title: Mouse embryo fibroblast-PBS rep3

city: Chengdu

first: Feihong

last: Gan

state: Sichuan

address: No.14, Third Section, Ren Min Nan Road

institute: Sichuan University

description: Sample 7

data_processing:
Quality control and mapping: Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster  analysis, GO and KEGG enrichment: FPKM value of each gene was calculated using cufflinks, and the read counts of each gene  were obtained by htseq-count. DEGs were identified using the DESeq R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment: If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2   and eXpress. DEGs were identified using the DESeq  functions estimateSizeFactors and nbinomTest. P value < 0.05 and  foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were  respectively performed using R based on the hypergeometric distribution.
Gene structure extension and novel transcripts identification: The reads were reassembled using StringTie . Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
Alternatively splicing analysis and SNP-INDEL calling: The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile. SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Mouse embryo fibroblast

extract_protocol:
Total RNA was extracted from cell lysates using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500) and 125bp/150bp paired-end reads were generated.

value: PBS

tag: disease state

value: Radiation injury


title: small intestine p53 on rep2

status: Public on Jun 30 2021

type: SRA

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
4-Hydroytamoxifen treated
small_intestine.txt
small_intestine_p53_on_2

library_source: transcriptomic

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16   --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

molecule: total RNA

organism: Mus musculus

source_name: small intestinal organoids

growth_protocol: Organoids were generated and propagated as described before (Sato and Clevers, 2013; Sato et al., 2009; Yui et al., 2012)

extract_protocol:
RNA was isolated according to manufacturer's protocol (Roboklon, Cat#E3598)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cre recombination was induced in vitro with 4-Hydroxytamoxifen (0.5 µM for SI organoids, 3.5 µM for COL organoids) or organoids were treated with ethanol as controls for 24 hours. SI organoid RNA was isolated 8 days, and COL organoid RNA was isolated 3 days after Cre recombination.

tag: strain

tag: tissue

value: small intestine

tag: genotype

tag: agent


title: mPFC_social defeat_susceptible_Right_replicate2

type: RNA

city: Daejeon

first: Sujin

last: Chae

address: 291 Daehak-ro

country: South Korea

institute: KAIST

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The prepared microarrays were scanned with an Illumina BeadArray reader

data_processing: The prepared microarrays were preprocessed by the Illumina GenomeStudio software (version 1.0.6). Raw signals of at least two biological replicates per condition were transformed to log2 scale and normalized by using the Bioconductor lumi package. Differentially expressed genes (DEGs) were identified by using the Bioconductor limma package with an false discovery rate (FDR) adjusted p-value cutoff of 0.05.

label: biotin

source_name: mouse right mPFC of susceptible of social defeat mice

label_protocol: Illumina

extract_protocol: Total RNA of each 7 representative mice was prepared by Trizol method then further purified by RNAeasy kit (Qiagen, USA). The left and right mPFC RNA of susceptible, resilient and control mice was used for microarray analysis with the MouseRef-8_V2 Expression BeadChip (Illumina).

tag: region

value: medial prefrontal cortex

value: brain


title: mPFC_social defeat_resilient_Right_replicate2

source_name: mouse right mPFC of resilient of social defeat mice


title: THP1.1000nM.GSK862.d4.n2 [S1-126]

city: Collegeville

first: Shawn

middle: W

last: Foley

state: PA

address: 1250 S. Collegeville Rd

department: Oncology

country: USA

institute: GlaxoSmithKline

description: processed data file: DNMT1_AML_fpkm_THP1_table.txt

data_processing:
Salmon_v0.12.0 transcript quantification
DEseq2 log2 fold change differential expression and normalized fpkm quantification
fGSEA gene set enrichment analysis
Genome_build: Human hg38
Supplementary_files_format_and_content: fpkm values for all quantifiable genes; log2 fold change values for all quantifiable genes

organism: Homo sapiens

growth_protocol: Cell lines were obtained from the American Type Culture Collection, the Deutsche Sammlung von Mikroorganismen und Zellbulturen, or AddexBio and maintained in the recommended cell culture media at 37°C in 5% CO2.

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini kit
Libraries were prepared at the NYU Medical Center Genome Technology Center
All 150 PE libraries were sequenced across 6 lanes for a total of 12 fastq samples per sample.

treatment_protocol: Cells were plated 24 hours before treatment with either DMSO, GSK3484862, GSK3685032, DAC, or GSK3510477 then grown for the indicated time before collection.

tag: cell line

tag: cell tye

value: AML cell line

tag: treatment

tag: dose

tag: time

tag: replicate


title: THP1.0nM.DMSO.d6.n2 [S1-128]

value: DMSO


title: THP1.10000nM.DAC.d4.n2 [S1-125]

value: DAC


title: THP1.2000nM.DAC.d4.n2 [S1-124]


title: small intestine Braf off rep2

description:
Ethanol treated control
small_intestine.txt
small_intestine_Braf_off_2

value: Ethanol control


title: small intestine p53 on rep1

description:
4-Hydroytamoxifen treated
small_intestine.txt
small_intestine_p53_on_1


title: Mouse embryo fibroblast-PBS rep1

country: China

description: Sample 3

tag: time point


title: Mouse embryo fibroblast-exosomes rep2

description: Sample 2

value: exosomes


title: THP1.400nM.DAC.d4.n2 [S1-123]


title: THP1.80nM.DAC.d4.n2 [S1-122]


title: small intestine Braf off rep1

description:
Ethanol treated control
small_intestine.txt
small_intestine_Braf_off_1


title: small intestine Braf on rep2

description:
4-Hydroytamoxifen treated
small_intestine.txt
small_intestine_Braf_on_2


title: small intestine Braf on rep1

description:
4-Hydroytamoxifen treated
small_intestine.txt
small_intestine_Braf_on_1


title: Mouse embryo fibroblast-exosomes rep1

description: Sample 1


title: Mouse embryo fibroblast-PBS rep2

description: Sample 6


title: Shox2_ProxE12.5limb_replicate2

city: Calgary

first: John

last: Cobb

state: AB

address: 2500 University Dr. NW

department: Biological Sciences

country: Canada

institute: University of Calgary

library_source: genomic

data_processing:
Library strategy: 4C-Seq
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014).
Reads were mapped to the mm10 (GRCm38) or mm9 (NCBI37) mouse genome assembly with bowtie2 version 2.2.1 (Langmead et al, 2012) with parameters “--end-to-end --sensitive -k 20”. The segtofrag files were obtained after mapping the 4C data on in silico generated restriction enzyme fragment library (NlaIII).
4C profiles (as used in figures) were generated using a running mean algorithm with a window size of eleven fragments. Normalisation is done by dividing the fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were produced through HTSstation using read counts per informative fragment., with smoothing.

molecule: genomic DNA

source_name: E12.5 Proximal Limb cells

extract_protocol:
E12.5 wild-type proximal forelimb segments were dissected in cold 10% fetal bovine Serum (FCS) in PBS. Dissected proximal forelimbs were pooled (10-13 pairs) and dissociated with collagenase (Sigma-Aldrich) and filtered through a 35 micron mesh to isolat
Nuclei were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) under dilute conditions to promote intramolecular ligation. Samples were then digested with DpnII (New England Biolabs) and again ligated with T4 DNA ligase HC (Promega) under dilute conditions. Templates were amplified with inverse PCR primers containing Illumina adapters using Expand long template polymerase (Roche). The sequences of primers for each viewpoint were (illumina adapters underlined):  Shox2 Forward/Reading primer: 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCCAATTAAGAAAATATGTGGCATG; Reverse Primer: CAAGCAGAAGACGGCATACGAAGAATGTGAAGTTTGGTCCC; LHB-A: Forward/Reading primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTACTGCTTAGTAAAGACTAATTATTCATG; Reverse Primer: CAAGCAGAAGACGGCATACGAAATGACATTATTATAAAATGCAATACTCT; PDE4: Forward/Reading primer:   AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGGCTGATTCTCCTGCATG  Reverse Primer: CAAGCAGAAGACGGCATACGAAGTTATAAAGATGATTAAGCTCTGATC  Libraries were sequenced together for each replicate on the Illumina HiSeq 2500 following the manufacturer's protocols. Viewpoint-specific primer sequences were used for subsequent demultiplexing.

value: Embryonic Proximal Forelimb

tag: embryonic day


title: Mouse embryo fibroblast-exosomes rep3

description: Sample 4


title: mPFC_social defeat_susceptible_Left_replicate1

source_name: mouse left mPFC of susceptible of social defeat mice


title: colon Braf p53 off rep1

description:
Ethanol treated control
colon.txt
colon_Braf_p53_off_1

source_name: colonic organoids

value: colon


title: colon Braf p53 off rep2

description:
Ethanol treated control
colon.txt
colon_Braf_p53_off_2


title: LHBA_ProxE12.5limb_replicate1


title: THP1.3.2nM.DAC.d4.n2 [S1-120]


title: PDE4_ProxE12.5limb_replicate1


title: THP1.10000nM.GSK032.d4.n2 [S1-119]


title: colon Braf p53 on rep2

description:
4-Hydroytamoxifen treated
colon.txt
colon_Braf_p53_on_2


title: THP1.16nM.DAC.d4.n2 [S1-121]


title: Shox2_ProxE12.5limb_replicate1


title: THP1.2000nM.GSK032.d4.n2 [S1-118]


title: colon Braf p53 on rep1

description:
4-Hydroytamoxifen treated
colon.txt
colon_Braf_p53_on_1


title: THP1.400nM.GSK032.d4.n2 [S1-117]


title: mPFC_social defeat_resilient_Right


title: THP1.80nM.GSK032.d4.n2 [S1-116]


title: colon p53 off rep2

description:
Ethanol treated control
colon.txt
colon_p53_off_2


title: mPFC_social defeat_control_Right_replicate1

source_name: mouse right mPFC of non-stressed control


title: RAS3

city: Rochester

first: Lilach

middle: O

last: O Lerman

state: Minnesota

address: 200 First St. SW

department: Division of Nephrology & Hypertension

institute: Mayo Clinic

data_processing:
10X Genomics cellranger v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: ischemic kidney

extract_protocol:
at 4 weeks, mice were euthanized, kidney were removed and dissociated for 20 min using Miltenyi Gentle Macs
kidneys were flow sorted to remove debris and dying cells

treatment_protocol: mice were subjected to renal ischemia for 4 weeks.

value: ischemic kidney

tag: age

value: 8 months


title: THP1.16nM.GSK032.d4.n2 [S1-115]


title: Sham4

source_name: normal kidney

value: normal kidney


title: mPFC_social defeat_resilient_Left

source_name: mouse left mPFC of resilient of social defeat mice


title: mPFC_social defeat_resilient_Right_replicate1


title: mPFC_social defeat_resilient_Left_replicate2


title: mPFC_social defeat_susceptible_Left


title: THP1.3.2nM.GSK032.d4.n2 [S1-114]


title: colon p53 off rep1

description:
Ethanol treated control
colon.txt
colon_p53_off_1


title: colon p53 on rep2

description:
4-Hydroytamoxifen treated
colon.txt
colon_p53_on_2


title: mPFC_social defeat_resilient_Left_replicate1


title: colon p53 on rep1

description:
4-Hydroytamoxifen treated
colon.txt
colon_p53_on_1


title: Sham3


title: RAS4


title: RAS2


title: THP1.0nM.DMSO.d4.n2 [S1-113]


title: RAS1


title: THP1.10000nM.GSK477.d2.n2 [S1-112]


title: colon Braf off rep2

description:
Ethanol treated control
colon.txt
colon_Braf_off_2


title: mPFC_social defeat_control_Left_replicate1

source_name: mouse left mPFC of non-stressed control


title: colon Braf off rep1

description:
Ethanol treated control
colon.txt
colon_Braf_off_1


title: THP1.1000nM.GSK862.d2.n2 [S1-111]


title: colon Braf on rep2

description:
4-Hydroytamoxifen treated
colon.txt
colon_Braf_on_2


title: mPFC_social defeat_control_Right


title: THP1.400nM.DAC.d2.n2 [S1-110]

description: processed data file: DNMT1_AML_fpkm_THP1_table.txt


title: Sham2


title: Sham1


title: THP1.400nM.GSK032.d2.n2 [S1-109]


title: p65_ChIPseq

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

institute: Chungbuk National University

data_processing:
Seq reads were mapped to reference mouse genome (mm10 assembly) using HISAT2 with default parameters.
We used the makeTagDirectory followed by findPeaks command from HOMER version 4.9.1 to identify peaks of ChIP-seq enrichment over background.
The total number of mapped reads in each sample was normalized to ten million mapped reads. ChIP-seq data were visualized by preparing custom tracks for the UCSC Genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Bone marrow-derived macrophage cells

