title: Khet_Eko2

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

data_processing:
Read Aligments: TopHat aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultra fast short read mapping program Bowtie 2.
Cufflinks assembles aligned RNA-Seq reads into transcripts, estimates their abundances, and tests for differential expression and regulation transcriptome-wide. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and gee count values for each sample

source_name: lung

growth_protocol: Lungs were minced and proteolytically digested with Dispase II (Corning) and 0.01 % DNase I (Sigma-Aldrich). After negative selection of immune cells via CD16/CD32 (BD Bioscience) coated dishes, remaining pneumocytes were cultured in F12 media (Gibco) supplemented with 2 % FBS, ITS supplements (Sigma-Aldrich), 0.8 mM CaCl2, 15 mM HEPES, 0.25 (w/v) % BSA and antibiotics. Purity of cell populations was verified by immunocytochemistry using antibodies against CC-10 and SPC (Santa Cruz).

extract_protocol:
RNA was isolated using Rneasy (QUIAGEN)
Stranded mRNA (Poly-A enrichment) library preparation

treatment_protocol: 72 hours post isolation cells were transduced with rAd.Cre at a MOI of 250. For the next three days, media was replaced daily wish fresh media, and cells were harvested 5 days following adenoviral transduction.

value: lung

value: alveolar type II cells

tag: strain

value: KRASG12D :EGFRdelta


title: Khet_Eko3

status: Public on Aug 29 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: Khet_Eko1


title: 109_3D

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

country: USA

institute: MGH Cancer Center

description: RNA-seq

data_processing:
SOLiD 5500 deep sequencer run (single, 50 nt) was performed with single index to generate color-space data in XSQ format.
XSQ files were subjected to generation of the color-space CSFASTA/QUAL read sequence files using Life Technologies XSQTools software package. The TopHat-Cufflinks pipeline with the Bowtie backend aligner was used to align the color space read data to the Xla_9.1 Xenpus reference gonome sequence to generate BAM files.
Cufflinks processed RNA-seq BAM files to generate normalized amounts of mRNA expression based on the Xla_9.1 annotation.
Genome_build: Xla_9.1 (Xenbase release 9.1)
Supplementary_files_format_and_content: Microsoft Excel xlsx spreadsheets including normalized relative intensity of mRNA expression
Supplementary_files_format_and_content: FPKM

organism: Xenopus laevis

source_name: X. lavis embryo (stage 10.5; pool of five embryos)

growth_protocol: Eggs from two clutches (labeled D and E) of female X. laevis were fertilized in vitro and embryos staged according to Nieuwkoop and Faber (1994).

extract_protocol:
Each dish was harvested at gastrula stage 10.5 in 5-embryo aliquots. Replicates were taken from two different clutches (D & E), and 5 replicates were analyzed within each clutch (10 replicates total). Each five embryo pool was homogenized in 200 μL of TriPure (Roche).  Total RNA was DNAse treated, LiCl precipitated, and 100 ng was reverse transcribed into cDNA using Ovation RNA Amplification System V2 (NuGEN).
Total RNA was subjected to cDNA synthesis using the Ovation RNA Amplification System V2 kit (NuGEN). Deep sequencing libraries were generated from the cDNA using the ABI SOLiD 5500 Fragment Library Core Kit (Life Technologies).

treatment_protocol: Stage 6-7 embryos were treated in groups of 25 in 60-mm glass Petri dishes with 10 mL of 0.1X MBS containing 1 μM RAR-selective agonist TTNPB, 1 μM RAR-selective inverse agonist (antagonist) AGN193109 or vehicle control (0.1% EtOH).

tag: exposure


title: Khet_3


title: Khet_2


title: Endothelial cells isolated from vehicle-treated ear, control mouse, replicate 5

type: RNA

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

description: Gene expression data of endothelial cells from mouse ears

hyb_protocol: Following fragmentation and terminal labeling, 5,5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Gene Chip Mouse Gene 2.1 ST array. GeneChips were washed and stained in the Affymetrix GeneCips fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan Multichannel instrument.

data_processing: RMA-normalised data were obtained using the Affymetrix Expression Console Software.

label: biotin

source_name: CD31+CD45-Ter119- endothelial cells, FACS-sorted from collagenase I-digested ears.

label_protocol: Biotinylated cRNA were prepared from 1ng total RNA and amplified according to manufacturers instructions, using the Affymetric GeneChip WT Pico kit.

growth_protocol: NICDiEC-OE mice with endothelial expression of constitutively active Notch1 were generated by combining RosaNICD/NICD with CDH5-iCre transgenics.

extract_protocol: RNA was extracted using the Qiagen RNEasy Plus Micro kit and amplified using the Affymetrix WT Pico Amplification kit, according to manufacturers description.

treatment_protocol: Mice were treated with 5 daily tamoxifen injections before the start of experiment. DNFB was applied dermally on two consecutive days (day 0 and 1) to promote sensitisation. Inflammation was elicited by a single application of DNFB to the ear pinna on day 5. Ears were harvested after 24 hours and digested in collagenase I. FACS was performed to isolate CD31+CD45-Ter119- endothelial cells. Cells were sorted directly into Qiagen RLT Plus lysis buffer.

value: ear

tag: cell population

value: CD31+CD45-Ter119- endothelial cells

tag: genotype/variation

value: control


title: Endothelial cells isolated from DNFB-treated ear, NICD1-EC-OE mouse, replicate 2

description: Gene expression data of endothelial cells from DNFB treated ears from mice with tamoxifen-induced endothelial overexpression of constitutively active Notch1

value: Pdgfb-CreERT2; R26-NICD


title: Endothelial cells isolated from DNFB-treated ear, control mouse, replicate 4

description: Gene expression data of endothelial cells from DNFB treated mouse ears


title: Endothelial cells isolated from DNFB-treated ear, control mouse, replicate 6


title: Endothelial cells isolated from vehicle-treated ear, NICD1-EC-OE mouse, replicate 1

description: Gene expression data of endothelial cells from ears from mice with tamoxifen-induced endothelial overexpression of constitutively active Notch1


title: 109_2D

description: RNA-seq


title: Khet_1


title: 109_1E

description: RNA-seq


title: Endothelial cells isolated from vehicle-treated ear, control mouse, replicate 3


