title: HD03_08_D02

city: Baltimore

first: Loyal

last: Goff

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Single-cell RNA-seq libraries were aligned with hisat2 version 2.0.1-beta to a mouse mm10 hisat2 index with the inserted CFP cDNA sequence included in the index.
Using samtools 1.2, sam files were compressed to bam files then sorted and indexed.
Using Cufflinks v2.2.1, indexed bam files were quantified against the Gencode mouse vM10 assembly and normalized across all samples
51 samples,  both in the bottom 5th percentile for total number of reads and for which less than 50% of reads were mapped, were removed. 22 PCA outliers were removed iteratively.
The remaining 1,296 samples (1,280 cells and 16 negative control wells) were normalized again, as before. 261 cells for which less than 1,000 genes were detected at non-zero fragments per kilobase of transcript per million mapped reads (FPKM) were removed, and 4 more cells were subsequently removed as PCA outliers. 28 cells were then removed due to a high ratio of mitochondrial to nuclear gene expression, indicating poor library quality.
1,003 cells and 0 negative control wells passed these quality control measures. The age, sex, and genotype of these 1,003 cells is as follows: 183 embryonic day (E)12.5 female RetCFP/+, 164 E12.5 male RetCFP/+, 173 E12.5 female RetCFP/CFP, 125 E12.5 male RetCFP/CFP, 161 E14.5 female RetCFP/+, 156 E14.5 male RetCFP/+, 37 E14.5 female RetCFP/CFP, and 4 E14.5 male RetCFP/CFP.
FPKM values were transformed to copies per cell (CPC) using the Census algorithm (Qiu et al., 2017).
Genome_build: mm10,  Transcriptome_build: Gencode vM10
Supplementary_files_format_and_content: feature_data.tsv is a tab-delimited text file containing gene (row) information for genes in the expression matrix'
Supplementary_files_format_and_content: pheno_data.tsv is a tab-delimited text file containing cell (column) phenotype information for cells in the expression matrix
Supplementary_files_format_and_content: exprs.mtx is a Matrix Market format (.mtx) file containing the gene x cells raw expression matrix of estimated RNA copies per cell

source_name: Sorted CFP-positive enteric neural crest cells and their differentiating progeny

growth_protocol: Mice heterozygous for the conditional Ret allele (Retfl/+)(Gould et al., 2008; Uesaka et al., 2008) were obtained from David Ginty (Harvard University, Boston, MA). Briefly, the floxed Ret allele (Retfl) was generated by inserting a gene cassette, comprising the floxed human RET9 cDNA with SV40 intron polyA sequence followed by a cyan fluorescent protein (CFP) cDNA with polyA sequence, into exon 1 of the mouse Ret gene. Ret CFP knock-in mice (RetCFP/+) were generated by crossing Retfl/+ mice to β-actin-Cre mice to remove the RET9 cDNA. All procedures were approved by the Johns Hopkins Animal Care and Use Committee (protocol number: MO21M56). All mouse experiments were conducted in accordance with the National Institutes of Health Guidance for the Care and Use of Laboratory Animals. All mice embryos used ranged from E12.5 to E14.5. Both males and females were used.

extract_protocol:
Whole gut tissue (stomach, fore and hind gut) from RetCFP/+ and RetCFP/CFP male and female embryos at E12.5 and E14.5 were dissociated into single cell suspensions using Accumax (Sigma, USA). The cells were filtered serially through a 100 μm and 40 μm cell strainer, and centrifuged at 2000 rpm for 5 m. The cell pellet was resuspended in 5% FBS, 4 mM EDTA in Leibovitz L-15 medium for cell sorting using MoFlo XDP (BD Biosciences) with a blue-violet excitation laser for CFP. Single cells were sorted directly into 96 well plates containing 1.9 μL Triton X-100 (Sigma-Aldrich, 0.2% v/v, #T9284), 1 μL dNTP mix (Amresco, 10 mM each, #N557), 1 μL 5’ biotinylated oligo-dT30VN primer (IDT, 10 μM), and 0.1 μL RNasin Plus (Promega, 40 U/μL, #N2615) per well.
Libraries were prepared from 2 embryos for each of the 8 conditions (RetCFP/+ and RetCFP/CFP, female and male, E12.5 and E14.5) with two exceptions: libraries were prepared from 1 RetCFP/CFP male E14.5 embryo and 4 RetCFP/CFP female E14.5 embryos owing to differential viability. Single-cell RNA-seq libraries were prepared following a modified Smart-seq2 protocol (Chevée et al., 2018; Picelli et al., 2014). Reverse transcription and preamplification (20 cycles for E12.5 cells, 22 cycles for E14.5 cells) followed the original Smart-seq2 protocol, with the exception of using 5’ biotinylated NGG template-switching oligonucleotides. Sequencing libraries were generated following the Nextera XT protocol (Illumina, #FC-131-1096) on a quartered scale, using approximately 200 pg input DNA per sample and 14 enrichment PCR cycles. Nextera XT v2 Index Sets (Illumina, #FC-131-2004) were diluted 1:5 in water prior to use. Libraries were sequenced (paired end, 50 bp read length) on an Illumina HiSeq 2500 to an average depth of 9.91x10^5 (standard deviation 7.43x10^5) paired-end reads per cell.

tag: Sex

value: female

value: RetCFP/CFP

value: hom

tag: batch

value: Whole gut (stomach, fore and hind gut)