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol:
The cells were fixed with 1% formaldehyde and processed for immunoprecipitaton using antibodies against KDM4B, CCAR1, MED1, and p65. The purified DNA and input genomic DNA were subjected to sequencing.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteoclast precursor cells with 30 ng/mL of macrophage colony-stimulating factor (M-CSF) were treated with 100 ng/mL of receptor activator of nuclear factor kappaB ligand (RANKL) for 30 min.

tag: cell type

value: Primary BMM cells

value: 6-8 weeks

tag: chip antibody


title: THP1.0nM.DMSO.d2.n2 [S1-108]


title: mPFC_social defeat_control_Left


title: small intestine replicate 4

description:
donor mouse 5
small_intestine_WT.txt

source_name: small intestinal crypts

extract_protocol:
Murine intestinal crypts were isolated by EDTA chelation, before RNA was subsequently purified according to manufacturer's protocol (Roboklon, Cat#E3598)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: female

value: wild type


title: small intestine replicate 3

description:
donor mouse 3
small_intestine_WT.txt

tag: strain

value: small intestine

value: male


title: CCAR1_ChIPseq


title: THP1.400nM.DAC.d1.n2 [S1-107]


title: colon Braf on rep1

description:
4-Hydroytamoxifen treated
colon.txt
colon_Braf_on_1

tag: tissue


title: small intestine replicate 2

description:
donor mouse 2
small_intestine_WT.txt

tag: genotype


title: THP1.400nM.GSK032.d1.n2 [S1-106]


title: input DNA


title: THP1.0nM.DMSO.d1.n2 [S1-105]


title: small intestine replicate 1

description:
donor mouse 1
small_intestine_WT.txt


title: MED1_ChIPseq


title: MV411.400nM.DAC.d6.n2 [S1-104]

description: processed data file: DNMT1_AML_fpkm_MV411_table.txt


title: MV411.400nM.GSK032.d6.n2 [S1-103]


title: colon replicate 3

description:
donor mouse 3
colon_WT.txt

source_name: colonic crypts


title: KDM4B_ChIPseq


title: 6pos

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to Ensembl mouse genome GRCm38 using STAR aligner 2.4.2a modified with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --chimSegmentMin 20 --twopassMode None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Raw counts calculated by STAR aligner with parameter --quantamode were merged to create count matrix. Counts on the second column of each file were used. Downstream paired differential expression analyses (between Grem1+ and Grem1- pairs) were performed in in R with Bioconductor edgeR Package version 3.28.0 Differentially expressed genes were defined as FDR < 0.05, and absolute value of logFC > 2
Subsequently, we used R package WGCNA (version 1.68), to mine the gene co expression pattern, and hence revealing the biological relevance through enrichment analyses. We used a subset of MSigDB that includes BIOCARTA, HALLMARK, GO, KEGG, PID and REACTOME for enrichment analyses.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv

source_name: Grem1 positive sorted brain cells

extract_protocol:
Total RNA
For RNAseq analysis, 1ug of total RNA was used for sequencing library preparation using a BIOO stranded Poly-A kit (PerkinElmer) according to the manufacturer’s instructions and sequenced on Illumina HiSeq to generate 1 x 100bp single-end reads.

tag: cell population

value: Grem1 positive sorted brain cells


title: 6neg

source_name: Grem1 negative sorted brain cells

value: Grem1 negative sorted brain cells


title: colon replicate 2

description:
donor mouse 2
colon_WT.txt


title: 5pos


title: colon replicate 4

description:
donor mouse 5
colon_WT.txt


title: colon replicate 1

description:
donor mouse 1
colon_WT.txt


title: VS13-5A [methylation]

type: genomic

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

description:
Donor:VS13 Egg:5A
Sample 24

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw data was processed using minfi package in R. FunctionalNormalization method was used for normalization. Average beta values were used for analysis.

label: cy3, cy5

source_name: Cumulus Cells

label_protocol: Illlumina Protocol

extract_protocol: Qiagen extraction protcol

treatment_protocol: In vivo ovarian stimulation according to long or short protocol

value: Female

tag: treatmentprotocol

value: Long

tag: donornum

tag: eggnum

tag: resultcontpreg

value: Neg

tag: resultpregtest


title: shIL13RA2 rep 3

city: Aurora

first: Diana

last: Cittelly

state: CO

department: Pathology

institute: University of Colorado AMC

data_processing:
Clean FASTQ files received from senquencing provider. Presence of adaptors, low-complexity or low-quality sequences of libraries was ruled out with FASTQC.
Total counts, Reads Per Kilobase of exon per Megabase of library size (RPKM) and differentially expressed genes were calculated using Cufflinks. In short, reads were mapped against the human genome assembly using hisat2 v2.1.0. Mapping BAM files were used to generate total counts and RPKM matrices with Cuffnormal (Cufflinks v2.21) and differentially expressed genes were determined with Cuffdiff (Cufflinks v2.21). It was used default parameters in all sofwares.
Genome_build: Human NCBI genome build: GRCh38.p13
Supplementary_files_format_and_content: Tab-delimited text file including FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 231BR cells

growth_protocol: 231BR cells expressing shEV or shRNA-8523 (0.5 million) were plated in triplicate in 10 cm plates in DMEM 10% FBS

extract_protocol:
Cells were collected in 1ml Trizol and isolated total RNA was further purified with RNeasy MinElute Cleanup Kit (Qiagen).
library was constructed by BGI Global genomic services

treatment_protocol: Cells were induced for shRNA expression for 96 hr with 1ug/ml doxy

tag: trophism

value: Brain trophic

value: MDA-MB-231 derived

value: mammary gland/breast; derived from metastatic site

tag: treatment

value: Expressing shRNA targeting IL13Ralpha2


title: MV411.1000nM.GSK862.d4.n2 [S1-100]

tag: cell line

tag: cell tye

value: AML cell line

tag: dose

tag: time

tag: replicate


title: VS8-4A [methylation]

description:
Donor:VS8 Egg:4A
Sample 19

tag: gender

value: Short


title: VS13-4A [methylation]

description:
Donor:VS13 Egg:4A
Sample 22


title: MV411.10000nM.DAC.d4.n2 [S1-99]

value: DAC


title: VS8-2A [methylation]

description:
Donor:VS8 Egg:2A
Sample 17


title: MV411.10000nM.GSK477.d4.n2 [S1-101]


title: VS11-1A [methylation]

description:
Donor:VS11 Egg:1A
Sample 18


title: VS9-3A [methylation]

description:
Donor:VS9 Egg:3A
Sample 21


title: 5neg

tag: strain


title: VS2-2A [methylation]

description:
Donor:VS2 Egg:2A
Sample 11

value: Pos


title: VS6-9A [methylation]

description:
Donor:VS6 Egg:9A
Sample 15

value: NotUsed


title: VS10-4A [methylation]

description:
Donor:VS10 Egg:4A
Sample 14


title: VS10-5A [methylation]

description:
Donor:VS10 Egg:5A
Sample 16


title: VS6-7A [methylation]

description:
Donor:VS6 Egg:7A
Sample 13


title: MV411.0nM.DMSO.d6.n2 [S1-102]

value: DMSO


title: VS9-5A [methylation]

description:
Donor:VS9 Egg:5A
Sample 23


title: MV411.2000nM.DAC.d4.n2 [S1-98]


title: 4pos


title: 3pos


title: shIL13RA2 rep 2

tag: cell type

tag: tissue


title: VS6-5A [methylation]

description:
Donor:VS6 Egg:5A
Sample 12


title: 4neg

tag: cell population


title: VS5-8A [methylation]

description:
Donor:VS5 Egg:8A
Sample 8

tag: treatmentprotocol


title: shEV rep 2

value: Expressing empty vector


title: shIL13RA2 rep 1


title: 2pos


title: MV411.400nM.DAC.d4.n2 [S1-97]


title: 3neg


title: 2neg


title: shEV rep 3


title: VS2-1A [methylation]

description:
Donor:VS2 Egg:1A
Sample 9

tag: donornum


title: VS6-1A [methylation]

description:
Donor:VS6 Egg:1A
Sample 10

tag: eggnum


title: MV411.80nM.DAC.d4.n2 [S1-96]


title: mt_d14_B2

city: Solna

first: Alexander

last: Goedel

address: Solnavägen 9

department: Department of Cell and Molecular Biology (CMB)

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequencing data was aligned and quantified by using the Cell Ranger Pipeline v3.1.0 (10x Genomics) with standard parameters.
Ambient RNA contamination was estimated through the levels of choriogonadotropins expression in epiblast (POU5F1 positive) cells and removed from the count matrix using SoupX (https://github.com/constantAmateur/SoupX).
Filtering of the count matrix was carried out as follows: Genes were kept if they showed expression in at least 3 cells per batch. Cells were kept when they had a mitochondiral gene count percentage of < 7.5% and > 2500 expressed genes (WT_d10_b1, WT_d10_b2, WT_d12_b1, mt_d10_b1) or > 1500 expressed genes (WT_d12_b2,  WT_d14_b1, WT_d14_b2, mt_d12_b1, mt_d12_b2, mt_d14_b2) or > 1000 expressed genes (mt_d14_b1)
Genome_build: Macaca_fascicularis_5.0 release 96
Supplementary_files_format_and_content: CM_filtered_uncoreccted.tsv.gz file contains a UMI (unique molecular identifier) read counts matrix of all samples after filtering genes and cells as described above.
Supplementary_files_format_and_content: CM_filtered_SoupX_corrected.tsv.gz file contains a UMI (unique molecular identifier) read counts matrix of all samples after correction for ambient RNA and filtering genes and cells as described above.

molecule: polyA RNA

organism: Macaca fascicularis

source_name: IVC embryo

growth_protocol: Frozen NHP blastocysts at 5-7 days post fertilization were thawed by Thawing Media (Kizatato, VT802) and cultured in an optimized condition based on a human embryo culture protocol. Briefly, blastocysts were cultured in blastocyst culture medium (BCM) for at least 4 hours to recover. Then they were treated with Acidic Tyrode’s solution (Sigma Aldrich, T1788) to remove the Zona pellucida, and transfer to a ibiTreat 8-well μ-plate (Ibidi) with 300 µL of pre-equilibrated in vitro culture medium 1 (IVC1). On the second day, carefully remove 150 µL of IVC1 and supply with 200 µL pre-equilibrated IVC2. Check the blastocyst growth and change medium every two days until the end of the experiments. IVC1: sterile filtered Advanced DMEM/F12 (Thermo Fisher Scientific), 20% (vol/vol) heat-inactivated FBS (Corning), 2 mM L-Glutamine (Thermo Fisher Scientific), 1x Penicillin/Streptomycin (Thermo Fisher Scientific), 1X ITS-X (Thermos Fisher Scientific). Add 8 nM β-estradiol (Sigma Aldrich), 200 ng/ml Progesterone (Sigma Aldrich), and 25 μM N-aceyl-L-cysteine (Sigma Aldrich) to the pre-filtered medium.  IVC2: sterile filter Advanced DMEM/F12 (Thermo Fisher Scientific), 30% (vol/vol) KnockOut Serum Replacement (Thermo Fisher Scientific), 2 mM l- Glutamine (Thermo Fisher Scientific), 1x Penicillin/Streptomycin (Thermo Fisher Scientific), 1X ITS-X (Thermo Fisher Scientific). Add 8nM β-estradiol (Sigma Aldrich), 200 ng/ml Progesterone (Sigma Aldrich), and 25 μM N-aceyl-L-cysteine (Sigma Aldrich) to the pre-filtered medium.

extract_protocol:
Blastocysts at Day 10, Day 12 and Day 14 were washed with PBS and treated with TrypLE Express Enzyme (Thermo Fisher Scientific) for 30 minutes at 37℃. Then dissociate single cells by mouth pipetting until no bulky cell clumps could be observed. Single cells were transferred into a RNase-free, low-cell-adhesion 1.5 mL tube and centrifuged at 300 ℊ for 5 minutes. Carefully remove the supernatant and resuspended the cell pellet with 40 µL of 2% BSA in PBS. Within 30 minutes after dissociation, cells were loaded into the 10x Genomics Chromium system.
Libraries for sequencing were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 according to the manufacturer’s instructions.

