title: placenta (584216_BS)

data_processing:
Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi
[MatrixProcessed.txt]  minfi-normalized Average Beta values

value: placenta


title: A3-CTRL-AM-like technical replicate 7

status: Public on Jan 04 2021

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: AM-like, CTRL, Animal A3, technical replicate 7

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
tab-delimited text files include gene counting for each sample
Genome_build: ss102 (Ensembl 91)
Supplementary_files_format_and_content: reads counts

molecule: total RNA

organism: Sus scrofa

source_name: AM-like

extract_protocol:
Total RNA from sorted cells was extracted using the Arcturus PicoPure RNA Isolation kit (ThermoFisher Scientiﬁc, St Aubin, France) according to the manufacturer’s instructions. The RNase-Free DNase Set (Qiagen, France) was used to remove contaminating DNA. RNA integrity was assessed using an RNA 6000 Pico kit on a Bioanalyzer 2100 (Agilent Technologies).
1 to 3 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina).

tag: strain

value: Large White

tag: cell type

value: AM-like

tag: infected

value: no

tag: virus

tag: original name (to remove)

tag: animal id


title: placenta (584160_BS)

type: genomic

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

country: USA

institute: Rollins School of Public Health at Emory University

hyb_protocol: bisulphite and oxidative bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Control Software using standard recommended Illumina scanner setting

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: human placenta, bisulfite converted

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from placenta samples, collected near term-equivalent age USA) and aliquoted into a standardized concentration for subsequent analyses

tag: infant sex

value: Female

tag: maternal age (years)

tag: birthweight (grams)

tag: gestational age (weeks)

tag: mother education

value: Any post graduate schooling

tag: tissue


title: A3-CTRL-AM-like technical replicate 9

description: AM-like, CTRL, Animal A3, technical replicate 9


title: PROseq_52R1

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

country: Germany

institute: Max Planck Institure for Biophysical Chemistry

data_processing:
Library strategy: PRO-seq
TT-seq and RNA-seq: Paired-end reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated for each condition. Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016). Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
PRO-seq: PRO-seq data were trimmed with cutadapt version 1.11 (Martin, 2011) using the following parameters: sample PROseq_25R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACATCGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_25R_Rep2: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGGTCAATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_52R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCTGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; and sample PROseq_52R_Rep: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGACGGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20 . The reads were mapped to the human genome (Genome Reference Consortium version GRCh38) of the human genome (from April 2014) and to the Drosophila melanogaster genome version BDGP6.28 with STAR (v2.6.1) (Dobin et al, 2013) using the following parameters: --outFilterMismatchNmax 3 --outFilterMultimapScoreRange 0 --alignIntronMax 500000. Resulting bam files were filtered using SAMTOOLS (v1.9) (Li et al, 2009) to remove alignments with mapping quality lower than 7 (-q 7). Only proper pairs (-f2) were retained. In order to calculate normalization factors for PRO-seq, HTSeq (v0.6.0) (Anders et al, 2015) with intersection-strict mode and --stranded=reverse parameter was used to calculate reads mapping to D.melanogaster transcripts (Drosophila_melanogaster.BDGP6.28.100.gtf.gz from Ensembl.org) followed by calculation of size factors with DESeq2 Bioconductor package (Love et al, 2014). PRO-seq sequencing Read1 mapping to the human genome was converted to reverse complement sequence and the last nucleotide incorporated by the RNAPII was determined (RNAPII position) - last base of the reversely complemented Read 1 for the “+” strand, and first base of the reversely complemented Read 1 for the “-” strand. Coverage for RNAPII position was calculated using coverage function from GRanges R Bioconductor package (Lawrence et al, 2013) and normalized using size factors determined with DESeq2 for D.melanogaster transcripts.  Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

source_name: U2OS osteosarcoma cells

growth_protocol: Human osteosarcoma U2OS cells (wild-type) were obtained from the Darzacq laboratory (Boehning et al, 2018). U2OS cells expressing CTD mutants were generated in the Darzacq laboratory (Boehning et al, 2018). RPB1-52R cells stably express RPB1 protein containing N-terminal HALO tag, N792D mutation conferring a-amanitin resistance and 52 CTD repeats present in the endogenous, wild type RPB1.  RPB1-25R mutant cells express only 25 repeats present in the wild type RPB1, which correspond to repeats 1-21 and 49-52. The cells are grown in DMEM(1X)+GlutaMAX-I medium (Gibco, #21885-025) with 10% FBS (Gibco, #10500-064) in the presence 100 U/ml of Penicillin-Streptomycin (Thermo Fisher, #15140122) in a humidified incubator with 5% CO2 at 37oC. Mutant cells we cultured with 1 ug/ml of a-Amanitin (Sigma-Aldrich, #A2263)

extract_protocol:
PRO-seq (Mahat et al, 2016)
PRO-seq (Mahat et al, 2016)

treatment_protocol: For activation experiments with TPA, the cells were treated with 200 nM TPA (12-O-Tetradecanoylphorbol 13-acetate) (Sigma Aldrich, #P1585) or DMSO (solvent control). DMSO was diluted 1:20000 in the culturing medium to prevent its possible side-effects on transcription (Verheijen et al, 2019)

tag: cell line

value: U2OS osteosarcoma cells

tag: rna fraction

value: Biotin-labeled RNA PolII-associated RNA

tag: genotype

value: U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018)

tag: treatment

value: no treatment


title: placenta (584260_BS)

value: Male


title: A3-CTRL-AM-like technical replicate 8

description: AM-like, CTRL, Animal A3, technical replicate 8


title: placenta (584160_oxBS)

source_name: human placenta, oxidative bisulfite converted


title: PROseq_25R2

value: U2OS cells expressing RPB1-CTD with 25 repeats (Boehning et al 2018)


title: placenta (584088_BS)

value: College graduate


title: placenta (584088_oxBS)


title: PROseq_25R1


title: A3-CTRL-AM-like technical replicate 6

description: AM-like, CTRL, Animal A3, technical replicate 6


title: A3-CTRL-AM-like technical replicate 4

description: AM-like, CTRL, Animal A3, technical replicate 4


title: placenta (584076_BS)

value: High school graduate


title: placenta (584068_BS)

value: Less than 11th grade


title: A3-CTRL-AM-like technical replicate 5

description: AM-like, CTRL, Animal A3, technical replicate 5


title: T_52R_Rep2

data_processing:
TT-seq and RNA-seq: Paired-end reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated for each condition. Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016). Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
PRO-seq: PRO-seq data were trimmed with cutadapt version 1.11 (Martin, 2011) using the following parameters: sample PROseq_25R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACATCGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_25R_Rep2: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGGTCAATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_52R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCTGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; and sample PROseq_52R_Rep: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGACGGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20 . The reads were mapped to the human genome (Genome Reference Consortium version GRCh38) of the human genome (from April 2014) and to the Drosophila melanogaster genome version BDGP6.28 with STAR (v2.6.1) (Dobin et al, 2013) using the following parameters: --outFilterMismatchNmax 3 --outFilterMultimapScoreRange 0 --alignIntronMax 500000. Resulting bam files were filtered using SAMTOOLS (v1.9) (Li et al, 2009) to remove alignments with mapping quality lower than 7 (-q 7). Only proper pairs (-f2) were retained. In order to calculate normalization factors for PRO-seq, HTSeq (v0.6.0) (Anders et al, 2015) with intersection-strict mode and --stranded=reverse parameter was used to calculate reads mapping to D.melanogaster transcripts (Drosophila_melanogaster.BDGP6.28.100.gtf.gz from Ensembl.org) followed by calculation of size factors with DESeq2 Bioconductor package (Love et al, 2014). PRO-seq sequencing Read1 mapping to the human genome was converted to reverse complement sequence and the last nucleotide incorporated by the RNAPII was determined (RNAPII position) - last base of the reversely complemented Read 1 for the “+” strand, and first base of the reversely complemented Read 1 for the “-” strand. Coverage for RNAPII position was calculated using coverage function from GRanges R Bioconductor package (Lawrence et al, 2013) and normalized using size factors determined with DESeq2 for D.melanogaster transcripts.  Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

extract_protocol:
TT-seq, RNA-seq (Schwalb et al, 2016; Wachutka et al., 2019)
TruSeq Stranded Total RNA Library Prep Gold (Illumina, #20020598)

value: Total fragmented RNA


title: A3-CTRL-AM-like technical replicate 3

description: AM-like, CTRL, Animal A3, technical replicate 3


title: T_WT_Rep1

value: wild-type U2OS cells


title: placenta (584240_oxBS)

value: placenta


title: placenta (584076_oxBS)


title: T_25R_Rep2


title: placenta (584068_oxBS)


title: placenta (584056_BS)


title: T_WT_Rep2


title: A3-CTRL-AM-like technical replicate 1

description: AM-like, CTRL, Animal A3, technical replicate 1

value: Large White


title: T_52R_Rep1


title: placenta (584056_oxBS)


title: placenta (584004_BS)


title: L_WT_Rep2

data_processing:
Library strategy: TT-seq
TT-seq and RNA-seq: Paired-end reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated for each condition. Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016). Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
PRO-seq: PRO-seq data were trimmed with cutadapt version 1.11 (Martin, 2011) using the following parameters: sample PROseq_25R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACATCGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_25R_Rep2: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGGTCAATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_52R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCTGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; and sample PROseq_52R_Rep: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGACGGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20 . The reads were mapped to the human genome (Genome Reference Consortium version GRCh38) of the human genome (from April 2014) and to the Drosophila melanogaster genome version BDGP6.28 with STAR (v2.6.1) (Dobin et al, 2013) using the following parameters: --outFilterMismatchNmax 3 --outFilterMultimapScoreRange 0 --alignIntronMax 500000. Resulting bam files were filtered using SAMTOOLS (v1.9) (Li et al, 2009) to remove alignments with mapping quality lower than 7 (-q 7). Only proper pairs (-f2) were retained. In order to calculate normalization factors for PRO-seq, HTSeq (v0.6.0) (Anders et al, 2015) with intersection-strict mode and --stranded=reverse parameter was used to calculate reads mapping to D.melanogaster transcripts (Drosophila_melanogaster.BDGP6.28.100.gtf.gz from Ensembl.org) followed by calculation of size factors with DESeq2 Bioconductor package (Love et al, 2014). PRO-seq sequencing Read1 mapping to the human genome was converted to reverse complement sequence and the last nucleotide incorporated by the RNAPII was determined (RNAPII position) - last base of the reversely complemented Read 1 for the “+” strand, and first base of the reversely complemented Read 1 for the “-” strand. Coverage for RNAPII position was calculated using coverage function from GRanges R Bioconductor package (Lawrence et al, 2013) and normalized using size factors determined with DESeq2 for D.melanogaster transcripts.  Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