tag: predicted parent celltype

value: neuron

tag: predicted celltype

tag: assigned cluster


title: HD03_06_H11

status: Public on Dec 30 2021

type: SRA

middle: A

state: MD

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: age

tag: genotype

value: RetCFP/+

value: het

tag: tissue

value: progenitor/glia


title: HD03_06_H07


title: HD03_06_H12


title: HD03_06_H01


title: HD03_06_G10


title: HD03_20_A01

value: male


title: HD03_20_B10


title: HD03_06_H02


title: HD03_20_B12


title: HD03_06_G07


title: HD03_06_G11


title: HD03_06_G08


title: HD03_06_H10


title: HD03_06_H03


title: HD03_06_G09


title: HD03_06_H05


title: HD03_08_A10


title: HD03_06_H04


title: HD03_06_G05


title: HD03_06_H08


title: HD03_06_H06


title: HD03_20_A09


title: HD03_06_G06


title: HD03_06_G02


title: HD03_06_G01


title: HD03_06_F12


title: HD03_06_G03


title: HD03_06_F11


title: HD03_06_G04


title: HD03_06_F10


title: HD03_06_F04


title: HD03_06_F03


title: HD03_06_F07


title: HD03_06_F05


title: HD03_06_F06


title: HD03_06_F01


title: HD03_06_E12


title: HD03_06_E11


title: HD03_06_E07


title: HD03_06_D11


title: HD03_06_E10


title: HD03_06_E04


title: HD03_06_E06


title: HD03_06_E03


title: HD03_06_E01


title: HD03_06_D12


title: HD03_06_E09


title: HD03_06_F08


title: HD03_06_F02


title: HD03_06_D08


title: HD03_06_D06


title: HD03_06_D09


title: HD03_06_D05


title: HD03_06_F09


title: HD03_06_E02


title: HD03_06_D04


title: HD03_06_D01


title: HD03_06_D03


title: HD03_06_C11


title: HD03_06_C10


title: HD03_06_D07


title: HD03_06_E08


title: HD03_06_C09


title: HD03_06_C05


title: HD03_06_C07


title: HD03_05_H12


title: HD03_05_H03


title: HD03_05_H06


title: HD03_05_H02


title: HD03_06_C06


title: HD03_05_H08


title: HD03_05_H01


title: HD03_05_G12


title: HD03_05_H07


title: HD03_05_G09


title: HD03_05_G10


title: HD03_05_G07


title: HD03_05_G08


title: HD03_05_G02


title: HD03_05_G06


title: HD03_05_G05


title: HD03_05_G03


title: HD03_06_C03


title: HD03_05_G01


title: HD03_05_F11


title: HD03_05_H09


title: HD03_05_F08


title: HD03_05_F05


title: HD03_05_F07


title: HD03_05_E12


title: HD03_05_E11


title: HD03_05_F04


title: HD03_05_E10


title: HD03_05_F03


title: HD03_05_E07


title: HD03_05_E06


title: HD03_05_F10


title: HD03_05_E05


title: HD03_05_C12


title: HD03_05_E01


title: HD03_05_E03


title: HD03_05_E04


title: HD03_05_E02


title: HD03_05_C09


title: HD03_05_C10


title: HD03_05_C08


title: HD03_05_F09


title: HD03_05_C05


title: HD03_05_C07


title: HD03_05_C04


title: HD03_05_C02


title: HD03_05_E09


title: HD03_05_C01


title: HD03_05_B12


title: HD03_05_B11


title: HD03_05_C11


title: HD03_05_B06


title: HD03_05_B07


title: HD03_05_B05


title: HD03_05_B10


title: HD03_05_B08


title: HD03_05_B04


title: HD03_05_B03


title: HD03_05_B02


title: HD03_05_A10


title: HD03_05_C03


title: HD03_04_H08


title: HD03_05_A08


title: HD03_05_F12


title: HD03_04_H06


title: HD03_04_G12


title: HD03_04_H01


title: HD03_04_F10


title: HD03_04_G09


title: HD03_04_F08


title: HD03_04_F09


title: HD03_04_F06


title: HD03_04_F07


title: HD03_04_F03


title: HD03_04_F01


title: HD03_04_E06


title: HD03_05_B01


title: HD03_04_D12


title: HD03_04_D11


title: HD03_04_H05


title: HD03_04_D10


title: HD03_04_D08


title: HD03_04_D06


title: HD03_04_D01


title: HD03_04_C11


title: HD03_04_D03


title: HD03_04_C12


title: HD03_04_D02


title: HD03_04_D07


title: HD03_04_F04


title: HD03_04_C09


title: HD03_04_C08


title: HD03_04_C02


title: HD03_04_C04


title: HD03_04_C03


title: HD03_04_C05


title: HD03_04_D09


title: HD03_04_B11


title: HD03_04_B12


title: HD03_04_B10


title: HD03_04_D05


title: HD03_04_B09


title: HD03_04_B08


title: HD03_04_B05


title: HD03_04_C10


title: HD03_04_B02


title: HD03_04_B04


title: HD03_04_A12


title: HD03_04_B03


title: HD03_04_B01


title: HD03_04_A10


title: HD03_04_A09


title: HD03_04_A07


title: HD03_04_A11


title: HD03_04_A02


title: HD03_04_A06


title: HD03_04_A03


title: HD03_04_A04


title: HD03_04_A08


title: HD03_04_A01


title: HD03_03_G12


title: HD03_03_G11


title: HD03_03_G09


title: HD03_03_G06


title: HD03_03_G10


title: HD03_03_G03


title: HD03_03_G07


title: HD03_03_G01


title: HD03_03_G05


title: HD03_03_F07


title: HD03_03_E08


title: HD03_06_D10


title: HD03_03_E01


title: HD03_03_E06


title: HD03_03_D12


title: HD03_03_D11


title: HD03_03_E07


title: HD03_03_D10


title: HD03_03_D08


title: HD03_03_G08


title: HD03_03_D07


title: HD03_03_D05


title: HD03_03_D02


title: HD03_03_D03


title: HD03_03_C12


title: HD03_03_D01


title: HD03_03_F12


title: HD03_03_C10


title: HD03_03_C11


title: HD03_03_C09


title: HD03_03_C07


title: HD03_03_C06


title: HD03_03_C08


title: HD03_03_C02


title: HD03_03_C01


title: HD03_03_C05


title: HD03_03_C03


title: HD03_03_D09


title: HD03_03_B12


title: HD03_03_B08


title: HD03_03_D04


title: HD03_03_B03


title: HD03_03_B01


title: HD03_03_A11


title: HD03_03_D06


title: HD03_03_A10


title: HD03_03_B09


title: HD03_02_F12


title: HD03_02_G01


title: HD03_03_B02


title: HD03_03_A03


title: HD03_02_F09


title: HD03_03_A07


title: HD03_03_A09


title: HD03_02_E11


title: HD03_03_A04


title: HD03_03_A01


title: HD03_02_F10


title: HD03_02_F08


title: HD03_02_F07


title: HD03_02_F06


title: HD03_02_F03


title: HD03_02_H05


title: HD03_02_F01


title: HD03_02_F02


title: HD03_03_B06


title: HD03_02_E10


title: HD03_02_H09


title: HD03_02_E07


title: HD03_02_E04


title: HD03_02_E09


title: HD03_02_F05


title: HD03_02_F11


title: HD03_02_E03


title: HD03_02_D08


title: HD03_02_E05


title: HD03_02_C12


title: HD03_02_E06


title: HD03_02_E02


title: HD03_02_C10


title: HD03_02_C11


title: HD03_02_C09


title: HD03_02_C07


title: HD03_02_C06


title: HD03_02_C05


title: HD03_02_C01


title: HD03_02_C02


title: HD03_02_B12


title: HD03_02_E08


title: HD03_02_B09


title: HD03_02_B07


title: HD03_02_B08


title: HD03_02_B06


title: HD03_02_B05


title: HD03_02_D01


title: HD03_02_B03


title: HD03_02_B04


title: HD03_02_A07


title: HD03_02_A09


title: HD03_02_A11


title: HD03_02_B01


title: HD03_02_A08


title: HD03_02_A06


title: HD03_02_A05


title: HD03_02_A10


title: HD03_01_H12


title: HD03_01_H08


title: HD03_02_A04


title: HD03_02_A03


title: HD03_01_H11


title: HD03_01_H09


title: HD03_01_H07


title: HD03_01_H04


title: HD03_01_H03


title: HD03_01_G05


title: HD03_01_H02


title: HD03_01_G03


title: HD03_01_F10


title: HD03_01_F12


title: HD03_02_D04


title: HD03_01_F11


title: HD03_01_F09


title: HD03_01_F08


title: HD03_01_F07


title: HD03_01_F06


title: HD03_01_H05


title: HD03_01_H06


title: HD03_01_F04


title: HD03_01_F02


title: HD03_01_F03


title: HD03_01_E09


title: HD03_01_E12


title: HD03_01_E10


title: HD03_01_E11


title: HD03_01_E03


title: HD03_01_D12


title: HD03_01_E02


title: HD03_01_E08


title: HD03_01_D08


title: HD03_01_D09


title: HD03_01_D07


title: HD03_01_D10


title: HD03_01_D06


title: HD03_01_D02


title: HD03_01_D01


title: HD03_01_C12


title: HD03_01_C10


title: HD03_01_C11


title: HD03_01_C09


title: HD03_01_C06


title: HD03_01_C08


title: HD03_01_C05


title: HD03_01_C04


title: HD03_01_C02


title: HD03_01_C03


title: HD03_01_B10


title: HD03_01_B09


title: HD03_01_B07


title: HD03_01_B06


title: HD03_01_D04


title: HD03_01_B02


title: HD03_01_A12


title: HD03_01_A09


title: HD03_01_A10


title: HD03_01_A07


title: HD03_01_A05


title: HD03_01_A04


title: HD03_01_A01


title: HD02_20_H12


title: HD03_01_A02


title: HD02_20_H11


title: HD02_20_H09


title: HD02_20_H10


title: HD02_20_H08


title: HD02_20_H06


title: HD02_20_H05


title: HD02_20_H04


title: HD03_01_A03


title: HD02_20_H07


title: HD02_20_H03


title: HD02_20_H01


title: HD02_20_G10


title: HD02_20_G09


title: HD02_20_G12


title: HD03_01_A06


title: HD02_20_G07


title: HD02_20_G08


title: HD02_20_G06


title: HD02_20_G04


title: HD02_20_G05


title: HD02_20_G02


title: HD02_20_F10


title: HD02_20_F12


title: HD02_20_F11


title: HD02_20_F09


title: HD02_20_F06


title: HD02_20_F05


title: HD02_20_F07


title: HD02_20_F02


title: HD02_20_F01


title: HD02_20_F03


title: HD02_20_E11


title: HD02_20_E12


title: HD02_20_E10


title: HD02_20_E09


title: HD02_20_E08


title: HD02_20_E07


title: HD02_20_G01


title: HD02_20_E05


title: HD02_20_E04


title: HD02_20_E03


title: HD02_20_E02


title: HD02_20_E01


title: HD02_20_F08


title: HD02_20_F04


title: HD02_20_D12


title: HD02_20_D10


title: HD02_20_D11


title: HD02_20_D09


title: HD02_20_D06


title: HD02_20_D05


title: HD02_20_D02


title: HD02_20_D03


title: HD02_20_D01


title: HD02_20_C12


title: HD02_20_C10


title: HD02_20_C08


title: HD02_20_C09


title: HD02_20_C07


title: HD02_20_C06


title: HD02_20_C11


title: HD02_20_C05


title: HD03_01_A08


title: HD02_20_C04


title: HD02_20_C03


title: HD02_20_B12


title: HD02_20_C01


title: HD02_20_B11


title: HD02_20_D08


title: HD02_20_D07


title: HD02_20_B07


title: HD02_20_B06


title: HD02_20_B03


title: HD02_20_B05


title: HD02_20_B01


title: HD02_20_A12


title: HD02_20_A10


title: HD02_20_B02


title: HD02_20_A11


title: HD02_20_A08


title: HD02_20_B09


title: HD02_20_A06


title: HD02_20_A07


title: HD02_20_B04


title: HD02_20_A04


title: HD02_20_A03


title: HD02_20_A02


title: HD02_19_H11


title: HD02_20_A05


title: HD02_19_H10


title: HD02_20_B10


title: HD02_19_H08


title: HD02_19_H07


title: HD02_19_H06


title: HD02_19_H05


title: HD02_19_H04


title: HD02_19_H03


title: HD02_19_H02


title: HD02_20_A09


title: HD02_19_G08


title: HD02_19_G07


title: HD02_19_G11


title: HD02_19_G10


title: HD02_20_G03


title: HD02_19_H01


title: HD02_19_G12


title: HD02_19_G03


title: HD02_19_G04


title: HD02_19_H09


title: HD02_19_F10


title: HD02_19_G02


title: HD02_19_F08


title: HD02_19_F07


title: HD02_19_G01


title: HD02_19_F09


title: HD02_19_F11


title: HD02_19_F06


title: HD02_19_F03


title: HD02_19_F04


title: HD02_19_F05


title: HD02_19_E12


title: HD02_19_F02


title: HD02_19_F01


title: HD02_19_E11


title: HD02_19_G09


title: HD02_19_E04


title: HD02_19_D12


title: HD02_19_E10


title: HD02_19_E06


title: HD02_19_G06


title: HD02_19_G05


title: HD02_19_D11


title: HD02_19_F12


title: HD02_19_E08


title: HD02_19_E09


title: HD02_19_E07


title: HD02_19_E02


title: HD02_19_E05


title: HD02_19_E03


title: HD02_19_E01


title: HD02_19_D10


title: HD02_19_D09


title: HD02_19_D08


title: HD02_19_D06


title: HD02_19_D07


title: HD02_19_D05


title: HD02_19_D03


title: HD02_19_C09


title: HD02_19_C11


title: HD02_19_C10


title: HD02_19_D01


title: HD02_19_C12


title: HD02_19_C08


title: HD02_19_D02


title: HD02_19_C07


title: HD02_19_C06


title: HD02_19_B12


title: N2 rep2 IP

city: Guangzhou

first: Weichao

last: Hao

state: Guangdong

address: No.1838 Guangzhou Avenue North, Baiyun District

country: China

institute: Southern Medical University

description:
RIP-seq of MEFs Ythdf3-IP RNA, replicate 2 of starvation
T6.S_IP

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.0.13 with default parameters.
The RIP targets were defined as peaks enriched in the IP (RIP/input≥2, and p<0.0001) and peaks were annotated by annotatePeaks.pl module of HOMER with default setting.
The differentially methylated sites were identified by diffReps with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Ythdf3 binding peaks

source_name: embryonic fibroblasts

growth_protocol: MEFs were isolated from mouse embryos at 13.5 days post-coitum, and cultured in high glucose DMEM (Corning, USA) supplemented with 10% FBS, 2mM glutaMAX, 1% non-essential amino acids, 50μM β-mercaptoethanol, and 100U/ml penicillin-streptomycin at 37°C under 5% CO2.

extract_protocol:
RIP was performed using Magna RIP Kit (Millipore) following the manufacturer's instructions and a Ythdf3 antibody targeting mouse endogenous Ythdf3 protein. The input and immunoprecipitated RNAs were recovered using RNAiso plus and extracted according to the manufacturer's protocol.
Libraries were constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (NEB).

treatment_protocol: The MEFs of nutrient starvation were treated with the nutrient-deprived medium for 2 hours.

tag: strain

tag: cell type

value: MEF

value: wild type

tag: passages

value: 5 to 6 passages

tag: rip antibody

value: anti-YTHDF3 (Santa Cruz, sc-377119)

tag: treatment

value: treated with nutrient-deprived medium for 2 hours


title: HD02_19_B06


title: N2 rep1 input

description:
RIP-seq of MEFs Input RNA, replicate 1 of starvation
T4.S_Input


title: HD02_19_B08


title: N0 rep2 IP

description:
RIP-seq of MEFs Ythdf3-IP RNA, replicate 2 of normal condition
T6.N_IP

value: untreated


title: HD02_19_B03


title: N0 rep1 IP

description:
RIP-seq of MEFs Ythdf3-IP RNA, replicate 1 of normal condition
T4.N_IP


title: HD02_19_B02


title: HD02_19_B01


title: N0 rep1 input

description:
RIP-seq of MEFs Input RNA, replicate 1 of normal condition
T4.N_Input


title: HD02_19_B07


title: HD02_19_C05


title: HD02_19_C04


title: HD02_19_C03


title: MeRIP_starv_rep2_IP

description: m6A-RIP mRNA obtained from MEFs with nutrient-deprived medium treatment for 2h (replicate 2)

data_processing:
Library strategy: MeRIP-Seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 software v2.0.4 with default parameters.
The methylated sites on peaks were identified by MACS2 peak-calling software.
The differentially methylated sites were identified by diffReps with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: differential peak text files

extract_protocol:
RNA was extracted from cells using RNAiso plus (Takara) according to the manufacturer's protocol. The mRNAs were further purified using Dynabeads™ mRNA Purification Kit (Invitrogen).
Libraries were constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (NEB).


title: HD02_19_A10


title: HD02_19_A11


title: MeRIP_starv_rep1_IP

description: m6A-RIP mRNA obtained from MEFs with nutrient-deprived medium treatment for 2h (replicate 1)


title: N0 rep2 input

description:
RIP-seq of MEFs Input RNA, replicate 2 of normal condition
T6.N_Input


title: HD02_19_C02


title: HD02_19_C01


title: HD02_19_B11


title: HD02_19_B10


title: HD02_19_B04


title: N2 rep1 IP

description:
RIP-seq of MEFs Ythdf3-IP RNA, replicate 1 of starvation
T4.S_IP


title: MeRIP_starv_rep2_Input

description: Input mRNA obtained from MEFs with nutrient-deprived medium treatment for 2h (replicate 2)


title: HD02_19_B09


title: MeRIP_norm_rep1_IP

description: m6A-RIP mRNA obtained from MEFs without nutrient-deprived medium treatment (replicate 1)


title: MeRIP_norm_rep2_Input

description: Input mRNA obtained from MEFs without nutrient-deprived medium treatment (replicate 2)


title: N2 rep2 input

description:
RIP-seq of MEFs Input RNA, replicate 2 of starvation
T6.S_Input


title: HD02_19_B05


title: HD02_19_A05


title: HD02_19_A04


title: HD02_19_A09


title: HD02_06_H03


title: HD02_19_A03


title: MeRIP_norm_rep2_IP

description: m6A-RIP mRNA obtained from MEFs without nutrient-deprived medium treatment (replicate 2)


title: HD02_19_A01


title: Sample_7_ASF_MUC_3

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Raw sequence reads were mapped to the mouse genome mm10/GRCm38 using the STAR aligner version 2.5.2b.
Mapped reads were counted at the gene level using the Rsubread R package. Lowly expressed genes were prefiltered, keeping only genes with 50 or more raw counts in at least 2 samples.
Library size normalization and further analysis was performed using the R package DESeq2 version 1.22.2
Differential expression was assessed using the Wald test as implemented in DESeq2, with a False Discovery Rate (FDR) threshold of 0.1 being used as a significance threshold.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

molecule: total RNA

growth_protocol: The colonic IEC weren collected by gentle scraping with a disposable, sterile inoculation loop

extract_protocol:
IEC were collected in Trizol and lysed by repeated passing through a 27G syringe needle. RNA was extracted by chloroform phase separation followed by RNA extraction with in-column DNase treatment using the Direct-zol RNA Kit
Poly-A pull-down was performed to enrich mRNAs from total RNA samples, followed by library construction using Illumina TruSeq chemistry.
Cluster generation and 50–base pair single-end 50 cycled sequencing was performed on the Illumina HiSeq4000 system

treatment_protocol: ASF mice were colonized with the mucosal consortium or PBS by oral gavage. A single litter of 9-week old animals was used for the experiment.

