title: T_Cell_500

value: 5mC, onBead, 500 cells, fixed


title: Myf6_KO_satellite_cell_biological_rep_2_technical_rep_4

status: Public on Oct 02 2020

type: SRA

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Illumina BaseSpace software was used for basecalling.
Sequenced reads were mapped to mm10 whole genome using hisat2 (v 2.1.0).
htseq-counts (v 0.11.2) (non stranded option) was used with Gencode.vM19 annotation to obtain reads mapped to genes in mm10.
Count tables were used by Deseq2 (v 1.24.0) to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files have read counts for genes in mm10, csv file has differentially expressed genes identified by deseq2

molecule: total RNA

organism: Mus musculus

extract_protocol:
Mouse hindlimb satellite cells were isolated by Fluorescence Activated Cell Sorting (FACS) by selecting for ITGA7+, Hoechst+, Lin- (CD45-, CD11b-, CD31-, SCA1-) cells. 3000 satellite cells per mouse were immediately lysed by sorting directly into reaction buffer (SMART-Seq V4 Ultra Low Input kit, Takara Bio).
RNA from lysed FACS-sorted satellite cells was converted into cDNA libraries using SMART-Seq V4 Ultra Low Input kit (Takara Bio). Illumina sequencing adapters were then added using the Nextera XT DNA library preparation kit (Illumina).

tag: age

value: 10 months-old

tag: genotype

value: Myf6 knockout

tag: cell type

value: satellite cells

tag: gender

value: female


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad007

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: strain


title: AEG 3482 rep2

city: Ann Arbor

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

data_processing:
Basecalling was performed by the Illumina HiSeq4000
FastQC was used for FASTQ file quality control
Sequences were aligned to the mm10 transcriptome using Kallisto v0.43.1 with parameters -b 100 --single -l 200 -s 20
Transcripts were counted and converted to genes using Tximport v1.8.0
Genome_build: mm10
Supplementary_files_format_and_content: csv files for TPMs (transcript per million counts) for each sample will be included

source_name: Primary tail fibroblast cell line

growth_protocol: The CCG-HTA-1 cells are grown in DMEM containing high glucose and no sodium pyruvate. This is supplemented with 10% FCS and a penicillin/streptomycin/antimycotic solution.

extract_protocol:
RNA was extracted from cells 48 hours after compound treatment using RNAzol, as per the manufacture, and ribodepleted using [WHAT KIT?????]
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: Cells were cultured in ambient oxygen at 37C with 10% CO2. Cells were added so that they would be approximately 80% confluent at the time of exposure to the chemicals being tested. 24 hours after cells were added the cells had attached and the chemicals were added to the culture media of the cells. After the appropriate time cells were harvested.

tag: cell line

tag: agent

tag: passage

value: Passage 4

value: Mice were 5-8 weeks when cells were collected


title: Para12_2

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

country: Germany

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor -  Pair1 - Experiment1

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters (Li and Durbin, 2010). The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapped by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Lung

growth_protocol: C57BL/6 mice were purchased from Charles River Laboratories. All mice were bred and housed under specific pathogen free conditions at the animal facilities of the University of Würzburg (ZEMM and Institute for Immunology and Virology), Memorial Sloan-Kettering Cancer Center, Max Planck Institute of Immunobiology and Epigenetics, Freiburg and Centre Immunologie Luminy and were used in accordance with institutional guidelines and as approved by the local authorities

extract_protocol:
Lungs were harvested, chopped into small pieces and incubated in digestion buffer DMEM (Gibco 31966021); 0.25 mg/ml LiberaseTM TL (Research Grade 05401020001, Roche); 10mM Hepes (Gipco 1563049) for 45 mins at 37°C on Eppendorf rotator at 120rpm. Digestion was stopped with 20ml RPMI 1640 medium Thermo Fisher Scientific; 31870074) added with 50μM 2-mercaptoethonal (AppliChem, A1108). Cells were meshed through 70um cell strainer (Falcon 3522350) and washed and collected in FACS Buffer or 1× MojoSort buffer (BioLegend; 480017). Bone marrow cells from ilia, femora, and tibiae were isolated by crushing the bones in 1× MojoSort buffer. Bone marrow cells were filtered (CellTrics, 30 μm; Sysmex) and washed and collected in 1x MojoSort buffer.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: tissue

value: Lung

value: 6-8 weeks + 3-4 weeks parabiosis prior to infection


title: AEG 3482 rep1


title: Para12_1

institute: Max Planck Institute of Immunobiology and Epigenetics

description: library of ILCs d15 post NB infection parabiotic C45.2 host_Cd45.1 donor  -  Pair1 - Experiment1


title: Para12_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A4_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A3_ad012


title: Myf6_KO_satellite_cell_biological_rep_2_technical_rep_2


title: T_Cell_25K

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

institute: New England Biolabs

data_processing:
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Sequenced reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program, then mapped to human (hg38) or mouse (mm10) reference genome using bowtie2 with parameters --dovetail --no-unal --no-mixed --no-discordant --very-sensitive -I 0 -X 1000.
Duplicated reads were then removed using picard tool MarkDuplicates and mitochondrial reads were also discarded using the samtools.
peaks were called using MACS2 with the following parameters: -f BAMPE -m 4 100 --bdg --SPMR
coverage track was generated using deepTools bamCoverage with RPKM (Reads Per Kilobase per Million mapped reads) normalization
genome build: human: hg38; mouse: mm10
processed data files format and content: bigWig; RPKM nomalized coverage
Library strategy: UniNicE-seq

source_name: cells

growth_protocol: HCT116 cell line were routinely grown in DMEM media with 10% fetal bovine serum respectively, media being replaced every 3 days. For human tissue section, we purchased it from US Biomax Inc under the agreement of only research purpose. FFPE slides of the liver sample were also custom ordered from BioChain, USA, with 24-48 hrs formalin fixation

extract_protocol:
After we isolated the nuclei from cultured cell or tissue section, the nuclei was labeling with Nt.CviPII, Biotinylated 5mC-dNTP mixture, decroslinked for O/N at 65 degree, and then genomic DNA was extracted using phenol-chloroform method.
Biotin-labeled open chromatin DNA was captured by streptavidin bead and the beads were washed with high salt buffer for 4 times, and followed the library preparation procedure using NEBNext Ultra II DNA library Prep Kit (E7370S, New England Biolabs, Inc)

value: Lymphocyte

value: T-cell lymphoma

tag: experimental variables

value: 5mC, onBead, 25K cells, fixed


title: Myf6_KO_satellite_cell_biological_rep_2_technical_rep_3


title: Clofilium tosylate rep2

value: Clofilium tosylate


title: Clofilium tosylate rep3


title: Para11_8

description: library of ILCs d15 post NB infection parabiotic C45.1 host_Cd45.2 donor -  Pair1 - Experiment1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A3_ad001


title: Myf6_KO_satellite_cell_biological_rep_2_technical_rep_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A3_ad010


title: Clofilium tosylate rep1


title: exp2_Para11_7

description: library of ILCs d15 post NB infection parabiotic C45.1 host_Cd45.2 donor -  Pair1 - Experiment2


title: Myf6_KO_satellite_cell_biological_rep_1_technical_rep_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A3_ad004


title: BerberineA rep3

value: BerberineA


title: Para11_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A3_ad002


title: Myf6_KO_satellite_cell_biological_rep_1_technical_rep_3


title: BerberineA rep2


title: Para11_4


title: Myf6_KO_satellite_cell_biological_rep_1_technical_rep_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A3_ad008


title: BerberineA rep1


title: Para11_3


title: Myf6_KO_satellite_cell_biological_rep_1_technical_rep_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A2_ad001


title: Para11_2


title: Myf6_WT_satellite_cell_biological_rep_2_technical_rep_3

value: wild type


title: d4_8

description: library of ILCs d4 post NB infection mouse1/mouse2

value: 6-8 weeks


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A2_ad007


title: Cardamonin rep2

value: Cardamonin


title: Cardamonin rep1


title: Para11_1


title: Myf6_WT_satellite_cell_biological_rep_2_technical_rep_4

value: 10 months-old


title: Para11_6


title: Myf6_WT_satellite_cell_biological_rep_2_technical_rep_1

value: satellite cells


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A2_ad004


title: Myf6_WT_satellite_cell_biological_rep_2_technical_rep_2

value: female


title: d4_7


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A2_ad006

value: CA


title: Diphenyleneiodonium Cl rep2

value: Diphenyleneiodonium Cl


title: d4_6


title: Myf6_WT_satellite_cell_biological_rep_1_technical_rep_4


title: Diphenyleneiodonium Cl rep1

value: Passage 4


title: Myf6_WT_satellite_cell_biological_rep_1_technical_rep_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A2_ad002

value: male


title: d4_5

value: Lung


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A12_ad012


title: Dihydrorotenone rep3

value: Dihydrorotenone

value: Mice were 5-8 weeks when cells were collected


title: d4_4


title: Cardamonin rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A2_ad010


title: Diphenyleneiodonium Cl rep3


title: Myf6_WT_satellite_cell_biological_rep_1_technical_rep_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A12_ad007


title: 133-E (miRNA-Seq)