value: 4sU-labeled RNA


title: A2-CTRL-AM-like technical replicate 11

description: AM-like, CTRL, Animal A2, technical replicate 11

value: AM-like

value: no


title: placenta (584040_BS)

value: Female


title: placenta (584040_oxBS)


title: A3-CTRL-AM-like technical replicate 2

description: AM-like, CTRL, Animal A3, technical replicate 2


title: placenta (584028_BS)


title: A2-CTRL-AM-like technical replicate 10

description: AM-like, CTRL, Animal A2, technical replicate 10


title: placenta (584028_oxBS)


title: T_25R_Rep1

value: U2OS osteosarcoma cells


title: A2-CTRL-AM-like technical replicate 9

description: AM-like, CTRL, Animal A2, technical replicate 9


title: Rag_D25_rep1

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
100-base paired-end reads were trimmed and aligned to the M. tuberculosis H37Rv genome to identify sites of himar1 insertion. Custom Perl programs available at https://github.com/sassettilab/Bellerose_et_al_mSystems_TnSeq_analyses were used for the read trimming and subsequently to summarize insertion counts at each genomic TA dinucleotide (see subdirectory 'TnSeq_insertion_counts_v6' under the aforementioned Github link).
Insertion mutant counts across all libraries were normalized by beta-geometric correction (DeJesus, M.A., Ambadipudi, C., Baker, R., Sassetti, C., and Ioerger, T.R. (2015). TRANSIT--A Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol: 11, e1004401), binned by gene, and replicate values for each mouse genotype averaged.
Genome_build: NC_018143.1
Supplementary_files_format_and_content: Tab-delimited text files generated in the custom data processing pipeline: col 1, genome coordinate; col 2, unique insertion counts

organism: Mycobacterium tuberculosis H37Rv

source_name: homogenized mouse spleen

extract_protocol:
Spleens from infected mice were homogenized and approximately 1.0E+06 CFU per mouse was plated on 7H10 agar with 20ug/mL kanamycin. After three weeks of growth, colonies were harvested by scraping, and genomic DNA was extracted as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. (2015) Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling, Methods Mol Biol: 1279:79-95.
Libraries were prepared for Illumina sequencing using custom primers as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015) Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95. In the majority of cases, two replicate mouse libraries were used per genotype. Only a single TnSeq library was obtained for CC010, CC031, CC037, CC059, CC016, and PWK/PhJ. Six replicate libraries were obtained for in vitro-grown libraries.

treatment_protocol: Mice were infected with 1.0E+06 CFU of saturated himar1 transposon mutants  delivered via intravenous tail vein injection. At various times over 16-28 days,  mice were euthanized and organs harvested.

tag: h37rv genotype

value: himar1 transposon library

tag: mouse strain

value: Rag

tag: infection length (days)


title: L_52R_Rep1

value: U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018)

value: no treatment


title: Rag_D25_rep2


title: PWK.PhJ_rep1


title: placenta (584016_BS)

value: Junior college graduate or equivalent


title: A2-CTRL-AM-like technical replicate 8

description: AM-like, CTRL, Animal A2, technical replicate 8

tag: strain

tag: cell type

tag: infected


title: A2-CTRL-AM-like technical replicate 12

description: AM-like, CTRL, Animal A2, technical replicate 12

tag: virus

tag: original name (to remove)

tag: animal id


title: placenta (584004_oxBS)

tag: infant sex

value: Male

tag: maternal age (years)

tag: birthweight (grams)

value: College graduate


title: placenta (584016_oxBS)

tag: gestational age (weeks)

tag: mother education

tag: tissue


title: Wsb.Eij_rep2


title: A2-CTRL-AM-like technical replicate 7

description: AM-like, CTRL, Animal A2, technical replicate 7


title: L_52R_Rep2

tag: cell line

tag: rna fraction

tag: genotype


title: Phox_rep1

tag: h37rv genotype

tag: mouse strain

value: Phox


title: NZO.H1LtJ_rep2

tag: infection length (days)


title: Phox_rep2


title: L_WT_Rep1

tag: treatment


title: NOS_rep1

value: NOS


title: NOS_rep2


title: A2-CTRL-AM-like technical replicate 5

description: AM-like, CTRL, Animal A2, technical replicate 5

tag: strain

tag: cell type

tag: infected


title: NOD.ShiLtJ_rep2


title: L_25R_Rep1

value: U2OS cells expressing RPB1-CTD with 25 repeats (Boehning et al 2018)


title: L_25R_Rep2


title: Fetal stromal and epithelium sample pool 5 - Gene Expression

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Gene expression of single cells from 6  fetal EPCAM+ and EPCAM- intestinal samples from 12, 17 and 19 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Pool_5_GEX

data_processing:
Raw sequence data for mRNA libraries were processed using 10x Genomics cellranger pipeline, version 3.1.0
Raw sequence data from hashing libraries were processed using CITE-Seq-Count, version 1.4.3
Genome_build: hg38
Supplementary_files_format_and_content: compressed raw UMI counts matrices from Cellranger outputs for mRNA libraries. Compressed raw UMI matrices from CITE-Seq-Count for antibody oligo tag counts.

source_name: Small and large fetal intestine

extract_protocol:
fetal intestinal samples were digested using either EDTA chelation protocol (EpCAM+/ epithelial pools) or milteyni umbilical cord digestion kit (EpCAM- / stromal pools) and then stained with either a oligonucleotide conjugated antibody to B2M/Cd298 (biolegend) or in EpCAM+ cells an additional EpCAM+ oligo conjugated antibody. In the case of the first pool 3 samples were digested fully without separation. All these libraries are 3 prime, scRNA seq processed using 10x v3 single cell RNA seq protocol and co-ordinate with a HTO library (in the case of single stain) or a HTO and ADT library (in EpCAM+ cells case) for demultiplexing
RNA libraries were processed as per 10x v3 single cell RNA seq protocol library preparation for illumina i7 sample indexes (CG000183, Rev C), HTO and ADT libraries were extracted from the protocol during SPRI clean up and amplified with custom tru-seq primers as per description in published protocol: https://doi.org/10.1186/s13059-018-1603-1

value: intestinal stromal and epithelial cells

tag: post-conceptual weeks


title: Fetal stromal and epithelium sample pool 6 - Gene Expression

description:
Gene expression of single cells from 3 whole fetal intestinal samples from 12, 17 and 19 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Pool_6_GEX


title: NOD.ShiLtJ_rep3


title: NOD.ShiLtJ_rep1


title: IFNG_D17_rep2

value: IFNG


title: IFNG_D17_rep1


title: A8 Slide

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Spaceranger (version 1.0) software
Genome_build: hg38
Supplementary_files_format_and_content: Spaceranger outputs - raw feature barcode matrix in mtx format, gene list in tab delimited format, spot barcodes in tab delimited format, spatial transcriptomics slide H&E image in jpeg format, spot position to image pixel coordinates.

source_name: whole colon section

extract_protocol:
adult and fetal intestinal samples were freshley frozen in OCT blocks and then sectioned onto an oligo-covered array with subsequent H&E, imaging, sample permeablilisation, RNA removal RT and amplification as per protocol for 10x visium spatial potocol (10x CG000239 Rev C)
illumina pair end constructs
Spatial Transcriptomics RNA-Seq

value: Fetal Small Intestine

tag: pcw


title: A7 Slide

source_name: whole small intestine section


title: CC065.Unc_rep2


title: A2-CTRL-AM-like technical replicate 3

description: AM-like, CTRL, Animal A2, technical replicate 3

value: Large White

value: AM-like

tag: virus

tag: original name (to remove)

tag: animal id


title: A9 Slide


title: CC065.Unc_rep1


title: A2-CTRL-AM-like technical replicate 2

description: AM-like, CTRL, Animal A2, technical replicate 2

value: no


title: A2-CTRL-AM-like technical replicate 4

description: AM-like, CTRL, Animal A2, technical replicate 4


title: CC051.TauUnc_rep2


title: A2-CTRL-AM-like technical replicate 6

description: AM-like, CTRL, Animal A2, technical replicate 6


title: CC042.GeniUnc_rep2


title: CC051.TauUnc_rep1


title: CC041.TauUnc_rep2


title: A1-CTRL-AM-like technical replicate 12

description: AM-like, CTRL, Animal A1, technical replicate 12


title: A2-CTRL-AM-like technical replicate 1

description: AM-like, CTRL, Animal A2, technical replicate 1


title: A6 Slide


title: CC041.TauUnc_rep1


title: CC042.GeniUnc_rep1


title: CC040.TauUnc_rep2


title: CC040.TauUnc_rep1


title: A4 Slide

value: Fetal Colon


title: A1-CTRL-AM-like technical replicate 10

description: AM-like, CTRL, Animal A1, technical replicate 10


title: A3 Slide


title: CC039.Unc_rep2

value: himar1 transposon library


title: A2 Slide

source_name: colon tissue

value: Adult colon

value: Adult


title: CC039.Unc_rep1


title: A1-CTRL-AM-like technical replicate 9

description: AM-like, CTRL, Animal A1, technical replicate 9


title: CC032.GeniUnc_rep1


title: CC025.GeniUnc_rep2


title: A1-CTRL-AM-like technical replicate 8

description: AM-like, CTRL, Animal A1, technical replicate 8


title: CC025.GeniUnc_rep1


title: A1 Slide


title: CC024.GeniUnc_rep1


title: IMR90_RAS_ATAC-seq [ATAC-19032015_S3]