value: ASF

value: Intestinal Epithelial Cells (Colon)

value: Colonized with mucosa associated fungi:C. albicans, S. cerevisiae, S. fibuligera


title: HD02_19_A12

value: female


title: HD02_19_A06


title: Sample_6_ASF_MUC_2


title: Sample_5_ASF_MUC_1


title: Sample_8_ASF_MUC_4


title: Sample_4_ASF_4


title: HD02_19_A08


title: MeRIP_starv_rep1_Input

description: Input mRNA obtained from MEFs with nutrient-deprived medium treatment for 2h (replicate 1)


title: Sample_3_ASF_3


title: HD02_19_A07


title: HD02_06_H06

value: RetCFP/CFP

value: hom


title: HD02_06_H02

value: Whole gut (stomach, fore and hind gut)


title: HD02_06_G12


title: MeRIP_norm_rep1_Input

description: Input mRNA obtained from MEFs without nutrient-deprived medium treatment (replicate 1)


title: Sample_1_ASF_1


title: HD02_19_A02

value: RetCFP/+


title: HHDST 2366

city: Boston

first: Alice

middle: H

last: Lichtenstein

state: MA

address: 711 Washington St

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

description: 10153 genes with 'Unique Gene Reads' data

data_processing:
After sequencing, raw data in FASTQ format was processed for quality using CLC Bio Genomic Workbench (Qiagen, Valencia, CA).
The transcriptome was assembled using the annotated porcine translational research database (version NR 112918) as a reference genome
Differential expression analysis was performed on using a two-factor model design matrix in edge R, a Bioconductor package based on a negative binomial distribution
To evaluate consistency of colonic mucosa sampling, the xCell tool [23] was used to analyze the RNA sequencing data (reads per kilobase million [RPKM]) that predicted enrichment of various cell types within each colon sample. One sample in the HHD-S group displayed low epithelial cell enrichment relative to all other samples (36% of the mean of other samples), suggesting low presence of colonic mucosa, and was therefore excluded from subsequent analyses, resulting in a final sample of n = 29.  Count data on annotated genes was filtered based on a minimum of at least one count per million across six samples in all groups and normalized using the trimmed mean of M values (TMM) method. The edge R two-factor model was designed to determine differential gene expression attributable to diet, statin, or a diet x statin interaction. Differentially expressed genes were identified using the Cox-Reid profile-adjusted likelihood method and likelihood ratio test. A Benjamini-Hochberg false discovery rate (FDR) method was used to adjust p-values for multiple comparisons
Thus, given the ancillary nature of this study genes were considered differentially expressed based on an FDR adjusted p <0.05 and absolute fold change ≥1.5. Fold change for genes identified by the edge R two-factor model were interpreted as diet effect: fold change of WD relative to HHD and statin effect: fold change of atorvastatin relative to no atorvastatin. Differentially expressed genes were only attributed to main effects (diet and statin).
Genome_build: The transcriptome was assembled using the porcine translational research database (version NR 112918) as a reference genome
Supplementary_files_format_and_content: comma-separated value files with Unique Gene Read counts for gene

organism: Sus scrofa

source_name: Colonic mucosa

growth_protocol: After one month of acclimatization to a “grower diet” and another month of a gradual shift to the experimental diets, the pigs were fed their respective diets in isocaloric amounts, with a gradual increase in total energy to meet growth requirements, for six months.

extract_protocol:
Colonic mucosa was homogenized and RNA was isolated using TRI reagent. Isolated RNA was treated with Turbo DNase (Ambion, Waltham, MA) to minimize genomic DNA contamination. RNA quality was assessed using the Experion RNA analysis electrophoresis kit (Bio-Rad, Hercules, CA). Only samples with an RNA Quality Indicator (RQI) greater than 8 were sequenced.
Prior to RNA sequencing (RNA-seq) samples were processed (mRNA purification and fragmentation, cDNA synthesis, end repair, 3’ adenylation, adaptor ligation, and DNA enrichment) using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) and AMPure XP beads (Beckman Coulter, Brea, CA) per the manufacturer’s instructions. DNA fragment size was determined using Experion DNA 1K chips (Bio-Rad, Hercules, CA) and library quantification was completed using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA). Raw data in FASTQ format was processed for quality using CLC Bio Genomic Workbench (Qiagen, Valencia, CA). The transcriptome was assembled using the annotated porcine translational research database (version NR 112918)  as a reference genome

treatment_protocol: Isocaloric diets were designed to represent typical Western and heart healthy dietary patterns consumed by humans. Detailed diet composition and ingredient sources have been reported previously. Briefly, both diets contained 38% of energy (E) as fat, 47% E as carbohydrate and 15% E as protein. The major differences between the WD and HHD were the types of carbohydrate and fat, and amount of fiber, cholesterol, fruits, vegetables, and fish oil. The WD was rich in saturated fat (butter fat), cholesterol, and refined carbohydrate (sugar, white flour), and low in fiber, whereas the HHD was rich in unsaturated fat (canola, soybean and corn oils), unrefined carbohydrate (whole wheat flour, oats), fruits/vegetables (freeze dried mix, Futureceuticals, Momence, IL) and fiber, and low in cholesterol. Pigs fed the HHD were administered fish oil capsules (Epanova 1000 mg [550 mg EPA + 200 mg DHA as free fatty acids], AstraZeneca, Cambridge, MA) three times per week. Pigs in the atorvastatin (Lipitor, Pfizer, New York, NY) groups were given 20 mg/day during the first three months and 40 mg/day during the latter three months of the intervention period.

tag: diet

value: Heart Healthy + Statin

tag: rna id


title: HD02_06_G06

value: neuron


title: HD02_06_G10

value: male

value: progenitor/glia


title: HD02_06_G03


title: HD02_06_F12


title: HHDST 2358


title: HHDST 2346


title: HD02_06_F09


title: HHDST 2339


title: HD02_06_F06


title: HD02_06_E11


title: HD02_06_F03


title: HD02_06_F01


title: Sample_2_ASF_2


title: HHDST 2328


title: HHDST 2329


title: HHD 2356

value: Heart Healthy


title: HHDST 2327


title: HHD 2357


title: HD02_06_F04


title: HD02_06_E06


title: HHD 2336


title: HD02_06_G11


title: HD02_06_E04


title: HHD 2330


title: HHD 2325


title: HHDST 2334


title: HD02_06_D11


title: HD02_06_D12


title: ARST 2362

value: Atherogenic + Statin


title: ARST 2352


title: HD02_06_D08


title: HD02_06_D06


title: HD02_06_E07


title: ARST 2345


title: ARST 2349


title: ARST 2340


title: HHD 2343


title: HD02_06_E03


title: HD02_06_C11


title: HD02_06_C02


title: ARST 2332


title: HD02_06_C09


title: ARST 2333


title: HD02_06_C04


title: HD02_06_C07


title: AR 2363

value: Atherogenic


title: AR 2348


title: HD02_06_B07


title: AR 2342


title: AR 2351


title: HD02_06_B10


title: HD02_06_B12


title: HD02_06_A09


title: HD02_06_A08


title: AR 2337


title: AR 2331


title: HD02_06_A06


title: AR 2338


title: HD02_05_H11

value: het


title: HD02_06_A05


title: HD02_05_H10


title: ARST 2326


title: HD02_05_H09


title: HD02_05_H08


title: HD02_05_H06


title: HD02_05_H07


title: HD02_05_H05


title: HD02_05_H04


title: HD02_05_G12


title: HD02_05_G11


title: HD02_05_H02


title: HD02_05_G08


title: HD02_05_G10


title: HD02_05_G09


title: HD02_05_H01


title: HD02_05_G07


title: shSRSF10 HCCLM3 cells

city: Hangzhou

first: Jianxiang

last: Chen

state: Zhejiang

address: No.58,Haishu Rd, Cangqian,

department: Pharmacy Institute and Department of Hepatology

institute: Hangzhou Normal University

description:
LM3-2
SRSF10 stable knockdown HCCLM3 cells
liver
39 years old man

data_processing:
HISAT\reference{hisat_ref} to perform genome mapping, HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads with equal or better accuracy than any other method.
rMATS \reference{rmats_ref} was used to detect differentially splicing gene (that is differential isoform relative abundance between samples), a computational tool to detect differential alternative splicing events from RNA-Seq data.
It calculates the inclusion isoform and skipping isoform, shown as Figure \figure{rmats_figure}. The statistical model of MATS calculates the P-value and false discovery rate (FDR) that the difference in the isoform ratio of a gene between two conditions, in our project, gene that with FDR <= 0.05 are defined as differentially splicing gene (DSG).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files.
Supplementary_files_format_and_content: *.A3SS.GeneDiffSplice.txt
Supplementary_files_format_and_content: *.A5SS.GeneDiffSplice.txt
Supplementary_files_format_and_content: *.MXE.GeneDiffSplice.txt
Supplementary_files_format_and_content: *.RI.GeneDiffSplice.txt
Supplementary_files_format_and_content: *.SE.GeneDiffSplice.txt

organism: Homo sapiens

source_name: human high metastatic hepatocellular carcinoma cells

growth_protocol: Hep3B and HCCLM3 cells were grown in DMEM (Thermo Fisher Scientific) supplemented with 10% dialysed FBS and 1% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from stable cells and harvested using Trizol reagent.
The suitable fragments are selected for the PCR amplification. During the QC steps, Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. Then the library is sequenced using Illumina HiSeq 4000 or other sequencer.

treatment_protocol: SRSF10 and scramble stable knockdown cells were selected by puromycin selection.

tag: cell line

tag: shRNA


title: HD02_05_G06

tag: Sex


title: shScramble control HCCLM3 cells

description:
LM3-1
scramble stable knockdown HCCLM3 cells
liver
39 years old man

value: high metastatic hepatocellular carcinoma cells

value: shScramble control


title: shSRSF10 Hep3B cells

description:
3B-2
SRSF10 stable knockdown Hep3B cells
liver
8 years juvenile

source_name: human hepatocellular carcinoma cells

value: hepatocellular carcinoma cells


title: Indisulam_dose1_16hours

city: London

first: Clare

last: Eckold

state: London

address: 10 Logan Place

country: United Kingdom

institute: (None)

data_processing:
Aligment HISAT version 2.1.0
Quantification Rsubread version 1.34.7
Genome_build: hg19

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) and rRNA was removed via ribodepletion (Illumina). Seven-five base paired end reads were sequenced using the HiSeq4000 (Illumina), resulting in 45 million reads per sample

value: Treated

tag: dose

tag: timepoint (h)


title: Indisulam_dose2_16hours


title: HD02_05_G05

tag: batch

tag: predicted parent celltype

tag: predicted celltype


title: HD02_05_G03

tag: age

tag: genotype

tag: assigned cluster


title: ProliHH_purox2_P5_rep1

type: RNA

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Proliferating hepatocytes (ProliHH) at passage5 cultured with irrMEF and EMUKK-05 medium. Puromycin-treated group (treatment concentration: 2ug/mL)

hyb_protocol: Hybridization and washing were performed according to Agilent's standard manual, and a Gene Expression Wash Pack (5188-5327: Agilent) was used for washing.

scan_protocol: An Agilent DNA Microarray Scanner was used to scan the microarrays.

data_processing: Agilent's Feature Extraction was used to quantify the scan results. Instructions for use followed the Agilent manual.

source_name: ProliHH, P5, purox2, replicate 1

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (5190-2305, Agilent) and the QIAGEN RNeasy mini kit (74104 : QIAGEN) according to the manufacturer's instructions. The amount of dye uptake and cRNA The quality of the labeled cRNA was monitored by Agilent 2100 Bioanalyzer, and the amount of dye incorporation and the yield of cRNA were confirmed by NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Proliferating hepatocytes (ProliHH) were cultured in irrMEF and EMUKK-05 medium.

extract_protocol: Total RNA was isolated using the miRNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and monitored for quality using an Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: with or without puromycin (at each passage)

tag: cell type

value: ProliHH


title: PHH_2064

description: Primary human hepatocytes (#2064)

source_name: PHH-2064, replicate 1

value: Primary hepatocytes


title: ProliHH_P6_rep1

description: Proliferating hepatocytes (ProliHH) at passage6 cultured with irrMEF and EMUKK-05 medium. No addition of puromycin.

source_name: ProliHH, P6, no-puro, replicate 1

tag: passages


title: Control_notreatment_16hours

value: No treatment


title: ProliHH_purox2_P25_rep1

description: Proliferating hepatocytes (ProliHH) at passage25 cultured with irrMEF and EMUKK-05 medium. Puromycin-treated group (treatment concentration: 2ug/mL)

source_name: ProliHH, P25, purox2, replicate 1


title: HD02_05_G02

tag: tissue

value: Whole gut (stomach, fore and hind gut)


title: ProliHH_P3_rep1

description: Proliferating hepatocytes (ProliHH) at passage3 cultured with irrMEF and EMUKK-05 medium. No addition of puromycin.

source_name: ProliHH, P3, no-puro, replicate 1


title: ProliHH_P15_rep1

description: Proliferating hepatocytes (ProliHH) at passage15 cultured with irrMEF and EMUKK-05 medium. No addition of puromycin.

source_name: ProliHH, P15, no-puro, replicate 1


title: PHH_2055

description: Primary human hepatocytes (#2055)

source_name: PHH-2055, replicate 1


title: ProliHH_purox1_P5_rep1

description: Proliferating hepatocytes (ProliHH) at passage5 cultured with irrMEF and EMUKK-05 medium. Puromycin-treated group (treatment concentration: 1ug/mL)

source_name: ProliHH, P5, purox1, replicate 1


title: Human_liver_totalRNA_636531

description: Human liver total RNA (636531, Clontech: Takara Bio, Shiga, Japan)

source_name: total RNA from human liver, replicate 1

value: isolated hepatocytes


title: ProliHH_P21_rep1

description: Proliferating hepatocytes (ProliHH) at passage21 cultured with irrMEF and EMUKK-05 medium. No addition of puromycin.