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Sequence reads were trimmed and filtered with Trimmomatic [v0.36] to remove adaptor sequences , low quality reads and reads shorter than 16 nucleotides.
The sRNAbench module from the sRNAtoolboxVM program was applied to map sequences to the reference genome, to profile the expression of known small RNAs from miRBase sheep miRNAs and to predict novel miRNAs. Rfam data was used to identify other small RNAs originating from rRNA, tRNA, snRNA and snoRNA and exclude them from the analysis.
The predicted new miRNAs were searched in the RNACentral database with blastn [v2.7.1] to known if they have been previously identified and to try to annotate them.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text file matrix with the raw counts of sequencing reads for miRNAs. The miRNAs are identified with the miRBase ID and the samples are identified by the name of the title column of the SAMPLES section.

organism: Ovis aries

source_name: Encephalon

growth_protocol: The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the EthicalCommittee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.

extract_protocol:
A sample from encephalon (parietal lobe cortex) was aseptically taken from each animal and tissue sections were preserved in RNAlater solution (Ambion, Austin, TX, USA) at −80 ⁰C. Total RNA was isolated from encephalon tissue using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and PureLink RNA Mini Kit (Invitrogen). 60 mg tissue samples were homogenized in 1 ml of TRIzol Reagent using Precellys®24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) combined with 1.4 and 2.8 mm ceramic beads mix lysing tubes (Bertin Technologies). RNA isolation was performed following manufacturer instructions and RNA was suspended in RNase free water and stored at −80 ⁰C. The TruSeq Small RNA library prep kit (Illumina, San Diego, CA, USA) was used for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The animals were treated with three different treatments: one group was inoculated with nine different commercial vaccines, other one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium, and other was treated with PBS. Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and June of 2106, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.

value: Parietal lobe cortex

tag: group

value: Control

tag: breed

value: Rasa Aragonesa


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A12_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A12_ad006


title: d4_2


title: Dihydrorotenone rep1

value: Mice were 8-11 weeks when cells were collected


title: d4_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A12_ad001


title: LOP9IL33rnegIl18P5P6

description: library of cultured Il18r1+Icos+ST2- ILCs on OP9 with IL2/IL7/IL1b/IL23 lineage positive output included


title: Antimycin A rep2

value: Antimycin A


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad012


title: 137-E (miRNA-Seq)


title: Antimycin A rep1


title: 135-E (miRNA-Seq)


title: 136-E (miRNA-Seq)


title: LOP9IL33rnegIl18

description: library of cultured Il18r1+Icos+ST2- ILCs on OP9 with IL2/IL7/IL1b/IL23

value: 6-8 weeks


title: RNA-MEF-dKO-rep3

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

description: dKO

data_processing:
The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover v0.9.2.
Reads were mapped to the mouse genome (mm9) using Tophat v2.0.14 and Bowtie v2-2.1.0.
Quantification of gene expression was performed using HTSeq v0.6.1 and gene annotations from Ensembl release 67.
Read counts have been normalized across WT and KO libraries with the method proposed by (Anders et al. 2010). Comparisons of interest were performed using the test for differential expression proposed by (Love et al. 2014) and implemented in the Bioconductor package DESeq2 (v1.16.1).
Resulting p-values were adjusted for multiple testing using the Benjamini and Hochberg method (Hochberg et al. 1990).
Genome_build: mm9
Supplementary_files_format_and_content: Processed expression data were summarized in an Excel file containing the following informations: gene name/ensemble_gene_id/raw read count/normalized read count for each sample, and for the differential gene expression analysis: log2 fold change/p-value/p-value adjusted for multi-testing.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs are grown in glutamine and pyruvate containing DMEM, supplemented with 10% serum, 1% penicillin-streptomycin

extract_protocol:
RNA samples were purified using standard methods from confluent MEF cultures.
Libraries of template molecules suitable for strand-specific high-throughput DNA sequencing were created using a TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (RS-122-2301; Illumina) as previously described (Papin et al. 2017).

treatment_protocol: H2A-Z.1flox/flox : H2A-Z.2 flox/flox MEFs were infected with control adenovirus or adenovirus expressing Cre recombinase (Ad-CMV-GFP or Ad-Cre-GFP respectively, Vector Biolabs, Philadelphia, Pennsylvania, USA) to generate control (WT) or double KO (dKO) cell lines. Viruses were diluted in the culture media for overnight infection. Infection media was replaced with fresh complete media the next day, and the cells were analyzed for knockout efficiency after 3 days.

value: Mouse embryonic fibroblasts

tag: genotype/variation

value: MEFs were derived from E13.5 embryos


title: Myf6_WT_satellite_cell_biological_rep_1_technical_rep_2

value: 10 months-old

value: wild type

value: satellite cells


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad010

value: CA


title: Dihydrorotenone rep2

value: Passage 4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad008

value: male


title: d4_3

value: Lung


title: RNA-MEF-dKO-rep2

description: dKO


title: LOP9IL33rnegP5P6


title: LOP9IL33rneg


title: 126-E (miRNA-Seq)

value: Vaccine


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad007


title: RNA-MEF-dKO-rep1

description: dKO


title: 124-E (miRNA-Seq)


title: Antimycin A rep3

value: Mice were 5-8 weeks when cells were collected


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad004


title: RNA-MEF-WT-rep3

description: WT

value: H2A-Z.1flox/flox :H2A-Z.2 flox/flox


title: BMOP9Il18negP7P5

source_name: BM

value: BM


title: BMOP9Il18negP7P5P6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad002


title: 121-E (miRNA-Seq)

value: Parietal lobe cortex

value: Rasa Aragonesa


title: RNA-MEF-WT-rep2

description: WT


title: 131-E (miRNA-Seq)

value: Control


title: BMOP9Il18negP8_2

description: library of cultured Il18r1+Icos+ST2-Il17rb- ILCs on OP9 with IL2/IL7/IL1b/IL23

value: 6-8 weeks


title: 117-E (miRNA-Seq)

value: Adjuvant


title: RNA-MEF-WT-rep1

description: WT

value: Mouse embryonic fibroblasts

value: MEFs were derived from E13.5 embryos


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A10_ad012


title: 5hmC_DIP_MEFs

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover.
Data were preprocessed with Cutadapt (http://journal.embnet.org/index.php/embnetjournal/article/view/200) v1.13 to remove the first 9 nucleotides and to trim trailing polyT sequences of at least 10 Ts. Cutdapt was used with the following parameters ‘-u 9 -a T{10}-discard-trimmed’.
Reads were mapped to the mouse genome (mm9) using Bowtie with default parameters except for “-p 3 –m 1 –strata –best –chunkmbs 128”.
Genome_build: mm9
Supplementary_files_format_and_content: WIG track files were generated using WigMaker. Scores represent tag numbers per total uniquely mapped reads.

growth_protocol: MEFs are grown in glutamine and pyruvate containing DMEM, supplemented with 10% serum, 1% penicillin-streptomycin.

extract_protocol:
Purified genomic DNA was first sonicated to ≈ 200 bp and modified-DNA was isolated using antibodies.
Librairies were prepared using the SMART cDNA Library Construction Kit and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

tag: strain background

value: wild type

value: E10.5 embryos

value: Mouse embryonic fibroblasts (MEFs)

tag: chip antibody

value: anti-5hmC (active motif, catalog number 39791)


title: BMOP9Il18negP8_1

tag: age


title: 116-E (miRNA-Seq)


title: LungOP9Il18negP8_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A10_ad010

value: CA

value: male


title: 5mC_DIP_MEFs

value: anti-5mC (active motif, catalog number 9649)


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A10_ad008


title: 115-E (miRNA-Seq)


title: LungOP9Il18negP8_1

value: Lung


title: 114-E (miRNA-Seq)


title: 122-E (miRNA-Seq)

value: Vaccine


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A10_ad007


title: Input_MEFs

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover.
Reads were mapped to the mouse genome (mm9) using Bowtie1 with the following arguments: -m 1 --strata --best -y -S –l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: WIG track files were generated using WigMaker. Scores represent tag numbers per total uniquely mapped reads.

extract_protocol:
Lysates were clarified from cross-linked and sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.


title: EPS_rep2

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

country: China

institute: Wuhan University

data_processing:
Bustard used for basecalling.
Sequenced reads were trimmed for adaptor sequence by cutadapt ,then mapped to hg38 whole genome using HISAT2 version 2.1.0 with parameters --rna-strandness RF --avoid-pseudogene
Use the bam file and Gencode.v29.gtf (protein_coding_gene) as input of featurecounts to generate Raw_counts
normalized_counts were caculated using DEseq2 ,Transcripts Per Kilobase Million(TPM) were generated by raw_counts and exon length
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Raw_counts ,TPM and normalized_counts by DEseq2 for each Sample

organism: Homo sapiens

source_name: extended pluripotent stem cell

extract_protocol:
Total RNA of human ESCs and EPSCs were prepared in duplicate with the HiPure Total RNA Mini Kit (Magen) according to the manufacturer’s instruction.
RNA libraries were prepared by NEB Next Ultra Directional RNA Library Prep Kit for Illumina.

value: extended pluripotent stem cell


title: DL1IL18pos_2_16

description: library of cultured Il18r1+Icos+ ILCs on OP9-DL1 with IL2/IL7/IL1b/IL23/IL18

value: BM


title: Input_H3.3_MEFs

description: A DNA element encoding the FLAG–FLAG–HA amino acids was inserted in frame with the N terminus of H3.3B. In addition, a loxP site was inserted on both ends of Exon 2.

