 μM indole-3-acetic acid (IAA)  1 hour and 6 hours respectively. For wild type mES cells treated with transcription inhibitors, Actinomycin D, Flavoporidol was used with 1 μM for 1 hour and DRB was used with 100 μM for 1 hour. Etoposide was used with 10 μM for 1 hour.


title: Pol2_IAA_1h_ATAC_rep1


title: Pol2_untreated_ATAC_rep1


title: Pol2_IAA_6h_Dhx9_4C_rep1


title: WT_Pol1_ChIP_B2T1


title: WT_Pol1_ChIP_B1T2


title: Pol2_IAA_1h_Dhx9_4C_rep1


title: WT_DRB_1h_Dhx9_4C_rep2

value: DRB treated mES


title: WT_Flavopiridol_1h_Dhx9_4C_rep1

value: Flavopiridol treated mES


title: Pol2_untreated_Dhx9_4C_rep2


title: Pol2_untreated_Dhx9_4C_rep1


title: WT_Flavopiridol_1h_Dhx9_4C_rep2


title: WT_DRB_1h_Dhx9_4C_rep1


title: WT_untreated_Dhx9_4C_rep2


title: WT_ActinomycinD_1h_Dhx9_4C_rep2

value: ActinomycinD treated mES


title: WT_untreated_Dhx9_4C_rep1


title: WT_ActinomycinD_1h_Dhx9_4C_rep1


title: RNA_ko-Tfh_2

city: Shanghai

first: Jinyi

last: Tang

address: Yueyang road 320

institute: IPS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were cleaned for trimming adaptor sequence, low-quality sequence (Q<20) from the 3' end, and filtering the reads with the length less than 20.
Cleaned reads were then quantified with the indexed mouse transcriptome Mus_musculus.GRCm38.cdna using the salmon program
The Salmon-generated quantification files were read in by DESeq2 package in R and generated normalized transcript quantification by "mean-ratio method".
Genome_build: ensembl reference transcriptome mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: tab-delimited text files of raw transcript quantification files(from salmon program) and normalized files (normalized by mean-ratio method)

extract_protocol:
Two populations from Transferred ly5.1 mice were isolated by cell sorting (Tfh: CD4+CD45.1+CXCR5hiPD-1hi, nonTfh: CD4+CD45.1+CXCR5-PD-1- ).
Total RNA were extracted using Trizol(Thermo),  and sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: WT OT-II or Tox2-/- SMARTA mice were transferred into Ly5.1 mice, followed by LCMV infection.