source_name: ProliHH, P21, no-puro, replicate 1


title: HD02_05_F12

value: RetCFP/+


title: ProliHH_purox1_P25_rep1

description: Proliferating hepatocytes (ProliHH) at passage25 cultured with irrMEF and EMUKK-05 medium. Puromycin-treated group (treatment concentration: 1ug/mL)

source_name: ProliHH, P25, purox1, replicate 1


title: Indisulam_dose1_6hours

tag: treatment


title: HD02_05_F11


title: shScramble control Hep3B cells

description:
3B-1
scramble stable knockdown Hep3B cells
liver
8 years juvenile


title: Control_notreatment_6hours


title: HD02_05_G04


title: HD02_05_F10


title: HD02_05_F09


title: HD02_05_F08


title: RNA_hPGHESC_2_P23_rep2

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
[Whole-genome bisulfite sequencing (WGBS)] Raw WGBS data were removed adaptors and low-quality bases using trim_galore (version: 0.1.3) with following parameters (--quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33). The clean reads were then paired mapped against the human reference genome hg19 using Bismark (version: 0.7.6)(Krueger and Andrews, 2011) with following parameters (--fastq --non_directional --phred33-quals). For improving the number of mapped reads, we re-mapped the unmapped reads with the single-end aligned mode. Only uniquely mapped reads were retained for the downstream analysis.
[RNA sequencing] Raw RNA-seq sequencing data were removed adaptors and low-quality based using the custom script. The clean reads were then mapped against the Ensembl human reference genome hg19 using TopHat (version: 2.0.12)(Trapnell et al., 2009) with the default parameters. Raw read were counted with HTSeq(Anders et al., 2015), and the gene expression level was quantified with the RPKM (reads per kilobase million).
Genome_build: hg19
Supplementary_files_format_and_content: WGBS BED files include the methylation rate information, and each column means the 'chr,start,end,base,strand,all_C,methylated_C,unmethylated_C,methylation_rate,ref,type'; RNA XLS files include the gene expression level of knonw genes, and each column means 'chr,start,end,strand,gene_ID,gene_name,gene_type,count,RPKM'.

molecule: genomic DNA

source_name: human parthenogenetic haploid embryonic stem cell

extract_protocol:
[RNA extraction] Total RNA was extracted from cell lines used in the WGBS study through a RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. Residual DNA was removed by RNase-free DNase Set (Qiagen)
[Whole-genome bisulfite sequencing (WGBS)] Genomic DNA was extracted from cell lines using the DNeasy Blood & Tissue Kit (Qiagen). There were two repetitions per cell line. For WGBS library construction, the DNA was fragmented into 300 bp by sonication using Covaris S2 instrument (Covaris), following end repair and A-tailing. Cytosine methylated adaptor-ligated DNA was treated with sodium bisulfite through a EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). Next, we used KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) to accomplish 4 cycles of PCR amplification. It should be noted that DNA was treated with sodium bisulfite twice to reach >99% bisulfite conversion rate and lambda DNA was added to assess the rate.
[RNA sequencing] For rRNA-depleted RNA-seq library preparation, total RNA was treated by a NEBNext rRNA Depletion Kit (NEB). The cDNAs were synthesized by a NEBNext RNA First Strand Synthesis Module (NEB) and the second strand was synthesized by a NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB). Final libraries were prepared using a Kapa Hyper Prep Kit (Kapa Biosystems) once again. Both WGBS and bulk RNA-seq libraries were sequenced on the HiSeq 4000 (Novogene).

tag: passage

value: passage 23

tag: replication

value: technology replication 2


title: HLC_iPSC-O

description: Hepatocyte-like cells from iPSC-O. iPSCs were generated from fibroblasts of the donor 2064 (iPSC-O) and the donor 2054 (iPSC-K).

source_name: HLC-O, replicate 1

value: iPSC-derived hepatocyte-like cells


title: HLC_iPSC-KI

description: Hepatocyte-like cells from iPSC-K

source_name: HLC-KI, replicate 1


title: RNA_hPGHESC_2_P18_rep2

value: human parthenogenetic haploid embryonic stem cell

value: passage 18


title: ProliHH_P1_rep1

description: Proliferating hepatocytes (ProliHH) at passage1 cultured with irrMEF and EMUKK-05 medium. No addition of puromycin.

source_name: ProliHH, P1, no-puro, replicate 1


title: RNA_hPGHESC_2_P23_rep1

value: technology replication 1


title: HD02_05_F07

source_name: Sorted CFP-positive enteric neural crest cells and their differentiating progeny

value: male

value: het

value: progenitor/glia


title: HD02_05_F06


title: ProliHH_purox2_P15_rep1

description: Proliferating hepatocytes (ProliHH) at passage15 cultured with irrMEF and EMUKK-05 medium. Puromycin-treated group (treatment concentration: 2ug/mL)

source_name: ProliHH, P15, purox2, replicate 1


title: RNA_hPGHESC_1_P15_rep2

value: passage 15


title: HD02_05_F04

value: neuron


title: RNA_hAGHESC_2_P7_rep2

source_name: human androgenetic haploid embryonic stem cell

value: passage 7


title: RNA_hAGHESC_2_P18_rep2

value: human androgenetic haploid embryonic stem cell


title: RNA_hPGHESC_2_P18_rep1


title: HD02_05_F03


title: RNA_hPGHESC_1_P15_rep1


title: RNA_hAGHESC_2_P7_rep1


title: RNA_hAGHESC_1_P5_rep2

value: passage 5


title: RNA_hAGHESC_2_P18_rep1


title: RNA_hAGHESC_1_P5_rep1


title: Indisulam_dose2_6hours

value: Treated


title: HD02_05_F01

value: Whole gut (stomach, fore and hind gut)


title: HD02_05_E09

value: RetCFP/+


title: HD02_05_F02


title: HD02_05_E08


title: HD02_05_E05


title: HD02_05_E12


title: HD02_05_E07


title: HD02_05_E11


title: RNA_hAGHESC_1_P15_rep2


title: RNA_hAGHESC_1_P15_rep1


title: HD02_05_E03


title: RNA_ICA2_P13_rep2

source_name: diploid semi-clone human embryonic stem cell

value: passage 13

value: biology replication 2, technology replication 2


title: HD02_05_D12


title: HD02_05_E01


title: HD02_05_D11


title: RNA_ICA1_P13_rep2

value: diploid semi-clone human embryonic stem cell

value: biology replication 1, technology replication 2


title: HD02_05_D09


title: RNA_ICA1_P13_rep1

value: biology replication 1, technology replication 1


title: HD02_05_D08


title: RNA_HUES42_P6_rep2

source_name: diploid human embryonic stem cell

value: diploid human embryonic stem cell

value: passage 9

value: technology replication 2


title: HD02_05_D05

value: male

value: het

value: progenitor/glia


title: HD02_05_D03


title: RNA_Blood_rep1

source_name: blood

value: blood

value: without culture

value: technology replication 1


title: HD02_05_D02


title: RNA_HUES42_P6_rep1


title: HD02_05_C12

value: neuron


title: HD02_05_D01

value: Whole gut (stomach, fore and hind gut)


title: HD02_05_C01

value: RetCFP/+


title: HD02_05_C05


title: HD02_05_C10


title: HD02_05_C08


title: HD02_05_B10


title: HD02_05_C04


title: HD02_05_C03


title: HD02_05_B11


title: HD02_05_C06


title: HD02_05_C11


title: HD02_05_C09


title: RNA_ICA2_P13_rep1

value: passage 13

value: biology replication 2, technology replication 1


title: HD02_05_C02


title: HD02_05_B08


title: HD02_05_B09


title: HD02_05_D06


title: RNA_Blood_rep2


title: HD02_05_B07


title: HD02_05_C07


title: HD02_05_B03


title: HD02_05_B01


title: HD02_05_A12


title: SH_R7

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw single-cell RNA-seq data was firstly trimmed the template switch oligo and polyA sequence using customer scripts, and then reads with adapters or low-quality bases were removed. Clean reads were then aligned into the human reference genome (hg19) using Tophat (version: 2.0.12), and HTSeq was used to count the unique UMI molecules based on the Ensembl hg19 annotation reference, that is to say, we only quantified the UMI once and removed the duplicated UMI.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include the UMI count information of Ensembl annotation genes

source_name: Human blastocyst cells

extract_protocol: Single cells were picked into the lysis buffer using a mouth pipette after washing in BSA for several times. And then single-cell RNA-seq libraries were generated following a modified STRT-seq protocol as previously described 4-6. In brief, an oligo-dT primer anchored with an 8 nt barcode and unique molecular identifiers (UMI) was used to capture mRNAs from cells and reverse transcribed for the first-strand cDNAs. Second-strand cDNAs were synthesised by 18 cycles of PCR amplification. Then the amplified cDNAs with different barcodes were pooled together followed by 4 cycles? PCR using biotinylated pre-indexed primers. After DNA fragmentation by Covaris S2 instrument (Covaris), the 3? cDNAs with biotin modification were captured through the use of Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific). Finally, the libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced by Illumina HiSeq 4000 platform with a 150-bp paired-end read strategy (Novogene).

value: Human blastocyst cells


title: SH_R9


title: HD02_05_A11


title: HD02_05_A10


title: HD02_05_A09


title: SH_R5


title: SH_R1


title: HD02_05_A06


title: HD02_05_A08


title: SH_R4


title: HD02_05_A05


title: HD02_05_A03


title: HD02_05_A07


title: w17_nuclei_2

city: Palo Alto

first: Jimena

last: Andersen

state: CA

address: 318 Campus Drive, Clark Center, 2nd floor/W200

institute: Stanford University

data_processing:
Quality control, UMI counting of Ensemble genes and aggregation of samples were performed by count and aggr functions in the Cell Ranger software (version 5.0.0 with default settings), with the 'include introns' option
Genome_build: Human: GRCh38 (2020-A)
Supplementary_files_format_and_content: Count matrices, barcodes, and features

source_name: Single nuclei of PCW17d5 human spinal cord

extract_protocol:
Dissociated single nuclei were loaded onto a Chromium single cell 3' Chip v3 (10x Genomics) and processed according to manufacturer's instructions.
cDNA libraries were generated with the Chromium Single cell 3' GEM, Library & Gel Bead Kit v3 accoring to manufacturer's instructions


title: HD02_05_B04


title: w17_nuclei_1

value: Single nuclei of PCW17d5 human spinal cord


title: SH_R3


title: HD02_05_A04


title: HD02_05_A02


title: SH_R8


title: SH_R2


title: w17_NeuN_1

source_name: NeuN-sorted single nuclei of PCW17d5 human spinal cord


title: SH_R6


title: w18_nuclei_2

source_name: Single nuclei of PCW18d2 human spinal cord


title: HD02_05_A01


title: w18_nuclei_1

value: Single nuclei of PCW18d2 human spinal cord


title: HD01_11_H11

value: female


title: HD01_11_H12

value: RetCFP/CFP

value: hom


title: w17_Thy1_2

source_name: Thy1-immunopanned single cells of PCW17 human spinal cord

extract_protocol:
Dissociated single cells were loaded onto a Chromium single cell 3' Chip v3 (10x Genomics) and processed according to manufacturer's instructions.
cDNA libraries were generated with the Chromium Single cell 3' GEM, Library & Gel Bead Kit v3 accoring to manufacturer's instructions


title: w17_NeuN_2

value: NeuN-sorted single nuclei of PCW17d5 human spinal cord


title: HD01_11_H10


title: w17_Thy1_1

value: Thy1-immunopanned single cells of PCW17 human spinal cord


title: HD01_11_H09

value: het

value: progenitor/glia


title: w17_cells_1

source_name: Single cells of PCW17 human spinal cord

value: Single cells of PCW17 human spinal cord


title: HD01_11_H07


title: w18_cells_8

source_name: Single cells of PCW18 human spinal cord, lumbar (L) region


title: HD02_05_D07

value: male


title: HD01_11_H06


title: w18_cells_6

source_name: Single cells of PCW18 human spinal cord, thoracic (T1) region


title: w18_cells_5

source_name: Single cells of PCW18 human spinal cord, cervical region (C)


title: HD01_11_H05


title: HD01_11_H03


title: w18_cells_4

value: Single cells of PCW18 human spinal cord, lumbar (L) region


title: w18_cells_1

value: Single cells of PCW18 human spinal cord, cervical region (C)


title: w18_cells_2

value: Single cells of PCW18 human spinal cord, thoracic (T1) region


title: HD01_11_H02

value: Whole gut (stomach, fore and hind gut)