extract_protocol:
Sub-confluent MEFs expressing FLAG-HA tagged endogenous H3.3 were lysed in hypotonic buffer (10 mM Tris-HCl at pH 7.65, 1.5 mM MgCl2, 10 mM KCl) and disrupted by Dounce homogenizer. The cytosolic fraction was separated from the nuclei by centrifugation at 4°C. Nuclei were re-suspended in sucrose buffer (20 mM Tris-HCl at pH 7.65, 15 mM KCl 60 mM NaCl, 0.15 mM spermine, 0.5 mM spermidine) adjusted with high-salt buffer (20 mM Tris-HCl at pH 7.65, 25 % glycerol, 1.5 mM MgCl2, 0.2 mM EDTA, 900 mM NaCl) to get a final NaCl concentration of 300 mM. The nuclear-soluble fraction was recovered by centrifugation at 4°C. The pellet containing chromatin fraction was incubated in sucrose buffer containing 1mM CaCl2, and MNase (2.5U/g of cells) 10 min at 37°C. Digestion was stopped with 4 mM EDTA and mononucleosomes were recovered by centrifugation at 4°C. Tagged nucleosomes were immunoprecipitated with anti-Flag M2-agarose (Sigma), eluted with Flag peptide (0.5 mg/mL), further affinity-purified with anti-HA antibody-conjugated agarose, and eluted with HA peptide (1 mg/mL). The HA and Flag peptides were first buffered with 50 mM Tris-Cl (pH 8.5), then diluted to 4 mg/mL in TGEN 150 buffer (20 mM Tris at pH 7.65, 150 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, 10% glycerol, 0 0.01% NP40), and stored at −20°C until use. Between each step, beads were washed in TGEN 150 buffer. Nucleosomes were submitted to RNase and proteinase K digestion, and DNA was extracted by phenolchloroform.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

value: C57BL/6 and 129S mixed

value: Conditional FH-H3.3B knock-in H3.3b fl/fl

value: E13.5 embryos


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A10_ad006


title: DL1IL18pos_1_15

value: 6-8 weeks


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A11_ad001


title: EPS_rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A10_ad002


title: LungOP9Il18negP8_3


title: DL1IL18neg_2_14

description: library of cultured Il18r1+Icos+ ILCs on OP9-DL1 with IL2/IL7/IL1b/IL23


title: Input_DIP_MEFs


title: FH_H3.3_MEFs

value: Double-immunoaffinity purification of native FLAG-HA tagged mononucleosomes


title: HUES8_rep2

source_name: embryonic stem cell

value: embryonic stem cell


title: DL1IL8neg_1_13

description: library of cultured Il18r1+Icos+ ILCs on OP9 -DL1with IL2/IL7/IL1b/IL23


title: HUES8_rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad001


title: OP9IL18pos_2_12

description: library of cultured Il18r1+Icos+ ILCs on OP9 with IL2/IL7/IL1b/IL23/IL18


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad012


title: Z1767_M9_Rep1

city: Edinburgh

first: Stephen

last: Fitzgerald

state: United Kingdom

address: Roslin Institute, University of Edinburgh, Easter Bush

country: United Kingdom

data_processing:
Prior to read mapping the reference strain 9000 was re-orientated to start at the origin of replicaiton OriC and re-annotated using Prodigal version 2.6. The loci of previously identified E. coli O157 sRNA (Tree et al, (2014) Mol. Cell) were found in strain 9000 using BLASTn and manually added to strain 9000_and_srna.gtf file.
RNA-sequencing reads were mapped to the strain 9000 reference genome using STAR version 2.7.0e with the following parameters (--quantMode GeneCounts and --sjdbGTFfeatureExon CDS)
Differential expressed (DE) genes were identified with edgeR (p-values =0.05) using the glmQLFit  +  glmQLFTest parameters.
Genome_build: CP018252.1; BioProject:PRJNA336330; BioSample:SAMN05544760
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample 1 - 24

organism: Escherichia coli O157

source_name: Bacteria

growth_protocol: 25 ml of LB or M9 media was inoculated with a single colony of each strain. Cultures were grown to OD600 = 0.7 and 17 ml (normalised to OD600 = 12) were harvested by centrifugation (4000rpm, 5 min). Harvested cells were washed with 1 ml of PBS and total RNA was extracted using mirVana™ microRNA extraction kit

extract_protocol:
Total RNA was extracted using a mirVana™ microRNA extraction kit
Total RNA samples were purified and concentrated using the Agencourt RNAClean XP kit (Beckman-Coulter). Ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). The ribodepleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C) and oligonucleotide adapters were then ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high-fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. Purified cDNA was pooled and sequenced on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: Strains were cultured in LB or M9 media to an OD600 = 0.7

tag: genotype

value: 1.2 Mbp inversion relative to 9000

tag: media


title: OP9IL18pos_1_11


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad010


title: Z1723_M9_Rep3

institute: Roslin Institute, University of Edinburgh

value: 220 kbp inverted duplication relative to 9000


title: OP9IL18neg_2_10

description: library of cultured Il18r1+Icos+ ILCs on OP9 with IL2/IL7/IL1b/IL23


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_RU486-treated_ZT12_Replicate-1

city: MILL VALLEY

first: Brian

middle: A

last: Hodge

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

description:
DR_CLK-DN1_ZT12_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_DR-cnt_vs_DR-CLK-DN1.txt

data_processing:
Trimming of Illumina specific adaptor sequences: Raw fastq reads were filtered by the Trimmomatic software (Trimmomatic-0.36) to remove Illumina-specific adapter sequences and the minimal length was set to 36 (MINLEN) for trimming sequences.
Read alignment: The paired-end filtered reads were aligned to the D. melanogaster dm6 genome (BDGP Release 6 + ISO1 MT/dm6) by HISAT2 to generate BAM files with the specific strand information set to “Reverse” (RF).
Generation of count files: Count files were generated by featureCounts and D. melanogaster reference refGene was utilized as the gene annotation file with specific strand information set to “stranded (Reverse)”.
Differential Expression Analyses: Count files (tabular format) were analyzed with DESEQ2 with fit type set to “local” and pvalues of less than 0.05 were considered differentially expressed between factor levels.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: DESeq2 output files (tabular) with annotation and normalized count reads. DESeq2 outputs include: mean normalized counts, averaged over all samples from both conditions; the logarithm (to basis 2) of the fold change; standard error estimate for the log2 fold change estimate; Wald statistic; p value for the statistical significance of this change; p value adjusted for multiple testing with the Benjamini-Hochberg procedure which controls false discovery rate (FDR), and normalized count reads from each sample.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on DR-diet for seven days (RU486 treated), collected at ZT12

growth_protocol: nCLK-Δ1 (Elav-GS-GAL4>UAS- nCLK-Δ1) adult flies were developed on standard stock food (1.5% yeast-extract) for four days.

extract_protocol:
Flies were flash frozen on dry-ice at ZT 0 and ZT 12 (lights-on and -off, respectively). Frozen flies were vortexed to collected heads and mRNA from each biological replicated of pooled heads were isolated with the Quick-RNA MiniPrep Kit (Zymo Research #11-328), per manufacturer's protocols.
Library preparation was performed by the Functional Genomics Laboratory (FGL), a QB3-Berkeley Core Research Facility at University of California, Berkeley. cDNA libraries were produced from the low-input RNA using the Takara SMART-Seq v4 Ultra-low input RNA kit. An S220 Focused-Ultrasonicator (Covaris®) was used to fragment the DNA, and library preparation was performed using the KAPA hyper prep kit for DNA (KK8504). Truncated universal stub adapters were used for ligation, and indexed primers were used during PCR amplification to complete the adapters and to enrich the libraries for adapter-ligated fragments. Samples were checked for quality on an AATI (now Agilent) Fragment Analyzer. Samples were then transferred to the Vincent J. Coates Genomics Sequencing Laboratory (GSL), another QB3-Berkeley Core Research Facility at UC Berkeley, where Illumina sequencing library molarity was measured with quantitative PCR with the Kapa Biosystems Illumina Quant qPCR Kits on a BioRad CFX Connect thermal cycler. Libraries were then pooled evenly by molarity and sequenced on an Illumina NovaSeq6000 150PE S4 flowcell, generating 25M read pairs per sample. Raw sequencing data was converted into fastq format, sample specific files using the Illumina bcl2fastq2 software on the sequencing centers local linux server system.

treatment_protocol: Three independent biological replicates of 100 mated female flies were reared on AL or DR diets treated with RU486 or vehicle control at 25±1 °C, under a light-dark (LD) 12:12h regimen for seven days. Diets were changed every 2 days until the seventh day.

value: heads

value: Elav-GS-GAL4>UAS-CLK-DN1 (BDSC:36318)

value: Female

tag: diet

value: Dietary restriction (0.5% yeast-extract)

tag: vehicle or ru486

value: RU486 treated (200µM)

tag: time of collection

value: ZT 12 (8:00pm, lights off)