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

data_processing:
Reads were mapped to the human reference (hg19). ChIP-seq and ATAC-seq samples were mapped using BWA (version 0.7.12) and RNA-seq samples using STAR aligner (version 2.6.0c).
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0).
H3K27AC, H3K27me3 and ATAC-seq samples: Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize parameter).
H3K9me3 samples: Enriched domains were called with EDD
ChIP-seq and ATAC-seq normalised coverage files (.bw) were generated using THOR.
RNA-seq counts were calculated using Rsubread.
Genome_build: hg19
Supplementary_files_format_and_content: .bw = coverage files
Supplementary_files_format_and_content: .narrowPeak/.bed = peak files
Supplementary_files_format_and_content: .txt = counts

growth_protocol: Keratinocytes were cultured in Epilife (Gibco) suppremented with human keratinocyte growth supprement (HKGS, Gibco).

extract_protocol:
For ChIP-seq, lysates were cralified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-seq, RNA was purified from using the Qiagen RNeasy plus kit according to the manufacturer's instructions.
For ChIP-seq, libraries were prepared using the NEB-Next Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer's instructions. For RNA-seq, libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: To induce differentiation in culture, keratinocytes were treated with 500 nM of phorbol 12-myristate 13-acetate (PMA, Sigma, P8139) for 48 h after become confluent.

value: Fibroblast

tag: passage

tag: condition

value: Ras Induced Senescence


title: A1-CTRL-AM-like technical replicate 7

description: AM-like, CTRL, Animal A1, technical replicate 7


title: IMR90_RAS_ATAC-seq [ATAC-19032015_S8]


title: A1-CTRL-AM-like technical replicate 6

description: AM-like, CTRL, Animal A1, technical replicate 6


title: CC023.GeniUnc_rep2


title: A1-CTRL-AM-like technical replicate 5

description: AM-like, CTRL, Animal A1, technical replicate 5


title: CC019.TauUnc_rep1


title: IMR90_RAS_ATAC-seq [ATAC-19032015_S1]


title: CC019.TauUnc_rep2


title: A1-CTRL-AM-like technical replicate 11

description: AM-like, CTRL, Animal A1, technical replicate 11


title: CrMTA1_3

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FDR < =0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

molecule: polyA RNA

source_name: Cell line HCT116

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 5ug of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 300-500 bps were purified, quantified and stored at -80 oC until used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina Next500 system for 150 nt pair-end sequencing by ABlife. Inc (Wuhan, China)。

tag: cell line

tag: tissue

value: colon

tag: morphology

value: epithelial

tag: disease

value: colorectal carcinoma


title: CC018.Unc_rep1

tag: h37rv genotype

tag: mouse strain


title: CC017.Unc_rep2

tag: infection length (days)


title: CrMTA1_2


title: CC017.Unc_rep1


title: CC015.Unc_rep1


title: A1-CTRL-AM-like technical replicate 4

description: AM-like, CTRL, Animal A1, technical replicate 4

tag: strain


title: A1-CTRL-AM-like technical replicate 3

description: AM-like, CTRL, Animal A1, technical replicate 3

tag: cell type


title: CC012.GeniUnc_rep2


title: CrMTA1_1


title: A1-CTRL-AM-like technical replicate 2

description: AM-like, CTRL, Animal A1, technical replicate 2

tag: infected


title: CC015.Unc_rep2


title: CC024.GeniUnc_rep2


title: WT_2


title: A1-CTRL-AM-like technical replicate 1

description: AM-like, CTRL, Animal A1, technical replicate 1


title: CC011.Unc_rep2


title: WT_3


title: CC012.GeniUnc_rep1


title: CC009.Unc_rep1


title: CC010.GeniUnc_rep1


title: WT_1


title: A3bis-FL-moDC technical replicate 12

description: moDC, FL, Animal A3bis, technical replicate 12

source_name: moDC

value: moDC

value: yes

value: FL


title: A3bis-FL-moDC technical replicate 11

description: moDC, FL, Animal A3bis, technical replicate 11


title: MTA1 rep1

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACT) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 2. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
Reads with overlap region on the locus of genome were clustered. The read number (N), read length and observed max depth were then counted for each cluster. For each gene, a same number of reads with coincident lengths were generated using computational simulation. The outputting reads were further randomly placed to same genes to generate max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p value ＜ 0.01) were selected, while the FTO peaks that have an overlap with control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files include MTA1 binding peaks for each sample

extract_protocol:
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate). Then, add 1% (vol/vol) 40U/ul Recombinant RNase Inhibitor（Takara,2313A） and 2% (vol/vol) 10mg/ml PMSF to the cell lysate, mix and rotate the mixture end over end at 4 °C for 30 min. Add 10 X RQ I buffer and DNase I(Promega,M610A). Incubate the tubes at 37 °C for 3 min,shaking at 1,000rpm. Immediately afterward a Stop solution was added to the lysates to quench DNase. Then, centrifuge 10,000 rpm for 10 min at 4 °C. Carefully collect the supernatant. Prepare a 1/50000 dilution of MNase(Thermo,EN0181).
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China) and Illumina GAIIx (Illumina, San Diego, CA, USA) 150 nt paird-end sequencing .

tag: antibody


title: CC018.Unc_rep2


title: CC006.TauUnc_rep1


title: CC006.TauUnc_rep2


title: A3bis-FL-moDC technical replicate 10

description: moDC, FL, Animal A3bis, technical replicate 10


title: Ctrl rep1

value: IgG


title: A3bis-FL-moDC technical replicate 9

description: moDC, FL, Animal A3bis, technical replicate 9


title: MTA1_2

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peakcalling with  default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: peaks bed

extract_protocol:
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of RIPA buffer( 50 mM Tris 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate).The cells lysates was sonicated to generate DNA fragments of 200-500 bp, centrifuged for 10 min at 12,000 g, and the supernatant was directly used for immunoprecipitation. Place the tube containing the Pierce™ ChIP-grade Protein A/G Magnetic Beads on the magnetic ,then, discard the supernatant. Wash the beads for three times with 1ml 0.1M sodium phosphate Buffer .
ChIP-seq was performed by using ThruPLEX® DNA-seq kit (R400427; Rubicon Genomics) according to manufacturer’s instructions. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 oC until used for sequencing. ChIP-Seq sequencing was performed on NextSeq500 platform with 151 bp paired-end sequencing.


title: CC004.TauUnc_rep2


title: CC005.TauUnc_rep2


title: A3bis-FL-moDC technical replicate 8

description: moDC, FL, Animal A3bis, technical replicate 8


title: A3bis-FL-moDC technical replicate 7

description: moDC, FL, Animal A3bis, technical replicate 7


title: CC003.Unc_rep1


title: CC011.Unc_rep1


title: CC002.Unc_rep2


title: Input_2


title: MTA1_1


title: CC002.Unc_rep1


title: A3bis-FL-moDC technical replicate 6

description: moDC, FL, Animal A3bis, technical replicate 6


title: Cast.EiJ_rep1


title: CC003.Unc_rep2


title: Cast.EiJ_rep2


title: A.J_rep2


title: Input_1


title: A3bis-FL-moDC technical replicate 4

description: moDC, FL, Animal A3bis, technical replicate 4


title: CC005.TauUnc_rep1


title: Trf1f/f Ad-GFP biological replicate 3

first: Simon

middle: J

last: Boulton

address: 1 Midland Rd

institute: The Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 19th February 2016. The parameters used were “--star-output-genome-bam --forward-prob 0 --paired-end”.
Differential expression analysis was performed with the DESeq2 package (version 1.28.0) (Love et al., 2014) within the R programming environment (version 4.0.0) (http://www.R-project.org/). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (Invitrogen), L-glutamine, and penicillin-streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The total RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent, Santa Clara, CA, USA) to insure RNA integrity and concentration before starting the procedure. mRNA libraries were generated using the KAPA mRNA Hyper Prep Kit (Roche) following manufacturer’s instructions. Library QC was reperformed on the BioAnalyser 2100 followed by sequencing on the Illumina HiSeq 2500 to generate 101bp strand-specific single-end reads.

treatment_protocol: Where applicable, cells were treated with 10uM TMPyP4 48 hours prior to the RNA collection.