title: wt_3

value: wild type


title: 109_1D

description: RNA-seq


title: wt_2


title: wt_1


title: Endothelial cells isolated from DNFB-treated ear, control mouse, replicate 5


title: CTRL_59_rep3

city: Olomouc

first: Petr

last: Vojta

address: Hnevotinska 5

department: Laboratory of experimental medicine

country: Czech Republic

institute: Palacky University

data_processing:
The reads were mapped to the reference genome of Hordeum vulgare (Hordeum_082214v1.30) by STAR aligner (STAR_2.4.2a)
Reads quantification was processed by subread-1.5.2 against GTF/GFF file (Hordeum_vulgare.082214v1.30.gtf)
Normalized counts were obtained by DESeq2 normalization
Genome_build: Hordeum_082214v1.30
Supplementary_files_format_and_content: DESeq2 normalized counts

organism: Hordeum vulgare

source_name: whole spike

growth_protocol: Plants were sawn in brown-earth soil with a density of 200 plants m-2 in 1.2 x 21 m plots. A mineral fertilizer containing 27% nitrogen was conventionally applied twice during springtime (30 kg per ha). In the vegetation period, plants were treated by herbicide (Mustang Forte) and fungicides (Acanto, Capalo)

extract_protocol:
3 µg of total RNA from each sample, extracted with RNAqueous kit (Thermo Fischer Scientific, Waltham, USA) and treated with TURBO DNA-free kit (Thermo Fischer Scientific, Waltham, USA) was used for cDNA library preparation by Illumina® TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, Madison, USA).
cDNA library was prepared by Illumina® TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, Madison, USA)

tag: cultivar

value: Golden Promise

value: whole spike

tag: developmental stage

value: BBCH scale - stage 59

value: azygous control


title: 109_2E

description: RNA-seq


title: Endothelial cells isolated from vehicle-treated ear, control mouse, replicate 4


title: CTRL_59_rep2


title: Endothelial cells isolated from DNFB-treated ear, control mouse, replicate 3


title: Endothelial cells isolated from vehicle-treated ear, control mouse, replicate 2


title: Endothelial cells isolated from vehicle-treated ear, control mouse, replicate 1


title: Endothelial cells isolated from DNFB-treated ear, control mouse, replicate 2


title: CTRL_49_rep3

value: BBCH scale - stage 49


title: Endothelial cells isolated from DNFB-treated ear, control mouse, replicate 1


title: CTRL_49_rep2


title: Core plus Ri rep4

city: Madison

first: Federico

last: Rey

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin-Madison

description: Sample name: HPP_R4

data_processing:
Sequencing reads were processed and filtered using the FastX Toolkit.
The first 10 bp of each read were removed to eliminate GC bias at the beginning of each read using the FastX Trimmer.
The 6-bp Illumina adapter sequences were then clipped using the FastX Clipper and a quality filter was applied to all reads to eliminate any reads with a quality score <30 as determined by the FastX Quality Filter.
Reads were then aligned to the mm9 mouse reference genome constructed to include only annotated genes (NM_RefSeqs) by Bowtie2 alignment.
Expression level determined using RSEM v 1.2.23.
Differential expression (fold change and PPDE) were calculated using Ebseq.
Genome_build: mm9
Supplementary_files_format_and_content: csv with abundance measurements

source_name: proximal large intestine

growth_protocol: Animal care and study protocols were approved by the University of Wisconsin - Madison Animal Care and Use Committee. Mice were housed in the Microbial Sciences Building vivarium. Germ-free (GF) ApoE KO mice, which were later colonized, were bred at the University of Wisconsin-Madison. GF mice were housed in plastic flexible vinyl gnotobiotic isolators. GF mice were inoculated via a single oral gavage with ~0.2 ml of the communities at 8-week-old. Mice were housed under standard conditions (12 h light:dark, temperature- and humidity-controlled conditions), and received ad libitum access to water and food. Diets were sterilized by irradiation and autoclaving. Sterility of germ-free animals was assessed by incubating freshly collected fecal samples under aerobic and anaerobic conditions using standard microbiology methods. Final dissection and data collection were performed at 26-weeks of age.

extract_protocol:
RNA was extracted first from frozen tissue using TRIzol and then using a Qiagen RNA-easy minikit with on column Dnase treatment.
Library was constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: Germ-free ApoE KO mice were colonized with (1) "core" community which do not produce butyrate, or (2) "core plus Roseburia intestinalis (butyrate-producing bacteria)"

value: ApoE knockout mice

tag: bacterial community

value: core plus Roseburia intestinalis

value: proximal large intestine

tag: age

value: 26 weeks


title: BR-IRGA 409 control rep3

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (Trimmomatic version 0.33)
Mapped to MH63 (indica subspecies) using HISAT v2.05.  Library type was set to firststrand and the rest of the parameters remained as the default.
The resulting bam files were then piped to HTseq count version 0.6.1. Using the options -f bam, -s reverse, and -m intersection-nonempty, counts per gene were generated for the annotated genes in MH63 genome. The identifiers can be found here: http://rice.hzau.edu.cn/rice_rs1/ and the link to the annotations file is at: http://rice.hzau.edu.cn/rice_rs1/download_ext/MH63_chr.gff.tar.gz
Genome_build: GCA_001623365.1
Supplementary_files_format_and_content: raw counts of sequencing reads,  gene as feature of interest.

organism: Oryza sativa

source_name: BR-IRGA 409 control_spikelet

growth_protocol: Rice plants were maintained until panicle exposure at greenhouse with climate control, when they were moved to controlled-environment chambers (Conviron BDW40), and subject to different temperature treatments. After, plants were returned to the greenhouse until the harvest.

extract_protocol:
Spikelets of the middle third of the panicle of flooded rice plants were sampled in each cultivar at the end of three days of heat stress and control condition and flash frozen on liquid nitrogen. Total RNA was extracted with Concert TM Plant RNA Reagent (Invitrogen). Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c  (9 am to 16 pm) during a period of three days at anthesis stage. Spikelets of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.