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_RU486-treated_ZT12_Replicate-3

description:
DR_CLK-DN1_ZT12_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_DR-cnt_vs_DR-CLK-DN1.txt

tag: Sex


title: OP9IL18neg_1_9

tag: strain


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_RU486-treated_ZT12_Replicate-2

description:
DR_CLK-DN1_ZT12_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_DR-cnt_vs_DR-CLK-DN1.txt


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad004

tag: brain region

value: CA

value: male


title: Z1723_M9_Rep2


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_Vehcle-treated_control_ZT12_Replicate-3

description:
DR_cnt_ZT12_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus vehicle for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_DR-cnt.txt
ZT12_DR-cnt_vs_DR-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on DR-diet for seven days (vehicle treated), collected at ZT12

value: Vehicle treated


title: Z1723_M9_Rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad006


title: LDL1IL18pos_2

value: Lung


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad002


title: Z1767_M9_Rep2


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_Vehcle-treated_control_ZT12_Replicate-1

description:
DR_cnt_ZT12_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus vehicle for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_DR-cnt.txt
ZT12_DR-cnt_vs_DR-CLK-DN1.txt


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_Vehcle-treated_control_ZT12_Replicate-2

description:
DR_cnt_ZT12_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus vehicle for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_DR-cnt.txt
ZT12_DR-cnt_vs_DR-CLK-DN1.txt


title: Z1615_M9_Rep3

value: 1.4 Mbp inversion relative to 9000


title: LDL1IL18pos_1


title: Z1767_M9_Rep3


title: Z1615_M9_Rep2


title: LDL1IL18neg_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_A1_ad008


title: LOP9IL18pos_2


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_RU486-treated_ZT12_Replicate-2

description:
AL_CLK-DN1_ZT12_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_AL-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on AL-diet for seven days (RU486 treated), collected at ZT12

value: Ad libitum (5% yeast-extract)


title: 9000_M9_ Rep3

value: Wildtype


title: LDL1IL18neg_1

value: 6-8 weeks


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_RU486-treated_ZT12_Replicate-3

description:
AL_CLK-DN1_ZT12_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_AL-CLK-DN1.txt


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_RU486-treated_ZT12_Replicate-1

description:
AL_CLK-DN1_ZT12_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_AL-CLK-DN1.txt


title: TG20_S20_L002_

city: Loughborough

first: Kin-Chow

last: Chang

state: Select State

address: College Street,, Sutton Bonington

department: School of Veterinary Medicine and Science

institute: University of Nottingham

data_processing:
Reads trimmed using skewer (version 0.2.2)
Alignment of reads and transcript abundance (output as transcripts per million) calculated using Kallisto (version 0.43.0)
Differential expression determined using Sleuth (version 0.28.1) in R (version 3.4.4)
Genome_build: GRCh38.p12 supplemented with OFL_ISL_21018
Supplementary_files_format_and_content: H5 files contain TPM values for each Sample

source_name: H1N1 TG donor 2 rep 2

extract_protocol: Preparation of Illumina libraries  TruSeq Stranded Total RNA libraries were generated from 18s rRNA depleted total RNA and sequenced using a HiSeq 3000 System at the SCIF Next Generation Sequencing Facility (University of Leeds, UK)

tag: agent

value: H1N1 TG

tag: cell type

value: Bronchial epithelial cells (BECs)


title: TG19_S19_L002_

source_name: H1N1 TG donor 2 rep1


title: Z1615_M9_Rep1


title: TG18_S18_L002_

source_name: H1N1 TG donor 1 rep2


title: LOP9IL18neg_2

tag: tissue


title: 9000_M9_ Rep2


title: TG17_S17_L002

source_name: H1N1 TG donor 1 rep1


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_Vehcle-treated_control_ZT12_Replicate-3

description:
AL_cnt_ZT12_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus vehicle for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_DR-cnt.txt
ZT12_AL-cnt_vs_AL-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on AL-diet for seven days (vehicle treated), collected at ZT12


title: DM16_S16_L002_

source_name: H1N1 DMSO donor 2 rep 2

value: H1N1 DMSO


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_Vehcle-treated_control_ZT12_Replicate-2

description:
AL_cnt_ZT12_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus vehicle for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_DR-cnt.txt
ZT12_AL-cnt_vs_AL-CLK-DN1.txt

value: heads


title: Z1767_LB_Rep3

value: 1.2 Mbp inversion relative to 9000

value: LB


title: LOP9IL18pos_1

source_name: Lung


title: DM15_S15_L002_

source_name: H1N1 DMSO donor 2 rep1


title: Z1767_LB_Rep2


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_RU486-treated_ZT0_Replicate-3

description:
DR_CLK-DN1_ZT0_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_DR-cnt_vs_DR-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on DR-diet for seven days (RU486 treated), collected at ZT0

value: Elav-GS-GAL4>UAS-CLK-DN1 (BDSC:36318)

value: Female

value: Dietary restriction (0.5% yeast-extract)

value: ZT 0 (8:00am, lights on)


title: LOP9IL18neg_1


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_Vehcle-treated_control_ZT12_Replicate-1

description:
AL_cnt_ZT12_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus vehicle for seven days and collected at ZT 12. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT12_AL-cnt_vs_DR-cnt.txt
ZT12_AL-cnt_vs_AL-CLK-DN1.txt

value: ZT 12 (8:00pm, lights off)


title: DM14_S14_L002_

source_name: H1N1 DMSO donor 1 rep2


title: Z1767_LB_Rep1


title: Progenit_3

description: library of I18r1+Icos+ST2-Il17rb- ILCs


title: DM13_S13_L002_

source_name: H1N1 DMSO donor 1 rep1


title: 9000_M9_ Rep1


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_RU486-treated_ZT0_Replicate-2

description:
DR_CLK-DN1_ZT0_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_DR-cnt_vs_DR-CLK-DN1.txt

value: RU486 treated (200µM)


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_RU486-treated_ZT0_Replicate-1

description:
DR_CLK-DN1_ZT0_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_DR-cnt_vs_DR-CLK-DN1.txt


title: Z1723_LB_Rep2

value: 220 kbp inverted duplication relative to 9000


title: Z1723_LB_Rep3


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_Vehcle-treated_control_ZT0_Replicate-3

description:
DR_cnt_ZT0_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus vehicle for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_DR-cnt.txt
ZT0_DR-cnt_vs_DR-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on DR-diet for seven days (vehicle treated), collected at ZT0

value: Vehicle treated


title: Progenit_1

description: library of I18r1+Icos+ST2-Il17rb- ILCs

value: Lung


title: TG7_S7_L001 _

source_name: Uninfected TG donor 2 rep1

value: Uninfected TG


title: Z1723_LB_Rep1

source_name: Bacteria


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_Vehcle-treated_control_ZT0_Replicate-2

description:
DR_cnt_ZT0_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus vehicle for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_DR-cnt.txt
ZT0_DR-cnt_vs_DR-CLK-DN1.txt


title: Z1615_LB_Rep3

value: 1.4 Mbp inversion relative to 9000


title: TG6_S6_L001_

source_name: Uninfected TG donor 1 rep2


title: BMILCPP9_4

description: library of Lin-Il18r1+Icos+/Lin-Icos+/Lin-Il18r1+ mouse2

source_name: BM

value: BM

value: 6-8 weeks


title: BMILCPP9_3


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_DR-diet_Vehcle-treated_control_ZT0_Replicate-1

description:
DR_cnt_ZT0_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on DR (0.55% yeast-extract) diet plus vehicle for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_DR-cnt.txt
ZT0_DR-cnt_vs_DR-CLK-DN1.txt


title: TG5_S5_L001_

source_name: Uninfected TG donor 1 rep1

value: Bronchial epithelial cells (BECs)


title: BMILCPP9_2


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_RU486-treated_ZT0_Replicate-3

description:
AL_CLK-DN1_ZT0_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_AL-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on AL-diet for seven days (RU486 treated), collected at ZT0

value: heads

value: Ad libitum (5% yeast-extract)


title: DM4_S4_L001_

source_name: Uninfected DMSO donor 2 rep 2

value: Uninfected DMSO


title: BMILCPP9_1


title: Z1615_LB_Rep1

value: LB


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_RU486-treated_ZT0_Replicate-2

description:
AL_CLK-DN1_ZT0_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_AL-CLK-DN1.txt

value: Elav-GS-GAL4>UAS-CLK-DN1 (BDSC:36318)

value: Female


title: DM3_S3_L001_

source_name: Uninfected DMSO donor 2 rep1


title: TG8_S8_L001_

source_name: Uninfected TG donor 2 rep 2


title: 9000_LB_ Rep3

value: Wildtype


title: Progenit_2

description: library of I18r1+Icos+ST2-Il17rb- ILCs


title: BMILCPP8_3

description: library of Lin-Il18r1+Icos+/Lin-Icos+/Lin-Il18r1+ mouse1


title: 9000_LB_ Rep2


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_RU486-treated_ZT0_Replicate-1

description:
AL_CLK-DN1_ZT0_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus RU486 (200µM) for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_AL-CLK-DN1.txt

value: ZT 0 (8:00am, lights on)


title: DM2_S2_L001_

source_name: Uninfected DMSO donor 1 rep2


title: DM1_S1_L001_

source_name: Uninfected DMSO donor 1 rep1


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_Vehcle-treated_control_ZT0_Replicate-3

description:
AL_cnt_ZT0_R3
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus vehicle for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the third of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_DR-cnt.txt
ZT0_AL-cnt_vs_AL-CLK-DN1.txt

source_name: 100 female heads from Elav-GS-GAL4>UAS-CLK-DN1 flies reared on AL-diet for seven days (vehicle treated), collected at ZT0