tag: tissue

value: Spleen

tag: genotype


title: RNA_ko-Tfh_1

tag: strain


title: RNA_wt-Tfh_2


title: RNA_ko-nonTfh1


title: RNA_wt-Tfh_1


title: GFP_Pol1_ChIP_rep1


title: Pol2_untreated_ATAC_rep2

tag: cell type

value: Untreated mES


title: Pol2_IAA_1h_Dhx9_4C_rep2

value: Pol II degron 1h mES


title: Sample 2785_Single mESC cell

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

source_name: Single mESC cell

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

value: Differentiated mESC

tag: day of differentiation

value: day 8


title: Sample 2784_Single mESC cell


title: Sample 2786_Single mESC cell


title: Sample 2779_Single mESC cell


title: Sample 2778_Single mESC cell


title: Sample 2780_Single mESC cell


title: Sample 2781_Single mESC cell


title: Sample 2782_Single mESC cell


title: Sample 2777_Single mESC cell


title: Sample 2776_Single mESC cell


title: Sample 2773_Single mESC cell


title: Sample 2775_Single mESC cell


title: Sample 2772_Single mESC cell


title: Sample 2770_Single mESC cell


title: Sample 2769_Single mESC cell


title: RNA_wt-nonTfh1


title: Sample 2768_Single mESC cell


title: Sample 2766_Single mESC cell


title: Sample 2764_Single mESC cell


title: Sample 2767_Single mESC cell


title: Sample 2765_Single mESC cell


title: Sample 2762_Single mESC cell


title: Sample 2783_Single mESC cell


title: Sample 2763_Single mESC cell


title: Sample 2759_Single mESC cell


title: Sample 2758_Single mESC cell


title: Sample 2760_Single mESC cell


title: Sample 2761_Single mESC cell


title: Sample 2774_Single mESC cell


title: Sample 2757_Single mESC cell


title: Sample 2754_Single mESC cell


title: Sample 2753_Single mESC cell


title: Sample 2749_Single mESC cell


title: Sample 2771_Single mESC cell


title: Sample 2751_Single mESC cell


title: Sample 2752_Single mESC cell


title: Sample 2747_Single mESC cell


title: Sample 2748_Single mESC cell


title: Sample 2750_Single mESC cell


title: Sample 2746_Single mESC cell


title: Sample 2744_Single mESC cell


title: Sample 2743_Single mESC cell


title: Sample 2745_Single mESC cell


title: Sample 2741_Single mESC cell


title: Sample 2742_Single mESC cell


title: Sample 2740_Single mESC cell


title: Sample 2738_Single mESC cell


title: Sample 2737_Single mESC cell


title: Sample 2736_Single mESC cell


title: Sample 2734_Single mESC cell


title: Sample 2732_Single mESC cell


title: Sample 2733_Single mESC cell


title: Sample 2735_Single mESC cell


title: Sample 2756_Single mESC cell


title: Sample 2755_Single mESC cell


title: Sample 2731_Single mESC cell


title: Sample 2727_Single mESC cell


title: Sample 2729_Single mESC cell


title: Sample 2728_Single mESC cell


title: Sample 2724_Single mESC cell


title: Sample 2726_Single mESC cell


title: Sample 2723_Single mESC cell


title: Sample 2725_Single mESC cell


title: Sample 2721_Single mESC cell


title: Sample 2722_Single mESC cell


title: Sample 2720_Single mESC cell


title: Sample 2719_Single mESC cell


title: Sample 2739_Single mESC cell


title: Sample 2717_Single mESC cell


title: Sample 2718_Single mESC cell


title: Sample 2716_Single mESC cell


title: Sample 2714_Single mESC cell


title: Sample 2713_Single mESC cell


title: Sample 2730_Single mESC cell


title: Sample 2712_Single mESC cell


title: Sample 2708_Single mESC cell


title: Sample 2710_Single mESC cell


title: Sample 2709_Single mESC cell


title: Sample 2715_Single mESC cell


title: Sample 2711_Single mESC cell


title: Sample 2705_Single mESC cell


title: Sample 2702_Single mESC cell


title: Sample 2703_Single mESC cell


title: Sample 2704_Single mESC cell


title: Sample 2701_Single mESC cell


title: Sample 2700_Single mESC cell


title: Sample 2706_Single mESC cell


title: Sample 2699_Single mESC cell


title: Sample 2707_Single mESC cell


title: Sample 2691_Single mESC cell


title: Sample 2693_Single mESC cell


title: Sample 2692_Single mESC cell


title: Sample 2697_Single mESC cell


title: Sample 2694_Single mESC cell


title: Sample 2698_Single mESC cell


title: Sample 2696_Single mESC cell


title: Sample 2695_Single mESC cell


title: Sample 2689_Single mESC cell


title: Sample 2685_Single mESC cell


title: Sample 2690_Single mESC cell


title: Sample 2684_Single mESC cell


title: Sample 2682_Single mESC cell


title: Sample 2680_Single mESC cell


title: Sample 2681_Single mESC cell


title: Sample 2679_Single mESC cell


title: Sample 2677_Single mESC cell


title: Sample 2678_Single mESC cell


title: Sample 2675_Single mESC cell


title: Sample 2676_Single mESC cell


title: Sample 2672_Single mESC cell


title: Sample 2673_Single mESC cell


title: Sample 2674_Single mESC cell


title: Sample 2671_Single mESC cell


title: Sample 2688_Single mESC cell


title: Sample 2687_Single mESC cell


title: Sample 2669_Single mESC cell


title: Sample 2668_Single mESC cell


title: Sample 2686_Single mESC cell


title: Sample 2661_Single mESC cell


title: Sample 2665_Single mESC cell


title: Sample 2664_Single mESC cell


title: Sample 2663_Single mESC cell


title: Sample 2659_Single mESC cell


title: Sample 2660_Single mESC cell


title: Sample 2683_Single mESC cell


title: Sample 2658_Single mESC cell


title: Sample 2657_Single mESC cell


title: Sample 2655_Single mESC cell


title: Sample 2656_Single mESC cell


title: Sample 2653_Single mESC cell


title: Sample 2654_Single mESC cell


title: Sample 2651_Single mESC cell


title: Sample 2650_Single mESC cell


title: Sample 2649_Single mESC cell


title: Sample 2652_Single mESC cell


title: Sample 2646_Single mESC cell


title: Sample 2647_Single mESC cell


title: Sample 2648_Single mESC cell


title: Sample 2670_Single mESC cell


title: Sample 2667_Single mESC cell


title: Sample 2666_Single mESC cell


title: Sample 2645_Single mESC cell


title: Sample 2662_Single mESC cell


title: Sample 2643_Single mESC cell


title: Sample 2644_Single mESC cell


title: Sample 2638_Single mESC cell


title: Sample 2640_Single mESC cell


title: Sample 2642_Single mESC cell


title: Sample 2635_Single mESC cell


title: Sample 2639_Single mESC cell


title: Sample 2641_Single mESC cell


title: Sample 2636_Single mESC cell


title: Sample 2637_Single mESC cell


title: Sample 2632_Single mESC cell


title: Sample 2631_Single mESC cell


title: Sample 2633_Single mESC cell


title: Sample 2634_Single mESC cell


title: Sample 2630_Single mESC cell


title: Sample 2627_Single mESC cell


title: Sample 2629_Single mESC cell


title: Sample 2626_Single mESC cell


title: Sample 2625_Single mESC cell


title: Sample 2624_Single mESC cell


title: Sample 2621_Single mESC cell


title: Sample 2623_Single mESC cell


title: Sample 2620_Single mESC cell


title: Sample 2622_Single mESC cell


title: Sample 2619_Single mESC cell


title: Sample 2613_Single mESC cell


title: Sample 2614_Single mESC cell


title: Sample 2617_Single mESC cell


title: Sample 2615_Single mESC cell


title: Sample 2618_Single mESC cell


title: Sample 2616_Single mESC cell


title: Sample 2611_Single mESC cell


title: Sample 2628_Single mESC cell


title: Sample 2609_Single mESC cell


title: Sample 2608_Single mESC cell


title: Sample 2607_Single mESC cell


title: Sample 2610_Single mESC cell


title: Sample 2606_Single mESC cell


title: Sample 2612_Single mESC cell


title: Sample 2603_Single mESC cell


title: Sample 2602_Single mESC cell


title: Sample 2601_Single mESC cell


title: Sample 2604_Single mESC cell


title: Sample 2598_Single mESC cell


title: Sample 2597_Single mESC cell


title: Sample 2595_Single mESC cell


title: Sample 2596_Single mESC cell


title: Sample 2592_Single mESC cell


title: Sample 2594_Single mESC cell


title: Sample 2593_Single mESC cell


title: Sample 2590_Single mESC cell


title: Sample 2591_Single mESC cell


title: Sample 2588_Single mESC cell


title: Sample 2589_Single mESC cell


title: Sample 2587_Single mESC cell


title: Sample 2586_Single mESC cell


title: Sample 2584_Single mESC cell


title: Sample 2605_Single mESC cell


title: Sample 2599_Single mESC cell


title: Sample 2585_Single mESC cell


title: Sample 2582_Single mESC cell


title: Sample 2600_Single mESC cell


title: Sample 2580_Single mESC cell


title: Sample 2577_Single mESC cell


title: Sample 2576_Single mESC cell


title: Sample 2575_Single mESC cell


title: Sample 2579_Single mESC cell


title: Sample 2578_Single mESC cell


title: Sample 2574_Single mESC cell


title: Sample 2581_Single mESC cell


title: Sample 2583_Single mESC cell


title: Sample 2573_Single mESC cell


title: Sample 2571_Single mESC cell


title: Sample 2572_Single mESC cell


title: Sample 2569_Single mESC cell


title: Sample 2568_Single mESC cell


title: Sample 2567_Single mESC cell


title: Sample 2563_Single mESC cell


title: Sample 2564_Single mESC cell


title: Sample 2570_Single mESC cell


title: Sample 2565_Single mESC cell


title: Sample 2562_Single mESC cell


title: Sample 2561_Single mESC cell


title: Sample 2559_Single mESC cell


title: Sample 2560_Single mESC cell


title: Sample 2557_Single mESC cell