value: BR-IRGA 409

tag: phenotype

value: tolerant to heat stress

tag: treatment

value: control condition (29C) for 7 hrs

tag: organ

value: panicle

value: spikelet


title: Core plus Ri rep3

description: Sample name: HPP_R3


title: Core plus Ri rep5

description: Sample name: HPP_R5


title: BR-IRGA 409 treated rep2

source_name: BR-IRGA 409 treated_spikelet

value: high temperature treatment (38C) for 7 hrs


title: BR-IRGA 409 treated rep1


title: BR-IRGA 409 control rep2


title: CTRL_49_rep1


title: BR-IRGA 409 treated rep3


title: Core plus Ri rep2

description: Sample name: HPP_R2


title: BR-IRGA 409 control rep1


title: KD-CKX1 17_10_59_rep3

value: KD-CKX1 line


title: S6_CHO-K6_Trast+Pert

city: Edmonton

first: Babak

last: Nami

state: Alberta

address: 8-35 Medical Sciences Building, 114 St.

department: Medical Genetics

country: Canada

institute: University of Alberta

hyb_protocol: 3 ug of each sample was hybridized to Affymetrix GeneChip® CHO Gene 2.0 ST array (Format 100) for 16 hours at 45 ºC with rotation at 60 rpm in an Affymetrix GeneChip® Hybridization Oven 645

scan_protocol: After hybridization, the arrays were washed and stained in an Affymetrix GeneChip® Fluidics Station FS450 and the fluorescent signals were measured with an Affymetrix GeneChip® Scanner 3000 7G

data_processing:
Row data was analyzed by Affymetrix Transcriptome Analysis Console (TAC) 3.0 software.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = CHOGene-2_0-st
program-name = Expression Console
program-version = 1.3.1.187

organism: Cricetulus griseus

source_name: Cultured cells treated for 24 h

label_protocol: 5.5 ug of fragmented ss cDNA were terminal labeled with biotin according to the standard Affymetrix protocol.

growth_protocol: The cells were cultured in RPMI-1640 medium containing 10% FBS by incubation in a standard cell culture condition.

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

treatment_protocol: Cell were treated with RPMI-1640 supplemented with 10% FBS and containing 10 ug/ml of trastuzumab or pertuzumab or their combination for 24 h.

tag: cell line

value: Epithelial cell line derived from the ovary of the Chinese hamster

value: stablely overexpressing human HER2

tag: treated with

value: trastuzumab and pertuzumab for 24 h


title: S5_CHO-K6_Pert

value: pertuzumab for 24 h


title: CTRL_59_rep1

value: Golden Promise

value: whole spike

value: BBCH scale - stage 59

value: azygous control


title: S4_CHO-K6_Trast

value: trastuzumab for 24 h


title: Core plus Ri rep1

description: Sample name: HPP_R1

value: ApoE knockout mice

value: core plus Roseburia intestinalis

value: proximal large intestine

value: 26 weeks


title: IRGA 428 treated rep3

source_name: IRGA 428 treated_spikelet

value: IRGA 428

value: sensitive to heat stress

value: panicle


title: Core rep3

description: Sample name: HPP_C5

value: core


title: S3_CHO-K6_Untreated

value: Epithelial cell line derived from the ovary of the Chinese hamster

value: none (untreated)


title: KD-CKX1 17_10_59_rep2

value: KD-CKX1 line


title: IRGA 428 treated rep2

value: high temperature treatment (38C) for 7 hrs

value: spikelet


title: KD-CKX1 17_10_59_rep1

value: Golden Promise

value: whole spike


title: H37Rv∆thrB_2.2 [RNA-seq]

city: Bronx

first: Erik

middle: James

last: Hasenoehrl

state: New York

address: 1301 Morris Park Ave. Price 569

department: Microbiology & Immunology

institute: Albert Einstein College of Medicine

description: H37Rv∆thrB after 2 days of threonine starvation, rep 2

data_processing:
Illumina reads were mapped to reference genome using bowtie2, which generated SAM files
SAM files were converted to coordinate-sorted BAM files using samtools
Reads per gene were countedusing featureCounts
Differential gene expression analysis was performed using DeSeq2
Data analysis protocol can be found in more detail in Benjak, et. Al., Methods Mol Biol, 2015
Genome_build: NC_000962.3
Supplementary_files_format_and_content: count files were produced from illumina fastq readfiles using fetureCounts and contain a raw count of reads per gene; DGE Analysis files were generated using DeSeq2 and contain analyzed read count comparisons between samples at time of starvation compared to time 0 (before starvation), these include p-values.

organism: Mycobacterium tuberculosis

extract_protocol:
Culture samples were collected and pelleted via centrifugation. Cell pellets were resuspended in Trizol reagent and RNA was harvested via phenol-chloroform extraction. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: threonine starved

tag: time

value: 2 days


title: S2_CHO-K1_Trast+Pert

value: wild type

value: trastuzumab and pertuzumab for 24 h


title: Core rep2

description: Sample name: HPP_C4

value: ApoE knockout mice

tag: tissue

value: proximal large intestine


title: H37Rv∆thrB_2.1 [RNA-seq]

description: H37Rv∆thrB after 2 days of threonine starvation, rep 1


title: IRGA 428 treated rep1

value: IRGA 428


title: KD-CKX1 17_10_49_rep3

value: BBCH scale - stage 49


title: Core rep1

description: Sample name: HPP_C3

value: 26 weeks


title: IRGA 428 control rep3

source_name: IRGA 428 control_spikelet

value: sensitive to heat stress

value: control condition (29C) for 7 hrs

value: panicle


title: H37Rv∆thrB_1.3 [RNA-seq]

description: H37Rv∆thrB after 1 day of threonine starvation, rep 3

value: 1 days


title: KD-CKX1 17_10_49_rep2

value: KD-CKX1 line


title: S1_CHO-K1_Untreated

tag: cell type

value: Epithelial cell line derived from the ovary of the Chinese hamster

value: none (untreated)


title: H37Rv∆thrB_1.2 [RNA-seq]

description: H37Rv∆thrB after 1 day of threonine starvation, rep 2


title: KD-CKX1 17_10_49_rep1

value: Golden Promise

value: whole spike

tag: genotype


title: IRGA 428 control rep2

value: spikelet


title: H37Rv∆thrB_0.3 [RNA-seq]

description: H37Rv∆thrB before threonine starvation, rep 3

source_name: H37Rv∆thrB before threonine starvation

value: before threonine starvation

value: 0 days


title: H37Rv∆thrB_0.2 [RNA-seq]

description: H37Rv∆thrB before threonine starvation, rep 2


title: H37Rv∆thrB_0.1 [RNA-seq]

description: H37Rv∆thrB before threonine starvation, rep 1


title: Cxxc1 cko DMC1-ChIP rep2

city: Bar Harbor

first: Hui

last: Tian

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

library_source: genomic

data_processing:
Fastq files  were trimmed using Trimmomatic (v0.32) and subsequently parsed for detection and selection of paired reads having homology at the 5’ and 3’ ends.
DMC1 files were aligned to mm10 genome using BWA (v.0.5.10-tpx) and bam files were parsed for detection and selection of reads containing true genomic sequence versus fill-in sequence at the homologous region.
DMC1 reads were selected from the original paired-end fastq files and single-ended fastq files were created containing only the true genomic sequences of single strand DNA reads.
The filtered DMC1 reads were then aligned to the mouse mm10 genome using BWA (v.0.5.10-tpx).
DMC1 peaks were called using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files of DMC1 peaks called by MACS2.