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_Vehcle-treated_control_ZT0_Replicate-2

description:
AL_cnt_ZT0_R2
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus vehicle for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the second of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_DR-cnt.txt
ZT0_AL-cnt_vs_AL-CLK-DN1.txt


title: BMILCPP8_4

description: library of Lin-IL18r1+Icos+/Lin-Icos+/Lin-Il18r1+ mouse1


title: C2C12-Msx1-3

city: Shanghai

first: Gang

last: Wang

address: 2005 Songhu Rd

department: School of life sciences

institute: Fudan university

data_processing:
The RNA-Seq FASTQ raw data were trimmed to remove low-quality reads and adapters using Trimmomatic. The trimmed reads were aligned to the mouse reference genome UCSC GRCm38/mm10 with HISAT2.
Gene and transcript quantification was performed using StringTie. The results of the mapping of the RNA-seq reads, transcript assembly and abundance estimation were reported as fragments per kilobase of exon per million fragments mapped (FPKM).
To identify genes that were differentially expressed, the fold changes of each gene were calculated by dividing the average FPKM for the case by the average FPKM for the control. To avoid infinite values, a value of 0.01 was added to the FPKM value of each gene before log2 transformation.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix text file include FPKM values for each Sample.

source_name: Myoblasts

extract_protocol:
RNA was harvested using Trizol reagent. cDNA sequencing libraries were prepared with an NEBNext® Ultra™ RNA Library Prep Kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Myoblasts

value: Msx1 overexpression


title: 9000_LB_ Rep1


title: BMILCPP8_2


title: Z1615_LB_Rep2


title: HHZ_root_rep3

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Read quality was checked using FastQC.
Adaptor and low quality reads of raw sequencing reads were trimmed using trim_galore. Adaptor of read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Adaptor of read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Cleaned reads were mapped to the rice reference genome (Os-Nipponbare-Reference-IRGSP-1.0) using STAR 2.5.3a with "--quantMode GeneCounts" option to report the read counts per gene.
Differentially expressed genes were determined using DESeq2 with read counts per gene as input.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene for each sample

organism: Oryza sativa

source_name: root of HHZ

growth_protocol: Two elite rice cultivars HHZ and 9311 were used for experiments. Dormancy of seeds was broken by incubation at 50 °C for 2 days. Germination was initiated in petri dishes with distilled water at 30 °C under dark for 4 days. The germinated seeds were transferred to mesh trays floating in culture solution in the growth chamber, with 96 plants per 1.4-l container. Seedlings were then transferred to the greenhouse at 10 days after germination (DAG), with 3 plants per 500-ml container. At 25 DAG, plants were transferred to 2-l containers, with 2 plants per container. Individual plants were arranged in 2-cm diameter holes drilled into container lids and fixed using sponge material wrapped around the stem. Temperature in the greenhouse was set to 27 °C, and the relative humidity was 60% -70%. Light was provided from 7 a.m. to 7 p.m., and the photon flux density (PFD) was about 400 μmol photons m-2 s-1. The culture solution was refreshed every 5 days. The composition of the culture solution was adapted from IRRI (International Rice Research Institute)’s protocol with 1 mmol L-1 NH4NO3, 0.6 mmol L-1 NaH2PO4·2H2O, 0.3 mmol L-1 K2SO4, 0.3 mmol L-1 CaCl2, 0.6 mmol L-1 MgCl2·6H2O, 50 μmol L-1 FeNaEDTA·3H2O, 50 μmol L-1 H3BO3, 9 μmol L-1 MnSO4·H2O, 0.3 μmol L-1 CuSO4·5H2O, 0.7 μmol L-1 ZnSO4·7H2O, 0.1 μmol L-1 Na2MoO4·2H2O, 7 μmol L-1 DCD-C2H4N4. The pH of the solution was 5.8-6.2.

extract_protocol:
At 50 days after germination (DAG), plants were transferred to NH4NO3-free solution for 2 days. Then, plants were transferred back to normal culture solution (containing 1 mM NH4NO3) for 3 hours. Then roots were sampled and frozen in liquid nitrogen immediately. Three replications were used. We used the PureLink RNA Mini Kit (Life Technologies Corporation) for RNA extraction from roots. To do this, we firstly grinded the root sample with liquid nitrogen, then followed the manufacture’s protocol for RNA extraction.
RNA libraries were prepared for sequencing based on standard Illumina protocols.

tag: growing stage

value: 50 days after germination

value: root

tag: cultivar

value: HHZ


title: BMILCPP8_1


title: D.Melanogaster_Elav-GS-Gal4>UAS-CLK-DN1_female_heads_AL-diet_Vehcle-treated_control_ZT0_Replicate-1

description:
AL_cnt_ZT0_R1
This sample is from mated females of the F1 generation from crossing the inducible pan-neuronal driver line, Elav-gene-switch-GAL4, and the UAS controlled dominant-negative clock protein (UAS-CLK-DN1, BDSC:36318). These flies were reared on AL (5% yeast-extract) diet plus vehicle for seven days and collected at ZT 0. RNA was extracted and pooled heads from approximately 100 flies. This sample is the first of three biological replicates.
nCLK-DN1-RNA-Seq_normalized_counts.txt
ZT0_AL-cnt_vs_DR-cnt.txt
ZT0_AL-cnt_vs_AL-CLK-DN1.txt

value: Vehicle treated


title: C2C12-Msx1-2


title: HHZ_root_rep2


title: HHZ_root_rep1


title: Stage 5 rRNA, COX2, COX3 deplete, 45ºC

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description:
xl_tpm.tsv
st5_rrna_cox_45

data_processing:
Reads were mapped to the X. laevis v9.2 or GRCz11 (zebrafish) genomes using HISAT2 v2.0.5 (--no-mixed --no-discordant)
Mapped reads were assigned to genes (Xenbase v9.2 models for X. laevis and Ensembl r99 for zebrafish) using featureCounts v1.5.1 in reversely-stranded paired-end mode with default parameters.
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: X. laevis v9.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited transcripts per million (TPM) per gene

organism: Xenopus laevis

source_name: Whole embryos

extract_protocol:
For X. laevis, 2 embryos were pooled for RNA extraction; for D. rerio, 20 embryos or 10 fin clips were pooled. Samples were snap frozen in a 1.5ul tube and homogenized with a pestle in 500ul of TRIzol Reagent (Invitrogen #15596026) followed by 100ul of chloroform. Tubes were spun at 18,000 x g at 4C for 15 minutes, the aqueous phase was transferred to a fresh tube with 340 ul of isopropanol and 1 ul of GlycoBlue (Invitrogen #AM9515), then precipitated at -80C for 1 hour. Precipitated RNA was washed with cold 75% ethanol and resuspended in 50ul of nuclease-free water. Concentration was determined by NanoDrop. RNA was stored at -80C until use.
For rRNA depletion, 1ul of antisense nuclear rRNA oligos (final concentration 0.4 uM per oligo) and 1ul of antisense mitochondrial rRNA (plus any other targeted gene) oligos (final concentration 0.1 uM per oligo) were combined with 1ug of total RNA in a 10ul buffered reaction volume (100mM Tris-HCl  pH 7.4, 200mM NaCl, 10mM DTT), heated at 95C for 2 minutes and cooled to 22C at a rate of 0.1C/s in a thermocycler. Next, 10U of thermostable RNaseH (NEB #M0523S) and 2uL of provided 10X RNaseH buffer were added and volume brought to 20uL with nuclease-free water. The reaction was incubated at 65C for 5 minutes (standard) or 45C for 30 minutes, then 5U of TURBO DNase (Invitrogen #AM2238) and 5uL of provided 10x buffer was added, volume brought to 50uL with nuclease-free water and incubated at 37C for 30 minutes. The reaction was purified and size selected to >200 nts using Zymo Clean and Concentrator-5 (Zymo #D4013) according to manufacturer’s protocol, eluting in 10uL of nuclease-free water. For poly(A) selection, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L) was used according to the manufacturer’s protocol: 1 ug of total RNA was denatured at 65C for 5 minutes then hybridized to buffered dT magnetic beads at room temperature for 2 minutes. Selected RNA was eluted in 50uL of Tris buffer at 80C for 2 minutes and rehybridized to the same beads for a second round of selection at room temperature for 2 minutes. Re-selected RNA was eluted in a final volume of 17 uL of Tris buffer. Strand-specific RNA-seq libraries were constructed using NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with fragmentation in first-strand buffer at 94C for 15 minutes. Following first and second strand synthesis, DNA was purified with 1.8X AmpureXP beads (Beckman #A63880), end repaired, then ligated to sequencing adaptors diluted 1:5. Ligated DNA was purified with 0.9X AmpureXP beads and PCR amplified for 8 cycles, then purified again with 0.9X AmpureXP beads. Libraries were verified by Qubit dsDNA high sensitivity (Invitrogen #Q32851) and Fragment Analyzer prior to multiplexed sequencing (paired end 38/37bp) on an Illumina NextSeq 500 at the Health Sciences Sequencing Core at Children's Hospital of Pittsburgh.