title: Sample 2558_Single mESC cell


title: Sample 2556_Single mESC cell


title: Sample 2555_Single mESC cell


title: Sample 2552_Single mESC cell


title: Sample 2551_Single mESC cell


title: Sample 2553_Single mESC cell


title: Sample 2554_Single mESC cell


title: Sample 2566_Single mESC cell


title: Sample 2546_Single mESC cell


title: Sample 2550_Single mESC cell


title: Sample 2549_Single mESC cell


title: Sample 2547_Single mESC cell


title: Sample 2544_Single mESC cell


title: Sample 2545_Single mESC cell


title: Sample 2543_Single mESC cell


title: Sample 2542_Single mESC cell


title: Sample 2536_Single mESC cell


title: Sample 2541_Single mESC cell


title: Sample 2537_Single mESC cell


title: Sample 2539_Single mESC cell


title: Sample 2538_Single mESC cell


title: Sample 2540_Single mESC cell


title: Sample 2534_Single mESC cell


title: Sample 2535_Single mESC cell


title: Sample 2533_Single mESC cell


title: Sample 2531_Single mESC cell


title: Sample 2532_Single mESC cell


title: Sample 2548_Single mESC cell


title: Sample 2528_Single mESC cell


title: Sample 2529_Single mESC cell


title: Sample 2527_Single mESC cell


title: Sample 2530_Single mESC cell


title: Sample 2526_Single mESC cell


title: Sample 2525_Single mESC cell


title: Sample 2523_Single mESC cell


title: Sample 2521_Single mESC cell


title: Sample 2524_Single mESC cell


title: Sample 2518_Single mESC cell


title: Sample 2520_Single mESC cell


title: Sample 2519_Single mESC cell


title: Sample 2522_Single mESC cell


title: Sample 2516_Single mESC cell


title: Sample 2517_Single mESC cell


title: Sample 2515_Single mESC cell


title: Sample 2512_Single mESC cell


title: Sample 2510_Single mESC cell


title: Sample 2509_Single mESC cell


title: Sample 2508_Single mESC cell


title: Sample 2511_Single mESC cell


title: Sample 2507_Single mESC cell


title: Sample 2506_Single mESC cell


title: Sample 2504_Single mESC cell


title: Sample 2503_Single mESC cell


title: Sample 2502_Single mESC cell


title: Sample 2501_Single mESC cell


title: Sample 2499_Single mESC cell


title: Sample 2500_Single mESC cell


title: Sample 2496_Single mESC cell


title: Sample 2497_Single mESC cell


title: Sample 2493_Single mESC cell


title: Sample 2498_Single mESC cell


title: Sample 2494_Single mESC cell


title: Sample 2492_Single mESC cell


title: Sample 2491_Single mESC cell


title: Sample 2514_Single mESC cell


title: Sample 2490_Single mESC cell


title: Sample 2513_Single mESC cell


title: Sample 2488_Single mESC cell


title: Sample 2486_Single mESC cell


title: Sample 2487_Single mESC cell


title: Sample 2485_Single mESC cell


title: Sample 2505_Single mESC cell


title: Sample 2483_Single mESC cell


title: Sample 2484_Single mESC cell


title: Sample 2482_Single mESC cell


title: Sample 2480_Single mESC cell


title: Sample 2481_Single mESC cell


title: Sample 2478_Single mESC cell


title: Sample 2477_Single mESC cell


title: Sample 2476_Single mESC cell


title: Sample 2475_Single mESC cell


title: Sample 2489_Single mESC cell


title: Sample 2495_Single mESC cell


title: Sample 2473_Single mESC cell


title: Sample 2467_Single mESC cell


title: Sample 2468_Single mESC cell


title: Sample 2470_Single mESC cell


title: Sample 2471_Single mESC cell


title: Sample 2474_Single mESC cell


title: Sample 2465_Single mESC cell


title: Sample 2464_Single mESC cell


title: Sample 2466_Single mESC cell


title: Sample 2479_Single mESC cell


title: Sample 2463_Single mESC cell


title: Sample 2459_Single mESC cell


title: Sample 2462_Single mESC cell


title: Sample 2461_Single mESC cell


title: Sample 2457_Single mESC cell


title: Sample 2456_Single mESC cell


title: Sample 2454_Single mESC cell


title: Sample 2450_Single mESC cell


title: Sample 2472_Single mESC cell


title: Sample 2449_Single mESC cell


title: Sample 2448_Single mESC cell


title: Sample 2447_Single mESC cell


title: Sample 2446_Single mESC cell


title: Sample 2445_Single mESC cell


title: Sample 2444_Single mESC cell


title: Sample 2460_Single mESC cell


title: Sample 2458_Single mESC cell


title: Sample 2443_Single mESC cell


title: Sample 2441_Single mESC cell


title: Sample 2442_Single mESC cell


title: Sample 2439_Single mESC cell


title: Sample 2440_Single mESC cell


title: Sample 2438_Single mESC cell


title: Sample 2451_Single mESC cell


title: Sample 2433_Single mESC cell


title: Sample 2434_Single mESC cell


title: Sample 2452_Single mESC cell


title: Sample 2469_Single mESC cell


title: Sample 2436_Single mESC cell


title: Sample 2435_Single mESC cell


title: Sample 2431_Single mESC cell


title: Sample 2432_Single mESC cell


title: Sample 2455_Single mESC cell


title: Sample 2428_Single mESC cell


title: Sample 2427_Single mESC cell


title: Sample 2453_Single mESC cell


title: Sample 2426_Single mESC cell


title: Sample 2425_Single mESC cell


title: Sample 2424_Single mESC cell


title: Sample 2423_Single mESC cell


title: Sample 2422_Single mESC cell


title: Sample 2437_Single mESC cell


title: Sample 2420_Single mESC cell


title: Sample 2419_Single mESC cell


title: Sample 2418_Single mESC cell


title: Sample 2421_Single mESC cell


title: Sample 2417_Single mESC cell


title: Sample 2416_Single mESC cell


title: Sample 2429_Single mESC cell


title: Sample 2414_Single mESC cell


title: Sample 2430_Single mESC cell


title: Sample 2412_Single mESC cell


title: Sample 2411_Single mESC cell


title: Sample 2413_Single mESC cell


title: Sample 2410_Single mESC cell


title: Sample 2406_Single mESC cell


title: Sample 2404_Single mESC cell


title: Sample 2405_Single mESC cell


title: Sample 2409_Single mESC cell


title: Sample 2408_Single mESC cell


title: Sample 2407_Single mESC cell


title: Sample 2402_Single mESC cell

value: day 4


title: Sample 2403_Single mESC cell


title: Sample 2401_Single mESC cell


title: Sample 2399_Single mESC cell


title: Sample 2398_Single mESC cell


title: Sample 2400_Single mESC cell


title: Sample 2396_Single mESC cell


title: Sample 2395_Single mESC cell


title: Sample 2397_Single mESC cell


title: Sample 2394_Single mESC cell


title: Sample 2415_Single mESC cell


title: Sample 2390_Single mESC cell


title: Sample 2391_Single mESC cell


title: Sample 2393_Single mESC cell


title: Sample 2389_Single mESC cell


title: Sample 2392_Single mESC cell


title: Sample 2388_Single mESC cell


title: Sample 2387_Single mESC cell


title: Sample 2386_Single mESC cell


title: Sample 2385_Single mESC cell


title: Sample 2384_Single mESC cell


title: Sample 2383_Single mESC cell


title: Sample 2381_Single mESC cell


title: Sample 2382_Single mESC cell


title: Sample 2378_Single mESC cell


title: Sample 2380_Single mESC cell


title: Sample 2379_Single mESC cell


title: Sample 2376_Single mESC cell


title: Sample 2375_Single mESC cell


title: Sample 2377_Single mESC cell


title: Sample 2372_Single mESC cell


title: Sample 2373_Single mESC cell


title: Sample 2371_Single mESC cell


title: Sample 2368_Single mESC cell


title: Sample 2366_Single mESC cell


title: Sample 2364_Single mESC cell


title: Sample 2365_Single mESC cell


title: Sample 2367_Single mESC cell


title: Sample 2362_Single mESC cell


title: Sample 2363_Single mESC cell


title: Sample 2361_Single mESC cell


title: Sample 2358_Single mESC cell


title: Sample 2357_Single mESC cell


title: Sample 2359_Single mESC cell


title: Sample 2360_Single mESC cell


title: Sample 2355_Single mESC cell


title: Sample 2353_Single mESC cell


title: Sample 2354_Single mESC cell


title: Sample 2356_Single mESC cell


title: Sample 2374_Single mESC cell


title: Sample 2350_Single mESC cell


title: Sample 2351_Single mESC cell


title: Sample 2370_Single mESC cell


title: Sample 2347_Single mESC cell


title: Sample 2345_Single mESC cell


title: Sample 2346_Single mESC cell


title: Sample 2344_Single mESC cell


title: Sample 2343_Single mESC cell


title: Sample 2348_Single mESC cell


title: Sample 2369_Single mESC cell


title: Sample 2341_Single mESC cell


title: Sample 2340_Single mESC cell


title: Sample 2337_Single mESC cell


title: Sample 2338_Single mESC cell


title: Sample 2339_Single mESC cell


title: Sample 2336_Single mESC cell


title: Sample 2334_Single mESC cell


title: Sample 2335_Single mESC cell


title: Sample 2352_Single mESC cell


title: Sample 2331_Single mESC cell


title: Sample 2332_Single mESC cell


title: Sample 2327_Single mESC cell


title: Sample 2329_Single mESC cell


title: Sample 2349_Single mESC cell


title: Sample 2326_Single mESC cell


title: Sample 2323_Single mESC cell


title: Sample 2328_Single mESC cell


title: Sample 2342_Single mESC cell


title: Sample 2322_Single mESC cell


title: Sample 2325_Single mESC cell


title: Sample 2324_Single mESC cell


title: Sample 2319_Single mESC cell


title: Sample 2318_Single mESC cell


title: Sample 2316_Single mESC cell


title: Sample 2321_Single mESC cell


title: Sample 2314_Single mESC cell


title: Sample 2320_Single mESC cell