title: HD01_11_H01

value: RetCFP/+


title: HD01_11_G12


title: HD01_11_H04

value: neuron


title: 11-CV

city: Córdoba

first: Jose

last: Echenique

state: Córdoba

address: Edificio Integrador, Medina Allende S/N, Ciudad Universitaria

department: Clinical Biochemistry

country: Argentina

institute: School of Chemistry Sciences, National University of Cordoba

data_processing:
Illumina Real Time Analysis (RTA) softwareused for basecalling
Primary analysis and de-multiplexing were performed using Illumina’s bcl2fastq software 2.20.  The result of the bcl2fastq workflow was de-multiplexed FASTQ files that were used for subsequent analysis by the mapping software and aligner.
The human assembly GRCh37 was downloaded from the Ensembl database; indexing was conducted with bowtie2, and the quality trimmed reads were mapped to the genome using TopHat (v 2.0.9). HTSeq was used to compute the read counts for each gene in each sample
The data of DEGs was normalized using the transfer matrix method (TMM). Next, the DEGs were screened with the software DESeq2. The p-values were adjusted with the Benjamini–Hochberg method for multiple comparison testing. Significance of DEGs was accepted at an adjusted p-value lower than 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: conjunctiva

extract_protocol:
Conjunctival tissues were removed, conserved in RNALater Stabilization Solution (Qiagen) and frozen at -80oC. RNA was isolated from individual tissue samples using GeneJET RNA Purification Kit (Thermo Fisher Scientific) following manufacturer's instructions and using PureLink® DNase Set (Invitrogen, Carlsbad, CA, USA) to remove DNA contamination from columns. Illumina Truseq Stranded mRNA Sample Preparation Kit (catalogue #RS-122-2103, Illumina) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: conjunctiva

tag: disease state

value: pterygium

tag: clinical variable

value: high exposure to UVR


title: HD01_11_G10

tag: Sex

value: female


title: HD01_11_G09

value: RetCFP/CFP

value: hom


title: 9-COC

value: normal exposure to UVR


title: 3-COC


title: HD01_11_G11


title: 13-CV


title: HD01_11_G08

value: het


title: 21-COC

value: pinguecula


title: w18_cells_7

source_name: Single cells of PCW18 human spinal cord, thoracic (T2) region


title: HD01_11_G06

source_name: Sorted CFP-positive enteric neural crest cells and their differentiating progeny


title: HD01_11_G07

value: progenitor/glia


title: w18_cells_3

value: Single cells of PCW18 human spinal cord, thoracic (T2) region


title: HD01_11_G05


title: 19-COC


title: 22-COC

value: normal conjunctiva


title: HD01_11_G04


title: HD01_11_G02


title: HD01_11_G03


title: 6-COC


title: HD01_11_G01


title: MATADOR_RNAseq_X642

city: Amsterdam

first: Mark

last: Opdam

address: 121, Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
RSEM package  Accurate transcript quantification from RNA-Seq data
reads were aligned using STAR
Genome_build: hg38
Supplementary_files_format_and_content: csv file matrix with read counts for all samples per gene

source_name: Primairy tumor before treatment FFPE

extract_protocol:
FFPE AllPrep DNA/RNA isolation mini kit according to the manufacturer’s instructions (Qiagen,  Hilden, Germany)
Libraries of cDNA were constructed  with the TruSeq RNA Access Library Prep Kit (Illumina, San Diego, California, USA)

value: Breast

tag: material

value: FFPE

value: 6 x AC dd


title: MATADOR_RNAseq_X71

value: 6 x TAC


title: MATADOR_RNAseq_X80


title: HD01_11_F07

value: RetCFP/+

value: Whole gut (stomach, fore and hind gut)