tag: developmental stage

tag: processing

value: rRNA depleted, COX2 and COX3 depleted


title: Progenit_4

description: library of I18r1+Icos+ST2-Il17rb- ILCs

source_name: Lung

value: Lung

tag: age

value: 6-8 weeks


title: NeoP8_3

description: library of 96 ST2+ILC and ST2- ILCs

value: postnatal day 4


title: C2C12-Ctrl-3

tag: genotype

value: control


title: NeoP8_2

description: library of 96 ST2+ILC and ST2- ILCs


title: 9311_root_rep3

source_name: root of 9311


title: 9311_root_rep2


title: C2C12-Ctrl-2


title: Stage 5 untreated

description:
xl_tpm.tsv
st5_untreat


title: NeoP8_1

description: library of 96 ST2+ILC and ST2- ILCs


title: C2C12-Ctrl-1


title: ep107_chem_rep

city: Ulsan

first: jaewon

last: lim

address: 50, UNIST-gil

country: South Korea

institute: ulsan national institute of science and technology

data_processing:
Sequencing: PacBio RS II
Mapping: Sequence reads generated from RNA-seq were mapped onto the reference genome (QHHM00000000) using bowtie with the maximum insert size of 1000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM: SAM files generated from bowtie.
Cufflinks: run Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM) with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: Genome build: reference genome (GenBank Accession: QHHM00000000)
Supplementary_files_format_and_content: tab-seperated text files include various values for each sample(The column name is shown on the first line)

organism: Lacticaseibacillus paracasei

source_name: bacteria

extract_protocol:
Total RNA from culture cells was extracted using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s recommended protocol.
The reaction was carried out with the 1st cDNA synthesis kit (Takara, Japan). The primer sequences were obtained from Takara (Japan).

tag: growth condition

value: with fermentation


title: HCT116_SB_NicE-seq

data_processing:
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Sequenced reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program, then mapped to human (hg38) reference genome using bwameth
Duplicated reads were then removed using samblaster
cytosine methylation was called using methyldackel
genome build: human: hg38
processed data files format and content: tab-delimited files with genomic coordinate, seuqence context and methylation information of each cytosine sites
Library strategy: Single-base NicE-seq

source_name: cell line

extract_protocol:
1 ug of genomic DNA was sheared by the standard sonication conditions of UniNicE-seq, pull downed by streptavidin C1 bead, followed the end-repair reaction, adaptor (methylated ) ligation reaction for O/N or 2 hr
Finally, EM-seq conversion reaction followed as suggested by EM-seq manufacturer (NEB, E7120). The library DNAs were amplified by 11 PCR cylces.

value: Colon

value: Colorectal cancer cells

tag: experimental variables

value: 5mC, EM-seq


title: ep107_nochem_rep

value: without fermentation


title: C2C12-Msx1-1


title: NeoP8_4

description: library of 96 ST2+ILC and ST2- ILCs


title: dmd mutant with NMES replicate #10

status: Public on Oct 01 2020

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Read quality control diagnostic analyses using FastQC version 0.11.8.
Reads were trimmed using Trimmomatic version 0.38.0.
Trimmed paired-end reads mapped to the Ensembl-annotated zebrafish transcriptome (Ensembl version 95) to generate read counts per gene using RSEM version 1.2.31 with bowtie version 1.1.2.
Analysis of differentially expressed Ensembl-annotated genes using DESeq2 version 1.22.2
Genome_build: GRCz11
Supplementary_files_format_and_content: RSEM output file

organism: Danio rerio

source_name: whole larvae

growth_protocol: Embryos collected from spawns of sapje^ta222a (dmd) mutant zebrafish were grown in embryo rearing media with methylene blue at 28.5 degrees Celsius. Embryos were manually dechorionated at 1 dpf and fed once daily beginning at 5 dpf

extract_protocol:
Zymo Direct-zol RNA microprep kit.
KAPA Stranded mRNA-Seq poly-A selected kit with 200-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input.

treatment_protocol: Neuromuscular electrical stimultation (NMES) or no NMES at 2, 3 and 4 days post fertilization.

value: dmd

tag: treatment

value: NMES


title: dmd mutant without NMES replicate #8


title: sibling with NMES replicate #2

value: sibling


title: dmd mutant without NMES replicate #7


title: sibling without NMES replicate #1


title: sibling with NMES replicate #3


title: sibling without NMES replicate #4


title: sibling with NMES replicate #1


title: sibling without NMES replicate #3


title: dmd mutant with NMES replicate #8


title: dmd mutant with NMES replicate #9


title: dmd mutant with NMES replicate #7


title: dmd mutant without NMES replicate #4


title: dmd mutant without NMES replicate #5


title: dmd mutant without NMES replicate #6


title: dmd mutant with NMES replicate #6


title: dmd mutant with NMES replicate #4


title: 9311_root_rep1

value: 50 days after germination


title: dmd mutant without NMES replicate #3


title: dmd mutant with NMES replicate #5


title: dmd mutant without NMES replicate #2


title: dmd mutant without NMES replicate #1


title: dmd mutant with NMES replicate #3


title: XXY63_3

city: Xinyang

first: Qingsong

last: Liu

state: Henan

address: No. 237, Nanhu road

institute: Xinyang Normal University

data_processing:
For transcriptome data, raw Illumina data of fastq format were first processed using in-house perl scripts. After removing reads containing adaptors, reads containing poly-N and low-quality reads from raw data, we obtained the clean data. The Q20, Q30, GC (guanine-cytosine)-content and sequence duplication level of the clean data were calculated. The clean reads were aligned to the reference genome IRGSP-1.0 (https://rapdb.dna.affrc.go.jp)using HISAT2 tools (version 2.09)
Feature Counts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated using fragments per kilobase of transcript per million mapped reads (FPKM) based on the length of the gene and reads count mapped to this gene. Differentially expressed genes analysis was performed using the DESeq2 R package.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each sample.

source_name: rice plant leaves

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and treated with RNase-free DNase I (NEB, USA) to remove any genomic DNA.
A total amount of 3 µg of total RNA per sample was used for the preparation of RNA-seq library. Sequencing libraries were prepared using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: During the rice plants tillering stage, leaf samples were collected for the analyses. From each plant, a leaf section (approximately 2 cm) was sampled from the middle part of 2nd leaf blade from top. Samples from five plants were pooled together as one biological replicate, and three replicates were collected for each rice line.

tag: line

tag: method

value: conventional cross-breeding

value: leaves

value: five weeks


title: sibling without NMES replicate #2


title: dmd mutant with NMES replicate #1


title: XXY63_2


title: XXY63_1


title: XS11_3


title: XIY63_2


title: T202_2


title: T1C-19_1

value: GE


title: XIY63_1


title: T1C-19_3


title: KMD2_2


title: MH63_1


title: KMD2_1


title: XS11_1


title: SY63_2


title: T202_1


title: SY63_1


title: KMD1_1


title: T202_3


title: JY63_3


title: SY63_3


title: JY63_1


title: JY63_2


title: XIY63_3


title: dmd mutant with NMES replicate #2


title: T1C-19_2


title: JH1_2


title: MH63_2


title: XS11_2


title: KMD1_3


title: KMD2_3


title: JH1_1


title: MH63_3


title: HH1_3


title: KMD1_2


title: HH1_1


title: JH1_3


title: CJ03_2


title: CJ03_3


title: HH1_2


title: CJ03_1


title: E02M_Fibroblast_P1

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Callithrix jacchus

source_name: Fibroblasts

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

value: Fibroblasts


title: E01F_A2_iNSLC_P11

source_name: Induced neural stem cell-like cells

value: Induced neural stem cell-like cells


title: I5386F_mA_2

growth_protocol: Fibroblasts were cultured in fibroblast medium consisting of DMEM supplemented with 10% inactivated FBS and 1% penicillin/streptomycin solution.

treatment_protocol: Fibroblasts transfected with the pPB-tetpA(hBCL2-miR9/9*-124)-iRPT and the TRE-ASCL1 lentivirus were used for neuronal conversion. First day of induction (PID 0), 1.0 × 10^5 cells were seeded on each well of a gelatin-coated 12-well plate (Iwaki) and fed with fibroblast medium containing 2 ug/mL doxycycline (Dox; Wako). On PID 2, cells were fed with fresh fibroblast medium containing Dox. On the PID 4, a 50 uL cell-drop consisted of fibroblast medium and 5.0 × 104 cells was added to each well of a poly-L-ornithine/laminin/fibronectin-coated plate, and fed with fibroblast medium after the cells attached. The following day (PID 5), the medium was switched to a neuronal reprogramming medium composed of a 1:1 mixture of Neurobasal Medium (Thermo Fisher) and DMEM/F-12 (Wako) supplemented with 1% N2 supplement (Thermo Fisher), 2% B27 supplement (Thermo Fisher), 1% non-essential amino acid solution (Sigma Aldrich), 1 mM L-glutamine (Nacalai tesque), 200 uM dbcAMP (Sigma Aldrich), 10 uM Forskolin, 10 uM Y-27632 (Wako), 3 uM CHIR99021 (Axon), 1 uM PD-0325901 (Wako), 0.5 uM A83-01 (Santa Cruz), 10 ng/mL recombinant human Leukemia inhibitory factor (Oriental Yeast), 1 mM valproic acid (Wako), 10 ng/mL Brain-derived neurotrophic factor (Peprotech), 10 ng/mL Glial cell line-derived neurotrophic factor (Peprotech), 10 ng/mL Neurotrophin-3 (Peprotech), 200 uM Ascorbic acid (Sigma Aldrich), 1 uM Retinoic acid (Sigma Aldrich), supplemented with Dox and penicillin/streptomycin. Medium was changed every four days.