molecule: genomic DNA

source_name: spermatocytes

extract_protocol:
Spermatocytes were isolated and fixed by 1% paraformaldehyde solution. The chromatin was sheared to ~1000 bp by sonication and used for ChIP.
For DMC1 library preparation,  DNA was firstly end repaired by incubation with T4 DNA Ligase Reaction Buffer with dNTP, T4 DNA polymerase, Klenow Enzyme and T4 PNK, followed by addition of 3’-A overhangs using Klenow Fragment 3’-5’ exo-. After denaturation of DNA , the adapters from TruSeq Nano DNA LD Library Prep Kit (set A, Illumina, FC-121-4001) were ligated with Quick Ligation kit. The libraries then were amplified using PCR Enhancer mix and primer cocktail (Illumina, FC-121-4001) for 12 cycles.

value: spermatocytes

value: adult

value: Cxxc1-CKO with Stra8-iCre

tag: antibody

value: DMC1 (Santa Cruz, sc-8973)


title: Cxxc1 het DMC1-ChIP rep2

value: Cxxc1 heterozygous with Stra8-iCre


title: Cxxc1 cko DMC1-ChIP rep1


title: KD-CKX1 5.8_49_rep3

value: BBCH scale - stage 49


title: KD-CKX1 5.8_59_rep1

value: BBCH scale - stage 59


title: HEK293T, NIH/3T3, A549 cells, sci-RNA-seq

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: sci-RNA-seq library

data_processing:
For sc-RNA-seq processing, read alignment and gene count matrix generation for single cell RNA-seq of co-assay was the same with sci-RNA-seq ("J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017).") with minor modifications: Reads were mapped to a chimeric reference genome of human (hg19) and mouse (mm10) for RNA-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for RNA-seq from mouse kidney experiment with STAR/v 2.5.2b, with gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse). For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
For reads processing for single cell ATAC-seq: base calls were converted to fastq format using Illumina’s bcl2fastq/ 2.16.0.10. Demultiplexing reads by PCR barcodes was done with custom python script tolerating one mismatched base in barcodes (edit distance (ED) < 2). The indexed Tn5 barcode for each reads was corrected to its nearest barcode (edit distance (ED) < 2) and reads with uncorrected barcodes (ED > 2) were removed. Demultiplexed reads were then adaptor clipped using trim_galore/0.4.1 with default settings. Trimmed reads were mapped to a chimeric reference genome of human (hg19) and mouse for ATAC-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for ATAC-seq from mouse kidney experiment with STAR/v 2.5.2b . Mapped reads were split into constituent cellular indices by further demultiplexing reads using the Tn5 index (ED < 2, including insertions and deletions). Duplicates for each cell were removed by samtools/v 1.3. For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of unique reads assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
Genome_build: human reference genome (hg19), mouse reference genome (mm10)
Supplementary_files_format_and_content: Processed data files are in txt format including a cell annotation file, gene (for RNA-seq) or peak (for ATAC-seq) annotation file, and a gene count sparse matrix (for RNA-seq) or peak count sparse matrix (for ATAC-seq).

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: HEK293T, NIH/3T3, A549 cells

growth_protocol: All mammalian cells were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) for HEK293T and NIH/3T3 cells or DMEM/F12 medium for A549 cells, both supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin). Cells were trypsinized with 0.25% typsin-EDTA (Gibco cat. no. 25200-056) and split 1:10 three times a week.