title: MATADOR_RNAseq_X652


title: HD01_11_F12


title: MATADOR_RNAseq_X604


title: HD01_11_F11


title: HD01_11_F09


title: HD01_11_F10


title: MATADOR_RNAseq_X628


title: MATADOR_RNAseq_X52


title: MATADOR_RNAseq_X572


title: HD01_11_F08

value: neuron


title: MATADOR_RNAseq_X657


title: MATADOR_RNAseq_X574


title: MATADOR_RNAseq_X577


title: HD01_11_F04


title: HD01_11_F03


title: HD01_11_F02


title: MATADOR_RNAseq_X50


title: MATADOR_RNAseq_X629


title: MATADOR_RNAseq_X44


title: HD01_11_E12


title: MATADOR_RNAseq_X41


title: HD01_11_E07


title: MATADOR_RNAseq_X40


title: MATADOR_RNAseq_X398


title: HD01_11_F06


title: HD01_11_E11


title: MATADOR_RNAseq_X419


title: HD01_11_E10


title: HD01_11_E05


title: HD01_11_E09


title: MATADOR_RNAseq_X321


title: MATADOR_RNAseq_X28


title: MATADOR_RNAseq_X163


title: HD01_11_F05


title: HD01_11_E03


title: MATADOR_RNAseq_X190


title: MATADOR_RNAseq_X508


title: MATADOR_RNAseq_X112


title: HD01_11_E02


title: MATADOR_RNAseq_X143


title: HD01_11_D07


title: MATADOR_RNAseq_X658


title: HD01_11_D10


title: MATADOR_RNAseq_X69


title: HD01_11_F01


title: HD01_11_E01


title: MATADOR_RNAseq_X637


title: MATADOR_RNAseq_X619


title: MATADOR_RNAseq_X618


title: MATADOR_RNAseq_X603


title: MATADOR_RNAseq_X606


title: HD01_11_D05


title: HD01_11_E04


title: HD01_11_D03


title: MATADOR_RNAseq_X598


title: HD01_11_D01


title: HD01_11_C11


title: MATADOR_RNAseq_X579


title: MATADOR_RNAseq_X569


title: HD01_11_C12


title: HD01_11_C10


title: HD01_11_C09


title: MATADOR_RNAseq_X567


title: HD01_11_C08


title: HD01_11_H08


title: MATADOR_RNAseq_X559


title: MATADOR_RNAseq_X55


title: HD01_11_C07


title: HD01_11_C05


title: HD01_11_D06


title: HD01_11_C04


title: MATADOR_RNAseq_X54


title: HD01_11_D02


title: MATADOR_RNAseq_X543


title: HD01_11_C03


title: MATADOR_RNAseq_X545


title: MATADOR_RNAseq_X523


title: MATADOR_RNAseq_X541


title: HD01_11_B11


title: HD01_11_C01


title: MATADOR_RNAseq_X521


title: HD01_11_C02


title: HD01_11_B09


title: HD01_11_B12


title: MATADOR_RNAseq_X591


title: HD01_11_B08


title: MATADOR_RNAseq_X552


title: HD01_11_B10


title: MATADOR_RNAseq_X51


title: MATADOR_RNAseq_X500


title: HD01_11_C06


title: HD01_11_B07


title: HD01_11_B04


title: HD01_11_B05


title: MATADOR_RNAseq_X489


title: HD01_11_B03


title: MATADOR_RNAseq_X473


title: MATADOR_RNAseq_X452


title: MATADOR_RNAseq_X387


title: HD01_11_B02


title: MATADOR_RNAseq_X451


title: MATADOR_RNAseq_X509


title: MATADOR_RNAseq_X363


title: MATADOR_RNAseq_X313


title: HD01_11_A12


title: MATADOR_RNAseq_X280


title: HD01_11_A11


title: MATADOR_RNAseq_X278


title: HD01_11_A10


title: MATADOR_RNAseq_X159


title: HD01_11_A06


title: HD01_11_A09


title: MATADOR_RNAseq_X232


title: MATADOR_RNAseq_X152


title: HD01_11_A05


title: HD01_11_A04


title: HD01_11_A03


title: HD01_09_H12


title: HD01_11_B01


title: MATADOR_RNAseq_X636


title: MATADOR_RNAseq_X106


title: HD01_11_A01


title: MATADOR_RNAseq_X640


title: HD01_11_A07


title: MATADOR_RNAseq_X660


title: MATADOR_RNAseq_X62


title: MATADOR_RNAseq_X630


title: HD01_09_H10


title: HD01_09_H09


title: MATADOR_RNAseq_X625


title: HD01_09_H11


title: MATADOR_RNAseq_X609


title: MATADOR_RNAseq_X145


title: MATADOR_RNAseq_X43


title: HD01_09_H07


title: MATADOR_RNAseq_X607


title: HD01_09_H04


title: HD01_09_H06


title: MATADOR_RNAseq_X587


title: MATADOR_RNAseq_X585


title: MATADOR_RNAseq_X580


title: HD01_09_H05


title: HD01_09_H03


title: HD01_09_G10


title: HD01_09_H02


title: MATADOR_RNAseq_X575


title: MATADOR_RNAseq_X53


title: HD01_09_H01


title: HD01_09_G11


title: MATADOR_RNAseq_X547


title: MATADOR_RNAseq_X560


title: MATADOR_RNAseq_X539


title: HD01_09_H08


title: HD01_09_G07


title: MATADOR_RNAseq_X536


title: MATADOR_RNAseq_X600


title: HD01_09_G06


title: MATADOR_RNAseq_X534


title: HD01_09_G05


title: MATADOR_RNAseq_X525


title: HD01_09_G04


title: MATADOR_RNAseq_X592


title: MATADOR_RNAseq_X498


title: HD01_09_G02


title: MATADOR_RNAseq_X470


title: MATADOR_RNAseq_X475


title: HD01_09_G03


title: MATADOR_RNAseq_X434


title: HD01_09_G09


title: MATADOR_RNAseq_X456


title: HD01_09_F10


title: MATADOR_RNAseq_X358


title: HD01_09_F11


title: MATADOR_RNAseq_X382


title: HD01_09_F08


title: MATADOR_RNAseq_X39


title: MATADOR_RNAseq_X517


title: HD01_09_F06


title: HD01_09_F09


title: HD01_09_F07


title: HD01_09_F05


title: MATADOR_RNAseq_X257


title: HD01_09_G01


title: MATADOR_RNAseq_X369


title: MATADOR_RNAseq_X219


title: HD01_09_F12


title: HD01_09_F03


title: HD01_09_F04


title: MATADOR_RNAseq_X188


title: HD01_09_F02


title: MATADOR_RNAseq_X161


title: MATADOR_RNAseq_X183


title: HD01_09_F01


title: MATADOR_RNAseq_X149


title: HD01_09_E11


title: MATADOR_RNAseq_X139


title: HD01_09_E10


title: MATADOR_RNAseq_X138


title: HD01_09_E09


title: MATADOR_RNAseq_X125


title: HD01_09_E08


title: HD01_09_E07


title: MATADOR_RNAseq_X85


title: MATADOR_RNAseq_X597


title: MATADOR_RNAseq_X593


title: HD01_09_E01


title: HD01_09_E05


title: MATADOR_RNAseq_X519


title: MATADOR_RNAseq_X527


title: MATADOR_RNAseq_X595


title: HD01_09_E06


title: HD01_09_E04


title: HD01_09_E02


title: HD01_09_E03


title: HD01_09_D12


title: MATADOR_RNAseq_X506


title: HD01_09_D11


title: HD01_09_D10


title: MATADOR_RNAseq_X486


title: MATADOR_RNAseq_X426


title: HD01_09_D08


title: HD01_09_D07


title: HD01_09_D09


title: HD01_09_D02


title: MATADOR_RNAseq_X424


title: MATADOR_RNAseq_X526


title: HD01_09_D03


title: MATADOR_RNAseq_X439


title: HD01_09_D01


title: MATADOR_RNAseq_X389


title: MATADOR_RNAseq_X391


title: HD01_09_C11


title: HD01_09_C12


title: MATADOR_RNAseq_X380


title: MATADOR_RNAseq_X381


title: MATADOR_RNAseq_X334


title: MATADOR_RNAseq_X487


title: HD01_11_A02


title: HD01_09_C09


title: MATADOR_RNAseq_X336


title: MATADOR_RNAseq_X464


title: MATADOR_RNAseq_X332


title: HD01_09_C07


title: HD01_09_C05


title: MATADOR_RNAseq_X330


title: HD01_09_D05


title: MATADOR_RNAseq_X331


title: HD01_09_C04


title: HD01_09_C06


title: HD01_09_C03


title: MATADOR_RNAseq_X272


title: MATADOR_RNAseq_X275


title: MATADOR_RNAseq_X273


title: MATADOR_RNAseq_X230


title: MATADOR_RNAseq_X271


title: HD01_09_B10


title: HD01_09_C01


title: HD01_09_B08


title: MATADOR_RNAseq_X182


title: HD01_09_B07


title: MATADOR_RNAseq_X128


title: HD01_09_B02


title: MATADOR_RNAseq_X179


title: MATADOR_RNAseq_X167


title: HD01_09_B11


title: MATADOR_RNAseq_X129


title: HD01_09_B06


title: MATADOR_RNAseq_X113


title: HD01_09_A12


title: HD01_09_B01


title: HD01_09_C02


title: MATADOR_RNAseq_X110


title: HD01_09_B12


title: MATADOR_RNAseq_X108


title: HD01_09_A09


title: HD01_09_A11


title: MATADOR_RNAseq_X263


title: MATADOR_RNAseq_X109


title: HD01_09_A07


title: MATADOR_RNAseq_X631


title: MATADOR_RNAseq_X626


title: HD01_09_A10


title: MATADOR_RNAseq_X627


title: MATADOR_RNAseq_X621


title: MATADOR_RNAseq_X124


title: HD01_09_A08


title: HD01_09_B04


title: HD01_09_A05


title: MATADOR_RNAseq_X589


title: MATADOR_RNAseq_X56


title: HD01_03_H12

value: male


title: MATADOR_RNAseq_X59


title: HD01_09_A04

value: female


title: HD01_03_H11

value: RetCFP/CFP


title: MATADOR_RNAseq_X505


title: MATADOR_RNAseq_X590


title: HD01_09_A03


title: HD01_03_H10


title: HD01_09_A02

value: hom


title: MATADOR_RNAseq_X57


title: HD01_03_H09


title: HD01_03_H07


title: HD01_03_H06


title: MATADOR_RNAseq_X494


title: MATADOR_RNAseq_X463


title: HD01_03_H05


title: MATADOR_RNAseq_X443


title: MATADOR_RNAseq_X440


title: HD01_03_H03


title: HD01_09_A01


title: MATADOR_RNAseq_X540


title: HD01_09_A06


title: HD01_03_H08


title: MATADOR_RNAseq_X492


title: MATADOR_RNAseq_X495


title: MATADOR_RNAseq_X303


title: MATADOR_RNAseq_X462


title: HD01_03_H04


title: MATADOR_RNAseq_X377


title: HD01_03_G10


title: HD01_03_G09


title: HD01_03_H02


title: MATADOR_RNAseq_X298


title: MATADOR_RNAseq_X421


title: MATADOR_RNAseq_X394


title: MATADOR_RNAseq_X378


title: MATADOR_RNAseq_X415


title: MATADOR_RNAseq_X24


title: MATADOR_RNAseq_X365


title: HD01_03_G07


title: HD01_03_G11


title: HD01_03_G06


title: HD01_03_G12


title: MATADOR_RNAseq_X314


title: HD01_03_G03


title: MATADOR_RNAseq_X241


title: HD01_03_G02


title: HD01_03_G05


title: HD01_03_G08


title: HD01_03_G04


title: HD01_03_F08


title: HD01_03_H01


title: MATADOR_RNAseq_X228


title: MATADOR_RNAseq_X224


title: MATADOR_RNAseq_X317


title: HD01_03_G01


title: MATADOR_RNAseq_X236


title: MATADOR_RNAseq_X220


title: HD01_03_F05


title: HD01_03_F07


title: MATADOR_RNAseq_X245


title: HD01_03_F04


title: HD01_03_F06


title: MATADOR_RNAseq_X364


title: MATADOR_RNAseq_X185


title: MATADOR_RNAseq_X186


title: HD01_03_F03


title: MATADOR_RNAseq_X164


title: MATADOR_RNAseq_X244


title: MATADOR_RNAseq_X165


title: HD01_03_F01


title: HD01_03_E12


title: MATADOR_RNAseq_X162


title: HD01_03_E11


title: HD01_03_E10


title: HD01_03_F09


title: MATADOR_RNAseq_X160


title: MATADOR_RNAseq_X157


title: HD01_03_E09


title: HD01_03_E08


title: MATADOR_RNAseq_X9


title: HD01_03_E07


title: HD01_03_E06


title: MATADOR_RNAseq_X201


title: MATADOR_RNAseq_X73


title: MATADOR_RNAseq_X74


title: HD01_03_E05


title: MATADOR_RNAseq_X646


title: MATADOR_RNAseq_X643


title: MATADOR_RNAseq_X63


title: HD01_03_E02


title: HD01_03_D12


title: HD01_03_E04


title: HD01_03_D10


title: HD01_03_D11


title: MATADOR_RNAseq_X551


title: MATADOR_RNAseq_X542


title: MATADOR_RNAseq_X501


title: MATADOR_RNAseq_X504


title: MATADOR_RNAseq_X555


title: HD01_03_D09


title: MATADOR_RNAseq_X49


title: HD01_03_D03


title: HD01_03_D07


title: MATADOR_RNAseq_X460


title: HD01_03_D08


title: HD01_03_D05


title: MATADOR_RNAseq_X448


title: HD01_03_D02


title: MATADOR_RNAseq_X459


title: MATADOR_RNAseq_X72


title: HD01_03_D06


title: HD01_03_D01


title: MATADOR_RNAseq_X414


title: MATADOR_RNAseq_X413


title: HD01_03_E01


title: HD01_03_C12


title: MATADOR_RNAseq_X412


title: HD01_03_E03


title: MATADOR_RNAseq_X5


title: HD01_03_C11


title: HD01_03_C10


title: MATADOR_RNAseq_X410


title: MATADOR_RNAseq_X497


title: HD01_03_C09


title: MATADOR_RNAseq_X351


title: HD01_03_C08


title: HD01_03_C07


title: HD01_03_C06


title: HD01_03_C04


title: MATADOR_RNAseq_X302


title: MATADOR_RNAseq_X299


title: HD01_03_C05


title: MATADOR_RNAseq_X262


title: HD01_03_C01


title: MATADOR_RNAseq_X350


title: MATADOR_RNAseq_X252


title: HD01_03_B12


title: MATADOR_RNAseq_X192


title: MATADOR_RNAseq_X355


title: MATADOR_RNAseq_X356


title: MATADOR_RNAseq_X251


title: HD01_03_B11


title: HD01_03_B08


title: MATADOR_RNAseq_X194


title: HD01_03_B10


title: HD01_03_C02


title: HD01_03_B06


title: MATADOR_RNAseq_X147


title: MATADOR_RNAseq_X156


title: MATADOR_RNAseq_X189


title: HD01_03_B07


title: MATADOR_RNAseq_X187


title: MATADOR_RNAseq_X301


title: HD01_03_B05


title: HD01_03_C03


title: MATADOR_RNAseq_X300


title: MATADOR_RNAseq_X136


title: HD01_03_B03


title: MATADOR_RNAseq_X146


title: MATADOR_RNAseq_X11


title: HD01_03_B02


title: MATADOR_RNAseq_X99


title: HD01_03_A12


title: HD01_03_A05


title: HD01_03_A07


title: MATADOR_RNAseq_X654


title: HD01_03_A08


title: HD01_03_B01


title: MATADOR_RNAseq_X659


title: MATADOR_RNAseq_X512


title: HD01_03_A11


title: MATADOR_RNAseq_X510


title: MATADOR_RNAseq_X588


title: MATADOR_RNAseq_X471


title: HD01_03_A06


title: MATADOR_RNAseq_X48


title: MATADOR_RNAseq_X478


title: HD01_03_A04


title: HD01_03_A01


title: HD01_03_A02


title: MATADOR_RNAseq_X46


title: MATADOR_RNAseq_X511


title: HD01_02_H12


title: MATADOR_RNAseq_X469


title: MATADOR_RNAseq_X428


title: MATADOR_RNAseq_X47


title: HD01_03_A09


title: MATADOR_RNAseq_X438


title: HD01_02_H10


title: MATADOR_RNAseq_X403


title: HD01_02_H06


title: HD01_02_H03


title: HD01_02_H07


title: HD01_02_H04


title: MATADOR_RNAseq_X324


title: MATADOR_RNAseq_X405


title: HD01_02_H02


title: HD01_02_H05


title: MATADOR_RNAseq_X268


title: MATADOR_RNAseq_X311


title: HD01_02_H08


title: HD01_03_A03


title: MATADOR_RNAseq_X310


title: MATADOR_RNAseq_X309


title: HD01_02_H01


title: HD01_02_H09


title: HD01_02_H11


title: MATADOR_RNAseq_X266


title: HD01_02_G12


title: HD01_03_B09


title: MATADOR_RNAseq_X265


title: MATADOR_RNAseq_X206


title: MATADOR_RNAseq_X199


title: HD01_02_G08


title: HD01_02_G06


title: HD01_02_G11


title: MATADOR_RNAseq_X200


title: MATADOR_RNAseq_X198


title: MATADOR_RNAseq_X312


title: HD01_02_G05


title: HD01_02_G04


title: MATADOR_RNAseq_X248


title: HD01_02_G07


title: HD01_02_G09


title: MATADOR_RNAseq_X18


title: HD01_02_G02


title: HD01_02_F11


title: MATADOR_RNAseq_X155


title: HD01_02_G03


title: MATADOR_RNAseq_X196


title: MATADOR_RNAseq_X151


title: MATADOR_RNAseq_X153


title: HD01_02_F10


title: MATADOR_RNAseq_X222


title: HD01_02_F08


title: HD01_02_F07


title: MATADOR_RNAseq_X92


title: HD01_02_F12


title: HD01_02_F09


title: MATADOR_RNAseq_X103


title: MATADOR_RNAseq_X107


title: MATADOR_RNAseq_X82


title: HD01_02_F04


title: HD01_02_F05


title: HD01_02_F02


title: HD01_02_F01


title: MATADOR_RNAseq_X582


title: HD01_02_F06


title: MATADOR_RNAseq_X86


title: MATADOR_RNAseq_X653


title: MATADOR_RNAseq_X568


title: MATADOR_RNAseq_X6


title: MATADOR_RNAseq_X558


title: HD01_02_E11


title: MATADOR_RNAseq_X556


title: HD01_02_E10


title: HD01_02_E08


title: MATADOR_RNAseq_X507


title: MATADOR_RNAseq_X553


title: HD01_02_E07


title: MATADOR_RNAseq_X484


title: HD01_02_E12


title: HD01_02_E06


title: MATADOR_RNAseq_X465


title: HD01_02_E05


title: HD01_02_E03


title: HD01_02_E01


title: HD01_02_D12


title: MATADOR_RNAseq_X450


title: HD01_02_D10


title: MATADOR_RNAseq_X447


title: MATADOR_RNAseq_X435


title: MATADOR_RNAseq_X411


title: MATADOR_RNAseq_X467


title: MATADOR_RNAseq_X427


title: HD01_02_E04


title: MATADOR_RNAseq_X401


title: HD01_02_E09


title: HD01_02_D07


title: HD01_02_E02


title: HD01_02_D06


title: HD01_02_D05


title: MATADOR_RNAseq_X354


title: MATADOR_RNAseq_X341


title: HD01_02_D02


title: MATADOR_RNAseq_X335


title: MATADOR_RNAseq_X444


title: MATADOR_RNAseq_X340


title: HD01_02_D01


title: HD01_02_C11


title: MATADOR_RNAseq_X319


title: HD01_02_C10


title: MATADOR_RNAseq_X30


title: MATADOR_RNAseq_X27


title: HD01_02_C05


title: MATADOR_RNAseq_X306


title: HD01_02_C07


title: MATADOR_RNAseq_X35


title: MATADOR_RNAseq_X357


title: MATADOR_RNAseq_X276


title: HD01_02_C09


title: MATADOR_RNAseq_X285


title: HD01_02_D09


title: HD01_02_D03


title: MATADOR_RNAseq_X25


title: HD01_02_C02


title: MATADOR_RNAseq_X22


title: MATADOR_RNAseq_X264


title: MATADOR_RNAseq_X326


title: HD01_02_C03


title: MATADOR_RNAseq_X21


title: HD01_02_B12


title: MATADOR_RNAseq_X1


title: HD01_02_C01


title: HD01_02_B11


title: MATADOR_RNAseq_X19


title: MATADOR_RNAseq_X195


title: HD01_02_B10


title: HD01_02_C06


title: HD01_02_C04


title: HD01_02_B08


title: HD01_02_B07


title: MATADOR_RNAseq_X10


title: MATADOR_RNAseq_X148


title: HD01_02_B05


title: HD01_02_B06


title: MATADOR_RNAseq_X13


title: MATADOR_RNAseq_X93


title: HD01_02_B04


title: HD01_02_B03


title: MATADOR_RNAseq_X8


title: HD01_02_B02


title: MATADOR_RNAseq_X84


title: MATADOR_RNAseq_X88


title: HD01_02_B01


title: MATADOR_RNAseq_X78


title: HD01_02_A11


title: MATADOR_RNAseq_X7


title: MATADOR_RNAseq_X77


title: HD01_02_A09


title: HD01_02_A08


title: MATADOR_RNAseq_X70


title: MATADOR_RNAseq_X68


title: MATADOR_RNAseq_X650


title: MATADOR_RNAseq_X656


title: HD01_02_A04


title: HD01_02_A05


title: HD01_02_A07


title: MATADOR_RNAseq_X64


title: MATADOR_RNAseq_X661


title: MATADOR_RNAseq_X635


title: HD01_02_A01


title: HD01_02_A02


title: MATADOR_RNAseq_X644


title: MATADOR_RNAseq_X632


title: head, ctct, i3xpos, rep1

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
Data was processed using the Hi-Cpro pipeline (Servant et al., 2015) to produce a list of valid interactions pairs with the Capture Hi-C option for the following region: chr3:34016000-35655100. This list was converted into cool and mcool files for visualization with higlass (Kerpedjiev et al., 2018). Following assessment of replicate reproducibility, the replicates of same condition were merged for visualization using Hi-Cpro followed again by conversion to cool and mcool files. 1D Capture Hi-C heatmaps are shown at 4kb resolution and 2D heatmaps for zoom ins at 2kb. Signal across all samples was normalized according to signal in WT samples. Differential 1D Capture Hi-C heatmaps were produced using the divisor function of higlass and signal from mutant lines was divided by WT Capture Hi-C. Heatmap values were then normalized to the sample with highest differential scores.
Genome_build: mm10
Supplementary_files_format_and_content: mcool files. Interaction frequency at Sox2 locus