title: Sample 2311_Single mESC cell


title: Sample 2315_Single mESC cell


title: Sample 2313_Single mESC cell


title: Sample 2310_Single mESC cell


title: Sample 2309_Single mESC cell


title: Sample 2330_Single mESC cell


title: Sample 2307_Single mESC cell


title: Sample 2333_Single mESC cell


title: Sample 2312_Single mESC cell


title: Sample 2305_Single mESC cell


title: Sample 2302_Single mESC cell


title: Sample 2301_Single mESC cell


title: Sample 2303_Single mESC cell


title: Sample 2308_Single mESC cell


title: Sample 2306_Single mESC cell


title: Sample 2300_Single mESC cell


title: Sample 2304_Single mESC cell


title: Sample 2296_Single mESC cell


title: Sample 2317_Single mESC cell


title: Sample 2295_Single mESC cell


title: Sample 2297_Single mESC cell


title: Sample 2299_Single mESC cell


title: Sample 2298_Single mESC cell


title: Sample 2294_Single mESC cell


title: Sample 2292_Single mESC cell


title: Sample 2293_Single mESC cell


title: Sample 2288_Single mESC cell


title: Sample 2286_Single mESC cell


title: Sample 2287_Single mESC cell


title: Sample 2285_Single mESC cell


title: Sample 2290_Single mESC cell


title: Sample 2289_Single mESC cell


title: Sample 2284_Single mESC cell


title: Sample 2282_Single mESC cell


title: Sample 2280_Single mESC cell


title: Sample 2278_Single mESC cell


title: Sample 2276_Single mESC cell


title: Sample 2277_Single mESC cell


title: Sample 2275_Single mESC cell


title: Sample 2273_Single mESC cell


title: Sample 2274_Single mESC cell


title: Sample 2272_Single mESC cell


title: Sample 2271_Single mESC cell


title: Sample 2270_Single mESC cell


title: Sample 2269_Single mESC cell


title: Sample 2291_Single mESC cell


title: Sample 2267_Single mESC cell


title: Sample 2266_Single mESC cell


title: Sample 2265_Single mESC cell


title: Sample 2264_Single mESC cell


title: Sample 2268_Single mESC cell


title: Sample 2262_Single mESC cell


title: Sample 2263_Single mESC cell


title: Sample 2283_Single mESC cell


title: Sample 2261_Single mESC cell


title: Sample 2258_Single mESC cell


title: Sample 2257_Single mESC cell


title: Sample 2281_Single mESC cell


title: Sample 2259_Single mESC cell


title: Sample 2260_Single mESC cell


title: Sample 2255_Single mESC cell


title: Sample 2256_Single mESC cell


title: Sample 2279_Single mESC cell


title: Sample 2252_Single mESC cell


title: Sample 2251_Single mESC cell


title: Sample 2253_Single mESC cell


title: Sample 2254_Single mESC cell


title: Sample 2249_Single mESC cell


title: Sample 2250_Single mESC cell


title: Sample 2247_Single mESC cell


title: Sample 2246_Single mESC cell


title: Sample 2245_Single mESC cell


title: Sample 2248_Single mESC cell


title: Sample 2244_Single mESC cell


title: Sample 2242_Single mESC cell


title: Sample 2241_Single mESC cell


title: Sample 2236_Single mESC cell


title: Sample 2237_Single mESC cell


title: Sample 2240_Single mESC cell


title: Sample 2239_Single mESC cell


title: Sample 2235_Single mESC cell


title: Sample 2232_Single mESC cell


title: Sample 2231_Single mESC cell


title: Sample 2230_Single mESC cell


title: Sample 2228_Single mESC cell


title: Sample 2227_Single mESC cell


title: Sample 2238_Single mESC cell


title: Sample 2225_Single mESC cell


title: Sample 2234_Single mESC cell


title: Sample 2226_Single mESC cell


title: Sample 2224_Single mESC cell


title: Sample 2233_Single mESC cell


title: Sample 2223_Single mESC cell


title: Sample 2222_Single mESC cell


title: Sample 2221_Single mESC cell


title: Sample 2220_Single mESC cell


title: Sample 2243_Single mESC cell


title: Sample 2219_Single mESC cell


title: Sample 2229_Single mESC cell


title: Sample 2218_Single mESC cell


title: Sample 2216_Single mESC cell


title: Sample 2215_Single mESC cell


title: Sample 2214_Single mESC cell


title: Sample 2213_Single mESC cell


title: Sample 2212_Single mESC cell


title: Sample 2210_Single mESC cell


title: Sample 2209_Single mESC cell


title: Sample 2211_Single mESC cell


title: Sample 2208_Single mESC cell


title: Sample 2207_Single mESC cell


title: Sample 2203_Single mESC cell


title: Sample 2204_Single mESC cell


title: Sample 2206_Single mESC cell


title: Sample 2201_Single mESC cell


title: Sample 2200_Single mESC cell


title: Sample 2198_Single mESC cell


title: Sample 2202_Single mESC cell


title: Sample 2199_Single mESC cell


title: Sample 2197_Single mESC cell


title: Sample 2195_Single mESC cell


title: Sample 2194_Single mESC cell


title: Sample 2196_Single mESC cell


title: Sample 2193_Single mESC cell


title: Sample 2191_Single mESC cell


title: Sample 2192_Single mESC cell


title: Sample 2217_Single mESC cell


title: Sample 2190_Single mESC cell


title: Sample 2188_Single mESC cell


title: Sample 2186_Single mESC cell


title: Sample 2187_Single mESC cell


title: Sample 2189_Single mESC cell


title: Sample 2185_Single mESC cell


title: Sample 2184_Single mESC cell


title: Sample 2183_Single mESC cell


title: Sample 2182_Single mESC cell


title: Sample 2205_Single mESC cell


title: Sample 2180_Single mESC cell


title: Sample 2173_Single mESC cell


title: Sample 2177_Single mESC cell


title: Sample 2178_Single mESC cell


title: Sample 2176_Single mESC cell


title: Sample 2171_Single mESC cell


title: Sample 2169_Single mESC cell


title: Sample 2170_Single mESC cell


title: Sample 2168_Single mESC cell


title: Sample 2164_Single mESC cell


title: Sample 2165_Single mESC cell


title: Sample 2161_Single mESC cell


title: Sample 2166_Single mESC cell


title: Sample 2167_Single mESC cell


title: Sample 2158_Single mESC cell


title: Sample 2162_Single mESC cell


title: Sample 2160_Single mESC cell


title: Sample 2156_Single mESC cell


title: Sample 2159_Single mESC cell


title: Sample 2157_Single mESC cell


title: Sample 2155_Single mESC cell


title: Sample 2163_Single mESC cell


title: Sample 2181_Single mESC cell


title: Sample 2179_Single mESC cell


title: Sample 2175_Single mESC cell


title: Sample 2172_Single mESC cell


title: Sample 2174_Single mESC cell


title: Sample 2152_Single mESC cell


title: Sample 2153_Single mESC cell


title: Sample 2154_Single mESC cell


title: Sample 2149_Single mESC cell


title: Sample 2150_Single mESC cell


title: Sample 2147_Single mESC cell


title: Sample 2144_Single mESC cell


title: Sample 2143_Single mESC cell


title: Sample 2146_Single mESC cell


title: Sample 2139_Single mESC cell


title: Sample 2142_Single mESC cell


title: Sample 2140_Single mESC cell


title: Sample 2141_Single mESC cell


title: Sample 2138_Single mESC cell


title: Sample 2133_Single mESC cell


title: Sample 2134_Single mESC cell


title: Sample 2136_Single mESC cell


title: Sample 2137_Single mESC cell


title: Sample 2132_Single mESC cell


title: Sample 2151_Single mESC cell


title: Sample 2128_Single mESC cell


title: Sample 2127_Single mESC cell


title: Sample 2129_Single mESC cell


title: Sample 2125_Single mESC cell


title: Sample 2124_Single mESC cell


title: Sample 2123_Single mESC cell


title: Sample 2148_Single mESC cell


title: Sample 2122_Single mESC cell


title: Sample 2121_Single mESC cell


title: Sample 2120_Single mESC cell


title: Sample 2119_Single mESC cell


title: Sample 2131_Single mESC cell


title: Sample 2116_Single mESC cell


title: Sample 2117_Single mESC cell


title: Sample 2135_Single mESC cell


title: Sample 2126_Single mESC cell


title: Sample 2118_Single mESC cell


title: Sample 2145_Single mESC cell


title: Sample 2130_Single mESC cell


title: Sample 2108_Single mESC cell


title: Sample 2111_Single mESC cell


title: Sample 2114_Single mESC cell


title: Sample 2110_Single mESC cell


title: Sample 2109_Single mESC cell


title: Sample 2105_Single mESC cell


title: Sample 2112_Single mESC cell


title: Sample 2104_Single mESC cell


title: Sample 2102_Single mESC cell


title: Sample 2103_Single mESC cell


title: Sample 2100_Single mESC cell


title: Sample 2099_Single mESC cell


title: Sample 2098_Single mESC cell


title: Sample 2096_Single mESC cell


title: Sample 2101_Single mESC cell


title: Sample 2097_Single mESC cell


title: Sample 2095_Single mESC cell


title: Sample 2093_Single mESC cell


title: Sample 2094_Single mESC cell


title: Sample 2113_Single mESC cell


title: Sample 2115_Single mESC cell


title: Sample 2091_Single mESC cell


title: Sample 2088_Single mESC cell


title: Sample 2089_Single mESC cell


title: Sample 2106_Single mESC cell


title: Sample 2090_Single mESC cell


title: Sample 2084_Single mESC cell


title: Sample 2083_Single mESC cell


title: Sample 2082_Single mESC cell


title: Sample 2086_Single mESC cell


title: Sample 2079_Single mESC cell


title: Sample 2087_Single mESC cell


title: Sample 2107_Single mESC cell


title: Sample 2085_Single mESC cell


title: Sample 2081_Single mESC cell


title: Sample 2077_Single mESC cell


title: Sample 2080_Single mESC cell


title: Sample 2078_Single mESC cell


title: Sample 2075_Single mESC cell


title: Sample 2074_Single mESC cell