extract_protocol:
All cell lines (A549, HEK293T and NIH/3T3 cells) were trypsinized, spun down at 300xg for 5 min (4°C) and washed once in 1X PBS. 5M cells were combined and lysed using 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630, 1% SUPERase In and 1% BSA). The isolated nuclei were then pelleted, washed twice with 500 µL cold lysis buffer without IGEPAL CA-630, and then resuspended in lysis buffer without IGEPAL CA-630 at a final concentration of 5000 nuclei/µL. For all washes, nuclei were pelleted through centrifugation at 500xg for 5 min at 4°C.
Mouse kidney was minced to small pieces by blade in cell lysis buffer and transferred to the top of a 40um cell strainer (Falcon). Kidney tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500g for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer. The samples were split to 5 tubes with 100ul in each tube and flash frozen in liquid nitrogen.
Nuclei were then distributed into one 96-well plate. For each well, 5,000 nuclei (2 µL) were mixed with 1 µl of 25 µM anchored oligo-dT primer (5′-ACGACGCTCTTCCGATCTNNNNNNNN[10bp index]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3′, where “N” is any base and “V” is either “A”, “C” or “G”; IDT) and 0.25 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 1.75 µL of first-strand reaction mix, containing 1 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 0.25 µl 100 mM DTT (Invitrogen), 0.25 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 0.25 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well. Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes). 3 μL cell lysis buffer without IGEPAL CA-630, 10 μL Nextera TD buffer (Illumina) and 1 to 2 μL indexed TDE1 enzyme (Illumina) were added to each well. Tagmentation was performed at 55°C for 30 min and stopped by adding 5 μl 2X stop solution (40 mM EDTA, 1 mM spermidine) to each well. All cells (or nuclei) were then pooled, stained with 4',6-diamidino-2-phenylindole (DAPI, Invitrogen) at a final concentration of 3 μM, and sorted at 25 nuclei per well into 5 μL EB buffer. Cells are gated based on DAPI stain such that singlets are discriminated from doublets and sorted into the each well. 0.66 μl mRNA Second Strand Synthesis buffer (NEB) and 0.34 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min. The reaction was then stopped by adding 6 μL DNA binding buffer (Zymo) and incubating at room temperature for 5 min. Each well was then purified using 24 uL AMPure XP beads (Beckman Coulter), eluted in 12.5 μL of buffer EB (Qiagen). Eluted product was then split (6 μL each) and transferred to two new 96-well plates.  For one plate (RNA-seq half), each well was mixed with 5 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (25nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. After tagmentation, each well was mixed with 0.4 μL 1% SDS, 0.4 μL BSA (NEB), and 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and incubated at 55°C for 15 min. Then each well was then added with 2 μL 10% Tween-20, 1.2 μL nuclease-free water, 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 18-22 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min. For sci-RNA-seq only branch of the workflow, after second strand synthesis, instead of cell lysis and ampure beads purification, all cells were used for tagmentation and following PCR reaction with the same procedure as co-assay. After PCR, samples were pooled and purified using 0.8 volumes of AMPure XP beads. Library concentrations were determined by Qubit (Invitrogen) and the libraries were visualized by electrophoresis on a 6% TBE-PAGE gel. All RNA-seq libraries were sequenced on the NextSeq 500 platform (Illumina) using a V2 75 cycle kit (Read 1: 18 cycles, Read 2: 52 cycles, Index 1: 10 cycles, Index 2: 10 cycles). The co-assay RNA-seq library was sequenced to saturate (~100k reads per cell) and the sci-RNA-seq library was sequenced to 16k reads per cell.  For the other plate (ATAC-seq half), each well was mixed with 1μL of 10 μM indexed P5 primer (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′; IDT), 1 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), 2 μL nuclease-free water, and 10 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 3 min, 98°C for 30 sec, 18-22 cycles of (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min. For sci-ATAC-seq only branch of the work flow, sorted cells were processed similarly with published method (31) with minor modifications: each well was mixed with 7 μL buffer EB (Qiagen), 0.4 μL 1% SDS, 0.4 μL BSA (NEB), and 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and incubated at 55°C for 15 min. Then each well was then added with 2 μL 10% Tween-20, 1.2 μL nuclease-free water, 2μL of 10 μM indexed P5 primer (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′; ID), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification procedure was the same with ATAC-seq in co-assay. After PCR, all samples were pooled and purified using 1 volumes of AMPure XP beads. Gel extraction was applied to remove primer dimers shorter than 200bp. Library concentrations were determined by Qubit (Invitrogen) and the libraries were visualized by electrophoresis on a 6% TBE-PAGE gel. Libraries were sequenced on a NextSeq 500 platform (Illumina) using a mid-output 300 cycle kit and a custom recipe (paired end 51bp reads with index reads that covered both the Tn5 barcode and the library amplification barcode) and custom primers as described before. The ATAC-seq libraries was sequenced to around 55,000 reads per cell. Fixed nuclei (by paraformaldehyde, mouse kidney) were process in similar steps of cultured cells with minor modifications: Thawed nuclei are permeabilized with 0.2% tritonX-100 for 3 minutes on ice, washed twice with nuclei wash buffer. After sorting, each well was mixed with 6 μL EB buffer, 0.5 μL 1% SDS, 0.5 μL protease K (Qiagen), and incubated at 65 °C for 16 hours to reverse crosslinking. 2 μL 10% tween-20 was added to each well, and 6 μL of mix was transferred to a fresh 96-well plate for ATAC-seq library preparation: each well was mixed with 2μL of 10 μM indexed P5 primer (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), 8 μL nuclease-free water, 1 μL 10% tween-20, 1 μL BSA (NEB) and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification program and following steps for ATAC-seq were the same with fresh nuclei.  The cell lysate for RNA-seq library preparation was purified using 2 volumes of AMPure XP beads and eluted in 5 μL elution buffer. 0.66 μl mRNA Second Strand Synthesis buffer (NEB) and 0.34 μl mRNA Second Strand S

treatment_protocol: A549 cells were treated with 100 nM DEX for 1 hr or 3 hr before harvest. Control cells were treated with same volume of EtOH.

value: 3 conditions:DEX 0 hour, 1 hour and 3 hour


title: KD-CKX1 5.8_49_rep2


title: 48h_rep2

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

country: China

institute: Xiamen University

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Tophat (2.1.1) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: back full skin

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time after cyp treatment

tag: strain

value: back full skin

value: wild type

tag: gender

value: male

value: 7-8 weeks


title: HEK293T, NIH/3T3, A549 cells, sci-CAR RNA-seq

description: sci-CAR library: single cell RNA-seq library part


title: HEK293T, NIH/3T3, A549 cells, sci-ATAC-seq

description: sci-ATAC-seq library


title: H37Rv∆thrB_1.1 [RNA-seq]

description: H37Rv∆thrB after 1 day of threonine starvation, rep 1

tag: genotype/variation

value: threonine starved

value: 1 days


title: Pea3 TKO_Rep1

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3). We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm10
Supplementary_files_format_and_content: Excel file with normalized values using De-seq

source_name: lacrimal gland epithelium

extract_protocol:
RNA extraction was performed by Nugen's Ovation RNA-seq System V2
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

treatment_protocol: Embryos were flash frozen in OCT

value: Le-cre, Pea3-/-, Ermfl/fl, Er81fl/fl

value: mixed background


title: Pea3 TKO_Rep3


title: IRGA 428 control rep1

tag: cultivar

value: IRGA 428

value: sensitive to heat stress

value: control condition (29C) for 7 hrs

value: panicle

value: spikelet


title: WT_Rep3

tag: age

value: Le-Cre


title: 48h_rep1


title: KD-CKX1 5.8_59_rep2

value: Golden Promise

value: whole spike

tag: developmental stage

value: KD-CKX1 line


title: RNA-seq [Sample 17]