source_name: E11.5 head (neural cells)

growth_protocol: Blastocysts derived from natural breeding of heterozygous transgenic mice were used for ES cell line establishment following a published protocol with some modifications (Czechanski et al., 2014). Presence of copulatory plug in the early morning was designated as E0.5. Blastocysts at E3.5 were harvested by flushing female uterine horns with M2 medium. 24hrs prior to embryo isolation, primary mouse embryonic fibroblasts (MEFs) were thawed and grown in 24 well plates in MEF culture medium containing Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher, #11965118), 10% FBS (VWR, #97068-091), 2 mM Glutamax (Thermo Fisher, #35050079) and penicillin–streptomycin (Thermo Fisher, #15140163). Isolated blastocysts were plated over MEFs in presence of serum free media combined with MEK/ERK pathway inhibitor (PD0325901, Reprocell, #04-0006-02), GSK3 signaling inhibitor (CHIR99021, Reprocell, #04-0004-02) and leukemia inhibition factor (LIF, Sigma, #ESG1107). Serum free media comprised of Neurobasal medium (Thermo Fisher, 21103049), DMEM/F12 Nutrient mixture (Thermo Fisher, 21103049), 1% penicillin–streptomycin (Thermo Fisher, #15140163), 2 mM Glutamax (Thermo Fisher, #35050079) and β-mercaptoethanol supplemented with N2 (Thermo Fisher, #17502001) and B-27 (Thermo Fisher, #17504001). Single blastocysts, plated in individual wells were cultured over feeders for 10 days at 37oC, 5% CO2 to allow ICM outgrowth and 50% of the medium was changed every 48 hrs. Embryos hatched out and attached to the feeder layer within 48-72 hrs of plating. Outgrowths were picked up using a mouth pipette without feeder carry-over and transferred into 96 well round bottom plates containing 50 ml of cold 0.05% trypsin and incubated for 5 minutes at 37oC. The outgrowth was disaggregated into small clumps of cells by pipetting up and down vigorously several times while observing under the microscope. Trypsin was quickly inactivated by adding 250 ml of 20% serum containing medium and LIF. From this cell suspension, 100 ul were lysed and used for genotyping and the remaining 200 ml were plated in 96 well plate containing feeders and grown for 48-72hrs in presence of ES serum containing media until ES colonies were visualized. Meanwhile genotype of each ES clone was determined, and wildtype and homozygous clones were propagated for additional 2-3 passages in presence of feeders and serum containing media. The growth and morphology of each ES clone was monitored before freezing the stocks (P3 or P4). Serum containing media comprised of Knockout Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher, #10829018) with 15% FBS (VWR, #97068-091), 2 mM Glutamax (Thermo Fisher, #35050079), 0.1 mM β-mercaptoethanol, 0.1 mM MEM non-essential amino acids (Thermo Fisher, #11140050), 1 mM sodium pyruvate (Thermo Fisher, #11360070), 1% penicillin–streptomycin (Thermo Fisher, #15140163) and Recombinant mouse LIF (Sigma, #ESG1107). Additionally, a fraction of these ES cell clones was feeder depleted and cultured in serum free media (2i + LIF) for at least 4-5 passages and frozen in freezing medium (95% FBS + 5% DMSO) once they adopted a round 3D morphology and good growth rate. For all our downstream experiments early passages of frozen stocks of ES cell clones were used without feeders grown in serum free media.

extract_protocol:
To stop fixation, Glycine was added at final concentration of 0.13M and incubated for 5 minutes at RT and 15 minutes on ice. Cells were then washed once in cold PBS, centrifuged at 2500g 4oC for 5 mins (these centrifugation conditions were used for all washes following fixation) and pellets frozen at -80oC. Thawed cell pellets were incubated in 1ml lysis buffer (10mM Tris-HCL pH8, 10mM NaCl, 0.2% Igepal CA-630, Roche Complete EDTA-free Sigma #11836170001). Following lysis, cells were dounced for a total of 40 strokes with the “tight pestle” and then washed in cold PBS. For DpnII digest, cells were resuspended in 50µl 0.5% SDS and incubated at 62oC for 10 minutes. Then 150µl of 1.5% Triton-X was added and cells incubated for 15 minutes at 37oC while shaking at 900rpm. 25µl of 10X DpnII restriction buffer (NEB) was added, and cells further incubated for 15 minutes while shaking. 200U of DpnII (NEB R0543M) were then added and incubated for 2h, then 200U more and incubated overnight. Next morning 200U more were added and incubated for 3h (total 600U of DpnII). DpnII was inactivated at 62oC for 20 minutes. Biotin fill-in was done by incubating cells with a mixture of 4.5 µl dCTP dTTP and dGTP at 3.3 mM, 8µl klenow polymerase (NEB M0210L) and 37.5µl Biotin-14-dATP (Thermo 19524016) for 4h at RT while shaking at 900rpm for 10 seconds every 5 minutes. Ligation was done overnight at 16oC also rotating at 900rpm for 10 seconds every 5 minutes by adding 120µl of 10X ligation buffer (NEB), 664µl water, 100µl 10% Triton-X, 6µl BSA 20mg/ml, and 2µl T4 ligase (NEB cat #M0202M). Crosslink removal was done overnight with 50µl of proteinase K in 300µl of following buffer (10mM Tris-HCl pH8.0, 0.5M NaCl, 1%SDS) while shaking at 1400rpm at 65oC. Following Sodium Acetate and 100% Ethanol -80oC precipitation, DNA was resuspended in 50µl 10mM Tris HCL. Sonication for Hi-C was done using Covaris onetube-10 AFA strips using the following parameters for a 300bp fragment size (Duration: 10secs, repeat for 12 times, total time 120 secs, peak power-20W, duty factor 40%, CPB-50) in a Covaris ME220 sonicator. Sonicated material was then size selected using SPRI beads with the following ratios: 0.55X and 0.75X. Hi-C material was then bound to 150µl Streptavidin C1 beads (Thermo 65002), washed and recovered following manufacturers recommendations. Bead-bound DNA was resuspended in 50µl 10mM Tris HCl.
Libraries were then amplified using 4 reactions per sample for a total of 200µl and 10 cycles, as recommended by manufacturer. For capture, 1µg of Hi-C library per sample was mixed with 5 μl of SureSelect XT HS and XT Low Input Blocker Mix (Agilent). Samples were denatured at 95oC for 5 minutes and pre-hybridized for 10 minutes at 65oC. 2 μl of SureSelect probes (Agilent) were mixed with 2 μl of 25% RNAse block, 6 μl of Hybridization buffer and 3 μl water. Following pre-hybridization, this probe mixture was added to pre-hybridized samples and incubated for 1 hour at 65 oC. For washing, samples and probes were bound to 50 μl Streptavidin C1 beads and washed using SureSelect wash buffers as recommended by the manufacturer. Washed material was resuspended in 25 μl of water and amplified by PCR using 14 cycles and Kappa polymerase.
Paired-end 50

treatment_protocol: Hi-C libraries for capture Hi-C were prepared as described in (Thompson et al., 2021). Briefly, for mouse ES cell lines, 1 million cells per sample were trypsinized, washed in growth media and fixed for 10 minutes at room temperature while rotating with 1% formaldehyde (Thermo: 28908) in 1ml of HBSS media. Heads of individual E11.5 embryos consisting of forebrain, midbrain and hindbrain were dissected in PBS with 10% FBS. After cutting specimen into small pieces with fine scissors, samples were incubated for 45 mins at 37oC in 300µl of 90%FBS/0.1mg/ml Collagenase I (Sigma:CO130) in PBS.  Following incubation, material was strained through 70µm filter and washed with cold PBS before incubating for 10 mins at RT in 1% formaldehyde. For isolation of AFG-derived tissues from Sox2-GFP heterozygous embryos, E11-E12.5 embryos were dissected in PBS with 10% FBS to isolate the lung and stomach primordia as well as the trachea and esophagus. These samples were then cut into small pieces and incubated for 45 minutes at 37 oC while shaking in a buffer containing: Collagenase IV (2.2 mg/mL; Gibco), BSA (0.1%; Jackson Laboratory), DNase (125 units/mL; Worthington), HEPES (20 mM), CaCl2 (1 mM), Pluronics (1%; (p-188 aka F-68; Thermo-Fisher) in Medium 199 (Gibco) (Zalc et al., 2021). Samples were then sorted in for GFP+ population using Hoechst staining to isolate living cells and using as control for setting gates, material isolated and processed in parallel from wt littermates. Following FACS, samples were fixed as described above.

tag: strain


title: MATADOR_RNAseq_X633


title: MATADOR_RNAseq_X612


title: MATADOR_RNAseq_X60


title: MATADOR_RNAseq_X583


title: MATADOR_RNAseq_X581


title: head, ctct, i18xpos, rep1


title: head, ctcf, i3xneg, rep1


title: head, ctct, i18xpos, rep2


title: head, ctct, i3xpos, rep2


title: head, ctcf, i3xneg, rep2


title: MATADOR_RNAseq_X573


title: head, ctcf, dc2c4, rep2


title: head, ctcf, i3xneg3xpos, rep1


title: head, ctcf, dc2c4, rep1


title: head, wt, rep2

value: wt


title: MATADOR_RNAseq_X532


title: MATADOR_RNAseq_X562


title: MATADOR_RNAseq_X533


title: head, wt, rep1


title: MATADOR_RNAseq_X518


title: es, ctcf, i3xpos, rep2

source_name: blastocyst-derived ES cells


title: MATADOR_RNAseq_X516


title: es, ctcf, i3xneg, rep2


title: es, ctcf, i3xpos, rep1


title: MATADOR_RNAseq_X515


title: es, ctcf, i3xneg, rep1


title: MATADOR_RNAseq_X477


title: es, ctcf, i3xneg3xpos, rep2


title: head, ctcf, i3xneg3xpos, rep2


title: MATADOR_RNAseq_X472


title: MATADOR_RNAseq_X571


title: MATADOR_RNAseq_X436


title: MATADOR_RNAseq_X457


title: es, ctcf, i3xneg3xpos, rep1


title: head, wt, rep3


title: es, ctcf, i18xpos, rep2


title: es, ctcf, dc5, rep2


title: es, ctcf, i18xpos, rep1


title: MATADOR_RNAseq_X432


title: MATADOR_RNAseq_X431


title: es, ctcf, dc5, rep1


title: MATADOR_RNAseq_X42


title: es, ctcf, dc2c4, rep1


title: MATADOR_RNAseq_X399


title: es, ctcf, dc2c4, rep2


title: MATADOR_RNAseq_X479


title: es, wt, rep2


title: afg, derivatives

source_name: cell type


title: es, wt, rep1


title: HGFT2

city: Chengdu

first: Xuan

address: NO.17 of Section 3, Renmin south Road

department: State Key Laboratory of Biotherapy and Cancer Center

institute: West China Hospital, Sichuan University

description:
Human hepatocellular carcinoma
HGF treated
HGFT2_HGFC2

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 GRCh38 whole genome using HISAT2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments per Kilobase per Millon Mapped Fragments (FPKM) were calculated using a protocol from Trapnell, C. et al, 2010. In short, Let FPKM(A) be the expression level of gene A, then F is the only number of Fragments aligned to gene A, N is the number of total Fragments that are uniquely aligned to the reference gene, and L is the length of the exon region of gene A. The FPKM method can eliminate the influence of gene length and sequencing difference on the calculation of gene expression. The calculated gene expression can be directly used to compare gene expression differences between different samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HGF treated

growth_protocol: All cells were cultured in DMEM (Hyclone) containing 10% FBS (PAN) and 100 U/mL of penicillin/streptomycin (Hyclone). All cells were grown at 37℃ in a humidified incubator with 5% CO2

extract_protocol:
HepG2 cells were lysed in Trizol and total RNA was extracted by a standard protocol. Illumina-compatible libraries were prepared using a TruSeq RNA library preparation kit (Illumina, USA) according to the manufacture’s instructions. Sequencing was performed using a HiSeqTM 2000 platform (Illumina, USA). RNA-Seq reads were mapped to the human genome using TopHat (Version 1.3.3), which uses Cufflinks software (version 1.2.1) to compare differentially expressed genes. Refere to supplementary materials for other details.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2 was treated for 4 days by HGF; control cells was treated by solvent of HGF for 4 days

tag: cell line

value: Hepatoblastoma cell line


title: MATADOR_RNAseq_X437


title: HGFC2

description:
Human hepatocellular carcinoma
Control
HGFT2_HGFC2

source_name: Control


title: HGFT1

description:
Human hepatocellular carcinoma
HGF treated
HGFT1_HGFC1


title: MATADOR_RNAseq_X374


title: MATADOR_RNAseq_X383


title: MATADOR_RNAseq_X366


title: MATADOR_RNAseq_X392


title: MATADOR_RNAseq_X34


title: MATADOR_RNAseq_X349


title: MATADOR_RNAseq_X346


title: MATADOR_RNAseq_X400


title: MATADOR_RNAseq_X344


title: HGFC1

description:
Human hepatocellular carcinoma
Control
HGFT1_HGFC1


title: MATADOR_RNAseq_X339


title: C8EB8ANXX_5_15

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

description: fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition

data_processing:
Sequence reads were mapped against the human reference genome (hg19) with the GEM split-mapper software (Marco-Sola et al., 2012) using the gencode_v21 annotation, and genes quantified with flux capacitor (Montgomery et al-. 2010).
The differential expression analysis was performed with the DESeq2 package using P Wald test, and considering the sex of the samples as a covariate of the generalized linear model
DESeq2: regularized log transformation of normalized RNA seq counts and further variance stabilizing transformation
Supplementary_files_format_and_content: Text files data log and variance stabilizing transformed for each Sample

source_name: fibroblasts

growth_protocol: Skin biopsies were obtained from sporadic and genetic forms of Parkinson’s disease and healthy controls. Fibroblasts were cultured in two conditions, high (25 mM) and low (5mM) glucose (DMEM; Gibco), and supplemented with 10% calf serum (CS) (Gibco) penicillin 100 U/mL, streptomycin 100 μg/mL, and heparin 125 μg/mL U/mL (DMEM/10% CS) (all Sigma, St Louis, Mo). Cells were grown at 37°C in 10% carbon dioxide and were passaged at confluence with a solution of trypsin/EDTA (Sigma).