value: Trf1f/f MEFs

tag: treatment

value: Ad-GFP infected


title: A3bis-FL-moDC technical replicate 5

description: moDC, FL, Animal A3bis, technical replicate 5

value: Large White

tag: virus


title: 129s1.SvImJ_rep1


title: 129s1.SvImJ_rep3


title: A3bis-FL-moDC technical replicate 3

description: moDC, FL, Animal A3bis, technical replicate 3

tag: original name (to remove)


title: A.J_rep1


title: CC004.TauUnc_rep1


title: Trf1f/f Ad-GFP biological replicate 1


title: Wsb.Eij_rep1


title: A3bis-FL-moDC technical replicate 2

description: moDC, FL, Animal A3bis, technical replicate 2

tag: animal id


title: Trf1f/f Ad-GFP biological replicate 2


title: Trf1f/f Ad-Cre biological replicate 3

value: Ad-Cre infected


title: in_vitro_rep6


title: Trf1f/f Ad-Cre biological replicate 2


title: in_vitro_rep5


title: A2-FL-moDC technical replicate 12

description: moDC, FL, Animal A2, technical replicate 12


title: in_vitro_rep3


title: Trf1f/f Ad-Cre biological replicate 1


title: A2-FL-moDC technical replicate 11

description: moDC, FL, Animal A2, technical replicate 11


title: Rtel1f/f Ad-GFP TMPyP4 biological replicate 3

value: Rtel1f/f MEFs

value: Ad-GFP infected; TMPyP4 treated


title: CC061.GeniUnc_rep2

value: himar1 transposon library


title: in_vitro_rep2


title: A2-FL-moDC technical replicate 10

description: moDC, FL, Animal A2, technical replicate 10


title: 129s1.SvImJ_rep2


title: Rtel1f/f Ad-GFP TMPyP4 biological replicate 2


title: CC059.TauUnc_rep1


title: CC061.GeniUnc_rep1


title: A2-FL-moDC technical replicate 9

description: moDC, FL, Animal A2, technical replicate 9


title: CC057.Unc_rep2


title: A2-FL-moDC technical replicate 8

description: moDC, FL, Animal A2, technical replicate 8


title: CC057.Unc_rep1


title: Rtel1f/f Ad-GFP biological replicate 3


title: CC056.GeniUnc_rep1


title: A2-FL-moDC technical replicate 7

description: moDC, FL, Animal A2, technical replicate 7


title: CC056.GeniUnc_rep2


title: A3bis-FL-moDC technical replicate 1

description: moDC, FL, Animal A3bis, technical replicate 1


title: in_vitro_rep4


title: Rtel1f/f Ad-GFP biological replicate 2


title: CC047.Unc_rep2


title: in_vitro_rep1


title: CC047.Unc_rep1


title: CC046.Unc_rep2


title: A2-FL-moDC technical replicate 6

description: moDC, FL, Animal A2, technical replicate 6


title: Rtel1f/f Ad-GFP biological replicate 1


title: CC046.Unc_rep1


title: Rtel1f/f Ad-Cre biological replicate 3


title: NZO.H1LtJ_rep1


title: A2-FL-moDC technical replicate 5

description: moDC, FL, Animal A2, technical replicate 5


title: Rtel1f/f Ad-Cre biological replicate 2


title: A2-FL-moDC technical replicate 4

description: moDC, FL, Animal A2, technical replicate 4


title: CC044.Unc_rep1


title: Rtel1f/f Ad-GFP RTEL1 CA biological replicate 3

value: Ad-GFP infected; RTEL1 C1252A/C1255A transduced


title: CC043.GeniUnc_rep2


title: A2-FL-moDC technical replicate 3

description: moDC, FL, Animal A2, technical replicate 3


title: A1-FL-moDC technical replicate 12

description: moDC, FL, Animal A1, technical replicate 12


title: Rtel1f/f Ad-GFP TMPyP4 biological replicate 1


title: CC045.GeniUnc_rep2


title: A2-FL-moDC technical replicate 1

description: moDC, FL, Animal A2, technical replicate 1


title: CC043.GeniUnc_rep1


title: CC037.TauUnc_rep1


title: Rtel1f/f Ad-Cre RTEL1 CA biological replicate 3

value: Ad-Cre infected; RTEL1 C1252A/C1255A transduced


title: CC034.Unc_rep1


title: CC038.GeniUnc_rep1


title: A1-FL-moDC technical replicate 10

description: moDC, FL, Animal A1, technical replicate 10


title: A2-FL-moDC technical replicate 2

description: moDC, FL, Animal A2, technical replicate 2


title: CC035.Unc_rep2


title: Rtel1f/f Ad-GFP RTEL1 CA biological replicate 2


title: CC035.Unc_rep1


title: Rtel1f/f Ad-GFP RTEL1 CA biological replicate 1


title: CC044.Unc_rep2


title: CC045.GeniUnc_rep1


title: A1-FL-moDC technical replicate 11

description: moDC, FL, Animal A1, technical replicate 11


title: CC034.Unc_rep2


title: CC030.GeniUnc_rep2


title: CC033.GeniUnc_rep1


title: Rtel1f/f Ad-Cre RTEL1 CA biological replicate 2


title: CC030.GeniUnc_rep1


title: A1-FL-moDC technical replicate 9

description: moDC, FL, Animal A1, technical replicate 9


title: CC027.GeniUnc_rep2


title: CC032.GeniUnc_rep2


title: Nf1-KO rep1

city: Berlin

first: Xiaoyan

last: Wei

address: Thielallee 63

institute: Free University of Berlin

data_processing:
Paired end reads were  mapping with mouse genome (mm9) using STAR 2.4.2a software.
Read counts were generated with R Studio function Summarize Overlaps and normalized to RPKM based on the number of uniquely mapped reads.
Differential expression analysis was performed with DESeq2 using default settings. Genes with an absolute fold change > 2 and adjusted p-value < 0.01 were assessed to be significantly differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Tibialis anterior muscle

extract_protocol:
TA muscle was removed followed by liquid nitrogen snap frozen and RNA was isolated using RNeasy Mini Kit (Qiagen). Illumina TruSeq RNA Library Preparation Kit v2 was used for the library preparation with 1ug of total RNA.
libraries were prepared based on the standard Illumina protocols

value: Tibialis anterior muscle

tag: genotype

tag: development stage

value: post natal day 21


title: CC028.GeniUnc_rep2


title: CC038.GeniUnc_rep2


title: CC031.GeniUnc_rep1


title: CC028.GeniUnc_rep1


title: Nf1-KO rep2


title: CC033.GeniUnc_rep2


title: A1-FL-moDC technical replicate 6

description: moDC, FL, Animal A1, technical replicate 6


title: A1-FL-moDC technical replicate 7

description: moDC, FL, Animal A1, technical replicate 7


title: A1-FL-moDC technical replicate 8

description: moDC, FL, Animal A1, technical replicate 8


title: CC027.GeniUnc_rep1


title: Rtel1f/f Ad-Cre RTEL1 CA biological replicate 1

tag: cell line


title: A1-FL-moDC technical replicate 5

description: moDC, FL, Animal A1, technical replicate 5


title: CC022.GeniUnc_rep2


title: A1-FL-moDC technical replicate 4

description: moDC, FL, Animal A1, technical replicate 4


title: CC023.GeniUnc_rep1


title: Het rep1

tag: tissue


title: CC021.Unc_rep1


title: CC021.Unc_rep2


title: CC022.GeniUnc_rep1


title: A1-FL-moDC technical replicate 3

description: moDC, FL, Animal A1, technical replicate 3


title: Sample 37_ChIPSeq_Treg_Input

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description:
Immunopreciptated DNA
Treg_ChIP_Input_NoIndex_L008

data_processing:
The raw bulk ATAC-Seq files were processed using the ENCODE-DCC pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) automated through Cromwell (https://github.com/broadinstitute/cromwell). Shortly, adapter sequences were trimmed (Cutadapt) prior to genome map with Bowtie2. Subsequently, mapped reads were filtered with Samtools. Next, sequencing enriched regions, associated to chromatin accessible peaks were called with MACS2 and filtered by running IDR, Irreproducible Discovery Rate, algorithm with a 10% threshold. Later, filtered peak regions were annotated by using HOMER software tools.
The raw bulk ChIP-Seq files were processed using the ENCODE-DCC pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) automated through Cromwell (https://github.com/broadinstitute/cromwell). Shortly, adapter sequences were trimmed by Cutadapt prior to the genome mapping with BWA and filtered subsequently using Samtools. Next, sequencing enriched regions associated to the transcription factor binding sites were called with SPP and filtered by running IDR, Irreproducible Discovery Rate, algorithm with a 5% threshold. Later, filtered peak regions were annotated by the HOMER software suite of tools. Comprehensive motif screening was performed with MEME-ChIP by using promoter originated, length-normalized reads to a 500 kb.
The raw fastq sequencing files were processed together with the gencode mouse annotation database (v. M21), by running kallisto (v. 0.46.0) to calculate the transcript abundances. Next, the abundance files were submitted to the sleuth (v. 0.30.0) pipeline based on R, for transcript abundance normalization, gene expression analysis and statistics. The quantified transcripts were combined into genes for the downstream analysis. Batch effects were evaluated through principal component analysis and removed with Limma. To capture significantly expressed genes we performed a likelihood ratio test between a null model and our experimental design using an adjusted p-value of 0.05 as threshold. The selected features were clustered using k-means and represented as a heatmap to define group gene signatures. Pairwise comparisons between groups were performed using the Wald-test and significant genes were considered for downstream analysis by having an adjusted p-value smaller than 0.05 and a log2 foldchange of 1.
The single cell RNA-Seq fastq files originated from the Chromium 10x libraries were processed with Cell Ranger (v. 3.0.2) for cell barcode aggregation, genome alignment, and UMI transcript quantification. The matrix of gene counts was analyzed with the Seurat (v. 3.1.2) package for the R environment. For downstream analysis, the top 3000 genes containing the highest standardized variance and expression were pre-selected. The detected cell clusters were visualized by performing Uniform Manifold Approximation and Projection (UMAP) algorithm. Cluster signatures were determined by the Wilcoxon Rank Sum test and genes containing adjusted p-values smaller than 0.01 were considered significant. For pseudotime trajectory analysis, the Seurat dataset was converted into a ‘SingleCellExperiment’ object and used within Slingshot and Monocle.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: kallisto abundances
Supplementary_files_format_and_content: h5: kallisto abundances and bootstrap estimates for sleuth
Supplementary_files_format_and_content: 10x mtx: UMI counts
Supplementary_files_format_and_content: 10x features.tsv: feature names
Supplementary_files_format_and_content: 10x barcodes.tsv: single cell barcodes
Supplementary_files_format_and_content: bb:  Indexed binary files containing annotated peaks
Supplementary_files_format_and_content: narrowpeak: text (BED6+4) files containing annotated peaks
Supplementary_files_format_and_content: bed: interval file containing annotated chip peaks
Supplementary_files_format_and_content: bigwig: Indexed binary files containing dense continuous data of read mapping