treatment_protocol: To generate ISL1 hypomorphic mutants, the zygotes were injected with mix of SpCas9 mRNA (200 ng/μL) and gRNAs (25 ng/μL each). Intracytoplasmic injections were performed by using the Nikon microinjection system under standard conditions. The embryos were cultured in embryo culture medium-9 (HECM-9) containing 10% fetal calf serum (Hyclone Laboratories) in 37°C incubator supplying 5% CO2. Genetic modified embryos with high quality from morula to blastocyst stage were used for further studies.

tag: developmental stage

value: Day 14

tag: genotype

tag: batch


title: ChIP-seq_Sox2_15h_rep2

city: Göttingen

first: Le

last: Xiong

address: Fassberg 11

department: Molecular Biology

institute: MPI for biophysical chemistry

data_processing:
For TT-seq data: Paired-end 42 bp reads were mapped to the mouse genome assembly mm10 using STAR 2.5.3 (Dobin et al., 2013) with the following parameters: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500,000. SAMtools (Li et al., 2009) were then used to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f 2) were selected. HTSeq-count (Anders et al., 2015) was used to calculate fragment counts for different features. R/Bioconductor package DESeq2 (Love et al., 2014) was used to call differentially expressed mRNAs and eRNAs applying DESeq2’s default size factor normalization. For both cases DESeq2 size factors were calcualted using counts for protein-coding genes. An adjusted P-value of 0.01 was used to identify significantly changed mRNAs or eRNAs by comparing each time point to the 0 hours measurement.  Further data processing was carried out using the R/Bioconductor environment.
For ATAC-seq data: Paired-end 76 bp reads were obtained for each of the samples and Nextera Transposase adapter sequence was removed using (Martin, 2011). Bowtie2 (Langmead and Salzberg, 2012) was used to align paired-end reads to the mouse genome assembly mm10 with the “--local” and “--no-discordant” options. SAMtools (Li et al., 2009) was then used to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f 2) were selected. Reads mapped to custom blacklist regions and mitochondria were removed. Two replicates were pooled and MACS2 (Zhang et al., 2008) was used to call chromatin opening peaks with options: -f BAMPE -g mm --broad --broad-cutoff 0.05. Peaks for all time point were then merged to create non-overlapping unified peaks. For quantitative comparison, HTSeq-count (Anders et al., 2015) was used to calculate fragment counts for the non-overlapping unified peaks and DESeq2 was used to call regions with significantly changed chromatin accessibility. For normalization, ATAC-seq peaks overlapping with promoters of protein-coding genes with unchanged mRNA expression were used to calculate DESeq2 size factors. An adjusted P-value of 0.01 was used to identify significantly changed regions by comparing each time point to the 0 hour measurement. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq data: Paired-end Oct4 and Sox2 ChIP-seq data processing was done as described for ATAC-seq data. For peak calling, MACS2 was used with the same option for each individual replicate. For Oct4 ChIP-seq data, data was normalized using added D. melanogaster RNA spike-ins. Normalization factors were obtained by dividing the total D. melanogaster spike-ins read counts for each sample by the total read counts of the sample with the lowest read counts. For Sox2 ChIP-seq data, data was normalized using total number of uniquely mapped reads. ChIP-seq coverages were divided by the respective normalization factors. HTSeq-count (Anders et al., 2015) was used to calculate fragment counts for peak features. Reads counts were divided by the respective normalization factors.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized coverage files for TT-seq, ATAC-seq, Oct4 and Sox2 ChIP-seq at each time point are provided in bigwig format. For ChIP-seq data, two replicates are merged.
Supplementary_files_format_and_content: Annotations of transcription unit, eRNA, Oct4-regulated eRNA, Oct4-bound transcribed enhancers, Oct4-sensitive and -insensitive enhancers are provided in gtf format.

source_name: ZHBTc4 mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cells (mESCs) harbouring a doxycycline repressible Pou5f1 transgene (ZHBTc4, Niwa et al.,  2000) were propagated on gelatin-coated plates in equal parts DMEM-F12 (Life Technology, 21331-020) and Neuralbasal (Life Technology, 21103-049) Medium supplemented with 2% Fetal Bovin Serum (Sigma Aldrich, G1393-100 ml), 2% Knockout Serum Replacement Medium (Gibco, 10828-028), 0.04 µg/ml Leukemia Inhibitory Factor (prepared in-house), Pennicilin/Streptomycin (Sigma Aldrich, P4333-100ml), 0.1 mM ß-Mercaptoethanol (Gibco, 31350-010), 0.5x B27 supplement (Life Technology, 12587-010), 0.5x N2 supplement (Gibco, AM9759, 3 µM CHIR99021 (Cayman Chemicals, 13122), 1 µM PD0325901 (Biomol, 103034-25). Cells were passaged using Accutase (Sigma Aldrich, 6964-100ml).

extract_protocol:
ChIP-seq
NEBNext® Ultra™ DNA Library Prep Kit

treatment_protocol: Pou5f1 expression was abolished by treatment with 1µg/ml doxycycline (Sigma Aldrich D9891-1G) for 3 hours, 6 hours, 9 hours, 12 hours and 15 hours.

value: ZHBTc4 mouse embryonic stem cell

tag: treatment condition

value: doxycycline (1ug/ml) treatment 15h, Sox2 antibody (Neuromics, GT15098)


title: MV411.2000nM.GSK032.d4.n2 [S1-92]

tag: cell line

tag: treatment


title: MV411.16nM.DAC.d4.n2 [S1-95]

tag: cell tye

tag: dose


title: Mouse_TD3 rep2

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

country: France

institute: Nice Sophia Antipolis

data_processing:
Library strategy: DRIP
Quality control of the RAW sequencing reads was performed using FastQC version 0.11.5. Trimming of bad-quality reads was performed using Trimmomatic version 0.36 30. Based on the FastQC results we cropped 10 nucleotides from the 5' end of each read, and trimmed bases with Phred score lower than 20 from heading and trailing of each read. Also the Illumina adapter sequences were removed, and the trimmed reads with a size less than 30 bp were removed. Hisat2 was used to align trimmed reads to the reference assembly (GRCm38). HOMER version 4.9 was used for peak finding and generating bedGraph files for visualization of alignment.
Samples were then directly quantified using Salmon v0.12.0 on an index created from the GRCm38 transcript using GENCODE vM18, tRNA and piRNA precursors. Then, transcript counts were imported into tximport for all downstream analysis and were then summed by gene symbol. Quantifications were also done using featureCounts.For differential transcript analysis, only protein-coding transcripts and long non-coding RNA that had at least 20 reads in each sample were fixed. Differential transcript analysis of the D and R fractions in mouse sperm RNA-seq samples was performed with DESeq2 and edgeR.
Genome-wide locations of TERRA repeats were found by aligning sequences of length 24 and 48 composed of 4 and 8 copies of TERRA to the reference genome using bowtie2 using “-a” argument to report all alignments
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file include TPM (Transcript Per Million) values for each Sample

source_name: Testis

extract_protocol:
Mouse spermatozoa were collected from the cauda epididymis. After sperm preparation TRIzol extracted  materials were ethanol precipitated and followed by overnight incubation at 56°C in Tris buffer 20 mM pH8, EDTA 50 mM, with 0.5% SDS, 20 µM dithiothreitol and 400 µg/ml Proteinase K. Two fractions of RNAs were prepared: 1- Free-RNA (R) from aqueous phase of Trizol extraction and, 2- DNAs associated RNAs from interface materials. Both fractions after proteinase K treatment were further purified by the ZR-DuetTM DNA/RNA MiniPrep Plus protocol according to the specifications of the manufacturer.
10-100 ng of RNA were recovered and analysed by high throughput sequencing on Illumina HiSeq 2500 or Illumina MiSeq

tag: age

value: 14 month-old

value: Testis

tag: molecule subtype

value: DNA-associated RNA


title: MV411.3.2nM.DAC.d4.n2 [S1-94]

tag: time

tag: replicate


title: VS11-5A [methylation]

description:
Donor:VS11 Egg:5A
Sample 20

tag: gender

value: Female

tag: resultcontpreg

value: Neg

tag: resultpregtest


title: ChIP-seq_Sox2_15h_rep1


title: ChIP-seq_Sox2_12h_rep1

value: doxycycline (1ug/ml) treatment 12h, Sox2 antibody (Neuromics, GT15098)


title: mt_d14_B1


title: MV411.400nM.GSK032.d4.n2 [S1-91]


title: mt_d12_B1

value: Day 12


title: MV411.10000nM.GSK032.d4.n2 [S1-93]

value: AML cell line


title: ChIP-seq_Sox2_12h_rep2


title: Mouse_TD3 rep1

tag: strain

tag: tissue


title: Mouse_TD1 rep1

value: 6 month-old


title: VS1-12A [methylation]

description:
Donor:VS1 Egg:12A
Sample 7

tag: treatmentprotocol

value: Long

tag: donornum

tag: eggnum


title: mt_d12_B2

tag: developmental stage

tag: genotype

tag: batch


title: ChIP-seq_Sox2_9h_rep2

tag: cell line

tag: treatment condition

value: doxycycline (1ug/ml) treatment 9h, Sox2 antibody (Neuromics, GT15098)


title: VS1-10A [methylation]

description:
Donor:VS1 Egg:10A
Sample 5

value: NotUsed


title: Mouse_TD1 rep2

tag: age


title: VS5-5A [methylation]

description:
Donor:VS5 Egg:5A
Sample 6


title: VS4-8A [methylation]

description:
Donor:VS4 Egg:8A
Sample 4

value: Pos


title: shEV rep 1

tag: trophism

value: Brain trophic

tag: cell type

value: MDA-MB-231 derived

value: mammary gland/breast; derived from metastatic site

tag: treatment

value: Expressing empty vector


title: Mouse_R3 rep2

source_name: Sperm

value: 14 month-old

value: Sperm

tag: molecule subtype

value: free-RNA


title: ChIP-seq_Sox2_9h_rep1

value: ZHBTc4 mouse embryonic stem cell


title: VS1-7A [methylation]

description:
Donor:VS1 Egg:7A
Sample 3

tag: gender

value: Female

tag: resultcontpreg

value: Neg


title: MV411.80nM.GSK032.d4.n2 [S1-90]

tag: cell tye

tag: dose

tag: time

tag: replicate


title: mt_d10_B1

value: Day 10


title: MV411.16nM.GSK032.d4.n2 [S1-89]

value: AML cell line


title: Mouse_R3 rep1

tag: strain

tag: tissue


title: ChIP-seq_Sox2_6h_rep2

value: doxycycline (1ug/ml) treatment 6h, Sox2 antibody (Neuromics, GT15098)


title: VS4-4A [methylation]

description:
Donor:VS4 Egg:4A
Sample 2

tag: treatmentprotocol

value: Long

tag: donornum

tag: eggnum

tag: resultpregtest


title: MV411.0nM.DMSO.d4.n2 [S1-87]

tag: cell line

value: DMSO


title: ChIP-seq_Sox2_6h_rep1

tag: treatment condition


title: Mouse_R1 rep2

tag: age

value: 6 month-old


title: Mouse_R1 rep1


title: WT_d12_B2

tag: developmental stage

value: Day 12

tag: genotype

value: wildtype

tag: batch


title: ChIP-seq_Sox2_3h_rep2

value: doxycycline (1ug/ml) treatment 3h, Sox2 antibody (Neuromics, GT15098)


title: WT_d14_B2

value: Day 14


title: Mouse_D3 rep2

tag: molecule subtype

value: DNA-associated RNA


title: WT_d12_B1


title: MV411.10000nM.GSK477.d2.n2 [S1-86]

tag: cell tye

tag: treatment


title: WT_d10_B2


title: Mouse_D3 rep1

value: 14 month-old


title: MV411.1000nM.GSK862.d2.n2 [S1-85]

tag: dose

tag: time


title: WT_d14_B1


title: ChIP-seq_Sox2_0h_rep2

value: untreated control 0h, Sox2 antibody (Neuromics, GT15098)


title: MV411.3.2nM.GSK032.d4.n2 [S1-88]

tag: replicate


title: Mouse_D1 rep2

tag: strain

tag: tissue

value: Sperm


title: ChIP-seq_Sox2_0h_rep1

value: ZHBTc4 mouse embryonic stem cell


title: MV411.400nM.DAC.d2.n2 [S1-84]