title: Sample 2076_Single mESC cell


title: Sample 2073_Single mESC cell


title: Sample 2070_Single mESC cell


title: Sample 2071_Single mESC cell


title: Sample 2092_Single mESC cell


title: Sample 2072_Single mESC cell


title: Sample 2069_Single mESC cell


title: Sample 2067_Single mESC cell


title: Sample 2068_Single mESC cell


title: Sample 2066_Single mESC cell


title: Sample 2065_Single mESC cell


title: Sample 2064_Single mESC cell


title: Sample 2063_Single mESC cell


title: Sample 2062_Single mESC cell


title: Sample 2061_Single mESC cell


title: Sample 2060_Single mESC cell

value: day 12


title: Sample 2058_Single mESC cell


title: Sample 2057_Single mESC cell


title: Sample 2059_Single mESC cell


title: Sample 2055_Single mESC cell


title: Sample 2056_Single mESC cell


title: Sample 2054_Single mESC cell


title: Sample 2053_Single mESC cell


title: Sample 2052_Single mESC cell


title: Sample 2048_Single mESC cell


title: Sample 2047_Single mESC cell


title: Sample 2045_Single mESC cell


title: Sample 2049_Single mESC cell


title: Sample 2050_Single mESC cell


title: Sample 2041_Single mESC cell


title: Sample 2044_Single mESC cell


title: Sample 2039_Single mESC cell


title: Sample 2038_Single mESC cell


title: Sample 2043_Single mESC cell


title: Sample 2037_Single mESC cell


title: Sample 2042_Single mESC cell


title: Sample 2036_Single mESC cell


title: Sample 2032_Single mESC cell


title: Sample 2033_Single mESC cell


title: Sample 2035_Single mESC cell


title: Sample 2030_Single mESC cell


title: Sample 2031_Single mESC cell


title: Sample 2029_Single mESC cell


title: Sample 2027_Single mESC cell


title: Sample 2051_Single mESC cell


title: Sample 2025_Single mESC cell


title: Sample 2023_Single mESC cell


title: Sample 2022_Single mESC cell


title: Sample 2026_Single mESC cell


title: Sample 2046_Single mESC cell


title: Sample 2024_Single mESC cell


title: Sample 2020_Single mESC cell


title: Sample 2040_Single mESC cell


title: Sample 2018_Single mESC cell


title: Sample 2017_Single mESC cell


title: Sample 2021_Single mESC cell


title: Sample 2019_Single mESC cell


title: Sample 2034_Single mESC cell


title: Sample 2015_Single mESC cell


title: Sample 2016_Single mESC cell


title: Sample 2014_Single mESC cell


title: Sample 2013_Single mESC cell


title: Sample 2009_Single mESC cell


title: Sample 2010_Single mESC cell


title: Sample 2011_Single mESC cell


title: Sample 2008_Single mESC cell


title: Sample 2028_Single mESC cell


title: Sample 2007_Single mESC cell


title: Sample 2006_Single mESC cell


title: Sample 2005_Single mESC cell


title: Sample 2004_Single mESC cell


title: Sample 2003_Single mESC cell


title: Sample 1999_Single mESC cell


title: Sample 2001_Single mESC cell


title: Sample 1998_Single mESC cell


title: Sample 1996_Single mESC cell


title: Sample 1995_Single mESC cell


title: Sample 1994_Single mESC cell


title: Sample 1992_Single mESC cell


title: Sample 1990_Single mESC cell


title: Sample 1989_Single mESC cell


title: Sample 1991_Single mESC cell


title: Sample 1993_Single mESC cell


title: Sample 2000_Single mESC cell


title: Sample 1988_Single mESC cell


title: Sample 2012_Single mESC cell


title: Sample 1986_Single mESC cell


title: Sample 1987_Single mESC cell


title: Sample 1985_Single mESC cell


title: Sample 1981_Single mESC cell


title: Sample 1982_Single mESC cell


title: Sample 2002_Single mESC cell


title: Sample 1980_Single mESC cell


title: Sample 1979_Single mESC cell


title: Sample 1984_Single mESC cell


title: Sample 1977_Single mESC cell


title: Sample 1983_Single mESC cell


title: Sample 1976_Single mESC cell


title: Sample 1975_Single mESC cell


title: Sample 1997_Single mESC cell


title: Sample 1978_Single mESC cell


title: Sample 1972_Single mESC cell


title: Sample 1967_Single mESC cell


title: Sample 1966_Single mESC cell


title: Sample 1964_Single mESC cell


title: Sample 1970_Single mESC cell


title: Sample 1973_Single mESC cell


title: Sample 1969_Single mESC cell


title: Sample 1965_Single mESC cell


title: Sample 1963_Single mESC cell


title: Sample 1960_Single mESC cell


title: Sample 1962_Single mESC cell


title: Sample 1961_Single mESC cell


title: Sample 1968_Single mESC cell


title: Sample 1971_Single mESC cell


title: Sample 1955_Single mESC cell


title: Sample 1958_Single mESC cell


title: Sample 1959_Single mESC cell


title: Sample 1949_Single mESC cell


title: Sample 1950_Single mESC cell


title: Sample 1948_Single mESC cell


title: Sample 1947_Single mESC cell


title: Sample 1974_Single mESC cell


title: Sample 1953_Single mESC cell


title: Sample 1954_Single mESC cell


title: Sample 1952_Single mESC cell


title: Sample 1946_Single mESC cell


title: Sample 1956_Single mESC cell


title: Sample 1944_Single mESC cell


title: Sample 1938_Single mESC cell


title: Sample 1957_Single mESC cell


title: Sample 1935_Single mESC cell


title: Sample 1936_Single mESC cell


title: Sample 1940_Single mESC cell


title: Sample 1943_Single mESC cell


title: Sample 1951_Single mESC cell


title: Sample 1941_Single mESC cell


title: Sample 1937_Single mESC cell


title: Sample 1939_Single mESC cell


title: Sample 1931_Single mESC cell


title: Sample 1934_Single mESC cell


title: Sample 1927_Single mESC cell


title: Sample 1933_Single mESC cell


title: Sample 1930_Single mESC cell


title: Sample 1928_Single mESC cell


title: Sample 1929_Single mESC cell


title: Sample 1925_Single mESC cell


title: Sample 1924_Single mESC cell


title: Sample 1942_Single mESC cell


title: Sample 1932_Single mESC cell


title: Sample 1923_Single mESC cell


title: Sample 1926_Single mESC cell


title: Sample 1945_Single mESC cell


title: Sample 1922_Single mESC cell


title: Sample 1921_Single mESC cell


title: Sample 1920_Single mESC cell


title: Sample 1919_Single mESC cell


title: Sample 1917_Single mESC cell


title: Sample 1918_Single mESC cell


title: Sample 1916_Single mESC cell


title: Sample 1915_Single mESC cell


title: Sample 1912_Single mESC cell


title: Sample 1911_Single mESC cell


title: Sample 1914_Single mESC cell


title: Sample 1913_Single mESC cell


title: Sample 1909_Single mESC cell


title: Sample 1907_Single mESC cell


title: Sample 1905_Single mESC cell


title: Sample 1908_Single mESC cell


title: Sample 1906_Single mESC cell


title: Sample 1904_Single mESC cell


title: Sample 1894_Single mESC cell


title: Sample 1910_Single mESC cell


title: Sample 1898_Single mESC cell


title: Sample 1900_Single mESC cell


title: Sample 1897_Single mESC cell


title: Sample 1899_Single mESC cell


title: Sample 1902_Single mESC cell


title: Sample 1893_Single mESC cell


title: Sample 1903_Single mESC cell


title: Sample 1896_Single mESC cell


title: Sample 1891_Single mESC cell


title: Sample 1892_Single mESC cell


title: Sample 1890_Single mESC cell


title: Sample 1895_Single mESC cell


title: Sample 1901_Single mESC cell


title: Sample 1888_Single mESC cell


title: Sample 1885_Single mESC cell


title: Sample 1887_Single mESC cell


title: Sample 1886_Single mESC cell


title: Sample 1884_Single mESC cell


title: Sample 1882_Single mESC cell


title: Sample 1877_Single mESC cell


title: Sample 1878_Single mESC cell


title: Sample 1883_Single mESC cell


title: Sample 1880_Single mESC cell


title: Sample 1875_Single mESC cell


title: Sample 1879_Single mESC cell


title: Sample 1881_Single mESC cell


title: Sample 1869_Single mESC cell


title: Sample 1871_Single mESC cell


title: Sample 1874_Single mESC cell


title: Sample 1870_Single mESC cell


title: Sample 1872_Single mESC cell


title: Sample 1873_Single mESC cell


title: Sample 1867_Single mESC cell


title: Sample 1868_Single mESC cell


title: Sample 1862_Single mESC cell


title: Sample 1861_Single mESC cell


title: Sample 1863_Single mESC cell


title: Sample 1864_Single mESC cell


title: Sample 1860_Single mESC cell


title: Sample 1866_Single mESC cell


title: Sample 1859_Single mESC cell


title: Sample 1858_Single mESC cell


title: Sample 1857_Single mESC cell


title: Sample 1856_Single mESC cell


title: Sample 1876_Single mESC cell


title: Sample 1855_Single mESC cell


title: Sample 1854_Single mESC cell


title: Sample 1848_Single mESC cell


title: Sample 1889_Single mESC cell


title: Sample 1847_Single mESC cell


title: Sample 1852_Single mESC cell


title: Sample 1845_Single mESC cell


title: Sample 1849_Single mESC cell


title: Sample 1844_Single mESC cell


title: Sample 1851_Single mESC cell


title: Sample 1865_Single mESC cell


title: Sample 1846_Single mESC cell


title: Sample 1841_Single mESC cell


title: Sample 1840_Single mESC cell


title: Sample 1842_Single mESC cell


title: Sample 1838_Single mESC cell


title: Sample 1837_Single mESC cell


title: Sample 1833_Single mESC cell


title: Sample 1834_Single mESC cell


title: Sample 1835_Single mESC cell


title: Sample 1832_Single mESC cell


title: Sample 1831_Single mESC cell


title: Sample 1830_Single mESC cell


title: Sample 1829_Single mESC cell