extract_protocol:
Atac-Seq: ATAC-Seq was performed on 5,000-40,000 FACS-purified cells from 2-9 mice. In brief, cells were lysed in lysis buffer for 1 minute and transposed with Tagment DNA Enzyme 1 (Illumina) for 30 minutes. DNA was cleaned up using a MinElute DNA purification Kit (Qiagen), followed by barcoding and library preparation by the Nextera DNA Library preparation kit (Illumina) according to manufacturer’s guidelines and sequenced on an Illumina Illumina NextSeq 500.
ChIP-Seq: Cells were fixed in 1% formaldehyde for 20min, quenched with 0.15M glycine and washed in PBS. 2x106 were then sorted and lysed for 30min at 4ºC. Cells were then sonicated for 22 minutes at 30 seconds on/off using the Bioruptor sonicator (Diagenode) and spun down. 10% was frozen for input, the remaining 90% was incubated with anti-ThPOK antibody bound to goat anti-rabbit M280 magnetic beads (Invitrogen) overnight at 4ºC prior to washing with RIPA buffer and overnight decrosslinking at 65ºC. DNA was then eluted off beads into TE buffer and, along with input, purified using the Zymogen DNA clean & concentrator kit. DNA was sequenced using NextSeq2500. To obtain Tregs, Foxp3RFP reporter mice were injected with IL-2/aIL-2 complex as previously described for 3 consecutive days for Treg expansion. CD4+ T cells were isolated from the spleen and mLNs and sorted as Thy1+TCRb+CD4+CD8a–RFP+.
RNA-Seq: Sorted cells (300-800) were lysed in TCL buffer (Qiagen, 1031576) supplemented with 1% βmercaptoethanol. RNA was isolated using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified. Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 550.
Single Cell Sequencing: Lymphocytes were sorted, counted for viability and immediately subjected to library preparation. The scRNA-Seq library was prepared using the 10x Single Cell Chromium system, according to the manufacturer’s instructions at the Genomics core of Rockefeller University and was sequenced on an Illumina NextSeq 550 to a minimum sequencing depth of 50,000 reads per cell using read lengths of 26 bp read 1, 8 bp i7 index, 98 bp read 2.

tag: strain background

tag: mouse id

tag: Sex

value: Female

value: In vivo expanded splenic regulatory Foxp3+ T cells


title: Sample 36_ChIPSeq_Treg_IP

description:
Immunopreciptated DNA
Treg_ChIP_ThPOK_IP_NoIndex_L002


title: CC013.GeniUnc_rep1

tag: h37rv genotype

tag: mouse strain


title: A1-FL-moDC technical replicate 1

description: moDC, FL, Animal A1, technical replicate 1

tag: strain

value: moDC


title: A1-FL-moDC technical replicate 2

description: moDC, FL, Animal A1, technical replicate 2

tag: cell type

value: yes


title: CC016.GeniUnc_rep1

tag: infection length (days)


title: Sample_ML6

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Mouse liver ERRBS by Illumina HiSeq 2500

data_processing:
Reads were aligned to the mouse genome using the Bismark alignment software.
The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) was calculated for each cytosine position in CpG, CHG, and CHH contexts (with H corresponding to A, C, or T nucleotides).
Genome_build: mm10
Supplementary_files_format_and_content: txt files of the percentage of bisulfite converted cytosines  and non-converted cytosines.

source_name: Liver

extract_protocol:
High molecular weight DNA was isolated from livers using the Gentra puregene tissue kit (Qiagen).
The Illumina TruSeq primers were used for the preparation of ERRBS libraries.
ERRBS

tag: group

value: Mother LIRKO


title: CC009.Unc_rep2


title: CC008.GeniUnc_rep1


title: CC008.GeniUnc_rep2


title: Sample_ML13


title: Sample_ML21


title: CC007.Unc_rep2


title: CC013.GeniUnc_rep2


title: A3-CTRL-moDC technical replicate 11

description: moDC, CTRL, Animal A3, technical replicate 11

tag: infected

value: no


title: Het rep2


title: Sample_ML1


title: A3-CTRL-moDC technical replicate 12

description: moDC, CTRL, Animal A3, technical replicate 12

tag: virus


title: A3-CTRL-moDC technical replicate 10

description: moDC, CTRL, Animal A3, technical replicate 10

tag: original name (to remove)


title: Sample_FL6

value: Father LIRKO


title: CC001.Unc_rep1


title: C57BL.6J_rep3


title: C57BL.6J_rep2


title: Sample_FL2


title: CC007.Unc_rep1


title: E12 chick retina, sample 4

city: Cambridge

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description:
E12 chick retina, whole retina
ChickenE12S4

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software (version 2.1.0, 10X Genomics)
Genome_build: GRCg6a
Supplementary_files_format_and_content: csv files including gene expression matrixes each development stage

organism: Gallus gallus

source_name: Retina

extract_protocol:
Cells were counted, resuspended in PBS with acetylated BSA, and processed with the Chromium Next GEM Single Cell 3’ Library Construction Kit (version 2) (10x Genomics, Pleasanton, CA; Zheng et al., 2017)
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells are partitioned into oil droplets containing single oligonucleotide-derivatized beads followed by cell lysis, barcoded reverse transcription of RNA, amplification, shearing, and attachment of 5’ adaptor and sample index oligos. Libraries were sequenced on the Illumina HiSeq 2500 (Paired end reads: Read 1, 26bp, Read 2, 98bp)

treatment_protocol: Animals were used in accordance with NIH guidelines and protocols approved by Institutional Animal Use and Care Committee at Harvard University. Fertilized chicken eggs (specific pathogen free) were obtained from Charles River Laboratories (Wilmington, MA), and incubated in a 1550 HATCHER (GQF MFG, Savannah, GA) at 37˚C. Retinas were dissected in Hanks’ balanced salt solution supplemented with 20 mM HEPES, pH 7.4 (HBSS).  After removing pigment epithelial cells and pecten, retinae were dissociated at 37˚C for 30min with papain (Papain dissociation system, LK003160, Worthington, Lakewood, NJ). The same volume of Neurobasal medium (Thermo Fischer, Waltham, MA) and 10 µg of deoxyribonuclease I (DN25, Sigma, St. Louis, MO) were added, and cells were triturated.  To remove debris, cells were then washed twice through a cushion of the ovomucoid protease inhibitor/BSA/HBSS in the papain dissociation system. To enrich RGCs, cells dissociated from E16 embryos as above immunopurified with a mouse monoclonal antibody to Thy-1 (BSJ-1: French and Jeffrey, 1986) using goat anti-mouse IgG conjugated magnetic beads (Miltenyi Biotec, Auburn, CA) (Yamagata et al., 2002). Cells were then resuspended in PBS with acetylated BSA, and processed as above.

tag: developmental stage

value: Retina


title: Sample_FL15


title: A3-CTRL-moDC technical replicate 9

description: moDC, CTRL, Animal A3, technical replicate 9

value: Large White

tag: animal id


title: A3-CTRL-moDC technical replicate 7

description: moDC, CTRL, Animal A3, technical replicate 7


title: A3-CTRL-moDC technical replicate 8

description: moDC, CTRL, Animal A3, technical replicate 8


title: E12 chick retina, sample 2

description:
E12 chick retina, whole retina
ChickenE12S2


title: Sample_FL12


title: E16 chick retina, sample 4

description:
E18 chick retina, enrich for RGC
ChickenvRGC2

value: Ventral retina


title: E12 chick retina, sample 1

description:
E12 chick retina, whole retina
ChickenE12S1


title: CC001.Unc_rep2


title: A3-CTRL-moDC technical replicate 5

description: moDC, CTRL, Animal A3, technical replicate 5


title: E16 chick retina, sample 3

description:
E18 chick retina, enrich for RGC
ChickenvRGC1


title: E16 chick retina, sample 2

description:
E18 chick retina, enrich for RGC
ChickendRGC2

value: Dorsal retina


title: A3-CTRL-moDC technical replicate 6

description: moDC, CTRL, Animal A3, technical replicate 6


title: Sample_C81

value: Control


title: E16 chick retina, sample 1

description:
E18 chick retina, enrich for RGC
ChickendRGC1


title: E18 chick retina, sample 4

description:
E18 chick retina, whole retina
Chicken1D


title: E18 chick retina, sample 3

description:
E18 chick retina, whole retina
Chicken1C


title: A3-CTRL-moDC technical replicate 4

description: moDC, CTRL, Animal A3, technical replicate 4


title: Sample_383

description: Mouse liver ERRBS by Illumina HiSeq 2500


title: C57BL.6J_rep1

value: himar1 transposon library


title: E18 chick retina, sample 2

description:
E18 chick retina, whole retina
Chicken1B


title: Rtel1f/f Ad-Cre biological replicate 1

value: Rtel1f/f MEFs

tag: treatment

value: Ad-Cre infected


title: ML 10

description:
SL113918
Mouse liver RNA-seq by Illumina HiSeq 2500

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file contains read counts.

extract_protocol:
Total RNA  was extracted using standard Trizol reagent (Invitrogen)  and cleaned up using RNeasy mini kit columns (Qiagen).
The NEBNext RNA first-strand synthesis module and NEBNExt Ultra Directional second strand synthesis kit (New England BioLabs) were used for the preparation of RNA sequencing (RNA-Seq) libraries.


title: E18 chick retina, sample 1

description:
E18 chick retina, whole retina
Chicken1A


title: Arabidopsis thaliana Tsu-0 rep4

city: East Lansing

first: Alan

last: Yocca

state: MI

address: 1066 Bogue St. Room A317

institute: Michigan State University

description: ATAC-seq processed

data_processing:
Raw reads were aligned to their respective genomes reported in the associated manuscript using Bowtie version 1.2.2 under the following settings: -S -v 2 -m 3 -q --chunkmbs 10000. In the case of the following genotypes, reference genomes were unavailable. Therefore they were aligned to the TAIR10 genome: Ad0, Hi, Og, Mt, En2
Peaks were called with MACS2 version 2.1.2 with the following parameters:  -g 1.35e8 --keep-dup all - q 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files are peak files output from MACS2