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

description:
X1275m_db_3
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt

data_processing:
We use Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value, 28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression level with RSEM.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: miRNA_Time course of DBTRG treated with dbcAMP.txt: Tab-delimited text file includes FPKM values for each Sample. D1 column represents the miRNA pattern of DBTRG treated with dbcAMP at 0h (FPKM); D2 column represents the miRNA pattern of DBTRG treated with dbcAMP at 6h (FPKM); D3 column represents the miRNA pattern of DBTRG treated with dbcAMP at 12h (FPKM); D4 column represents the miRNA pattern of DBTRG treated with dbcAMP at 24h (FPKM); D5 column represents the miRNA pattern of DBTRG treated with dbcAMP at 48h (FPKM).
Supplementary_files_format_and_content: RNA_dbcAMP_miR1275_DBTRG.txt: Tab-delimited text file includes FPKM values for each Sample. NC_1/NC_2/NC_3 were the DBTRG-05MG cells treated with control-media on day3 (FPKM); NC_db_1/NC_db_2/NC_db_3 were the DBTRG-05MG cells treated with dbcAMP on day3 (FPKM); X1275m_1/X1275m_2/X1275m_3 were the DBTRG-05MG cells treated with miR-1275 mimics on day3 (FPKM); and X1275m_db_1/X1275m_db_2/X1275m_db_3 were the DBTRG-05MG cells treated with combined dbcAMP and miR-1275 mimics on day3 (FPKM).

organism: Homo sapiens

growth_protocol: The cells were cultured according to the guideline of ATCC.

extract_protocol:
miRNA-seq for Sample 1-5: Total RNA was extracted using miRNeasy kit (QIAGEN) and was processed for reverse transcriptase with a miScript II RT kit and via qPCR using standard protocols. RNA-seq for Sample 6-17: Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Samples 1-5 were the microRNA-seq data of DBTRG-05MG treated with dbcAMP at 0/6/12/24/48 hours. Sample 6-17 were the analysis of DBTRG-05MG cells treated with control-media, dbcAMP, miR-1275 mimics and combined dbcAMP and miR-1275 mimics on day3.

tag: treatment

value: 1mM dbcAMP combined miR-1275 48h


title: Cxxc1 het DMC1-ChIP rep1

value: spermatocytes

value: adult

value: Cxxc1 heterozygous with Stra8-iCre

value: DMC1 (Santa Cruz, sc-8973)


title: WT_Rep2


title: Pea3 TKO_Rep2


title: HEK293T, NIH/3T3, A549 cells, sci-CAR ATAC-seq

description: sci-CAR library: single cell ATAC-seq library part

value: 3 conditions:DEX 0 hour, 1 hour and 3 hour


title: 24h_rep2

value: back full skin

value: wild type

value: male

value: 7-8 weeks


title: KD-CKX1 5.8_49_rep1

value: BBCH scale - stage 49


title: 24h_rep1


title: WT_Rep1

value: mixed background


title: RNA-seq [Sample 16]

description:
X1275m_db_2
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: RNA-seq [Sample 14]

description:
X1275m_3
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: RNA-seq [Sample 15]

description:
X1275m_db_1
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: HF-SD5

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

description: Gene expression data from hypothalamus following 2 months of diet

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA was hybridized for 20 hr on Rat Transcriptome 1.0 ST arrays incubated at 48°C in the Affymetrix GeneChip Hybridization Oven 645. Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Rat Transcriptome 1.0ST arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was analyzed using Affymetrix Expression Console software (normalized using RMA) and the Transcriptome Analysis Console software (ANOVA with false discovery rate)

organism: Rattus norvegicus

source_name: rat hypothalamus after 2 months of diet feeding

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip WT PLUS Affymetrix protocol from 100 ng total RNA.

growth_protocol: Sprague-Dawley rats (6-7 weeks) were received from Charles River. Rats were housed in environmentally controlled rooms with ad libitum access to water and diets.

extract_protocol: Rats were sacrificed with carbon dioxide after 2 months of the diet. Brains were rapidly collected and processed on dry ice. The hypothalamus was micro-dissected by using the anterior commissure as a horizontal reference and the line between the mammillary bodies in the posterior hypothalamus as the caudal limit.

treatment_protocol: Rats were randomly assigned to one of 3 experimental diet groups: low-fat control diet providing 16% kcal from soybean oil, high-fat diet containing 35% kcal from flaxseed oil, or high-fat diet containing 35% kcal from safflower oil.

tag: Sex

value: hypothalamus

value: 14-15 weeks

tag: diet

value: high-fat diets (35% kcal/d) containing either safflower (linoleic acid) oil for 2 months


title: HF-SD4


title: 12h_rep2


title: HF-SD3


title: mouse kidney , sci-CAR ATAC-seq

source_name: kidney

value: kidney

value: 8 weeks adult

value: B6 background


title: RNA-seq [Sample 13]

description:
X1275m_2
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: mouse kidney , sci-CAR RNA-seq


title: 12h_rep1


title: 6h_rep2


title: RNA-seq [Sample 12]

description:
X1275m_1
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: 6h_rep1


title: RNA-seq [Sample 11]

description:
NC_db_3
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt

value: 1mM dbcAMP 48h


title: 0h_rep2


title: H37Rv∆thrA at T7, biological rep3

description:
thrA7.3
Biological replicate 3 of 4.

hyb_protocol: Each pair of differentially labeled probes was resuspended in 60 ml of hybridization buffer (500 ml formamide, 250 ml 206 SSC, 5 ml 10% SDS, 245 ml ultrapure water) and hybridized to the microarray slide overnight in a 42C water bath. Slides were then washed in increasingly stringent wash conditions (3 times 5 min 16SSC 0.1% SDS, 3 times 5 min 0.16 SSC 0.1% SDS, 3 times 5 min 0.16 SSC and a final dip in 0.22 mm-filtered MQ water).

scan_protocol: Arrays were scanned in a Genepix 4000A scanner Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Spots quantified with TIGR Spotfinder. The data was then processed in TIGR MIDAS. Two color tiff images of the microarrays were visually inspected for defects and obvious spatial biases. Prior to normalization pin-tip (block) intensity box plots were used to detect slides exhibiting spatial and/or pin biases, with post-normalization intensity box plots and MA plots used to assess the effectiveness of normalization in correcting these biases. RI plots were also used to identify outlier slides and for assessing the effectiveness of the normalization process, and Z-score histograms were used to look for slides with abnormal intensity distributions. Slides that did not pass the quality control process were rejected, and repeat hybridizations were performed. Post normalization (Total Intensity and LOWESS) the in-slide replicate spots were averaged before expression ratios were calculated. The results from 3 biological replicates including two dye swaps were then subjected to a t-test without false discovery correction in TIGR MeV software.