title: Sample 1828_Single mESC cell


title: Sample 1826_Single mESC cell


title: Sample 1850_Single mESC cell


title: Sample 1853_Single mESC cell


title: Sample 1827_Single mESC cell


title: Sample 1843_Single mESC cell


title: Sample 1825_Single mESC cell


title: Sample 1824_Single mESC cell


title: Sample 1820_Single mESC cell


title: Sample 1822_Single mESC cell


title: Sample 1819_Single mESC cell


title: Sample 1823_Single mESC cell


title: Sample 1815_Single mESC cell


title: Sample 1836_Single mESC cell


title: Sample 1812_Single mESC cell


title: Sample 1839_Single mESC cell


title: Sample 1811_Single mESC cell


title: Sample 1817_Single mESC cell


title: Sample 1808_Single mESC cell


title: Sample 1810_Single mESC cell


title: Sample 1814_Single mESC cell


title: Sample 1813_Single mESC cell


title: Sample 1806_Single mESC cell


title: Sample 1809_Single mESC cell


title: Sample 1807_Single mESC cell


title: Sample 1805_Single mESC cell


title: Sample 1803_Single mESC cell


title: Sample 1801_Single mESC cell


title: Sample 1802_Single mESC cell


title: Sample 1799_Single mESC cell


title: Sample 1821_Single mESC cell


title: Sample 1818_Single mESC cell


title: Sample 1798_Single mESC cell


title: Sample 1797_Single mESC cell


title: Sample 1816_Single mESC cell


title: Sample 1796_Single mESC cell


title: Sample 1790_Single mESC cell


title: Sample 1789_Single mESC cell


title: Sample 1792_Single mESC cell


title: Sample 1788_Single mESC cell


title: Sample 1791_Single mESC cell


title: Sample 1787_Single mESC cell


title: Sample 1783_Single mESC cell


title: Sample 1786_Single mESC cell


title: Sample 1785_Single mESC cell


title: Sample 1779_Single mESC cell


title: Sample 1781_Single mESC cell


title: Sample 1780_Single mESC cell


title: Sample 1784_Single mESC cell


title: Sample 1777_Single mESC cell


title: Sample 1804_Single mESC cell


title: Sample 1778_Single mESC cell


title: Sample 1775_Single mESC cell


title: Sample 1773_Single mESC cell


title: Sample 1774_Single mESC cell


title: Sample 1794_Single mESC cell


title: Sample 1771_Single mESC cell


title: Sample 1793_Single mESC cell


title: Sample 1776_Single mESC cell


title: Sample 1769_Single mESC cell


title: Sample 1772_Single mESC cell


title: Sample 1767_Single mESC cell


title: Sample 1768_Single mESC cell


title: Sample 1795_Single mESC cell


title: Sample 1763_Single mESC cell


title: Sample 1766_Single mESC cell


title: Sample 1782_Single mESC cell


title: Sample 1764_Single mESC cell


title: Sample 1762_Single mESC cell


title: Sample 1761_Single mESC cell


title: Sample 1760_Single mESC cell


title: Sample 1765_Single mESC cell


title: Sample 1759_Single mESC cell


title: Sample 1757_Single mESC cell


title: Sample 1755_Single mESC cell


title: Sample 1800_Single mESC cell


title: Sample 1758_Single mESC cell


title: Sample 1754_Single mESC cell


title: Sample 1752_Single mESC cell


title: Sample 1770_Single mESC cell


title: Sample 1751_Single mESC cell


title: Sample 1753_Single mESC cell


title: Sample 1750_Single mESC cell


title: Sample 1748_Single mESC cell


title: Sample 1747_Single mESC cell


title: Sample 1746_Single mESC cell


title: Sample 1745_Single mESC cell


title: Sample 1744_Single mESC cell


title: Sample 1743_Single mESC cell


title: Sample 1742_Single mESC cell


title: Sample 1741_Single mESC cell


title: Sample 1740_Single mESC cell


title: Sample 1739_Single mESC cell


title: Sample 1737_Single mESC cell


title: Sample 1738_Single mESC cell


title: Sample 1736_Single mESC cell


title: Sample 1735_Single mESC cell


title: Sample 1733_Single mESC cell


title: Sample 1756_Single mESC cell


title: Sample 1734_Single mESC cell


title: Sample 1749_Single mESC cell


title: Sample 1731_Single mESC cell


title: Sample 1728_Single mESC cell


title: Sample 1732_Single mESC cell


title: Sample 1730_Single mESC cell


title: Sample 1726_Single mESC cell


title: Sample 1725_Single mESC cell


title: Sample 1724_Single mESC cell


title: Sample 1723_Single mESC cell


title: Sample 1721_Single mESC cell


title: Sample 1720_Single mESC cell


title: Sample 1719_Single mESC cell


title: Sample 1729_Single mESC cell


title: Sample 1718_Single mESC cell


title: Sample 1722_Single mESC cell


title: Sample 1717_Single mESC cell


title: Sample 1716_Single mESC cell


title: Sample 1715_Single mESC cell


title: Sample 1710_Single mESC cell


title: Sample 1711_Single mESC cell


title: Sample 1714_Single mESC cell


title: Sample 1707_Single mESC cell


title: Sample 1708_Single mESC cell


title: Sample 1713_Single mESC cell


title: Sample 1727_Single mESC cell


title: Sample 1712_Single mESC cell


title: Sample 1706_Single mESC cell


title: Sample 1703_Single mESC cell


title: Sample 1704_Single mESC cell


title: Sample 1701_Single mESC cell


title: Sample 1705_Single mESC cell


title: Sample 1700_Single mESC cell


title: Sample 1699_Single mESC cell


title: E14_pal_KO2

city: Chapel Hill

first: Karl

middle: B.

last: Shpargel

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

description: 25bp paired end sequencing

data_processing:
Aligned RNA-seq to get bam-file: tophat2 with options: --library-type fr-firststrand -p 1 --no-novel-juncs --mate-inner-dist 315 --mate-std-dev 150 --no-mixed --no-discordant -G MM9_UCSC_genes.gtf MM9_UCSC_Bowtie2Index_genome R1.fastq.gz R2.fastq.gz
Calculated RNA-seq read counts for each gene: samtools view bam-file put into htseq-count with options: --stranded=reverse -m intersection-nonempty - MM9_UCSC_genes.gtf
Genome_build: mm9
Supplementary_files_format_and_content: counts.txt files are TSV htseq-count rna read counts per gene

source_name: dissected palatal shelf

extract_protocol:
For RNA isolation, dissected palatal shelves were dissociated in Trizol  and processed accordingly.
RNA-seq: KAPA KK8580 Stranded mRNA-seq Kit for mRNA isolation, cDNA production, KAPA KK8722 dual index adapter ligation, and library amplification.

treatment_protocol: 3 biological replicates of E14.25 paired palatal shelves from WT and KMT2D neural crest cell knockout mouse embryos were dissected and snap frozen in Trizol

tag: developmental stage

value: Embryonic day E14.25

value: Kmt2dfl/fl Wnt1-Cre


title: E14_pal_WT4

description: 25bp paired end sequencing

value: WT


title: E14_pal_KO1

description: 25bp paired end sequencing


title: E14_pal_WT2

description: 25bp paired end sequencing


title: Sample 1698_Single mESC cell


title: Sample 1697_Single mESC cell


title: Sample 1696_Single mESC cell


title: Sample 1709_Single mESC cell


title: Sample 1695_Single mESC cell


title: Sample 1694_Single mESC cell


title: Sample 1693_Single mESC cell


title: Sample 1692_Single mESC cell


title: (+)siD1_10 FGC1198_s_2

city: Miinneapolis

first: Jeffrey

middle: H

last: Albrecht

state: MN

address: One Veterans Drive

department: Medicine - Gastroenterology

institute: University of Minnesota

description:
FBS(+) Cyclin-D1 siRNA rep-10
(+)siD1_10
RawTranscriptCounts_AML12.xls

data_processing:
Illumina's bcl2fastq-v2.17.1.14 software was used to convert BCL basecall files to fastq files.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to respective genomes and Refseq transcriptome. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
ChIP-Seq: Peak calling on HNF4a ChIP samples was done using HOMER in factor mode and FDR cut off of 0.01 with respect to corresponding Input. Bioconductor's diffBind package was used for differential binding analysis.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Excel file with raw transcript counts
Supplementary_files_format_and_content: Tab-delimited peak files listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.

source_name: AML12 cells (ATCC® CRL-2254™)

growth_protocol:
RNA-Seq: AML12, HepG2, and Sk-Hep1 cells were cultured in the presence or absence of serum along with control or cyclin D1 siRNA (see PMID 27351284 and 22751438 for the culture conditions). HepG2 and SK-HEP-1 cells were cultured in the presence of control or cyclin D1 siRNA (see PMID 27351284 for the culture conditions)
ChIP-Seq: Male BALB/c mice were transduced with recombinant adenoviruses encoding cyclin D1-HA-FLAG or cyclin D1-RD-FLAG (see PMID: 22751438 and 27351284 for details). Livers were harvested 24 hours later for ChIP-seq.

extract_protocol:
RNA-Seq: RNA was extracted using Qiazol followed by purification using the miRNeasy kit (Qiagen)
ChIP-Seq: DNA was exgtracted from mouse liver as previously described (PMID: 18556755).
RNA-Seq: Libraries were prepared using TruSeq Stranded mRNA HT kit using standard Illumina protocols
ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions.

treatment_protocol:
RNA-Seq: AML 12 cells were cultured in 10% FBS (FBS(+)) or had withdrawal of serum 24 hours before harvest (FBS(-)). 45 hours before harvest, AML 12, HepG2 and SK-Hep-1 cells were treated with control or cyclin D1 siRNA (Dharmacon On-Target plus SMARTpool, catalog # L-042441-00-0020).
ChIP-Seq:  Mice were treated with recombinant adenoviruses as above.