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Plants were grown in growth chambers at 22 degrees Celcius with a 16hr light, 8hr dark photoperiod.

extract_protocol: DNA was extracted after Tn5 integration using a QIAGEN minielute kit. More details can be found in Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ. 2017. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res. 45:e41.

tag: accession

value: leaf


title: Sample_189


title: Sample_C30


title: E12 chick retina, sample 3

description:
E12 chick retina, whole retina
ChickenE12S3

tag: tissue


title: ML 8

description:
SL113916
Mouse liver RNA-seq by Illumina HiSeq 2500

extract_protocol:
Ttotal RNA  was extracted using standard Trizol reagent (Invitrogen)  and cleaned up using RNeasy mini kit columns (Qiagen).
The NEBNext RNA first-strand synthesis module and NEBNExt Ultra Directional second strand synthesis kit (New England BioLabs) were used for the preparation of RNA sequencing (RNA-Seq) libraries.


title: A3-CTRL-moDC technical replicate 3

description: moDC, CTRL, Animal A3, technical replicate 3

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
tab-delimited text files include gene counting for each sample
Genome_build: ss102 (Ensembl 91)
Supplementary_files_format_and_content: reads counts

extract_protocol:
Total RNA from sorted cells was extracted using the Arcturus PicoPure RNA Isolation kit (ThermoFisher Scientiﬁc, St Aubin, France) according to the manufacturer’s instructions. The RNase-Free DNase Set (Qiagen, France) was used to remove contaminating DNA. RNA integrity was assessed using an RNA 6000 Pico kit on a Bioanalyzer 2100 (Agilent Technologies).
1 to 3 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina).


title: A3-CTRL-moDC technical replicate 2

description: moDC, CTRL, Animal A3, technical replicate 2


title: A2-CTRL-moDC technical replicate 11

description: moDC, CTRL, Animal A2, technical replicate 11


title: A2-CTRL-moDC technical replicate 12

description: moDC, CTRL, Animal A2, technical replicate 12


title: A3-CTRL-moDC technical replicate 1

description: moDC, CTRL, Animal A3, technical replicate 1


title: Arabidopsis thaliana old rep3

description: ATAC-seq processed

value: old


title: FL 6

description:
SL113914
Mouse liver RNA-seq by Illumina HiSeq 2500


title: Arabidopsis thaliana Per-1 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Per-1 rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Per-1 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana old rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Tsu-0 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Per-1 rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Tsu-0 rep1

description: ATAC-seq processed


title: A2-CTRL-moDC technical replicate 9

description: moDC, CTRL, Animal A2, technical replicate 9


title: A2-CTRL-moDC technical replicate 10

description: moDC, CTRL, Animal A2, technical replicate 10


title: Arabidopsis thaliana old rep2

description: ATAC-seq processed


title: FL 5

description:
SL113913
Mouse liver RNA-seq by Illumina HiSeq 2500


title: Arabidopsis thaliana Og rep4

description: ATAC-seq processed

value: Og


title: Arabidopsis thaliana Tsu-0 rep3

description: ATAC-seq processed


title: Arabidopsis thaliana old rep1

description: ATAC-seq processed


title: A2-CTRL-moDC technical replicate 8

description: moDC, CTRL, Animal A2, technical replicate 8


title: FL 7

description:
SL113915
Mouse liver RNA-seq by Illumina HiSeq 2500


title: ML 9

description:
SL113917
Mouse liver RNA-seq by Illumina HiSeq 2500


title: Control 4

description:
SL113912
Mouse liver RNA-seq by Illumina HiSeq 2500

value: Controls


title: Arabidopsis thaliana Og rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Og rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Og rep2

description: ATAC-seq processed


title: Control 3

description:
SL113911
Mouse liver RNA-seq by Illumina HiSeq 2500


title: A2-CTRL-moDC technical replicate 6

description: moDC, CTRL, Animal A2, technical replicate 6

value: moDC


title: Arabidopsis thaliana Nw rep3

description: ATAC-seq processed

value: Nw


title: Control 2

description:
SL113910
Mouse liver RNA-seq by Illumina HiSeq 2500


title: A2-CTRL-moDC technical replicate 5

description: moDC, CTRL, Animal A2, technical replicate 5


title: Control 1

description:
SL113909
Mouse liver RNA-seq by Illumina HiSeq 2500


title: Arabidopsis thaliana Nw rep4

description: ATAC-seq processed


title: Arabidopsis thaliana No rep4

description: ATAC-seq processed

value: No


title: Arabidopsis thaliana Nw rep2

description: ATAC-seq processed


title: Arabidopsis thaliana No rep3

description: ATAC-seq processed


title: Arabidopsis thaliana No rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Nw rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Col-0 untreated rep4

description: Untreated


title: A2-CTRL-moDC technical replicate 3

description: moDC, CTRL, Animal A2, technical replicate 3

value: no


title: 4952RNAseq

city: Indianapolis

first: Jing

last: Su

state: Indiana

address: 410 W. 10th Street, HITS 3000

department: Department of Biostatistics

institute: Indiana University School of Medicine

data_processing:
RNA-Seq analysis was performed following the standard pipeline established by The Cancer Genome Atlas (TCGA) and the National Cancer Institute Genomic Data Commons (GDC). Briefly, quality of raw sequencing reads was assessed by FASTQC analysis (Babraham Bioinformatics). Sequence reads were aligned using the Spliced Transcripts Alignment to a Reference (STAR) sequence aligner with a two-pass approach and gene counts determined using HTSeq software. The RNA-Seq data was reported as raw counts, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and FPKM-UQ (Upper 75% Quantile).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Brain metastatic tissue from solid tumor

extract_protocol:
Prior to analysis, frozen tumor block was assessed by a board-certified pathologist (SQ) to assess for adequate tumor content. Total RNA was purified from tumor specimens using the RNeasy Plus Micro Kit (Qiagen) with genomic DNA removal. RNA integrity (RIN) was determined by electrophoretic tracing using an Agilent Bioanalyzer. RNAseq libraries were constructed from samples (RIN >7.0) using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero rRNA depletion. Indexed libraries were sequenced on an Illumina NextSeq 500 DNA sequencer using 150x150-nt paired end reads, generating >40 million reads per sample (12 samples per flow cell) with >80% of sequences achieving >Q30 Phred quality scores. RNA-Seq analysis was performed following the standard pipeline established by The Cancer Genome Atlas (TCGA) and the National Cancer Institute Genomic Data Commons (GDC). Briefly, quality of raw sequencing reads was assessed by FASTQC analysis (Babraham Bioinformatics). Sequence reads were aligned using the Spliced Transcripts Alignment to a Reference (STAR) sequence aligner with a two-pass approach and gene counts determined using HTSeq software. The RNA-Seq data was reported as raw counts, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and FPKM-UQ (Upper 75% Quantile).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain Metastatic Tissue

tag: gender

value: Female

tag: age

tag: survival time

tag: survival

tag: prognostic subtype

value: Poor


title: Arabidopsis thaliana Col-0 untreated rep2

description: Untreated


title: Arabidopsis thaliana Col-0 untreated rep3

description: Untreated


title: A2-CTRL-moDC technical replicate 2

description: moDC, CTRL, Animal A2, technical replicate 2

tag: strain

value: Large White


title: 4955RNAseq

value: Good


title: 4945RNAseq

value: Others


title: A2-CTRL-moDC technical replicate 1

description: moDC, CTRL, Animal A2, technical replicate 1

tag: cell type


title: Arabidopsis thaliana Col-0 untreated rep1

description: Untreated


title: 4931RNAseq

value: Male

value: Cluster 1


title: A1bis-CTRL-moDC technical replicate 12

description: moDC, CTRL, Animal A1bis, technical replicate 12


title: Arabidopsis thaliana Mt rep3

description: ATAC-seq processed

value: Mt


title: A2-CTRL-moDC technical replicate 4

description: moDC, CTRL, Animal A2, technical replicate 4


title: 4826RNASeq


title: Arabidopsis thaliana Mt rep2

description: ATAC-seq processed

value: leaf


title: Arabidopsis thaliana Mt rep4

description: ATAC-seq processed


title: Arabidopsis thaliana No rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Mt rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Ler-0 rep3

description: ATAC-seq processed


title: A2-CTRL-moDC technical replicate 7

description: moDC, CTRL, Animal A2, technical replicate 7


title: Arabidopsis thaliana Ler-0 rep4

description: ATAC-seq processed


title: A1bis-CTRL-moDC technical replicate 9

description: moDC, CTRL, Animal A1bis, technical replicate 9


title: Arabidopsis thaliana Ler-0 rep1

description: ATAC-seq processed


title: 4687RNASeq


title: 4739RNASeq


title: Arabidopsis thaliana Ler-0 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Kn rep4

description: ATAC-seq processed

value: Kn


title: A1bis-CTRL-moDC technical replicate 7

description: moDC, CTRL, Animal A1bis, technical replicate 7


title: 4671RNASeq

value: Cluster 2


title: Arabidopsis thaliana Kn rep1

description: ATAC-seq processed


title: 4722-RNAseq


title: Arabidopsis thaliana Kn rep3

description: ATAC-seq processed


title: A1bis-CTRL-moDC technical replicate 8

description: moDC, CTRL, Animal A1bis, technical replicate 8


title: Arabidopsis thaliana Kn rep2

description: ATAC-seq processed


title: 4636RNAseq


title: A1bis-CTRL-moDC technical replicate 6

description: moDC, CTRL, Animal A1bis, technical replicate 6


title: A1bis-CTRL-moDC technical replicate 11

description: moDC, CTRL, Animal A1bis, technical replicate 11


title: A1bis-CTRL-moDC technical replicate 10

description: moDC, CTRL, Animal A1bis, technical replicate 10


title: Arabidopsis thaliana Kil rep3

description: ATAC-seq processed

value: Kil


title: 4632RNASeq


title: A1bis-CTRL-moDC technical replicate 5

description: moDC, CTRL, Animal A1bis, technical replicate 5

value: moDC


title: Arabidopsis thaliana Kil rep2

description: ATAC-seq processed


title: 4595RNASeq


title: Arabidopsis thaliana Kil rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Jm rep4