value: DAC


title: MV411.400nM.GSK032.d2.n2 [S1-83]


title: Mouse_D1 rep1


title: VS1-4A [methylation]

description:
Donor:VS1 Egg:4A
Sample 1

tag: gender

value: Female

tag: treatmentprotocol

tag: donornum

tag: resultcontpreg

value: Neg

value: Pos


title: Liver, T27_ALIOS-diet/DEN

city: Newcastle Upon Tyne

first: Helen

last: Reeves

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Northern Institute for Cancer Research

data_processing:
Sequenced reads mapped to mm10 whole genome using STAR
Per-gene read counts were quantified using ht-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes per-gene raw count values for each sample

source_name: liver

extract_protocol:
10-20 mg of non-tumor and tumor tissues were shipped in RNAlater on dry ice to AROS Applied Technology (Denmark), where RNA was extracted and the quality of each sample checked using a Bioanalyzer (Agilent). Only samples with at least 400ng of total RNA and a RNA Integrity Number (RIN) greater than 8.0 were included.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed with control or ALIOS diet for 48 weeks. Additional two study groups were fed with dietary intervention with coadminstration of the liver carcinogen DEN

tag: diet

value: ALIOS-diet

value: DEN

value: liver

tag: tissue type

value: Tumor

tag: harvest time

value: 48 weeks


title: MV411.400nM.DAC.d1.n2 [S1-81]

tag: cell line

value: AML cell line


title: MV411.0nM.DMSO.d1.n2 [S1-79]

value: DMSO


title: MV411.0nM.DMSO.d2.n2 [S1-82]


title: Liver, T25_ALIOS-diet/DEN


title: ChIP-seq_Sox2_3h_rep1

tag: treatment condition

value: doxycycline (1ug/ml) treatment 3h, Sox2 antibody (Neuromics, GT15098)


title: MV411.400nM.GSK032.d1.n2 [S1-80]


title: Liver, T26_ALIOS-diet/DEN


title: NOMO1.400nM.GSK032.d6.n1 [S1-77]

description: processed data file: DNMT1_AML_fpkm_NOMO1_table.txt


title: NOMO1.400nM.DAC.d6.n1 [S1-78]


title: Liver, T24_ALIOS-diet/DEN


title: Liver, T23_ALIOS-diet/DEN


title: WT_d10_B1

tag: developmental stage

value: Day 10

tag: genotype

value: wildtype

tag: batch


title: NOMO1.0nM.DMSO.d6.n1 [S1-76]

tag: cell tye

tag: treatment

tag: dose


title: Liver, T21_control-diet/DEN

tag: strain

value: control-diet


title: Liver, T20_control-diet/DEN

tag: tissue


title: Liver, T19_control-diet/DEN


title: NOMO1.10000nM.GSK477.d4.n1 [S1-75]

tag: time

tag: replicate


title: Liver, T18_control-diet/DEN


title: JVM13 CycD1 T286A, replicate 3

city: Barcelona

first: Santiago

last: Demajo

state: Barcelona

address: Rosselló 153

country: Spain

institute: IDIBAPS - Hospital Clínic Barcelona

description: Gene expression data from JVM13 cells after inducing cyclin D1 with T286A mutation

hyb_protocol: 6.6 ug of fragmented and labeled cRNA were hybridized on Affymetrix Human Genome U219 Array Plate for 16 hr at 45ºC, using the automated GeneTitan System, which includes the hybridization oven and Fluidic Station.

scan_protocol: Scanning was performed using the automated GeneTitan System.

data_processing: Data analysis was performed using R software v3.5.0. Data were normalized using the robust multiarray average (RMA) method.

source_name: JVM13 cell line with CycD1 T286A overexpression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: JVM13 cells were cultured at 37°C and 5% CO2 in RPMI supplemented with 10% FBS.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol.

treatment_protocol: Cells were induced with 0.1 μg/mL doxycycline.


title: JVM13 CycD1 T286A, replicate 2


title: NOMO1.10000nM.DAC.d4.n1 [S1-73]


title: NOMO1.2000nM.DAC.d4.n1 [S1-72]


title: Liver, T17_control-diet/DEN


title: Liver, T22_ALIOS-diet/DEN


title: NOMO1.80nM.DAC.d4.n1 [S1-70]


title: Liver, T16_ALIOS-diet/DEN


title: JVM13 CycD1 T286A, replicate 1


title: NOMO1.400nM.DAC.d4.n1 [S1-71]


title: JVM13 control, replicate 2

description: Gene expression data from JVM13 cells with empty vector

source_name: JVM13 cell line with empty vector


title: JVM13 CycD1 wt, replicate 3

description: Gene expression data from JVM13 cells after inducing wild-type cyclin D1

source_name: JVM13 cell line with CycD1 wt overexpression


title: JVM13 control, replicate 1


title: Liver, T15_ALIOS-diet/DEN


title: Liver, T14_ALIOS-diet


title: NOMO1.1000nM.GSK862.d4.n1 [S1-74]


title: NOMO1.16nM.DAC.d4.n1 [S1-69]


title: NOMO1.3.2nM.DAC.d4.n1 [S1-68]


title: JVM13 CycD1 wt, replicate 1


title: JVM13 CycD1 wt, replicate 2


title: Liver, T13_ALIOS-diet


title: NOMO1.2000nM.GSK032.d4.n1 [S1-66]


title: Liver, T11_ALIOS-diet


title: NOMO1.400nM.GSK032.d4.n1 [S1-65]


title: NOMO1.80nM.GSK032.d4.n1 [S1-64]


title: Liver, T9_ALIOS-diet


title: AC TNF 6h

city: Tokushima

first: Keiko

last: Aota

address: 3-18-15 Kuramoto-Cho

department: Oral Medicine

country: Japan

institute: Tokushima University Graduate sChool

hyb_protocol: 7.5 µg fragmented and labeled aRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlasTM fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlasTM imaging station.

data_processing: The robust multichip average (RMA) method was used background correction and normalization with GeneSpring GX 12.1 software

label: Biotin

source_name: Salivary gland_TNF

label_protocol: 10 ng of total RNA was labeled using a GeneAtlasTM 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: NS-SV-AC cells were incubated in a humidified atomosphere of 95% air and 5% CO2 at 37℃

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: NS-SV-AC cells were treated with or without 20 ng/ml of TNF-a for 2, 6, 12 or 24 h.

tag: cell type

value: Immortalized human salivary gland acinar cells

value: salivary gland

value: NS-SV-AC


title: Liver, T8_ALIOS-diet


title: AC BSA 6h

source_name: Salivary gland_BSA


title: AC TNF 12h


title: AC BSA 24h


title: AC TNF 2h


title: IRF7-/- c-kit+3(C3)

city: Tianjin

first: Hao

last: Wang

state: Tianjin

address: 288 nanjing Road

institute: institute of blood

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: c-kit+ leukemic cells from bone marrow

extract_protocol:
c-kit+ cells were isolated from AML-WT  and AML-IRF7-/- mice. c-kit- cells were isolated from AML-WT mice. Total RNA was isolated from these enriched c-Kit+ cells following standard protocol with TRIzol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GFP+ leukemia cells were transplanted into 6-8 weeks old C57BL/6J mice (1×106 cells/mouse) without irradiation. The mice were sacrified at day 18 and the leukemia cells were sorted from BM. RNA-seq libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocol.

value: Bone Marrow

value: IRF7-/--GFP overexpression

value: acute myeloid leukemia (AML)


title: WT c-kit+3(B3)

value: control-GFP overexpression


title: IRF7-/- c-kit+2(C2)


title: WT c-kit+2(B2)


title: AC BSA 2h


title: Liver, T7_control-diet


title: NOMO1.3.2nM.GSK032.d4.n1 [S1-62]


title: WT c-kit+1(B1)


title: WT c-kit-3(A3)

source_name: c-kit- leukemic cells from bone marrow


title: Liver, T12_ALIOS-diet

value: ALIOS-diet


title: Liver, T6_ALIOS-diet

value: liver


title: NOMO1.0nM.DMSO.d4.n1 [S1-61]


title: AC BSA 12h


title: IRF7-/- c-kit+1(C1)


title: NOMO1.10000nM.GSK477.d2.n1 [S1-60]


title: AC TNF 24h


title: NOMO1.16nM.GSK032.d4.n1 [S1-63]


title: Liver, T10_ALIOS-diet

value: Tumor


title: Liver, T5_ALIOS-diet

value: 48 weeks


title: NOMO1.10000nM.GSK032.d4.n1 [S1-67]

value: AML cell line


title: Liver, T4_ALIOS-diet


title: NOMO1.1000nM.GSK862.d2.n1 [S1-59]


title: WT c-kit-1(A1)


title: 708OE_PEG_repeat2

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Initial quality-control analysis for sequencing reads was performed using FastQC (Andrews S et al, 2013) . Raw sequencing reads were trimmed to remove the adapters and bases with low quality score (< 20) using Cutadapt (Martin 2011) . The trimmed reads were aligned to the Oryza sativa genome (MSU7) with HISAT2 (Kim, Langmead et al. 2015) with parameter "--rna-strandness RF". SAMtools (Li, Handsaker et al. 2009) was used to gain high quality mapped reads (samtools view -q 20), sort reads (samtools sort), add index (samtools index) and estimate the number of uniquely mapped reads (samtools view -F 4 -c). FeatureCounts (Liao, Smyth et al. 2014) was empolyed to assign aligned reads to genes with parameters "-p -s 2 -t exon -g gene_id ". Differentially expressed genes (DEGs) were called with DESeq2 (Love, Huber et al. 2014) filtering the genes without expression in all samples. Genes were considered to be significantly differentially expressed between mutant and wild-type when |log2foldchange| ≥ log2(1.5) and the P value ≤ 0.05.
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files generated using DeepTools with binsize of 10. The matrix including log2Foldchange and pvalue generated by DESeq2

organism: Oryza sativa

growth_protocol: The husked rice seeds were surface-sterilized by treatment with 0.1% HgCl2 for 30 min and washed with sterilized water. After sterilization, seeds were then cultured grown in solid half-strength Murashige and Skoog medium in artificial growth chambers under a short-day photoperiod (10 h light, 30°C; 14 h dark, 28°C) and 60% relative humidity for 7 days. Then, seedlings were transferred to liquid rice medium and cultured under short-day photoperiod conditions for 7 days.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen).  PolyA+ RNA was enriched by selection with two rounds of oligo(dT) Dynabeads (Invitrogen).
Stranded RNA-seq library was constructed according to KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17; www.kapabiosystems.com).

treatment_protocol: For dehydration treatment, seedlings were treated with 20% PEG8000 solution for 3 h.

value: seedling

tag: development stage

value: PEG


title: 708OE_PEG_repeat3


title: NOMO1.400nM.DAC.d2.n1 [S1-58]

value: DAC


title: Medulloblastoma MYC-Gfi1-N1ICD (in Math1+ cells)_rep2

city: Trento

first: Luca

last: Tiberi

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology - CIBIO

country: Italy

institute: University of Trento

data_processing:
Reads were aligned to mm10 reference using STAR 2.4.1d
Gene expression counts were computed with htseq-count tool 0.6.1
Quality control was performed with Qualimap v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression counts

source_name: Medulloblastoma

growth_protocol: Cerebellar tumors were isolated from mice and fresh frozen

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Life Technologies) according to manufacturer's instructions
Libraries were prepared from the extracted RNAs using the QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria) using 0.5-1 μg of RNA per library and following the manufacturers’ instructions. We modified the standard protocol adding Unique Molecular Identifiers (UMI) during the second strand synthesis step. Indices from the Lexogen i7 6nt Index Set and i5 6nt Dual Indexing Add-on Kits (Cat. No. 044.96 and 047.96, Lexogen) were used, and 15-19 cycles of library amplification were performed. Libraries were eluted in 30 μL of the kit’s Elution Buffer. The double-stranded DNA concentration was quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher), ranging from 3 to 12 ng/μL. The molar concentration of cDNA molecules in the individual libraries was calculated from the double-stranded DNA concentration and the single library average size (determined on a PerkinElmer Labchip GX). An equal number of cDNA molecules from each library were pooled and the final pool was purified once more in order to remove any free primer and prevent index-hopping.