source_name: H37Rv∆thrA after 7 days of homoserine starvation

label_protocol: Labeling was performed using protocols SOP# M007 from The Institute of Genomic Research (TIGR)

extract_protocol: Cells were collected by centrifugation and resuspended in 1 ml TRIzol reagent (Life Technologies, Fisher, Grand Island, NY). The suspension was transferred to Fast-Prep Blue Cap tubes and processed 2x for 45 s at speed 6 in a Fast-Prep apparatus (MP Bio, Irvine, CA). After a brief incubation on ice, the debris was spun down and the supernatant (~750 ml) further process with Direct-zol™ RNA MiniPrep (Zymo Research Corporation, Irvine, CA) according to manufacturer’s protocol.

value: before homoserine starvation

value: 0 days

value: homoserine starved

value: 7 days

source_name: H37Rv∆thrA during exponential phase growth with homoserine supplementation


title: H37Rv∆thrA at T7, biological rep4

description:
thrA7.4
Biological replicate 4 of 4.


title: RNA-seq [Sample 10]

description:
NC_db_2
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: 0h_rep1

value: back full skin


title: RNA-seq [Sample 9]

description:
NC_db_1
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: HF-FD3

value: high-fat diets (35% kcal/d) containing flaxseed (alpha-linolenic acid) oil for 2 months


title: HF-FD4

value: male


title: HF-SD1


title: HF-SD2


title: Input DNA

city: Ithaca

first: Hualiang

last: Pi

state: NY

address: 125 Wing Dr.

department: Microbiology

institute: Cornell University

data_processing:
The sequence reads generated from ChIP-seq were trimmed and mapped onto the reference genome B. subtilis 168 (NC_000964) using CLC genomic workbench software version 8.5.1.
A shape-based peak caller of the CLC genomic workbench software version 8.5.1 was used to compare experiment alignments and control (input DNA) to identify ChIP peaks.
The threshold for signal to noise ratio (S/N) was set as 1.5 and the P-value threshold was set as 0.05.
Genome_build: B. subtilis 168 (NC_000964)
Supplementary_files_format_and_content: wig files

organism: Bacillus subtilis

source_name: bacterial cells

growth_protocol: Cells were grown in LB medium amended with 25 µM FeSO4 to OD600 of ~0.25 and 1 mM IPTG was added to cell culture to induce expression of FrvA as indicated. At different time points, 40 ml aliquots were harvested and the pellets were kept at −80 °C.

extract_protocol:
The cell pellets were washed and resuspended with buffer CA (10 mM Na2HPO4, 2 mM KH2PO4, pH 7.4, 137 mM NaCl, and 2.7 mM KCl). The samples were incubated with 1% formaldehyde at room temperature for 10 min for crosslinking and then incubated with 133 mM glycine (pH7.5) at 4 °C for 30 min to quench the crosslinking. Cells were spun down, washed twice with buffer CB (50 mM Tris–HCl pH7.4, 150 mM NaCl and 1 mM EDTA), and then resuspended in 0.5 ml buffer CB followed by sonication for cell lysis and DNA fragmentation. Supernatant was collected after centrifugation and the total protein concentration was quantified using a Bradford assay. Aliquots of 400 µg of total protein were kept at −80 °C. Aliquots of 1% volume of the lysate were diluted with CB buffer and kept at −80 °C to serve as the input-control (1% of input DNA). For immunoprecipitation, α-FLAG M2 magnetic agarose beads (Sigma, Cat# M8823) were washed and resuspended in 400 μl buffer CB. Aliquots of 400 µg of total protein were diluted, mixed with the washed magnetic beads, and incubated on a rotation mixer overnight in a cold room (40C). The bead slurry was recovered by using a magnetic stand and washed twice with 500 μl of buffer CB. The protein–DNA complexes were eluted with 3X FLAG peptide according to the manufacture’s protocol. All samples including 1% input DNA samples were treated at 650C for overnight to reverse crosslinking. Co-immunoprecipitated DNA was purified using a PCR purification Kit (Omega Biotek, Norcross, GA), quantified by NanoDrop spectrophotometer.
Fifty to one hundred nanograms of ChIP or input DNA was used for DNA library preparation at the Cornell University Life Sciences Core Laboratories Center.

treatment_protocol: A high-affinity ferrous iron efflux transporter FrvA from Listeria monocytogenes was utilized as an inducible genetic tool to impose iron limitation. Bacillus wild-type cells with C-terminal FLAG-tagged Fur at its native locus and an ectopic copy of frvA integrated at amyE locus were grown in LB medium amended with 25 µM iron to ensure Fur repression. After the cell culture reaches OD600 of ~0.25, an aliquot of cell culture was harvested to study Fur-dependent regulation under iron sufficient conditions. Then 1 mM IPTG was added to the cell culture to induce expression of FrvA to deplete intracellular iron pools. Fur loses its cofactor iron and falls off most of its targeted sites by 30 min as confirmed by ChIP-qPCR. Thus cells were harvested at 30 min to study Fur-dependent regulation under iron deficient conditions.

value: Bacillus subtilis CU1065

tag: chip antibody


title: Fur Deficient Iron #2

tag: condition

value: iron deficient

value: α-FLAG antibody (Sigma, Cat# M8823)


title: H37Rv∆thrA at T7, biological rep2

description:
thrA7.2
Biological replicate 2 of 4.

tag: time


title: H37Rv∆thrA at T7, biological rep1

description:
thrA7.1
Biological replicate 1 of 4.


title: RNA-seq [Sample 8]

description:
NC_3
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt

value: cultured media RPMI-1640 48h


title: HF-FD2

tag: tissue

value: hypothalamus

value: 14-15 weeks


title: RNA-seq [Sample 7]

description:
NC_2
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt

tag: cell type


title: H37Rv∆thrA at T4, biological rep4

description:
thrA4.4
Biological replicate 4 of 4.

source_name: H37Rv∆thrA after 4 days of homoserine starvation

value: 4 days


title: H37Rv∆thrA at T4, biological rep3

description:
thrA4.3
Biological replicate 3 of 4.