title: Sample 1702_Single mESC cell


title: (+)siD1_10 FGC1198_s_3


title: (+)siD1_9 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-9
(+)siD1_9
RawTranscriptCounts_AML12.xls


title: (+)siD1_10 FGC1198_s_1


title: E14_pal_KO3

description: 25bp paired end sequencing


title: Sample 1691_Single mESC cell


title: (+)siD1_9 FGC1198_s_2


title: (+)siD1_9 FGC1198_s_1


title: (+)siD1_9 FGC1198_s_3


title: Sample 1688_Single mESC cell


title: Sample 1689_Single mESC cell


title: (+)siD1_7 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-7
(+)siD1_7
RawTranscriptCounts_AML12.xls


title: E14_pal_WT3

description: 25bp paired end sequencing


title: (+)siD1_7 FGC1198_s_3


title: (+)siD1_7 FGC1198_s_2


title: (+)siD1_10 FGC1198_s_4


title: Sample 1686_Single mESC cell


title: Sample 1684_Single mESC cell


title: Sample 1687_Single mESC cell


title: (+)siD1_7 FGC1198_s_1


title: (+)siD1_6 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-6
(+)siD1_6
RawTranscriptCounts_AML12.xls


title: Sample 1683_Single mESC cell


title: (+)siD1_6 FGC1198_s_2


title: (+)siD1_6 FGC1198_s_3


title: (+)siD1_6 FGC1198_s_1


title: Sample 1685_Single mESC cell


title: Sample 1690_Single mESC cell


title: (+)siD1_5 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-5
(+)siD1_5
RawTranscriptCounts_AML12.xls


title: (+)siD1_5 FGC1198_s_3


title: (+)siD1_5 FGC1198_s_2


title: Sample 1679_Single mESC cell


title: (+)siD1_5 FGC1198_s_1


title: (+)siD1_4 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-4
(+)siD1_4
RawTranscriptCounts_AML12.xls


title: (+)siD1_4 FGC1198_s_3


title: Sample 1677_Single mESC cell


title: Sample 1678_Single mESC cell


title: Sample 1680_Single mESC cell


title: (+)siD1_4 FGC1198_s_2


title: (+)siD1_4 FGC1198_s_1


title: Sample 1681_Single mESC cell


title: Sample 1676_Single mESC cell

value: day 0


title: (+)siD1_3 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-3
(+)siD1_3
RawTranscriptCounts_AML12.xls


title: Sample 1675_Single mESC cell


title: Sample 1674_Single mESC cell


title: Sample 1673_Single mESC cell


title: Sample 1672_Single mESC cell


title: (+)siD1_3 FGC1198_s_1


title: Sample 1682_Single mESC cell


title: (+)siD1_3 FGC1198_s_2


title: (+)siD1_1 FGC1198_s_4

description:
FBS(+) Cyclin-D1 siRNA rep-1
(+)siD1_1
RawTranscriptCounts_AML12.xls