treatment_protocol: No treatment for isolated cells

value: Medulloblastoma

tag: oncogenes

tag: conditional expression

value: Math1-positive cells


title: NOMO1.400nM.GSK032.d2.n1 [S1-57]

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini kit
Libraries were prepared at the NYU Medical Center Genome Technology Center
All 150 PE libraries were sequenced across 6 lanes for a total of 12 fastq samples per sample.


title: NOMO1.0nM.DMSO.d2.n1 [S1-56]

value: DMSO


title: NIP_PEG_repeat3_Lane1

value: wild-type


title: Liver, T1_ALIOS-diet

tag: diet

tag: tissue type

tag: harvest time


title: Medulloblastoma MYC-Gfi1-N1ICD (in Math1+ cells)_rep3


title: Liver, T2_ALIOS-diet


title: Liver, NT23_ALIOS-diet

value: Non-tumor


title: 708OE_PEG_repeat1


title: Medulloblastoma MYC-Gfi1 (in S100b+ cells)_rep3

value: S100b-positive cells


title: Liver, T3_ALIOS-diet


title: NOMO1.400nM.DAC.d1.n1 [S1-55]

tag: cell line


title: NIP_PEG_repeat2_Lane2

tag: genotype


title: Liver, NT22_ALIOS-diet


title: Medulloblastoma MYC-Gfi1-N1ICD (in Math1+ cells)_rep1


title: NOMO1.400nM.GSK032.d1.n1 [S1-54]


title: Medulloblastoma MYC-Gfi1 (in S100b+ cells)_rep2


title: NIP_PEG_repeat2_Lane1


title: NOMO1.0nM.DMSO.d1.n1 [S1-53]


title: Liver, NT21_ALIOS-diet


title: WT c-kit-2(A2)

value: Bone Marrow


title: NIP_PEG_repeat1_Lane2


title: Liver, NT20_ALIOS-diet


title: NIP_PEG_repeat3_Lane2


title: snATAC_10x_MOp-2_rep2

city: La Jolla

first: Yang

last: Li

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

description:
MM_148
Replicate 2
snATAC-seq

data_processing:
The cellranger-atac demux pipeline is used for generating FASTQs for the R1 (R1_001.fastq) and R2 (R3_001.fastq) paired-end reads as well as the sample index (R2_001.fastq).
Sequencing reads were aligned to reference genome using bwa, with snaptools command: https://github.com/r3fang/SnapTools
HDF5 format files (*.snap) are generated by using SnapTools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *snap: HDF5 matrix files.
Supplementary_files_format_and_content: *.metadata.tsv: Metadata of single nuclei.

source_name: dissection part 2 of the primary motor cortex

extract_protocol:
A step-by-step protocol for library preparation is available here: https://www.protocols.io/view/sequencing-open-chromatin-of-single-cell-nuclei-sn-pjudknw/abstract
Libraries were prepared according to 10x Genomics's instructions.

value: Primary motor cortex

tag: brain dissection

tag: region name

tag: platform

value: Single Cell ATAC - 10x Genomics


title: NIP_PEG_repeat1_Lane1

tag: treatment


title: THP1.400nM.GSK032.d6.n1 [S1-51]

city: Collegeville

first: Shawn

last: Foley

institute: GlaxoSmithKline

data_processing:
Salmon_v0.12.0 transcript quantification
DEseq2 log2 fold change differential expression and normalized fpkm quantification
fGSEA gene set enrichment analysis
Genome_build: Human hg38
Supplementary_files_format_and_content: fpkm values for all quantifiable genes; log2 fold change values for all quantifiable genes

tag: cell tye

tag: dose


title: snATAC_10x_MOp-2_rep1

description:
MM_147
Replicate 1
snATAC-seq

tag: tissue


title: THP1.0nM.DMSO.d6.n1 [S1-50]

tag: time

tag: replicate


title: Liver, NT18_ALIOS-diet

tag: strain

value: ALIOS-diet


title: THP1.10000nM.GSK477.d4.n1 [S1-49]


title: Sham_mg4

city: Hangzhou

first: Jianmin

last: Zhang

address: 88 Jiefang Road

institute: Zhejiang University

data_processing:
cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined
The mapped reads of each sample were assembled using stringtie-1.3.0(ccb.jhu.edu/software/stringtie/) with default parameters (command line: stringtie -p 2 -G genome.gtf -o output.gtf -l mapped.bam). Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using gffcompare (github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kb)]).
Genome_build: mm9
Supplementary_files_format_and_content: xlsx files include FPKM values and counts for each Sample

source_name: Microgla

extract_protocol:
Total RNA from Microglia sorted by FACS was isolated using TRIzol (Invitrogen, CA, USA) according to the manufacture’s protocol.
Sequence libraries were constructed according to the standard SMART-seq protocol, and paired-end sequencing was performed with Illumina Novaseq 6000 (LC bio) following the vendor’s recommended protocol.

value: Brain

tag: cell type

value: Microglia

tag: disease state

value: Sham opreation

tag: time point

value: 3 days post operation


title: 708RNAi_PEG_repeat2

value: seedling

tag: development stage

value: SDG708-knockdown lines 708Ri-1-1


title: Sham_mg3


title: 708RNAi_PEG_repeat1

value: PEG


title: THP1.1000nM.GSK862.d4.n1 [S1-48]

address: 1250 S. Collegeville Rd

value: AML cell line


title: Liver, NT17_ALIOS-diet

tag: diet

value: liver

tag: tissue type

tag: harvest time

value: 48 weeks


title: Medulloblastoma MYC-Gfi1 (in S100b+ cells)_rep1

value: Medulloblastoma

tag: oncogenes

tag: conditional expression


title: Liver, NT15_ALIOS-diet

value: Non-tumor


title: THP1.10000nM.DAC.d4.n1 [S1-47]

tag: cell line

value: DAC


title: THP1.400nM.DAC.d6.n1 [S1-52]

tag: treatment


title: Liver, NT14_ALIOS-diet


title: Sham_mg1


title: WT_PEG_repeat2

tag: genotype

value: wild-type


title: WT_PEG_repeat1


title: THP1.2000nM.DAC.d4.n1 [S1-46]

tag: cell tye

tag: dose


title: Liver, NT19_ALIOS-diet

tag: tissue


title: WT_control_repeat3


title: 708RNAi_PEG_repeat3


title: SAH_mg3

value: Subarachnoid hemorrhage


title: THP1.400nM.DAC.d4.n1 [S1-45]

tag: time

tag: replicate


title: WT_control_repeat2


title: SAH_mg4

tag: strain

tag: cell type


title: THP1.80nM.DAC.d4.n1 [S1-44]


title: Liver, NT13_ALIOS-diet


title: Liver, NT12_control-diet

value: control-diet


title: SAH_mg2

tag: disease state

tag: time point


title: Liver, NT16_ALIOS-diet

tag: diet

value: ALIOS-diet


title: Ophiocordyceps sinensis_FB rep3_miRNA-seq

city: Chengdu

first: Han

address: No.1166 Liutai Avenue

department: College of Pharmacy

institute: Chengdu University of Traditional Chinese Medicine

description: miRNA-seq

data_processing:
Illumina NovaSeq6000 used for basecalling
Small RNA raw data in fastq format were first processed through cutadapt and fastp to obtain clean data, excluding reads with an “N” content ≥ 10%, reads without a 3′-adaptor sequences, low-quality reads, and sequences shorter than 18 nt or longer than 30 nt.
miDeep2(miRDeep2.pl reads_collapsed.fa genome.fa)was used to predict new miRNAs from unidentified miRNA reads
miRNA target genes were predicted using miRanda(miranda -sc 150 -en -7) and Targetscan(v3.1)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with miRNA counts for every miRNA and every sample

organism: Ophiocordyceps sinensis

source_name: fruiting body

extract_protocol:
Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer's protocol.
5 μg of total RNA was ligated to 5′-RNA and 3′-RNA adaptors according to the NEBNext® Multiplex Small RNA Library Prep Set for Illumina protocol (NEB, MA, USA)

value: fruiting body


title: Liver, NT11_control-diet

tag: tissue type


title: Sham_mg2

value: Brain

value: Microglia


title: THP1.16nM.DAC.d4.n1 [S1-43]


title: WT_control_repeat1

tag: development stage


title: 20uM ATRA Treated Replicate 6

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
For each allelic sequence pair (each allele having up to 10 unique RNA barcodes), mean of the rna/dna ratios from above calculated for each sample --> t-test of sample mean expression values between the alleles of each biallelic sequence
Genome_build: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary_files_format_and_content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

source_name: Cell line

growth_protocol: Cells were grown without changing medium for 72 hours at 37°C, 5% CO2.

extract_protocol:
Cells lifted in 250uL PBS and 750µL Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Turbo DNAse-free kit was used to remove incidental DNA, followed by a second cleanup using the Zymo kit to achieve a higher final concentration of RNA.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Basal medium (2% FBS in DMEM), with 1% penicillin-streptomycin in the medium before transfection and >6hrs after plus 20µM final concentration all-trans retinoic acid in 100% DMSO, or an equivalent amount of 100% DMSO for vehicle treatment. Medium prepared and refreshed daily with freshly added ATRA from light-protected frozen aliquots

value: 20µM all-trans retinoic acid (ATRA)


title: SAH_mg1

value: 3 days post operation


title: Liver, NT10_control-diet

tag: harvest time


title: THP1.3.2nM.DAC.d4.n1 [S1-42]


title: 20uM ATRA Treated Replicate 5


title: Ophiocordyceps sinensis_FB rep2_miRNA-seq

description: miRNA-seq


title: Ophiocordyceps sinensis_FB rep1_miRNA-seq

description: miRNA-seq


title: THP1.2000nM.GSK032.d4.n1 [S1-40]


title: Liver, NT8_control-diet


title: THP1.10000nM.GSK032.d4.n1 [S1-41]


title: Liver, NT9_control-diet


title: 20uM ATRA Treated Replicate 4


title: THP1.400nM.GSK032.d4.n1 [S1-39]


title: Liver, NT7_control-diet


title: 20uM ATRA Treated Replicate 3


title: Ophiocordyceps sinensis_ST rep3_miRNA-seq

description: miRNA-seq

source_name: sclerotium

value: sclerotium


title: Liver, NT6_control-diet


title: THP1.80nM.GSK032.d4.n1 [S1-38]


title: Ophiocordyceps sinensis_ST rep1_miRNA-seq

description: miRNA-seq


title: Ophiocordyceps sinensis_ST rep2_miRNA-seq

description: miRNA-seq


title: 20uM ATRA Treated Replicate 2


title: THP1.16nM.GSK032.d4.n1 [S1-37]


title: Ophiocordyceps sinensis_MC rep3_miRNA-seq

description: miRNA-seq

source_name: mycoparasite complex

value: mycoparasite complex


title: 20uM ATRA Treated Replicate 1


title: Liver, NT4_control-diet


title: THP1.3.2nM.GSK032.d4.n1 [S1-36]

value: AML cell line


title: Vehicle Treated, Replicate 6

value: vehicle (100% DMSO)


title: Liver, NT3_control-diet

value: liver

value: 48 weeks


title: THP1.0nM.DMSO.d4.n1 [S1-35]

value: DMSO


title: Ophiocordyceps sinensis_MC rep2_miRNA-seq

description: miRNA-seq


title: Ophiocordyceps sinensis_MC rep1_miRNA-seq

description: miRNA-seq


title: Vehicle Treated, Replicate 5


title: Liver, NT2_control-diet

value: Non-tumor


title: THP1.10000nM.GSK477.d2.n1 [S1-34]


title: Ophiocordyceps sinensis_FB rep3_mRNA-seq

data_processing:
Illumina NovaSeq6000 used for basecalling
RNA-seq raw data in the high-throughput sequencing, the Fast QC Toolkit (Version 0.11.9) was used, adaptor sequences and low-quality reads were removed
HISAT2(v2.0.4) was used to  map to the reference genome
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with clean gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer's protocol.
1μg of total RNA per group was used as input material for the RNA sample preparations using a NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA).