description: ATAC-seq processed

value: Jm


title: A1bis-CTRL-moDC technical replicate 4

description: moDC, CTRL, Animal A1bis, technical replicate 4


title: Arabidopsis thaliana Jm rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Jm rep2

description: ATAC-seq processed


title: 4588RNASeq


title: A1bis-CTRL-moDC technical replicate 3

description: moDC, CTRL, Animal A1bis, technical replicate 3


title: Arabidopsis thaliana Jm rep1

description: ATAC-seq processed


title: 4582RNASeq


title: A1bis-CTRL-moDC technical replicate 2

description: moDC, CTRL, Animal A1bis, technical replicate 2


title: Arabidopsis thaliana Is rep3

description: ATAC-seq processed

value: Is


title: A1bis-CTRL-moDC technical replicate 1

description: moDC, CTRL, Animal A1bis, technical replicate 1

value: no


title: Arabidopsis thaliana Kil rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Is rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Is rep1

description: ATAC-seq processed


title: 4578RNASeq

value: Brain Metastatic Tissue


title: Arabidopsis thaliana Is rep4

description: ATAC-seq processed


title: 4579RNASeq

value: Female


title: Arabidopsis thaliana Hi rep1

description: ATAC-seq processed

value: Hi


title: 4567RNAseq


title: Arabidopsis thaliana Gr-1 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Hi rep2

description: ATAC-seq processed


title: IgG ChIPSeq

city: singapore

first: SU E

last: YU

state: SINGAPORE

address: NUS, MD7, level 4

department: Biochemistry

country: Singapore

institute: NUS

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2.
Data were filtered using the following specifications: PCR duplication.
Peaks were called using Partek 6.6 software with an average fragment size of 300bps and 0.05 as the cutoff p-value of Mann-Whitney U test for separation of forward and reverse reads in a peak.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files.

source_name: E14 murine embryonic stem cells, IgG ChIP

growth_protocol: Murine ES cells (E14) were cultured in ES cell medium consisting of Glasgow Minimum Essential Medium (GMEM; Invitrogen), 15% ES cell qualified fetal bovine serum (FBS; Invitrogen), 0.055 mM β-mercaptoethanol (Sigma), 100 mM sodium pyruvate (Invitrogen), 0.1 mM MEM nonessential amino acid (NEAA, Invitrogen) and 1,000 units/ml of LIF (Millipore).

extract_protocol:
Lysates were clarified from sonicated nuclei and Npac-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: Murine embryonic stem cells

tag: chip antibody

value: Rb IgG (sc-2027, Santa Cruz)


title: Npac ChIPSeq

source_name: E14 murine embryonic stem cells, Npac ChIP

value: Npac (14833-1-AP, Proteintech Group)


title: 4558RNASeq

value: Good


title: Arabidopsis thaliana Gr-1 rep3

description: ATAC-seq processed


title: 4559-RNAseq

value: Male

value: Cluster 1


title: Arabidopsis thaliana Gr-1 rep1

description: ATAC-seq processed

value: leaf


title: Arabidopsis thaliana Gr-1 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Hi rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Gd-1 rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Hi rep4

description: ATAC-seq processed


title: 4526RNAseq

value: Others


title: 4500RNAseq


title: Arabidopsis thaliana Gd-1 rep4

description: ATAC-seq processed


title: 4497RNAseq


title: Arabidopsis thaliana Est rep4

description: ATAC-seq processed

value: Est


title: Arabidopsis thaliana Gd-1 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Est rep2

description: ATAC-seq processed


title: Arabidopsis thaliana En-2 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Gd-1 rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Est rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Est rep1

description: ATAC-seq processed


title: 4482RNAseq


title: EX_H_47P

type: RNA

city: Olsztyn

first: Piotr

last: Kaczynski

address: Tuwima 10

department: Department of Hormonal Action Mechanisms

country: Poland

institute: Institute of Animal Reproduction and Food Research of Polish Academy of Sciences

description:
Endometrial sample collected from gilt assigned to the experimental group (hormone-treated)
Gene expression after 24h of treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to gilent 4x44k Porcine Gene Expression microarrays (G2519F-026440) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for Agilent 4x44k Porcine Gene Expression microarrays (G2519F-026440).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Expression signals were filtered based on “well above background” flags (detection in 5 of 10 samples in control group, and in 5 of 6  samples in experimental group) and normalized with the BioConductor package VSN (Huber et al. 2002).

source_name: porcine endometrial tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from endometrial samples using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Purity and concentration of isolated RNA was measured with NanoDrop spectrophotometer (Thermo Fisher Scientific). RNA integrity was assessed by using Agilent Eukaryote Total RNA Nano chips and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Randomly selected horns within each gilt received hormonal infusions: PGE2 (200 µg/infusion) simultaneously with E2 (33.3 µg/infusion). The contralateral horn received placebo infusions. In the control group each horn received intrauterine placebo infusions. Treatments were administered every 4 h for 24 h on days 11-12 after the onset of estrus.

value: endometrium

value: female

value: 8 months


title: Arabidopsis thaliana En-2 rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Cvi-0 rep3

description: ATAC-seq processed


title: Arabidopsis thaliana En-2 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Cvi-0 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana En-2 rep3

description: ATAC-seq processed


title: EX_H_41P


title: 4512RNAseq


title: EX_H_44P


title: 33-4559RNASeq


title: 2015-955RNAseq


title: EX_H_40L


title: EX_H_36P


title: EX_C_47L

description:
Endometrial sample collected from gilt assigned to the experimental group (placebo-treated)
Gene expression after 24h of treatment


title: EX_C_44L


title: EX_H_38P


title: Arabidopsis thaliana Col-0 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Col-0 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Cvi-0 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Cvi-0 rep1

description: ATAC-seq processed


title: EX_C_41L


title: 2015-1834RNAseq


title: Arabidopsis thaliana Col-0 rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Col-0 rep1

description: ATAC-seq processed


title: 2015-109RNAseq


title: 2013-2873RNAseq


title: 2014-1511RNAseq


title: Arabidopsis thaliana Chat-1 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Chat-1 rep3

description: ATAC-seq processed


title: Arabidopsis thaliana Chat-1 rep2

description: ATAC-seq processed


title: Arabidopsis thaliana Bur rep4

description: ATAC-seq processed

value: Bur


title: Arabidopsis thaliana Bur rep3

description: ATAC-seq processed


title: 2015-1335RNAseq

value: Poor


title: 2013-1795RNAseq

value: Brain Metastatic Tissue

value: Cluster 2


title: Arabidopsis thaliana Bur rep2

description: ATAC-seq processed


title: EX_C_36L


title: Arabidopsis thaliana Chat-1 rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Bur rep1

description: ATAC-seq processed


title: CTRL_P_46P

description:
Endometrial sample collected from gilt assigned to the control group (Placebo infused into both uterine horns)
Gene expression after 24h of treatment


title: Arabidopsis thaliana Bd-0 rep4

description: ATAC-seq processed


title: Arabidopsis thaliana Bd-0 rep3

description: ATAC-seq processed


title: 2012-1354-RNAseq

value: Female


title: CTRL_P_14P


title: Arabidopsis thaliana Bd-0 rep1

description: ATAC-seq processed


title: Arabidopsis thaliana Ad-0 rep 4

description: ATAC-seq processed


title: Arabidopsis thaliana Ad-0 rep 3

description: ATAC-seq processed


title: 2012-1807RNAseq


title: 2012-1430RNAseq


title: 2009-1104RNAseq


title: Arabidopsis thaliana Ad-0 rep 1

description: ATAC-seq processed


title: 2008-1840RNAseq


title: CTRL_L_28L


title: Arabidopsis thaliana Ad-0 rep 2

description: ATAC-seq processed


title: LJX_miRNA

city: Zhengzhou

first: Zhaohui

last: Zheng

address: 1 Eastern Jianshe Road

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina bcl2fastq 2.0 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
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: kidney tissues

extract_protocol:
Total RNA was extracted from renal tissues using the Trizol LS reagent . After total RNA quality check, the rRNA was removed using the Ribo-ZeroTM rRNA removal kit and purification and fragmentation of RNA was performed at the same time. First-strand cDNA was synthesized via reverse transcription, followed by second-strand cDNA synthesis. After terminal repair and purification, the cDNA library was amplified through PCR. Finally, samples were sequenced using a 2×150 base paired-end configuration with the Illumina Hiseq 2500 (Illumina, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

tag: sample type


title: WC_miRNA


title: ZJL_miRNA


title: Arabidopsis thaliana Bd-0 rep2

description: ATAC-seq processed


title: 2007-563RNAseq


title: XQY_miRNA


title: 2007-45RNAseq


title: CTRL_P_28P


title: 2007-263-RNAseq


title: CTRL_P_9P


title: CTRL_L_46L


title: FB, Hypoxia, Technical Replicate 3

city: Silver Spring

first: Ian

last: Bellayr

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

description:
Gene expression comparison between normoxia and hypoxia cell culture conditions for iPSCs
N - Normoxia; Hy - Hypoxia
Induced Pluripotent Stem Cell (iPSC)

hyb_protocol: Assembled slide chambers were placed in the hybridization oven set to 55oC with a rotator speed of 20rpm for 20 hours.  See manuscript for more detailed description

scan_protocol: All images were produced using the DNA microarray scanner with surescan high-resolution technology (Agilent Technologies).  Slides were scanned at 446 nm for the Cy3 dye and a resolution of 2 µm double pass.  See manuscript for more detailed description

data_processing:
The spots were annotated through the Agilent Feature Extraction (AFE) 11.0 software.  All methods and analyses used in this study were implemented in JMP Genomics, which included normalization, principle component analysis, clustering, box plots and statistics.  See manuscript for more detailed description.
Data was normalized by the quantile normalization method.