value: Adult marmoset (I5386F)

value: Fibroblast-derived induced neurons


title: E02M_B0_7_iPS_P13

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: E95_GE_neurosphere

source_name: Embryo-derived neurospheres

value: Embryo-derived neurospheres


title: I5061F_B0_iNSLC_P1


title: CTXNS2_B1_iPS_P5


title: I5061F_B3_15_iPS_P10


title: I5061F_Fibroblast_P1


title: I5061F_B3_iNSLC_P5


title: E01F_Fibroblast_EPB_NSM_day6


title: CM421F_Fibroblast_P1


title: E01F_A2_2_iPS_P10


title: I5386F_Fibroblast


title: I5332F_mA_2

value: Adult marmoset (I5332F)


title: CTXNS1_B1_iPS_P7


title: I5332F_Fibroblast


title: I5332F_mA_1


title: I5386F_mA_1


title: E02M_mA_2

value: Embryonic marmoset (E02M)


title: I5061F_B3_3_iPS_P11


title: E01F_Fibroblast_EPB_NSM_day15


title: E02M_mA_1


title: E01F_mA_2

value: Embryonic marmoset (E01F)


title: E01F_mA_1


title: PA1359_3

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

description:
Adaptor-ligated sheared genomic DNA
DAPseq_7XRE.xlsx

data_processing:
Library strategy: DAP-seq
Read trimming using Trimmomatic.
Alignment using Bowtie2.
Peak calling using MACS2.
Closest features called with BEDtools.
Genome_build: PAO1
Supplementary_files_format_and_content: DAPseq_7XRE.xlsx: Excel table, MACS2 analysis results with closest features.

organism: Pseudomonas aeruginosa PAO1

source_name: Purified genomic DNA from liquid cultures

extract_protocol:
Purified proteins bound to magnetic beads were incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: protein


title: neg_3

value: Negative control


title: PA4499_2


title: PA5301_3


title: PA1884_3


title: PA0535_3


title: PA4987_2


title: PA1359_2


title: PA4987_1


title: neg_2


title: PA0535_2


title: PA1884_2


title: PA4499_1


title: PA4987_3


title: PA5301_2


title: PA2312_3


title: PA5301_1


title: PA1359_1


title: PA2312_2


title: neg_1


title: PA2312_1


title: PA0535_1


title: PA5301_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

data_processing:
Read trimming using Trimmomatic.
Alignment using Bowtie2.
Feature count using htseq-count.
Differential expression analysis using DESeq2.
Genome_build: PAO1
Supplementary_files_format_and_content: RNAseq_7XRE.xlsx: Excel table, DESeq2 analysis results.

source_name: LB liquid culture at OD=1

growth_protocol: LB liquid culture at OD=1.

extract_protocol:
Hot Phenol RNA Extraction.
RNA were treated with DNase I, then rRNA were depleted using the Invitrogen RiboMinus kit. Libraries were constructed using the NEBNext Ultra II Directional RNA lib prep kit from NEB.

tag: genotype/variation

value: PA5301 mutant


title: PA5301_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: PA4987_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: PA4987 mutant


title: PA4499_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: PA4499 mutant


title: PA4499_3


title: PA4987_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: PA1884_1


title: PA1884_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: PA1884 mutant


title: PA0535_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: PA0535 mutant


title: PA0535_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: PAO1_WT_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: WT


title: PAO1_WT_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: D3 - Mock #18 [11-18CT]

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
STAR v2.5.2b used for mapping and read qualtification
Reads were normalised using VST approach from DESeq2 package in R
Differential gene expression was calculated using DESeq2 in R
Genome_build: Meleagris gallopavo Turkey_5.1
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized (DESeq2) values for each Sample.

organism: Meleagris gallopavo

source_name: control_Day 3_CT

extract_protocol:
Tissue was preserved in RNALAter, flash frozen on in liquid notrogen, and total RNA was harvested using mirVana and Trizol reagents. Illumina HiSeq3000 RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: status

value: Control

tag: day

value: Day 3

value: Cecal tonsils (CT)


title: D3 - Mock #20 [11-20CT]

tag: tissue


title: D3 - Mock #11 [11-11CT]


title: PA1359_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: PA1359 mutant


title: D1 - Mock #5 [11-5CT]

source_name: control_Day 1_CT

value: Day 1


title: D3 - Mock #15 [11-15CT]


title: D3 - Mock #17 [11-17CT]


title: D1 - Mock #4 [11-4CT]


title: PA2312_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx

value: PA2312 mutant


title: D1 - Mock #8 [11-8CT]


title: D3 - CcK #20 [9-20CT]

source_name: CcK colonized_Day 3_CT

value: Treated; CcK colonized


title: PA2312_mut_2

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: D3 - Mock #19 [11-19CT]


title: D1 - Mock #1 [11-1CT]


title: D1 - Mock #3 [11-3CT]


title: D3 - CcK #19 [9-19CT]


title: D3 - Mock #16 [11-16CT]


title: D1 - Mock #2 [11-2CT]


title: PA1359_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: D1 - Mock #10 [11-10CT]


title: PA1884_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: D1 - Mock #7 [11-7CT]


title: PA4499_mut_1

description:
rRNA-depleted RNA
RNAseq_7XRE.xlsx


title: D3 - CcK #18 [9-18CT]


title: D3 - Mock #13 [11-13CT]


title: D3 - CcK #16 [9-16CT]


title: D3 - CcK #17 [9-17CT]


title: D3 - CcK #14 [9-14CT]


title: D3 - CcK #13 [9-13CT]


title: D3 - CcK #11 [9-11CT]


title: D1 - CcK #10 [9-10CT]

source_name: CcK colonized_Day 1_CT


title: D1 - CcK #7 [9-7CT]


title: D1 - CcK #9 [9-9CT]


title: D1 - CcK #6 [9-6CT]


title: D1 - CcK #1 [9-1CT]


title: D1 - CcK #4 [9-4CT]


title: D1 - CcK #3 [9-3CT]


title: D1 - CcK #2 [9-2CT]


title: PP_5241_3

city: Berkeley

first: Alexey

last: Kazakov

address: 1 Cyclotron Road

department: Environmental Genomics and Systems Biology Division

institute: Lawrence Berkeley National Laboratory

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_5241
PP_5241_3_S76_L002

data_processing:
library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie
Peak calling using SPP
Closest features were called using dap-seq-utils(https://github.com/novichkov-lab/dap-seq-utils)
Genome_build: GCF_000327065.1, GCF_001623525.1, GCF_000007565.2, GCF_001307275.1
Supplementary_files_format_and_content: wig

organism: Pseudomonas putida

source_name: purified genomic DNA from liquid cultures

growth_protocol: Pseudomonas strains were cultured in either LB or minimal media.

extract_protocol:
Genomic DNA was extracted with Promega wizard genomic kit according to the manufacturers protocols for gram negative bacteria. 6XHIS-tagged DNA-binding response regulator proteins were heterologously expressed in E. coli, purified with metal affinity resin, and mixed with 60 uL DNA binding buffer before elution. DNA binding buffer contained  0.4 ng/uL sheared adapter-ligated Pseudomonas genomic DNA, 10 mM imidazole, 0.1% Tween20 with or without 50 mM acetyl phosphate in TBS buffer pH 7.4. To enrich for specific protein-DNA interactions, resin bound protein-DNA was washed in a low concentration of imidazole before elution in a high concentration of imidazole. DNA was then amplified with index primers and sequenced with Illumina NovaSeq 6000.
DNA libraries were prepared for sequencing using a protocol from Chiniquy et al., BMC Genomics, 2020.