extract_protocol:
RNA was performed using the Allprep DNA RNA Protein Minikit from Quiagen following manufacter instructions. Starting material included three times PBS washed cellular pellets of 106 cells. DNA and RNA concentration were determined on a NanoDrop ND-3300 Fluorospectrometer, and RNA integrity was examined with the Bioanalyzer 2100 (Agilent).
RNA sequencing (RNA-seq) was performed at the Centro Nacional de Análisis Genómico (CNAG) in Barcelona, Catalonia. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,) with minor modifications.

tag: status

value: sporadic Parkinson's disease

tag: glucose

value: low 5 mM

tag: gender


title: C8EB8ANXX_3_11

treatment_protocol: Fibroblasts were cultured in two conditions, high (25 mM) and low (5mM) glucose (DMEM; Gibco)

value: healthy control


title: C8EB8ANXX_5_14


title: C8EB8ANXX_6_16


title: C8EB8ANXX_3_10


title: MATADOR_RNAseq_X296


title: MATADOR_RNAseq_X297


title: C8DHYANXX_3_9

value: LRRK2 Parkinson's disease (G2019S mutation)


title: MATADOR_RNAseq_X294

value: Breast


title: C8EB8ANXX_4_12


title: C8EB8ANXX_4_13


title: C8DHYANXX_7_25


title: C8DHYANXX_8_27


title: MATADOR_RNAseq_X293

value: FFPE


title: MATADOR_RNAseq_X292

value: 6 x AC dd


title: C8DHYANXX_6_23


title: C6H19ANXX_7_11

description: fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition

value: high 25 mM


title: MATADOR_RNAseq_X282


title: MATADOR_RNAseq_X277

value: 6 x TAC


title: MATADOR_RNAseq_X348


title: MATADOR_RNAseq_X288


title: C6H19ANXX_5_9


title: C6GVLANXX_2_8


title: C6H19ANXX_6_7


title: MATADOR_RNAseq_X258


title: C6H19ANXX_6_6


title: MATADOR_RNAseq_X240


title: MATADOR_RNAseq_X239


title: MATADOR_RNAseq_X217


title: C6H19ANXX_7_2


title: MATADOR_RNAseq_X209


title: C6GVLANXX_1_4


title: C6H19ANXX_5_5


title: MATADOR_RNAseq_X218


title: MATADOR_RNAseq_X237


title: C6H19ANXX_4_1

description: fibroblasts RNA seq comparison of controls versus overall Parkinson's disease at high glucose culture condition


title: C6GVLANXX_2_10


title: MATADOR_RNAseq_X204


title: MATADOR_RNAseq_X171


title: MATADOR_RNAseq_X177


title: MATADOR_RNAseq_X180


title: MATADOR_RNAseq_X169


title: Infected 4 - 20wpi

city: Seattle

first: Hazem

last: Abdelaal

state: WA

address: 1900 9th street

institute: Seattle Children's Researcch Institute

data_processing:
Raw RNA-Seq reads were uploaded to CLC Genomics Workbench 8.5 (Qiagen, Redwood City, CA, USA) for processing
Trimmed reads were mapped to the reference genome sequence of Bos taurus (assembly ARS-UCD1.2), and read counts generated against the reference genome annotation tracks were compiled and tabulated
Normalization and differential gene expression analysis in R using the package DESeq2 version 1.16.1 (84). Differentially expressed (DE) transcripts were defined as transcripts with fold changes $62.0, and P value , 0.05 when compared to the naive control group.
DEGs analyses were conducted to search for overrepresented pathways, gene set enrichment, and signaling pathway impact
Network analysis was performed using  the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING)on the DE transcripts identified in this study
Supplementary_files_format_and_content: Excel file has all samples' genes normalized counts

organism: Bos taurus

source_name: Whole blood

extract_protocol:
RNA was extracted from whole blood samples using the RiboPure RNA purification kit (Ambion) following the manufacturer’s recommendation. TURBO DNA-Free DNase Treatment (Ambion) was used to eliminate residual genomic DNA. RNA quantity and quality were assessed using the RNA Pico Series Chip on the Bioanalyzer 2100 (Agilent). RNA integrity numbers (RINs) . 8 were obtained for all total RNA samples purified.
Libraries were prepared according to Illumina's instructions. RNA extracted from the whole blood of cows at 8 and 20 wpi, or at the same time for the uninfected control group (12 biological replicates per group), was subjected to RNA sequencing at the University of Wisconsin–Madison Biotechnology Center. A total of 1 mg of RNA was used as input for TruSeq RNA Sample Prep Rev.F (March 2014; Illumina). Single-end RNA sequencing was performed on the Illumina HiSeq 2000 sequencer according to manufacturer’s instructions

treatment_protocol: Aerosol infection of calves was performed by nebulization of virulent M. bovis strain 10–7428

value: Whole blood cell population

value: Holstein

value: Infected at 20 weeks postinfection


title: Infected 3 - 20wpi


title: Infected 6 - 8wpi

value: Infected at 8 weeks postinfection


title: Infected 5 - 20wpi


title: Infected 1 - 20wpi


title: MATADOR_RNAseq_X256


title: Infected 5 - 8wpi


title: Infected 2 - 20wpi


title: MATADOR_RNAseq_X210


title: Infected 6 - 20wpi


title: Infected 4 - 8wpi


title: MATADOR_RNAseq_X141


title: MATADOR_RNAseq_X142


title: MATADOR_RNAseq_X166


title: C6H19ANXX_4_3

value: male


title: MATADOR_RNAseq_X12


title: MATADOR_RNAseq_X135


title: MATADOR_RNAseq_X123


title: Uninfected 6 - 20wpi

value: Uninfected at 20 weeks postinfection


title: Infected 2 - 8wpi


title: Infected 3 - 8wpi


title: Infected 1 - 8wpi


title: Uninfected 5 - 20wpi


title: MATADOR_RNAseq_X121


title: Uninfected 4 - 20wpi


title: MATADOR_RNAseq_X120


title: Uninfected 3 - 20wpi


title: MATADOR_RNAseq_X102


title: Uninfected 1 - 20wpi


title: Uninfected 2 - 20wpi


title: MATADOR_RNAseq_X100


title: Uninfected 5 - 8wpi

value: Uninfected at 8 weeks postinfection


title: MATADOR_RNAseq_X101


title: MATADOR_RNAseq_X98


title: Uninfected 4 - 8wpi


title: Uninfected 3 - 8wpi


title: Uninfected 2 - 8wpi


title: MATADOR_RNAseq_X122


title: MATADOR_RNAseq_X91


title: Uninfected 1 - 8wpi


title: MATADOR_RNAseq_X66


title: 530c

city: Austin

first: Grace

last: Chappell

state: TX

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

institute: ToxStrategies, Inc.

description: RNA extracted from FFPE tissue

data_processing:
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Genome_build: probe-based targeted sequencing
Supplementary_files_format_and_content: comma-separated text files include raw count values for each gene_probe

source_name: FFPE duodenum_crypt_180ppm Cr(VI) 7 days

growth_protocol: female B6C3F1 mice were bred, reared, and administered test compounds at Charles River Laboratories

extract_protocol:
Crypt and villus compartments from formalin-fixed, paraffin-embedded duedenum tissue were selectively scraped from sections mounted to glass slides directly into lysis buffer.
RNA was amplified using targeted oligomers according to the TempO-Seq (BioSpyder Industries) whole transcriptpome expression assay protocol for library construction.

treatment_protocol: B6C3F1 mice were exposed to 0-180ppm Cr(VI) as sodium dichromate dihydrate (SDD) in the drinking water (ad libitum) for 7 or 90 days.

value: crypt

value: 180ppm Cr(VI) 7 days

tag: genotype

value: wildtype


title: MATADOR_RNAseq_X90


title: 530v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_180ppm Cr(VI) 7 days

value: villus


title: MATADOR_RNAseq_X104


title: 529c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X651


title: MATADOR_RNAseq_X649


title: MATADOR_RNAseq_X608


title: MATADOR_RNAseq_X570


title: 528c

description: RNA extracted from FFPE tissue


title: 528v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X605


title: MATADOR_RNAseq_X453


title: MATADOR_RNAseq_X94


title: 526c

description: RNA extracted from FFPE tissue


title: Uninfected 6 - 8wpi


title: 526v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X449


title: MATADOR_RNAseq_X530


title: 529v

description: RNA extracted from FFPE tissue


title: 490v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_180ppm Cr(VI) 90 days

value: 180ppm Cr(VI) 90 days


title: MATADOR_RNAseq_X347

value: Breast


title: MATADOR_RNAseq_X429

value: FFPE


title: MATADOR_RNAseq_X420


title: 490c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_180ppm Cr(VI) 90 days


title: 488c

description: RNA extracted from FFPE tissue


title: 485c

description: RNA extracted from FFPE tissue


title: 527c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X418

value: 6 x AC dd


title: 485v

description: RNA extracted from FFPE tissue


title: 484v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X367


title: MATADOR_RNAseq_X33


title: MATADOR_RNAseq_X368


title: MATADOR_RNAseq_X338


title: MATADOR_RNAseq_X529


title: 484c

description: RNA extracted from FFPE tissue


title: 450v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_60ppm Cr(VI) 7 days

value: 60ppm Cr(VI) 7 days


title: MATADOR_RNAseq_X337


title: 483c

description: RNA extracted from FFPE tissue


title: 483v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X430

value: 6 x TAC


title: MATADOR_RNAseq_X325


title: MATADOR_RNAseq_X290


title: MATADOR_RNAseq_X329


title: MATADOR_RNAseq_X32


title: 450c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_60ppm Cr(VI) 7 days


title: 488v

description: RNA extracted from FFPE tissue


title: 449c

description: RNA extracted from FFPE tissue


title: 449v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X281


title: MATADOR_RNAseq_X255


title: MATADOR_RNAseq_X279


title: MATADOR_RNAseq_X254


title: MATADOR_RNAseq_X216


title: 448c

description: RNA extracted from FFPE tissue


title: 447v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X23


title: 447c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X214


title: 446c

description: RNA extracted from FFPE tissue


title: 446v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X215


title: MATADOR_RNAseq_X17


title: 406c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_60ppm Cr(VI) 90 days

value: 60ppm Cr(VI) 90 days


title: MATADOR_RNAseq_X213


title: MATADOR_RNAseq_X175


title: 405c

description: RNA extracted from FFPE tissue


title: 405v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_60ppm Cr(VI) 90 days


title: 404v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X174


title: 448v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X16


title: 403v

description: RNA extracted from FFPE tissue


title: 404c

description: RNA extracted from FFPE tissue


title: 403c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X137


title: MATADOR_RNAseq_X140


title: 402c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X133


title: 406v

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X132


title: 370c

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_crypt_20ppm Cr(VI) 7 days

value: 20ppm Cr(VI) 7 days


title: MATADOR_RNAseq_X118

source_name: Primairy tumor before treatment FFPE


title: MATADOR_RNAseq_X89


title: MATADOR_RNAseq_X117


title: MATADOR_RNAseq_X87


title: MATADOR_RNAseq_X647


title: 369c

description: RNA extracted from FFPE tissue


title: 369v

description: RNA extracted from FFPE tissue

source_name: FFPE duodenum_villus_20ppm Cr(VI) 7 days


title: 367v

description: RNA extracted from FFPE tissue


title: 368c

description: RNA extracted from FFPE tissue


title: 367c

description: RNA extracted from FFPE tissue


title: MATADOR_RNAseq_X576


title: MATADOR_RNAseq_X564


title: 366v

description: RNA extracted from FFPE tissue