title: THP1.1000nM.GSK862.d2.n1 [S1-33]


title: Liver, NT1_control-diet


title: Vehicle Treated, Replicate 4


title: Ophiocordyceps sinensis_FB rep2_mRNA-seq


title: Vehicle Treated, Replicate 3


title: Vehicle Treated, Replicate 2


title: Type7 OC 3

city: Memphis

first: Xiaolong

last: Chen

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “-D C-CGG -w 100 -s 12 -v 0.1 -m 32 -x 1000 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

source_name: oocyte in antral follicle

extract_protocol:
Harvested oocytes were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. After lysed for 3h at 50°C, naked genomic DNA were relesed.
The released naked DNA was digested by MspI(Fermentas,ER0541),The digested DNA was then end-repaired and tailed with an extra A to the 3'blunted ends.Illumina standard premethylated indexed adaptors were ligated with the dA-tailed DNA fragments. Bisulfite conversion was then performed using the MethyCode bisulfite conversion kit (Invitrogen,MECOV-50) followed by two rounds of PCR enrichment.After PCR enrichment, DNA fragments between 200 and 700bp were size-selected by a 12% native polyacrylamide TBE gel.

value: oocyte in antral follicle


title: Ophiocordyceps sinensis_FB rep1_mRNA-seq


title: Ophiocordyceps sinensis_ST rep3_mRNA-seq


title: THP1.400nM.GSK032.d2.n1 [S1-31]


title: Liver, NT5_control-diet


title: Ophiocordyceps sinensis_ST rep2_mRNA-seq


title: Type7 OC 2


title: Vehicle Treated, Replicate 1


title: Type7 OC 1


title: snRNA-seq MOCK

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing: Single-nuclei RNA-seq data was processed using mkfastq and count command from 10X Genomics CellRanger v3.0.1.

source_name: Cortex

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol.

value: Cortex

tag: age

value: post natal day 60

tag: infection

value: mock


title: Ophiocordyceps sinensis_MC rep3_mRNA-seq


title: Ophiocordyceps sinensis_ST rep1_mRNA-seq


title: snRNA-seq ZIKV

value: zika virus


title: THP1.400nM.DAC.d1.n1 [S1-29]

tag: cell line

tag: treatment

value: DAC


title: THP1.0nM.DMSO.d1.n1 [S1-27]

tag: cell tye


title: Type6 OC 2


title: THP1.400nM.GSK032.d1.n1 [S1-28]

tag: dose


title: Emseq-Mock4

data_processing:
Library strategy: Methyl-seq
The adaptor sequences and low quality bases were trimmed from the reads using the Trim Galore tool ver. 0.6.5.
Reads were aligned to the mouse genome using the Bismark alignment software.
The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) was calculated by bismark_methylation_extractor
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

extract_protocol:
NEBNext Enzymatic Methyl-Seq  Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
300ng of DNA was used for library construction using the NEBNext Enzymatic Methyl-Seq (NEB), respectively.

tag: tissue


title: Type6 OC 3


title: THP1.400nM.DAC.d2.n1 [S1-32]

tag: time


title: Ophiocordyceps sinensis_MC rep2_mRNA-seq


title: Emseq-Mock3


title: Ophiocordyceps sinensis_MC rep1_mRNA-seq


title: Type5b OC 3

source_name: oocyte in secondary follicle

value: zygote

value: oocyte in secondary follicle


title: Emseq-Mock2


title: Type6 OC 1


title: MV411.400nM.GSK032.d6.n1 [S1-25]

tag: replicate


title: Type5b OC 2

tag: strain


title: THP1.0nM.DMSO.d2.n1 [S1-30]


title: Type5b OC 1

value: trophectoderm


title: MV411.0nM.DMSO.d6.n1 [S1-24]


title: Emseq-Zikv4


title: Emseq-Mock1


title: Emseq-Zikv3


title: Type5a OC 7


title: 2-year TBI brain 3

city: Charleston

first: Amer

last: Toutonji

state: SC

address: 173 Ashley Ave, CRI204

institute: Medical University of South Carolina

hyb_protocol: followed the manufacturer's instructions: NanoString (Seattle, WA)

data_processing: number of reads was normalized by housekeeping genes in the panel using nCounter® nSolver software

label: Nanostring

source_name: TBI-injured brain

label_protocol: the extract wasn't labeled

extract_protocol: mRNA was extracted from up to 1 mg of brain tissue using the RNeasy Lipid Tissue Mini Kit (Qiagen)

tag: injury

value: TBI (CCI)

tag: time point post tbi

value: year 2

tag: age (weeks)


title: MV411.10000nM.GSK477.d4.n1 [S1-23]

value: AML cell line


title: 2-year TBI brain 2

scan_protocol: followed the manufacturer's instructions: NanoString (Seattle, WA)


title: MV411.1000nM.GSK862.d4.n1 [S1-22]


title: Type5a OC 6


title: 2-year TBI brain 1


title: Emseq-Zikv2


title: Emseq-Zikv1


title: MV411.400nM.DAC.d6.n1 [S1-26]


title: MV411.2000nM.DAC.d4.n1 [S1-20]


title: 1-year TBI brain 3

value: year 1


title: 1-year TBI brain 2


title: Type5a OC 5

value: inner cell mass


title: MV411.400nM.DAC.d4.n1 [S1-19]


title: Srsf3fl/fl;Wnt1-Cre+/Tg_3

city: Aurora

first: Katherine

middle: Ann

last: Fantauzzo

address: 12801 East 17th Avenue, MS 8120

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

description:
cKO_3tube_13_S89_L004
Srsf3fl_Wnt1-CreTg_cKO_3

data_processing:
For alternative splicing analysis, fastq were trimmed to remove adapter sequence contamination and cropped to 125 bp using BBDuk (v35.85). Alignment to the mouse vM19 GENCODE genome was performed with STAR (v2.7.0). BAM files were used as the imput for rMATS (v4.0.1) to detect alternative splicing events.
For differential expression analysis, fastq were quantified at the transcript level via Salmon (v1.1.0) with GENCODE vM19 genome. Abundance was summarized at the gene level using tximport (v1.16.1) and DESeq2 (v1.28.1).
Genome_build: mm10 (GENCODE vM19)
Supplementary_files_format_and_content: CSV count matrices of Salmon abundance and estimated counts
Supplementary_files_format_and_content: Excel file of simplified DESeq2 output, rMATS JCEC output

extract_protocol:
Secondary palatal shelves (PS) and maxillary processes (MxP) were dissected on ice and the overlying ectoderm removed by digestion with 20 mg/mL trypsin for 15-20 min at 4°C. PS and MxP were subsequently rinsed in 10% fetal bovine serum for 1 min followed by 1x phosphate buffered saline (PBS). Excess PBS was removed and PS and MxP were submerged in 200 uL Invitrogen RNAlater stabilization solution for overnight storage at 4°C. The following day excess RNAlater was removed and the samples were stored at -80°C. Total RNA was simultaneously isolated from all samples using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.
PolyA selection was performed and sequencing libraries were synthesized using NuGen Universal Plus mRNA-Seq with NuQuant kit at the University of Colorado Genomics and Microarray Core. Libraries were sequenced on an Illumina NovaSeq6000.

tag: strain background

tag: genotype

tag: developmental stage

value: maxillary process mesenchyme


title: Type5a OC 4

tag: development stage


title: Srsf3fl/fl;Wnt1-Cre+/Tg_2

description:
cKO_2tube_12_S88_L004
Srsf3fl_Wnt1-CreTg_cKO_2


title: Type4 OC 6


title: 28-day TBI brain 3

value: day 28


title: MV411.16nM.DAC.d4.n1 [S1-17]

department: Oncology


title: Srsf3fl/fl;Wnt1-Cre+/Tg_1

description:
cKO_1tube_8_S87_L004
Srsf3fl_Wnt1-CreTg_cKO_1


title: 1-year TBI brain 1


title: Srsf3fl/fl;Wnt1-Cre+/+_2

description:
control_2tube_4_S85_L004
Srsf3fl_Wnt1-CreTg_Control_2


title: Type4 OC 5


title: Srsf3fl/fl;Wnt1-Cre+/+_3

description:
control_3tube_6_S86_L004
Srsf3fl_Wnt1-CreTg_Control_3


title: 28-day TBI brain 2


title: MV411.3.2nM.DAC.d4.n1 [S1-16]


title: Type4 OC 4


title: MV411.10000nM.DAC.d4.n1 [S1-21]


title: MV411.10000nM.GSK032.d4.n1 [S1-15]


title: 28-day TBI brain 1


title: 7-day TBI brain 3

value: day 7


title: MV411.2000nM.GSK032.d4.n1 [S1-14]


title: MV411.80nM.DAC.d4.n1 [S1-18]


title: Type4 OC 1


title: PdgfraPI3K/PI3K_3

description:
MUT_3_S92_L002
PdgfraPI3K_MUT_3

value: palatal shelf mesenchyme


title: Srsf3fl/fl;Wnt1-Cre+/+_1

description:
control_1tube_2_S84_L004
Srsf3fl_Wnt1-CreTg_Control_1


title: PdgfraPI3K/PI3K_2

description:
MUT_2_S91_L002
PdgfraPI3K_MUT_2


title: 7-day TBI brain 2


title: Type5a OC 1


title: Type4 OC 2


title: MV411.80nM.GSK032.d4.n1 [S1-12]


title: PdgfraPI3K/PI3K_1

description:
MUT_1_S90_L002
PdgfraPI3K_MUT_1


title: Type3b OC 2

source_name: oocyte in primary follicle

value: oocyte in primary follicle


title: Type3b OC 3


title: Type3b OC 1


title: Pdgfra+/+_3

description:
WT_3_S89_L002
PdgfraPI3K_WT_3

value: Pdgfra+/+


title: MV411.16nM.GSK032.d4.n1 [S1-11]


title: MV411.400nM.GSK032.d4.n1 [S1-13]


title: 7-day TBI brain 1


title: MV411.3.2nM.GSK032.d4.n1 [S1-10]


title: 3-day TBI brain 3

value: day 3


title: 3-day TBI brain 2


title: MV411.0nM.DMSO.d4.n1 [S1-09]

value: DMSO


title: Pdgfra+/+_2

description:
WT_2_S88_L002
PdgfraPI3K_WT_2


title: Pdgfra+/+_1

description:
WT_1_S87_L002
PdgfraPI3K_WT_1


title: MV411.10000nM.GSK477.d2.n1 [S1-08]


title: Type3a OC 4


title: Type3a OC 2


title: 3-day TBI brain 1


title: 2-year-old Sham brain 3

source_name: normal mouse brain

value: sham

value: not applicable


title: 2-year-old Sham brain 2


title: Type3a OC 1


title: MV411.1000nM.GSK862.d2.n1 [S1-07]


title: Type2 OC 3

source_name: oocyte in promordial follicle

value: oocyte in promordial follicle


title: E17-5-9 scATAC-seq

city: Los angeles

first: Xue

last: Liu

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

data_processing:
Raw sequencing data is demultiplexed and converted to fastq format by using bcl2fastq v2.20. Cell Ranger ATAC software v1.1.0 (10X Genomics) is used for barcodes identification, reads alignment, duplicate marking, peak calling and cell calling with default parameter. Briefly, each barcode sequence is checked against a ‘whitelist’ of correct barcode sequences, and the frequency of each whitelist barcode is counted.
Raw reads are aligned to the human reference genome GRCm38 using BWA-MEM with default parameters, then duplicated reads that have identical mapping positions on the reference are marked. For peak calling, the number of transposition events at each base-pair along the genome is counted, then signal above a threshold are determined as peak signal after modeling. For cell calling, barcodes with high fraction of fragments overlapping called peak are selected, then odds ratio of 100000 is used to separate the barcodes that correspond to real cells from the non-cell barcodes. Finally, a count matrix is generated consisting of the counts of fragments ends within each peak region for each barcode.
For further QC, clustering and gene accessibility visualization were performed following online vignette (https://satijalab.org/signac/articles/mouse_brain_vignette.html). Briefly, a Seurat object was generated on count matrix and fragments, and QC was performed by removing cells that are outliers for QC metrics: pct_reads_in_peaks, peak_region_fragments, blacklist_ratio, nucleosome_signal. After normalization and linear dimensional reduction, non-linear dimension reduction and clustering, gene accessibilities were visualized by UMAP. Cell types and mesenchymal cell sub-clusters were defined by checking unknown cell type markers.