title: Sample 1670_Single mESC cell


title: Sample 1668_Single mESC cell


title: Sample 1669_Single mESC cell


title: Sample 1666_Single mESC cell


title: (+)siD1_1 FGC1198_s_2


title: (+)siC_8 FGC1198_s_4

description:
FBS(+) Control siRNA rep-8
(+)siC_8
RawTranscriptCounts_AML12.xls


title: Sample 1665_Single mESC cell


title: (+)siD1_1 FGC1198_s_1


title: (+)siC_8 FGC1198_s_2


title: Sample 1664_Single mESC cell


title: (+)siD1_3 FGC1198_s_3


title: (+)siC_7 FGC1198_s_4

description:
FBS(+) Control siRNA rep-7
(+)siC_7
RawTranscriptCounts_AML12.xls


title: (+)siC_8 FGC1198_s_1


title: (+)siC_8 FGC1198_s_3


title: Sample 1659_Single mESC cell


title: Sample 1663_Single mESC cell


title: Sample 1662_Single mESC cell


title: Sample 1671_Single mESC cell


title: (+)siC_7 FGC1198_s_3


title: Sample 1660_Single mESC cell


title: (+)siC_7 FGC1198_s_1


title: (+)siD1_1 FGC1198_s_3


title: (+)siC_6 FGC1198_s_4

description:
FBS(+) Control siRNA rep-6
(+)siC_6
RawTranscriptCounts_AML12.xls


title: Sample 1657_Single mESC cell


title: (+)siC_6 FGC1198_s_3


title: Sample 1658_Single mESC cell


title: Sample 1656_Single mESC cell


title: (+)siC_6 FGC1198_s_2


title: (+)siC_6 FGC1198_s_1


title: Sample 1667_Single mESC cell


title: Sample 1655_Single mESC cell


title: Sample 1653_Single mESC cell


title: Sample 1654_Single mESC cell


title: Sample 1661_Single mESC cell


title: (+)siC_5 FGC1198_s_4

description:
FBS(+) Control siRNA rep-5
(+)siC_5
RawTranscriptCounts_AML12.xls


title: Sample 1652_Single mESC cell


title: (+)siC_5 FGC1198_s_3


title: (+)siC_7 FGC1198_s_2


title: Sample 1651_Single mESC cell


title: (+)siC_5 FGC1198_s_2


title: (+)siC_5 FGC1198_s_1


title: Sample 1649_Single mESC cell


title: Sample 1650_Single mESC cell


title: Sample 1648_Single mESC cell


title: (+)siC_4 FGC1198_s_4

description:
FBS(+) Control siRNA rep-4
(+)siC_4
RawTranscriptCounts_AML12.xls


title: (+)siC_4 FGC1198_s_2


title: (+)siC_4 FGC1198_s_1


title: Sample 1647_Single mESC cell


title: (+)siC_4 FGC1198_s_3


title: Sample 1646_Single mESC cell


title: (+)siC_3 FGC1198_s_2

description:
FBS(+) Control siRNA rep-3
(+)siC_3
RawTranscriptCounts_AML12.xls


title: Sample 1645_Single mESC cell


title: (+)siC_3 FGC1198_s_4


title: (+)siC_3 FGC1198_s_1


title: (+)siC_3 FGC1198_s_3


title: (+)siC_2 FGC1198_s_4

description:
FBS(+) Control siRNA rep-2
(+)siC_2
RawTranscriptCounts_AML12.xls


title: Sample 1644_Single mESC cell


title: Sample 1643_Single mESC cell


title: Sample 1641_Single mESC cell


title: Sample 1642_Single mESC cell


title: (+)siC_2 FGC1198_s_3


title: (+)siC_2 FGC1198_s_2


title: Sample 1640_Single mESC cell


title: Sample 1639_Single mESC cell


title: (+)siC_2 FGC1198_s_1


title: (+)siC_1 FGC1198_s_3

description:
FBS(+) Control siRNA rep-1
(+)siC_1
RawTranscriptCounts_AML12.xls


title: (+)siC_1 FGC1198_s_4


title: Sample 1637_Single mESC cell


title: Sample 1636_Single mESC cell


title: (+)siC_1 FGC1198_s_2


title: Sample 1635_Single mESC cell


title: (+)siC_1 FGC1198_s_1


title: Sample 1634_Single mESC cell


title: Sample 1632_Single mESC cell


title: (-)_siC_6 FGC1198_s_2

description:
FBS(-) Control siRNA rep-6
(-)_siC_6
RawTranscriptCounts_AML12.xls


title: (-)_siC_6 FGC1198_s_3


title: Sample 1638_Single mESC cell


title: Sample 1631_Single mESC cell


title: (-)_siC_5 FGC1198_s_3

description:
FBS(-) Control siRNA rep-5
(-)_siC_5
RawTranscriptCounts_AML12.xls


title: (-)_siC_5 FGC1198_s_4


title: (-)_siC_6 FGC1198_s_1


title: Sample 1629_Single mESC cell


title: Sample 1630_Single mESC cell


title: (-)_siC_6 FGC1198_s_4


title: Sample 1626_Single mESC cell


title: (-)_siC_5 FGC1198_s_1


title: Sample 1628_Single mESC cell


title: Sample 1627_Single mESC cell


title: (-)_siC_5 FGC1198_s_2


title: Sample 1625_Single mESC cell


title: Sample 1624_Single mESC cell


title: (-)_siC_4 FGC1198_s_4

description:
FBS(-) Control siRNA rep-4
(-)_siC_4
RawTranscriptCounts_AML12.xls


title: (-)_siC_4 FGC1198_s_2


title: Sample 1623_Single mESC cell


title: (-)_siC_4 FGC1198_s_3


title: Sample 1622_Single mESC cell


title: Sample 1633_Single mESC cell


title: (-)_siC_4 FGC1198_s_1


title: (-)_siC_3 FGC1198_s_3

description:
FBS(-) Control siRNA rep-3
(-)_siC_3
RawTranscriptCounts_AML12.xls


title: Sample 1621_Single mESC cell


title: Sample 1620_Single mESC cell


title: Sample 1619_Single mESC cell


title: (-)_siC_3 FGC1198_s_2


title: Sample 1617_Single mESC cell


title: Sample 1616_Single mESC cell


title: Sample 1618_Single mESC cell


title: (-)_siC_3 FGC1198_s_1


title: (-)_siC_2 FGC1198_s_4

description:
FBS(-) Control siRNA rep-2
(-)_siC_2
RawTranscriptCounts_AML12.xls


title: (-)_siC_2 FGC1198_s_3


title: Sample 1615_Single mESC cell


title: (-)_siC_2 FGC1198_s_2


title: (-)_siC_1 FGC1198_s_4

description:
FBS(-) Control siRNA rep-1
(-)_siC_1
RawTranscriptCounts_AML12.xls


title: Sample 1614_Single mESC cell


title: Sample 1613_Single mESC cell


title: (-)_siC_2 FGC1198_s_1


title: (-)_siC_1 FGC1198_s_3


title: (-)_siC_1 FGC1198_s_1


title: (-)_siC_3 FGC1198_s_4


title: (-)_siC_1 FGC1198_s_2


title: Sample 1609_Single mESC cell


title: Sample 1606_Single mESC cell


title: Sample 1605_Single mESC cell


title: Sample 1604_Single mESC cell


title: Sample 1607_Single mESC cell


title: Sample 1603_Single mESC cell


title: Sample 1601_Single mESC cell


title: Sample 1602_Single mESC cell


title: Sample 1600_Single mESC cell


title: Sample 1599_Single mESC cell


title: Sample 1597_Single mESC cell


title: Sample 1596_Single mESC cell


title: Sample 1595_Single mESC cell


title: Sample 1594_Single mESC cell


title: Sample 1593_Single mESC cell


title: Sample 1589_Single mESC cell


title: Sample 1611_Single mESC cell


title: Sample 1592_Single mESC cell


title: Sample 1587_Single mESC cell


title: Sample 1591_Single mESC cell


title: Sample 1612_Single mESC cell


title: Sample 1582_Single mESC cell


title: Sample 1585_Single mESC cell


title: Sample 1584_Single mESC cell


title: Sample 1588_Single mESC cell


title: Sample 1579_Single mESC cell


title: Sample 1610_Single mESC cell


title: Sample 1608_Single mESC cell


title: Sample 1586_Single mESC cell


title: Sample 1578_Single mESC cell


title: Sample 1580_Single mESC cell


title: Sample 1583_Single mESC cell


title: Sample 1570_Single mESC cell


title: Sample 1590_Single mESC cell


title: Sample 1569_Single mESC cell


title: Sample 1571_Single mESC cell


title: Sample 1577_Single mESC cell


title: Sample 1598_Single mESC cell


title: Sample 1576_Single mESC cell


title: Sample 1575_Single mESC cell


title: Sample 1574_Single mESC cell


title: Sample 1564_Single mESC cell


title: Sample 1573_Single mESC cell


title: Sample 1566_Single mESC cell


title: Sample 1572_Single mESC cell


title: Sample 1567_Single mESC cell


title: Sample 1565_Single mESC cell


title: Sample 1555_Single mESC cell


title: Sample 1561_Single mESC cell


title: Sample 1562_Single mESC cell


title: Sample 1559_Single mESC cell


title: Sample 1557_Single mESC cell


title: Sample 1556_Single mESC cell


title: Sample 1558_Single mESC cell


title: Sample 1552_Single mESC cell


title: Sample 1549_Single mESC cell


title: Sample 1546_Single mESC cell


title: Sample 1568_Single mESC cell


title: Sample 1550_Single mESC cell


title: Sample 1548_Single mESC cell


title: Sample 1544_Single mESC cell


title: Sample 1551_Single mESC cell


title: Sample 1542_Single mESC cell


title: Sample 1543_Single mESC cell


title: Sample 1545_Single mESC cell


title: Sample 1581_Single mESC cell


title: Sample 1560_Single mESC cell


title: Sample 1540_Single mESC cell


title: Sample 1563_Single mESC cell


title: Sample 1554_Single mESC cell


title: Sample 1539_Single mESC cell


title: Sample 1553_Single mESC cell


title: Sample 1538_Single mESC cell


title: Sample 1537_Single mESC cell


title: Sample 1536_Single mESC cell


title: Sample 1535_Single mESC cell


title: Sample 1547_Single mESC cell


title: Sample 1534_Single mESC cell


title: Lkyn_Cut_6_2

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

data_processing:
Reads were aligned to the genome using Bowtie2, followed by readcount using htseq-count
Expression data were normalized using Deseq2
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Normalized expression reads for all replicates

organism: Arabidopsis thaliana

source_name: Cut apical root meristems

growth_protocol: Seedslings were germinated on 1/2MS agar plates containing 0.5% sucrose. Following 2 days at 4c, plates were move to a 22c for 16h light/8h dark cycle for 7 days

extract_protocol:
Root tips were flash frozen, grinded and RNA extracted using RNeasy micro-kit (Qiagen) according to the manufacturer instructions
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.

treatment_protocol: For L-Kyn treatments, 7 days old seedlings were

value: L-kyn 6h


title: Lkyn_Cut_6_3


title: Lkyn_Cut_3_2

value: L-kyn 3h


title: Lkyn_Cut_6_1


title: Sample 1531_Single mESC cell


title: Lkyn_Cut_3_1


title: Mock_Cut_6_2

value: mock 6h after cut


title: Sample 1532_Single mESC cell


title: Sample 1541_Single mESC cell


title: Sample 1530_Single mESC cell


title: 12-TC83-P1

city: Louisville

first: Dylan

middle: MacGregor

last: Johnson

state: KY

address: 505 S Hancock St., CTRB RM642B

department: Microbiology & Immunology

institute: University of Louisville, School of Medicine

description: rRNA depleted total RNA

data_processing:
Trimmomatic (Galaxy Version 0.36.6) Sliding window trimming across 4 average bases with 20 average quality required
Bowtie2 (Galaxy Version 2.3.4.2) Alignment to TC-83 or V4020 reference sequence with default settings, unaligned reads to new fastq file
Samtools mpileup (Galaxy Version 2.1.4) on Bowtie2 BAM files with TC-83 or V4020 reference sequence
Filter pileup (Galaxy Version 1.0.2)
HiSat2 (Galaxy Version 2.1.0) alginment of unalinged reads fastq from Bowtie2 to mm10 genome
htseq-count (Galaxy version 0.9.1) on HiSat2 alignment
DESeq2 (Galaxy Version 2.11.40.2) both by passage and with a virus x passage facor model
goseq (Galaxy Version 1.26.0)
Genome_build: L01443.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet containing filtered pileup data from each virus alignment. Also includes analysis of mutation rate, read depth, and nucleotide variation.
Supplementary_files_format_and_content: Excel spreadsheet containing the output from DESeq2 showing differential expression from both a "virus x passage" model and each individual passage, along with normalized read counts.

source_name: brain

growth_protocol: BALB/c mice were inoculated via the intracranial route with 10^5 PFU of serial passaged VEEV strain V4020 or strain TC-83. Two days post inoculation, mice were sacrificed and brain tissue was collected in Trizol reagent for total RNA isolation.

extract_protocol:
Tissue was placed in 1 ml trizol (ThermoFisher #15596018) with glass beads,  homogenized on an omni bead-beater, and isolated with BCP according to the manufactuer's protocol.
RNA was DNAse I treated (Zymo Research, #E1010) and purified with an Rneasy mini kit (Quiagen, #74104) followed by rRNA depletion (NEB, #E6310), and Illumina library prep (NEB, #7775).

value: BALB/c

tag: veev strain

value: VEEV strain TC-83

value: Brain

tag: passage

value: Passage 1


title: 67-TC83-P3

description: rRNA depleted total RNA

value: Passage 3


title: 117-TC83-P5

description: rRNA depleted total RNA

value: Passage 5


title: 42-TC83-P2

description: rRNA depleted total RNA

value: Passage 2


title: 92-TC83-P4

description: rRNA depleted total RNA

value: Passage 4


title: Mock_Cut_6_1


title: 11-TCC83-P1

description: rRNA depleted total RNA


title: Sample 1529_Single mESC cell

tag: cell line

value: Differentiated mESC


title: Sample 1528_Single mESC cell


title: Mock_Cut_3_3

value: mock 3h after cut


title: Sample 1527_Single mESC cell


title: Sample 1533_Single mESC cell


title: Mock_Cut_3_1


title: 107-V4020-P5

description: rRNA depleted total RNA

value: VEEV strain V4020


title: 106-V4020-P5

description: rRNA depleted total RNA


title: 81-V4020-P4

description: rRNA depleted total RNA


title: 57-V4020-P3

description: rRNA depleted total RNA


title: Sample 1525_Single mESC cell


title: Lkyn_Uncut_6_1


title: Lkyn_Uncut_6_2

source_name: Apical root meristem


title: Mock_Cut_3_2


title: Sample 1524_Single mESC cell


title: Sample 1526_Single mESC cell


title: Lkyn_Uncut_3_3


title: Sample 1523_Single mESC cell


title: 56-V4020-P3

description: rRNA depleted total RNA


title: 2-V4020-P1

description: rRNA depleted total RNA


title: 32-V4020-P2

description: rRNA depleted total RNA