source_name: Fibroblast

label_protocol: Individual RNA material was labeled with Cy3.  See manuscript for more detailed description

growth_protocol: MSCs were expanded at initial plating densities of ~60 cells/cm2 using standard MSC growth medium (alpha-minimum essential media (αMEM), 1% L-glutamine, 1% penicillin-streptomycin (PS), 16% fetal bovine serum (FBS)) following established protocols.

extract_protocol: Total RNA were isolated from samples using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocols.

treatment_protocol: Cell were grown under normoxia (37C, 5% CO2, ...) and Hypoxia (37C,….) conditions

value: Hypoxia


title: CTRL_L_9L


title: FB, Normoxia, Technical Replicate 3

value: Normoxia


title: FB, Hypoxia, Technical Replicate 1


title: FB, Normoxia, Technical Replicate 2


title: FB, Hypoxia, Technical Replicate 2


title: CTRL_L_14L


title: FB, Normoxia, Technical Replicate 1


title: EB1, Hypoxia, Technical Replicate 3

source_name: iPSC-Fibroblast


title: EB1, Hypoxia, Technical Replicate 1


title: EB1, Normoxia, Technical Replicate 3


title: WC_RNA


title: EB1, Hypoxia, Technical Replicate 2


title: EB1, Normoxia, Technical Replicate 2


title: 2007-550RNAseq


title: EB1, Normoxia, Technical Replicate 1


title: LLD_miRNA


title: LJX_RNA


title: Zheng1-JJL_RNA


title: 2006-262-RNAseq


title: DF, Hypoxia, Technical Replicate 3


title: EX_C_38L


title: 2007-109RNASeq


title: LLD_RNA


title: DF, Hypoxia, Technical Replicate 1


title: THP1_III

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

description: miRNA

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
TRIM GALORE! was used to remove adapters, low quality regions and sequences of less than 17 nucleotides.
Filtered reads were mapped onto the human genome (hg38) using the Bowtie.
HTSeq was used to obtain read counts. A GTF containing pre-miRNAs annotations (mirBase - Release 22.1) was used.
Differentially expressed genes were determined with EdgeR in R using HTSeq counts from the all reads analysis and a FDR < 0.05 as the significance cutoff.
Target genes of miRNAs were obtained from the recorded pairs in miRTarBase database.
In order to discuss the relationship between miRNAs from modulated macrophages and the pathogenicity of T.rubrum, the databases miRBase, miRTarBase and PantherDB were used.
Genome_build: Human genome (hg38), Broad T. rubrum strain CBS118892 genome.
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and EdgeR output in TXT format containing logFC, logCPM, LR and p value.

source_name: THP1 - control, replicate III

growth_protocol: The Trichophyton rubrum strain CBS 118892 was cultured on Sabouraud dextrose agar for 15 days at 28ºC. Keratinocytes were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) at 37ºC in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA extraction of T. rubrum and  THP-1 were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
Micro RNA libraries were prepared for sequencing according to Illumina guidelines.

treatment_protocol: Pre-cultured conidia and heat inactive of T. rubrum were added to THP-1 cell line and the co-culture was incubated for 24 h at 37ºC in a humidified atmosphere containing 5% CO2.

tag: human cell line


title: Zheng1-JJL_miRNA


title: XQY_RNA


title: DF, Hypoxia, Technical Replicate 2


title: DF, Normoxia, Technical Replicate 2


title: Fetal stromal and epithelium sample pool 6 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) libraryof single cells from 3 whole fetal intestinal samples from 12, 17 and 19 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Pool_6_HTO

data_processing:
Raw sequence data for mRNA libraries were processed using 10x Genomics cellranger pipeline, version 3.1.0
Raw sequence data from hashing libraries were processed using CITE-Seq-Count, version 1.4.3
Genome_build: hg38
Supplementary_files_format_and_content: compressed raw UMI counts matrices from Cellranger outputs for mRNA libraries. Compressed raw UMI matrices from CITE-Seq-Count for antibody oligo tag counts.

source_name: Small and large fetal intestine

extract_protocol:
fetal intestinal samples were digested using either EDTA chelation protocol (EpCAM+/ epithelial pools) or milteyni umbilical cord digestion kit (EpCAM- / stromal pools) and then stained with either a oligonucleotide conjugated antibody to B2M/Cd298 (biolegend) or in EpCAM+ cells an additional EpCAM+ oligo conjugated antibody. In the case of the first pool 3 samples were digested fully without separation. All these libraries are 3 prime, scRNA seq processed using 10x v3 single cell RNA seq protocol and co-ordinate with a HTO library (in the case of single stain) or a HTO and ADT library (in EpCAM+ cells case) for demultiplexing
RNA libraries were processed as per 10x v3 single cell RNA seq protocol library preparation for illumina i7 sample indexes (CG000183, Rev C), HTO and ADT libraries were extracted from the protocol during SPRI clean up and amplified with custom tru-seq primers as per description in published protocol: https://doi.org/10.1186/s13059-018-1603-1

value: intestinal stromal and epithelial cells

tag: post-conceptual weeks


title: THP1_II

description: miRNA

source_name: THP1 - control, replicate II


title: DF, Normoxia, Technical Replicate 3


title: ZJL_RNA


title: 2006-76RNASeq

value: Good


title: THP1_I

description: miRNA

source_name: THP1 - control, replicate I


title: siS_2

description: HepG2 cells RNA-seq by Illumina HiSeq 2500

data_processing:
Reads were aligned to the human genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: HepG2 cells

tag: sirna

value: Scramble


title: 2004-950RNAseq

value: Male


title: DF, Normoxia, Technical Replicate 1

tag: treatment


title: WB, Hypoxia, Technical Replicate 1


title: WB, Hypoxia, Technical Replicate 2


title: Fetal stromal and epithelium sample pool 5 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 6  fetal EPCAM+ and EPCAM- intestinal samples from 12, 17 and 19 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Pool_5_HTO


title: WB, Normoxia, Technical Replicate 1


title: WB, Normoxia, Technical Replicate 2


title: siS_1


title: siS_3


title: siN_3

value: siNREP


title: siN_2


title: siN_1


title: Mouse_thyroid_knockout_rep4

city: Greifswald

first: Janine

last: Golchert

address: Felix-Hausdorff-Str. 8

department: Department of Functional Genomics

institute: University Medicine Greifswald

hyb_protocol: 2.5 µg of fragmented and biotinylated cDNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing:
Quality of hybridizations was assessed using Expression Console software and microarray data were analyzed using Rosetta Resolver software including RMA normalization.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

label_protocol: Biotinylated cDNA were prepared according to the GeneChip® Whole Transcript PLUS Reagent Kit manual starting from 200 ng total RNA.

extract_protocol: Extraction of total RNA was performed with TRIzol reagent and homogenization in a bead mill dismembrator. After purification of total RNA, quality control was performed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Ctsk-/-/Mct8-/y/Mct10-/- was generated by crossbreeding sexually mature mice at the age of 6 to 8 weeks to generate homozygous littermates. Thyroid tissue of male mice at 5 to 8 months of age was isolated and snap-frozen in liquid nitrogen.

tag: strain background

tag: genotype/variation

value: Ctsk-/-/Mct8-/y/Mct10-/- knockout

value: thyroid tissue


title: Mouse_thyroid_wild-type_rep4

value: wild type

tag: tissue


title: RNA_FE3

city: xiamen

first: kunzhao

last: du

address: jimei

institute: huaqiao university

description:
RNA_FE3 represents the Fto(f/f，Emx1-cre) sample biological repeat 3 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt

data_processing:
For RNA-seq, In first step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reads mapping to the reference genome was performed.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool,and three sets of raw reads were obtained.
For Ribo-seq, Ribo-seq used TopHat2 for genome mapping.
Quantification of mapped results to gene level was carried out using HTSeq.
For samples with biological replicates, DESeq2 R package (1.14.1) was used for differential expression analysis. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
Genome_build: mm10
Supplementary_files_format_and_content: Ribo-seq_ read_count.txt include raw gene count for each Sample in Ribo-seq
RNA-seq_ read_count.txt include raw gene count for each Sample in RNA-seq
Ribo-seq_ FPKM.txt include FPKM values for each Sample in Ribo-seq
Ribo-seq_ RPKM.txt include RPKM for each Sample in RNA-seq

source_name: cerebral cortex

extract_protocol:
For RNA-seq, cerebral cortices of mice were removed, and RNA was harvested using Trizol reagent.NEBNext® UltraTM RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.  For Ribo-Seq, three groups of E15.5 mouse cerebral cortices were rapidly washed twice in ultra-pure water, and grind thoroughly with liquid nitrogen to powder. Sample was treated with specific lysis buffer with cycloheximide (50mg/mL) to acquire the lysate. Concentration of the lysate was measured by the NanoDrop™ 2000 Spectrophotometer. To digest the RNA other than RPFs, cell or tissue lysate was treated with unspecific endoribonuclease RNase I. Isolation of monosomes was performed by size-exclusion chromatography with MicroSpin S-400 HR columns. The RNA samples were then treated with rRNA depletion kit to deplete the samples of as much rRNA contamination as possible before PAGE purification of the relatively short (20~38 nt) RPFs. Following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR. After library construction, the concentration of library was measured by The Qubit® 2.0 Fluorometer and adjusted to 1ng/uL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the insert size and concentration of the library was identical, the samples can then be subjected for sequencing. Raw data (raw reads) of FASTQ format were firstly processed through cut adapt.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cerebral cortex

tag: age

value: embryonic day 15.5

tag: genotype

value: Fto(f/f, Emx1-cre)

tag: rna fraction

value: total RNA


title: Mouse_thyroid_knockout_rep3


title: RNA_FE2

description:
RNA_FE2 represents the Fto(f/f，Emx1-cre) sample biological repeat 2 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt


title: Mouse_thyroid_wild-type_rep1