source_name: embryonic mouse lung single cells

extract_protocol:
Dissociated cells resuspended in PBS + 0.04% BSA were treated with DNase I prior to nuclei isolation.  Specifically, cells were pelleted, the supernatant removed, and the cell pellet resuspended in DNase Solution (1X TBS, 1X Reaction Buffer with MgCl2 (ThermoFisher Scientific, Waltham, MA), 0.1 U/l DNase I (ThermoFisher Scientific), nuclease-free water).  Cells were then incubated for 5 mins, pelleted, and washed twice with PBS + 0.04% BSA.  The cell suspension was passed through a 40 m Flowmi Cell Strainer (VWR, Radnor, PA), and the cell concentration determined before proceeding to nuclei isolation. For nuclei isolation, up to 1x106 cells were pelleted, followed by removal of the supernatant, and resuspension in chilled 0.1X Lysis Buffer (1 mM Tris-HCl pH 7.4, 1 mM NaCl, 0.3 mM MgCl2, 0.01% Tween-20, 0.01% Nonidet P40 Substitute, 0.001% Digitonin (Sigma-Aldrich, St. Louis, MO), 0.1% BSA (Miltenyi Biotec, Bergisch Gladbach, Germany), and nuclease-free water) for a pre-determined optimal cell lysis time.  Wash Buffer was added to dilute the lysis buffer, then the nuclei were immediately pelleted.  The supernatant was removed, and the isolated nuclei were resuspended in 1X Nuclei Buffer (10x Genomics, Pleasanton, CA).  Finally, nuclei concentration was determined and scATAC-Seq transposition and library construction was immediately performed.
scATAC-Seq transposition and library construction was performed according to the manufacturer’s protocol using the Chromium Next GEM Single Cell ATAC v 1.1 reagent kit (10x Genomics).  Transposition of single nuclei obtained in the previous step was performed in bulk, followed by capture of the transposed, single nuclei into GEMs (Gel Bead-In-Emulsions) using the Chromium Controller (10x Genomics).  GEM cleanup and library size selection was performed using Dynabeads MyOne Silane beads (10x Genomics) and SPRIselect reagent (Beckman Coulter B23318), respectively.  Sample index PCR was performed for 10 cycles.  Indexed sequencing libraries were quantified by qPCR using the Collibri Library Quantification Kit for Illumina platforms (ThermoFisher Scientific).  Libraries were sequenced on the NovaSeq (Illumina, San Diego, CA) at 2x50bp at a sequencing depth of ~25K reads per nuclei.

tag: mouse lung cells

value: E17.5 WT lung single cells

tag: assay

value: scATAC-sequencing


title: Type2 OC 2


title: 2-year-old Sham brain 1


title: MV411.400nM.DAC.d2.n1 [S1-06]

tag: cell line

value: DAC


title: E17-5-7 scATAC-seq


title: 1-year-old Sham brain 3


title: MV411.400nM.GSK032.d2.n1 [S1-05]

value: AML cell line

tag: treatment


title: Type2 OC 1


title: Type1 OC 3

value: zygote


title: 1-year-old Sham brain 2


title: 1-year-old Sham brain 1


title: MV411.0nM.DMSO.d2.n1 [S1-04]

tag: cell tye


title: 12-week-old Sham brain 3


title: Type1 OC 1


title: MV411.400nM.GSK032.d1.n1 [S1-02]

tag: dose


title: Type1 OC 2

tag: tissue


title: 12-week-old Sham brain 1


title: MV411.0nM.DMSO.d1.n1 [S1-01]

tag: time


title: 12-week-old Sham brain 2


title: E17-5-8 scATAC-seq


title: MV411.400nM.DAC.d1.n1 [S1-03]

tag: replicate


title: GS_L3C_H12

status: Public on Jun 29 2021

city: Natal

first: Diego

middle: Marques

last: Coelho

state: RN

address: Av. Nascimento de Castro, 2155

department: Bioinformatics

country: Brazil

institute: UFRN

description: Single cell RNA-Seq library from FACS sorted CAG-mRFP;Hes5p-GFP E13.5 mouse brain

data_processing:
Illumina Hiseq 2500 default software for basecalling.
Paired-end reads were aligned to the mouse reference genome (mm10) using hisat2 (Kim et al, 2015) with the default parameters except: -p 6.
Quantified against a modified reference transcriptome (GENCODE vM15; (Frankish et al., 2018)) with cuffquant.
Data were analyzed using Seurat R package v2 (Butler et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited with log-normalized count reads for every gene and sample
Supplementary_files_format_and_content: Tab-delimeted with raw gene counts for every gene and sample

source_name: Brain

extract_protocol:
Fluorescence-activated cell sorting (FACS) to separate single-labeled CAG+ cells (only CAG promoter active, mRFP+GFP- cells) and double-labeled CAG+/Hes5+ cells (both promoters active, mRFP+GFP+ cells)
Viable sorted cells of both types collected individually were lysed and libraries were generated using a modified Smart-seq 2 protocol for subsequent scRNA sequencing as described (Chevée et al., 2018).

treatment_protocol: In utero electroporation with a dual promoter plasmid containing two fluorescent proteins under the control of two different promoters: the CAG promoter driving mRFP and the Hes5 promoter driving GFP

tag: strain

value: cerebral cortex

tag: age

value: embrionic day 13.5

tag: marker


title: GS_L3C_H05


title: GS_L3C_H10


title: GS_L3C_H06


title: GS_L3C_H11


title: GS_L3C_H09


title: GS_L3C_H08


title: Q- rep3

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

country: India

institute: Centre for cellular and molecular biology (CCMB)

data_processing:
QC check was performed using FastQC; version 0.11.9
Reads were mapped to the reference genome using RNA-STAR; version 2.7.8a
The raw counts of genes were quantified using featureCounts; version 2.0.1
Differential gene expression analysis was performed using DEseq2; version 1.30.1
Panther and KEGG were used for downstream analysis of GO and pathways, respectively
Genome_build: GCA_001927405.2_ASM192740v2
Supplementary_files_format_and_content: Raw counts from featureCounts in .txt format

organism: Xanthomonas oryzae pv. oryzae

source_name: Bacterial cell pellet

growth_protocol: Xoo strains were grown at 28ᵒC to OD600 1.0 in peptone sucrose medium

extract_protocol:
Total RNA was extracted using MN RNA isolation kit (740955) with on-column Dnase treatment.
NEBNext® UltraTM II Directional was used for library preparation after rRNA depletion using NEBNext® rRNA Depletion Kit (Bacteria). The library was generated using RNA Library Prep Kit for Illumina® and quality checked using Agilent TapeStation; average library size was 270bp. The libraries were sequenced to obtain 2x100bp sequences with an output of greater than 30 million reads per sample.

treatment_protocol: Not Applicable

value: XopQ-


title: Q- rep1


title: Q- rep2


title: BXO43 rep1

value: WT


title: BXO43 rep3


title: GS_L3C_H01


title: GS_L3C_H04


title: Sorted_BFP+_PI-_Survivors_Induced

city: Boston

first: Charles

middle: Lee

last: Evavold

state: MA

address: 300 Longwood Avenue

department: Immunology

institute: Harvard University

data_processing:
Library strategy: CRISPR screen
Multiplexed sequencing data was deconvoluted based on construct and sample barcodes. In brief data processing was as in Doench et al. 2016 using PoolQ webtools from the Broad GPP. Raw read counts mapped to sgRNA barcodes are presented as processed data. Data was further processed to generate a ranked hit list. Log-normalized sgRNA abundance from the sorted survivors was subtracted with log-normalized sgRNA abundance from the combined input sample to account for bias in the starting population after cellular library creation. A strict Chip file (CP1139 from Broad GPP) was used to map perturbations to sites in the genome, and the normalized data was subjected to hypergeometric analysis without replacement to generate a ranked hit list based on log-fold change and p-value significance.
Genome_build: CP1139 chip file from Broad GPP for annotated mapping of sgRNA sequences to genome sites.
Supplementary_files_format_and_content: Raw read counts for each sgRNA barcode for Input and Sorted survivor conditions are presented as .txt files.

source_name: Bone marrow derived macrophages, immortalized with J2 retrovirus

growth_protocol: R26-Cas9-KI Bone marrow derived macrophages were differentiated in 30% L929 M-CSF containing supernatants in complete high glucose DMEM with L-glut and sodium pyruvate and Pen/Strep with 10% FBS. Primary macrophages were immortalized by J2 retrovirus and sequential starving of M-CSF concentration. Immortalized macrophages were engineered to express Tet3G transactivator protein and a doxycycline-inducible caspase-cleavage fragment of GSDMD tagged with the fluorescent protein tagBFP.

extract_protocol:
Genomic DNA from cell pellets was purified using the Nucleospin Blood XL kit from Clontech according to the manufacturer’s protocol. Isolated DNA was cleaned of PCR inhibitors using the PCR inhibitor clean up columns from Zymo Research.  DNA concentration was then measured with a Nanodrop and diluted to the desired concentration and number of wells as specified by Broad GPP protocols. PCR plate with diluted gDNA was shipped to the Broad Institute on dry ice for PCR amplification and next generation sequencing.
Libraries were prepared according to Illumina's instructions. After DNA extraction as described above, barcodes were PCR amplified from genomic DNA and subjected to next generation sequencing using Illumina 2500 High Output.

treatment_protocol: A cellular library of genome wide perturbations was created by transducing engineered Cas9 transgenic iBMDMs with the Brie lentiviral sgRNA expression library with a blasticidin resistance marker. Macrophages were either left uninduced (no doxycylcine in complete DMEM) to serve as input population to account for population sgRNA bias (enrichment for tumor suppressors, depletion for essential genes for examples) or induced (doxycycline 0.5 μg/ml induction of the NT-GSDMD-tagBFP pore forming toxic molecule for 16 hours).