tag: strain

value: 50 mM acetyl phosphate


title: PP_input_1

description:
adaptor-ligated sheared genomic DNA
PP_input_1_S1_L002

value: untreated


title: PP_5320_2

description:
adaptor-ligated sheared genomic DNA bound by PP_5320
PP_5320_2_S87_L002


title: PP_5320_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_5320
PP_5320_4_S89_L002


title: PP_5320_1

description:
adaptor-ligated sheared genomic DNA bound by PP_5320
PP_5320_1_S86_L002


title: PP_5241_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_5241
PP_5241_4_S77_L002


title: PP_5320_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_5320
PP_5320_3_S88_L002


title: PP_input_2

description:
adaptor-ligated sheared genomic DNA
PP_input_2_S13_L002


title: PP_1651_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_1651
PP_1651_4_S53_L002


title: PP_3551_2

description:
adaptor-ligated sheared genomic DNA bound by PP_3551
PP_3551_2_S63_L002


title: PP_1651_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_1651
PP_1651_3_S52_L002


title: PP_1651_2

description:
adaptor-ligated sheared genomic DNA bound by PP_1651
PP_1651_2_S51_L002


title: PP_1651_1

description:
adaptor-ligated sheared genomic DNA bound by PP_1651
PP_1651_1_S50_L002


title: PP_1401_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_1401
PP_1401_3_S40_L002


title: PP_1401_2

description:
adaptor-ligated sheared genomic DNA bound by PP_1401
PP_1401_2_S39_L002


title: PP_1401_1

description:
adaptor-ligated sheared genomic DNA bound by PP_1401
PP_1401_1_S38_L002


title: PP_1066_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_1066
PP_1066_3_S28_L002


title: PP_1401_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_1401
PP_1401_4_S41_L002


title: PP_3551_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_3551
PP_3551_4_S65_L002


title: PP_1066_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_1066
PP_1066_4_S29_L002


title: PP_3551_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_3551
PP_3551_3_S64_L002


title: PP_5241_1

description:
adaptor-ligated sheared genomic DNA bound by PP_5241
PP_5241_1_S74_L002


title: PP_0534_2

description:
adaptor-ligated sheared genomic DNA bound by PP_0534
PP_0534_2_S15_L002


title: PP_1066_2

description:
adaptor-ligated sheared genomic DNA bound by PP_1066
PP_1066_2_S27_L002


title: PP_0534_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_0534
PP_0534_4_S17_L002


title: PP_0534_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_0534
PP_0534_3_S16_L002


title: PP_5241_2

description:
adaptor-ligated sheared genomic DNA bound by PP_5241
PP_5241_2_S75_L002


title: PP_3551_1

description:
adaptor-ligated sheared genomic DNA bound by PP_3551
PP_3551_1_S62_L002


title: Pf6N2E2_5565_1

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_5565
Pf6N2E2_5565_1_S54_L002

organism: Pseudomonas fluorescens


title: Pf6N2E2_5565_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_5565
Pf6N2E2_5565_3_S56_L002


title: PP_0263_1

description:
adaptor-ligated sheared genomic DNA bound by PP_0263
PP_0263_1_S2_L002


title: Pf6N2E2_5565_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_5565
Pf6N2E2_5565_4_S57_L002


title: PP_0263_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_0263
PP_0263_4_S5_L002


title: Pf6N2E2_5487_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_5487
Pf6N2E2_5487_4_S45_L002


title: Pf6N2E2_5565_2

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_5565
Pf6N2E2_5565_2_S55_L002


title: Pf6N2E2_5487_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_5487
Pf6N2E2_5487_3_S44_L002


title: Pf6N2E2_5487_1

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_5487
Pf6N2E2_5487_1_S42_L002


title: Pf6N2E2_5487_2

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_5487
Pf6N2E2_5487_2_S43_L002


title: PP_1066_1

description:
adaptor-ligated sheared genomic DNA bound by PP_1066
PP_1066_1_S26_L002


title: Pf6N2E2_4066_2

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_4066
Pf6N2E2_4066_2_S31_L002


title: Pf6N2E2_3883_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_3883
Pf6N2E2_3883_4_S21_L002


title: Pf6N2E2_4066_1

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_4066
Pf6N2E2_4066_1_S30_L002


title: Pf6N2E2_3883_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_3883
Pf6N2E2_3883_3_S20_L002


title: PP_0534_1

description:
adaptor-ligated sheared genomic DNA bound by PP_0534
PP_0534_1_S14_L002


title: Pf6N2E2_3883_2

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_3883
Pf6N2E2_3883_2_S19_L002


title: Pf6N2E2_1724_2

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_1724
Pf6N2E2_1724_2_S7_L002


title: Pf6N2E2_3883_1

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_3883
Pf6N2E2_3883_1_S18_L002


title: N2E2_input_1

description:
adaptor-ligated sheared genomic DNA
N2E2_input_1_S25_L002


title: N2E2_input_2

description:
adaptor-ligated sheared genomic DNA
N2E2_input_2_S37_L002


title: Pf6N2E2_1724_1

description:
adaptor-ligated sheared genomic DNA bound by Pf6N2E2_1724
Pf6N2E2_1724_1_S6_L002


title: Pf6N2E2_1724_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_1724
Pf6N2E2_1724_4_S9_L002


title: Pf6N2E2_1724_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_1724
Pf6N2E2_1724_3_S8_L002


title: PP_0263_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated PP_0263
PP_0263_3_S4_L002


title: PP_0263_2

description:
adaptor-ligated sheared genomic DNA bound by PP_0263
PP_0263_2_S3_L002


title: N2C3_input_2

description:
adaptor-ligated sheared genomic DNA
N2C3_input_2_S85_L002


title: AO356_25435_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_25435
AO356_25435_4_S96_L002


title: N2C3_input_1

description:
adaptor-ligated sheared genomic DNA
N2C3_input_1_S73_L002


title: AO356_25435_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_25435
AO356_25435_3_S72_L002


title: AO356_25435_2

description:
adaptor-ligated sheared genomic DNA bound by AO356_25435
AO356_25435_2_S71_L002


title: AO356_22615_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_22615
AO356_22615_4_S84_L002


title: AO356_25435_1

description:
adaptor-ligated sheared genomic DNA bound by AO356_25435
AO356_25435_1_S70_L002


title: AO356_22615_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_22615
AO356_22615_3_S60_L002


title: AO356_22615_2

description:
adaptor-ligated sheared genomic DNA bound by AO356_22615
AO356_22615_2_S59_L002


title: AO356_22615_1

description:
adaptor-ligated sheared genomic DNA bound by AO356_22615
AO356_22615_1_S58_L002


title: Pf6N2E2_4066_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_4066
Pf6N2E2_4066_4_S33_L002


title: Pf6N2E2_4066_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Pf6N2E2_4066
Pf6N2E2_4066_3_S32_L002


title: AO356_18205_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_18205
AO356_18205_3_S48_L002


title: AO356_18205_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_18205
AO356_18205_4_S95_L002


title: AO356_18205_2

description:
adaptor-ligated sheared genomic DNA bound by AO356_18205
AO356_18205_2_S47_L002


title: AO356_18205_1

description:
adaptor-ligated sheared genomic DNA bound by AO356_18205
AO356_18205_1_S46_L002


title: AO356_17800_1

description:
adaptor-ligated sheared genomic DNA bound by AO356_17800
AO356_17800_1_S34_L002


title: AO356_17800_2

description:
adaptor-ligated sheared genomic DNA bound by AO356_17800
AO356_17800_2_S35_L002


title: AO356_17800_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_17800
AO356_17800_3_S36_L002


title: AO356_11000_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_11000
AO356_11000_4_S94_L002


title: AO356_11000_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_11000
AO356_11000_3_S24_L002


title: AO356_11000_1

description:
adaptor-ligated sheared genomic DNA bound by AO356_11000
AO356_11000_1_S22_L002


title: AO356_10065_1

description:
adaptor-ligated sheared genomic DNA bound by AO356_10065
AO356_10065_1_S10_L002


title: AO356_10065_2

description:
adaptor-ligated sheared genomic DNA bound by AO356_10065
AO356_10065_2_S11_L002


title: AO356_11000_2

description:
adaptor-ligated sheared genomic DNA bound by AO356_11000
AO356_11000_2_S23_L002


title: AO356_10065_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_10065
AO356_10065_4_S82_L002


title: AO356_10065_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_10065
AO356_10065_3_S12_L002


title: 8_BT-12_M4_1

city: Houston

first: Filippo

last: Giancotti

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

data_processing:
RNA-seq reads were aligned to the human reference genome (hg19) using Tophat (v2.1.1; https://ccb.jhu.edu/software/tophat/index.shtml). gene models of Refgene were downloaded from the Illumina's iGenomes project (https://support.illumina.com/sequencing/sequencing_software/igenome.html). FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using cufflinks (v2.2.1; http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: hg19
Supplementary_files_format_and_content: Assembled FPKM values across all samples generated by CummeRbund R package with the gct format

growth_protocol: BT-12 cells are grown in DMEM plus 10% FBS.

extract_protocol:
Total RNA were extracted from cell lines using TRIzol (Invitrogen, USA).
Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to doublestrand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end,  then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.  Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to doublestrand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end,  then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.

tag: cell line

tag: cell type

value: Atypical teratoid/rhabdoid tumor (AT/RT) cell line

tag: primary tumor site

value: Posterior fossa

tag: passage

value: stable expression of SMARCB1


title: 6_BT-12_WT_2


title: 9_BT-12_M4_2


title: 7_BT-12_M4_0


title: 5_BT-12_WT_1


title: 2_BT-12_Vector_1

value: vector


title: 4_BT-12_WT_0


title: 1_BT-12_Vector_0


title: 3_BT-12_Vector_2


title: Brain_CK1

city: Guangzhou

first: shuibin

last: lin

state: Guangdong

address: Nonglin street

department: Center for Translational Medicine

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
SOAPnuke software used for filtering.
Sequenced reads mapped to mm10 whole genome using Bowtie2 to obtain the alignment results. Then RSEM was used to calculate gene and transcript expression levels.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

source_name: Brain

extract_protocol:
Brains were removed and RNA was harvested using Trizol reagent.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces and then cDNA was generated using random hexamer-primed reverse transcription and amplified by PCR for construction of sequencing libraries.

value: brain

tag: age

value: post natal day 28

value: wild type


title: Brain_KO1

tag: genotype


title: Brain_KO3


title: Brain_CK3


title: Brain_CK2