value: Induced sorted survivors

tag: cell type

value: Macrophage


title: GS_L3C_G12


title: Combined_Input_Uninduced

value: Uninduced, population bias


title: BXO43 rep2


title: GS_L3C_G07


title: GS_L3C_G06


title: GS_L3C_G08


title: GS_L3C_G05


title: GS_L3C_G03


title: GS_L3C_G02


title: GS_L3C_G09


title: GS_L3C_H03


title: GS_L3C_F05


title: GS_L3C_F06


title: GS_L3C_E11


title: GS_L3C_G01


title: GS_L3C_G10


title: GS_L3C_E09


title: GS_L3C_F08


title: GS_L3C_H02


title: GS_L3C_F09


title: GS_L3C_F04


title: GS_L3C_F03


title: GS_L3C_F12


title: GS_L3C_G04


title: GS_L3C_E08


title: GS_L3C_E04


title: GS_L3C_E02


title: GS_L3C_F10


title: GS_L3C_F07


title: GS_L3C_F01


title: GS_L3C_E10


title: GS_L3C_E01


title: GS_L3C_E05


title: GS_L3C_D12


title: GS_L3C_D11


title: GS_L3C_F11


title: GS_L3C_E03


title: GS_L3C_E12


title: GS_L3C_E07


title: GS_L3C_D10


title: GS_L3C_D08


title: GS_L3C_D06


title: GS_L3C_D09


title: GS_L3C_D03


title: GS_L3C_D02


title: GS_L3C_C09


title: GS_L3C_C11


title: GS_L3C_C07


title: GS_L3C_C03


title: GS_L3C_C10


title: GS_L3C_C02


title: GS_L3C_C08


title: GS_L3C_B11


title: GS_L3C_B10


title: GS_L3C_C05


title: GS_L3C_B09


title: GS_L3C_C01


title: GS_L3C_B04


title: GS_L3C_B08


title: GS_L3C_B06


title: GS_L3C_B12


title: GS_L3C_B03


title: GS_L3C_B02


title: GS_L3C_B01


title: GS_L3C_A11


title: GS_L3C_D05


title: GS_L3C_C12


title: GS_L3C_A12


title: GS_L3C_A09


title: GS_L3C_A10


title: GS_L3C_A08


title: GS_L3C_A07


title: GS_L3C_A06


title: GS_L3C_B07


title: GS_L3C_A05


title: GS_L3C_A03


title: GS_L3C_A02


title: GS_L2D_H10


title: GS_L3C_B05


title: GS_L3C_A04


title: GS_L2D_H08


title: GS_L2D_H06


title: GS_L2D_H12


title: GS_L2D_H07


title: GS_L2D_H03


title: GS_L2D_H09


title: GS_L2D_H05


title: GS_L2D_H02


title: GS_L2D_H11


title: GS_L2D_H01


title: GS_L2D_G11


title: GS_L2D_G10


title: GS_L2D_G12


title: GS_L2D_H04


title: GS_L2D_G09


title: GS_L2D_G07


title: GS_L2D_G06


title: GS_L2D_G04


title: GS_L2D_G03


title: GS_L2D_G08


title: GS_L2D_G01


title: GS_L2D_F12


title: GS_L2D_G02


title: GS_L2D_F11


title: GS_L2D_F10


title: GS_L2D_F09


title: GS_L2D_F08


title: GS_L2D_F07


title: GS_L2D_F04


title: GS_L2D_F03


title: GS_L2D_F01


title: GS_L2D_F05


title: GS_L2D_E10


title: GS_L2D_E08


title: GS_L2D_E07


title: GS_L2D_E05


title: GS_L2D_E04


title: GS_L2D_E03


title: GS_L2D_E01


title: GS_L2D_D11


title: GS_L2D_E02


title: GS_L2D_D12


title: GS_L2D_D10


title: GS_L2D_D08


title: GS_L2D_D03


title: GS_L2D_D07


title: GS_L2D_F02


title: GS_L2D_D02


title: GS_L2D_E12


title: GS_L2D_C12


title: GS_L2D_E11


title: GS_L2D_E09


title: GS_L2D_C07


title: GS_L2D_C05


title: GS_L2D_C09


title: GS_L2D_D01


title: GS_L2D_E06


title: GS_L2D_C04


title: GS_L2D_C02


title: GS_L2D_C10


title: GS_L2D_C08


title: GS_L2D_C01


title: GS_L2D_B12


title: GS_L2D_B11


title: GS_L2D_B09


title: GS_L2D_D09


title: GS_L2D_B08


title: GS_L2D_B10


title: GS_L2D_B06


title: GS_L2D_B07


title: GS_L2D_C11


title: GS_L2D_B01


title: GS_L2D_A12


title: GS_L2D_A11


title: GS_L2D_B03


title: GS_L2D_A09


title: GS_L2D_A10


title: GS_L2D_B04


title: GS_L2D_A06


title: GS_L2D_B02


title: GS_L2D_A08


title: GS_L2D_A07


title: GS_L2A_H12


title: GS_L2A_H11


title: GS_L2D_C03


title: GS_L2D_A05


title: GS_L2D_A02


title: GS_L2A_H09


title: GS_L2D_A04


title: GS_L2A_H10


title: GS_L2D_A03


title: GS_L2D_A01


title: GS_L2A_H03


title: GS_L2A_H04


title: GS_L2A_H02


title: GS_L2A_H07


title: GS_L2A_H01


title: GS_L2A_H05


title: GS_L2A_H06


title: GS_L2A_G12


title: GS_L2A_G11


title: GS_L2A_G10


title: GS_L2A_G03


title: GS_L2A_G01


title: GS_L2A_F12


title: GS_L2A_F11


title: GS_L2A_G08


title: GS_L2A_F05


title: GS_L2A_F10


title: GS_L2A_G06


title: GS_L2A_F09


title: GS_L2A_F08


title: GS_L2A_E12


title: GS_L2A_F01


title: GS_L2A_F03


title: GS_L2A_H08


title: GS_L2A_F07


title: GS_L2A_F04


title: GS_L2A_E09


title: GS_L2A_E10


title: GS_L2A_E11


title: GS_L2A_E06


title: GS_L2A_E05


title: GS_L2A_E02


title: GS_L2A_E08


title: GS_L2A_E04


title: GS_L2A_E07


title: GS_L2A_E01


title: GS_L2A_G04


title: GS_L2A_D12


title: GS_L2A_D11


title: GS_L2A_D10


title: GS_L2A_F02


title: GS_L2A_D09


title: GS_L2A_D07


title: GS_L2A_D06


title: GS_L2A_D02


title: GS_L2A_D03


title: GS_L2A_C12


title: GS_L2A_C10


title: GS_L2A_C11


title: GS_L2A_C08


title: GS_L2A_C05


title: GS_L2A_C07


title: GS_L2A_C06


title: GS_L2A_C02


title: GS_L2A_C03


title: GS_L2A_C04


title: GS_L2A_B11


title: GS_L2A_B12


title: GS_L2A_C01


title: GS_L2A_B09


title: GS_L2A_B10


title: GS_L2A_B04


title: GS_L2A_B07


title: GS_L2A_B05


title: GS_L2A_B08


title: GS_L2A_B03


title: GS_L2A_B01


title: GS_L2A_D08


title: GS_L2A_B02


title: GS_L2A_A12


title: GS_L2A_A11


title: GS_L2A_A09


title: GS_L2A_A08


title: GS_L2A_A06


title: GS_L2A_A07


title: GS_L2A_A05


title: GS_L2A_A04


title: GS_L2A_A03


title: GS_L2A_A01


title: GS_L1B_H10


title: GS_L1B_H07


title: GS_L1B_H08


title: GS_L1B_H06


title: GS_L1B_H09


title: GS_L1B_H11


title: GS_L1B_H04


title: GS_L1B_H05


title: GS_L1B_H01


title: GS_L1B_G11


title: GS_L2A_A10


title: GS_L1B_H02


title: GS_L1B_G09


title: GS_L1B_G08


title: GS_L1B_G07


title: GS_L1B_G10


title: GS_L1B_G12


title: GS_L1B_G05


title: GS_L1B_G03


title: GS_L1B_G06


title: GS_L1B_G04


title: GS_L1B_G02


title: GS_L1B_F12


title: GS_L2A_A02


title: GS_L1B_G01


title: GS_L1B_F11


title: GS_L1B_F10


title: GS_L1B_H12


title: GS_L1B_F09


title: GS_L1B_F07


title: GS_L1B_F08


title: GS_L1B_F05


title: GS_L1B_F04


title: GS_L1B_F02


title: GS_L1B_F03


title: GS_L1B_E12


title: GS_L1B_F01


title: GS_L1B_E11


title: GS_L1B_E09


title: GS_L1B_E08


title: GS_L1B_E04


title: GS_L1B_E07


title: GS_L1B_E05


title: GS_L1B_E03


title: GS_L1B_E02


title: GS_L1B_E01


title: GS_L1B_D12


title: GS_L1B_D11


title: GS_L1B_D08


title: GS_L1B_D06


title: GS_L1B_D09


title: GS_L1B_D07


title: GS_L1B_D03


title: GS_L1B_D05


title: GS_L1B_D01


title: GS_L1B_C12


title: GS_L1B_C09


title: GS_L1B_C05


title: GS_L1B_C08


title: GS_L1B_C07


title: GS_L1B_C11


title: GS_L1B_C06


title: GS_L1B_E06


title: GS_L1B_C01


title: GS_L1B_C03


title: GS_L1B_B11


title: GS_L1B_B12


title: GS_L1B_B07


title: GS_L1B_C02


title: GS_L1B_B08


title: GS_L1B_B10


title: GS_L1B_D10


title: GS_L1B_B09


title: GS_L1B_B05


title: GS_L1B_B04


title: GS_L1B_D02


title: GS_L1B_A12


title: GS_L1B_A11


title: GS_L1B_A09


title: GS_L1B_A08


title: GS_L1B_A10


title: GS_L1B_A07


title: GS_L1B_A06


title: GS_L1B_C04


title: GS_L1B_A05


title: GS_L1B_A03


title: GS_L3B_H08

value: pCAG-mRFP


title: GS_L3B_H10


title: GS_L3B_H09


title: GS_L1B_B02


title: GS_L3B_H07


title: GS_L3B_H06


title: GS_L1B_B01


title: GS_L3B_H04


title: GS_L3B_G10


title: GS_L3B_G09


title: GS_L3B_H03


title: GS_L3B_G08


title: GS_L3B_G05


title: GS_L3B_G12


title: GS_L3B_G11


title: GS_L3B_G04


title: GS_L3B_H01


title: GS_L3B_G06


title: GS_L3B_H02


title: GS_L1B_A01


title: GS_L1B_A02


title: GS_L3B_G01


title: GS_L3B_H12


title: GS_L3B_F05


title: GS_L3B_H11


title: GS_L3B_G03


title: GS_L3B_F07


title: GS_L3B_G02


title: GS_L3B_F11


title: GS_L3B_F04


title: GS_L3B_H05


title: GS_L3B_F03


title: GS_L3B_E12


title: GS_L3B_F02


title: GS_L3B_F01


title: GS_L3B_E10


title: GS_L3B_E09


title: GS_L3B_E07


title: GS_L3B_E06


title: GS_L3B_E08


title: GS_L3B_E04


title: GS_L3B_D10


title: GS_L3B_E01


title: GS_L3B_E02


title: GS_L3B_D12


title: GS_L3B_D08


title: GS_L3B_D07


title: GS_L3B_D09


title: GS_L3B_D06


title: GS_L3B_D03


title: GS_L3B_D05


title: GS_L3B_C11


title: GS_L3B_C12


title: GS_L3B_C10


title: GS_L3B_C09


title: GS_L3B_C08


title: GS_L3B_C07


title: GS_L3B_C04


title: GS_L3B_C05


title: GS_L3B_E11


title: GS_L3B_B12


title: GS_L3B_C02


title: GS_L3B_B11


title: GS_L3B_B10


title: GS_L3B_E03


title: GS_L3B_B08


title: GS_L3B_B07


title: GS_L3B_B06


title: GS_L3B_B05


title: GS_L3B_B04


title: GS_L3B_B01


title: GS_L3B_A12


title: GS_L3B_A11


title: GS_L3B_B03


title: GS_L3B_A06


title: GS_L3B_A07


title: GS_L3B_D01


title: GS_L3B_A05


title: GS_L3B_A04


title: GS_L3B_A08


title: GS_L3B_A03


title: GS_L3B_A02


title: GS_L2C_H09


title: GS_L3B_B09


title: GS_L3B_A09


title: GS_L2C_H07


title: GS_L2C_H10


title: GS_L2C_H12


title: GS_L2C_H11


title: GS_L2C_H08


title: GS_L2C_H06


title: GS_L2C_H04


title: GS_L2C_H03


title: GS_L2C_H01


title: GS_L2C_H02


title: GS_L2C_G12


title: GS_L2C_G10


title: GS_L2C_G09


title: GS_L2C_G08


title: GS_L2C_G04


title: GS_L2C_G07


title: GS_L2C_G03


title: GS_L2C_G02


title: GS_L2C_F08


title: GS_L2C_G01


title: GS_L2C_F12


title: GS_L2C_F05


title: GS_L2C_F07


title: GS_L2C_H05


title: GS_L2C_F04


title: GS_L2C_F02


title: GS_L2C_F03


title: GS_L2C_E11


title: GS_L2C_E07


title: GS_L2C_E12


title: GS_L2C_E10


title: GS_L2C_G11


title: GS_L2C_F09


title: GS_L2C_E06


title: GS_L2C_E04


title: GS_L2C_E05


title: GS_L2C_E02


title: GS_L2C_E01


title: GS_L2C_D12


title: GS_L2C_D10


title: GS_L2C_E03


title: GS_L2C_F10


title: GS_L2C_F11


title: GS_L2C_F01


title: GS_L2C_D05


title: GS_L2C_D06


title: GS_L2C_D03


title: GS_L2C_D02


title: GS_L2C_E08


title: GS_L2C_C09


title: GS_L2C_C08


title: GS_L2C_C02


title: GS_L2C_C10


title: GS_L2C_C01


title: GS_L2C_C05


title: GS_L2C_C12


title: GS_L2C_B10


title: GS_L2C_D01


title: GS_L2C_B11


title: GS_L2C_C11


title: GS_L2C_C04


title: GS_L2C_C03


title: GS_L2C_C06


title: GS_L2C_C07


title: GS_L2C_B06


title: GS_L2C_B12


title: GS_L2C_B08


title: GS_L2C_B07


title: GS_L2C_D08


title: GS_L2C_D07


title: GS_L2C_B05


title: GS_L2C_B04


title: GS_L2C_B01


title: GS_L2C_B03


title: GS_L2C_A11


title: GS_L2C_A12


title: GS_L2C_B02


title: GS_L2C_A09


title: GS_L2C_A08


title: GS_L2C_A06


title: GS_L2C_A07


title: GS_L2C_A05


title: GS_L1D_H12


title: GS_L2C_A03


title: GS_L1D_H09


title: GS_L1D_H08


title: GS_L2C_A04


title: GS_L2C_A02


title: GS_L1D_H07


title: GS_L1D_G11


title: GS_L1D_G10


title: GS_L1D_H05


title: GS_L1D_H02


title: GS_L1D_H11