title: Fur Deficient Iron #1


title: gAtac_rluc3: gonad ATAC-seq rep1

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: ATACseq

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5’end coordinate of the – strand read was less than or equal to the 5’end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as will as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors.
bedGraph files were generated from replicate concatenated processed ATAC-seq reads .bed files using bedtools genomecov v2.23 (-scale 1/(library size - chrM reads/100000)) which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
UMIs from RNA-seq reads were extracted with UNI-tools followed by read trimming with fastx_trimmer and mapping with STAR. Mapped files were deduplicated with UNI-tools and remapped with STAR to generate bam and bedGraph files
RNA-seq normalized bedGraph files were converted to bigWig format with bedGraphToBigWig and replicates were averaged using bamCompare from the deeptools suite.
RNA-seq count tables were generated using RSEM and differential expression determined using DESeq2
UMIs from ChIP-seq reads were extracted using UMI-tools followed by read trimming with fastx_trimmmer and mapping with Bowtie2.
Uniquely mapping ChIP-seq reads were converted to bed files of the full fragment lengths then to library normalized bigWig files using bamCoverage from the deepTools suite. BigWig files were then normalized to input controls using bamCompare from the deepTools suite with --ratio substract for worm and --ratio ratio for human
Windows around annotated transcription start sites were counted for intersections with full-paired-end-fragment ChIP-seq reads using bedtools intersect and windows containing significant signal determined using DESeq2
Genome_build: ce10, hg19
Supplementary_files_format_and_content: library-normalized bigWig files of processed ATAC-seq reads, mapped RNA-seq reads, and input-normalized ChIP-seq reads
Supplementary_files_format_and_content: Gene count tables for RNA-seq reads and promoter-window count tables for full-paired-end-fragment ChIP-seq reads

organism: Caenorhabditis elegans

source_name: worm gonads

growth_protocol: C. elegans strains were maintained on OP50 bacteria and NGM agar plates at 15ºC. Worms were transferred to fresh food once a week.

extract_protocol:
Synchronized L4 animals were washed 5 times in M9 buffer and collected on ice. 20 gonads per sample were isolated by hand. Nuclei were isolated using a glass Dounce homogenizer with 50 strokes tight-fitting insert in buffer A (15 mM Tris–HCl pH7.5, 2 mM MgCl2, 340 mM sucrose, 0.2 mM spermine, 0.5 mM spermidine, 0.5 mM phenylmethanesulfonate [PMSF], 1mM DTT, 0.1% Trition X-100 and 0.25% NP-40 substitute). The debris were removed by spinning at 100×g for 5 min and the nuclei were pelleted by spinning at 1000×g for 10 min and proceeded immediately to transposition step of the ATACseq protocol
Library preparation was done following a protocol published in Buenrostro et al. 2013. Cell pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase) (Illumina Nextera DNA Library preparation kit, #FC-121-1030). The transposition reaction was carried out for 60 min at 37ºC. The samples were purified using Zymo DNA Clean & Concentrator kit; following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 12 to 14 cycles and sequenced using paired-end-sequencing length of 75 nucleotides using NextSeq 500/550 High Output v2 kit (Illumina) on a NextSeq500 machine (Illumina) following manufacturer's protocol.

value: worm gonads

tag: passages/stage


title: LF-CD4

value: low-fat (16% kcal/d) diet)


title: RNA-seq [Sample 6]

description:
NC_1
mRNA
processed data file: RNA_dbcAMP_miR1275_DBTRG.txt


title: HF-FD1


title: LF-CD3


title: LF-CD2


title: gAtac_rluc2: gonad ATAC-seq rep1

description: ATACseq


title: Fur Sufficient Iron #2

value: iron sufficient


title: Fur Sufficient Iron #1


title: microRNA-seq [Sample 4]

description:
D4
micro-RNA
processed data file: miRNA_Time course of DBTRG treated with dbcAMP.txt

value: 1mM dbcAMP_24h


title: hmg3haChIP2: Hmg3-HA ChIP-seq rep2

description: ChIP-seq

source_name: whole worms

extract_protocol:
Worms were frozen in liquid nitrogen prior to pulverization using a hammer as well as mortar and pestle. The resulting powder was fixed in 1,1 % formaldehyde. The sample was sonicated twice using a Bioruptor (Diagenode) for 15 times 30 sec ON, 30 sec OFF on high settings at 4°C. 5% of the supernatant was taken off as input and the protein concentration was determined using Bradford assay. The input was digested with 1 µl RNase A for 1 h at 37°C, the crosslink was reversed as described for the ChIP sample. 2-4 mg of extract was used for ChIPs.
Library preparation was done following standard Bioo Scientific protocol and NEXTflex® qRNA-Seq™ Kit v2 (Bioo Scientific). Libraries were sequnced using single end sequencing length of a 75 nucleotides on a HiSeq400 machine (Illumina).

value: whole worms


title: microRNA-seq [Sample 3]

description:
D3
micro-RNA
processed data file: miRNA_Time course of DBTRG treated with dbcAMP.txt

value: 1mM dbcAMP_12h


title: gAtac_rluc1: gonad ATAC-seq rep1

description: ATACseq


title: hmg3haChIP1: Hmg3-HA ChIP-seq rep1

description: ChIP-seq


title: microRNA-seq [Sample 2]

description:
D2
micro-RNA
processed data file: miRNA_Time course of DBTRG treated with dbcAMP.txt

value: 1mM dbcAMP_6h


title: wormChIPInput: Hmg3-HA input

description: ChIP-seq ctrl


title: H37Rv∆thrA at T4, biological rep1

description:
thrA4.1
Biological replicate 1 of 4.

value: homoserine starved

value: before homoserine starvation

value: 0 days


title: H37Rv∆thrA at T4, biological rep2

description:
thrA4.2
Biological replicate 2 of 4.


title: microRNA-seq [Sample 1]

description:
D1
micro-RNA
processed data file: miRNA_Time course of DBTRG treated with dbcAMP.txt

value: 1mM dbcAMP_0h


title: H37Rv∆thrA at T2, biological rep4

description:
thrA2.4
Biological replicate 4 of 4.

source_name: H37Rv∆thrA after 2 days of homoserine starvation


title: H37Rv∆thrA at T2, biological rep3

description:
thrA2.3
Biological replicate 3 of 4.

value: 2 days


title: microRNA-seq [Sample 5]

description:
D5
micro-RNA
processed data file: miRNA_Time course of DBTRG treated with dbcAMP.txt

value: 1mM dbcAMP_48h


title: H37Rv∆thrA at T2, biological rep2

description:
thrA2.2
Biological replicate 2 of 4.


title: H37Rv∆thrA at T2, biological rep1

description:
thrA2.1
Biological replicate 1 of 4.


title: Mixed tPBAT Library - 1.2 fmol

status: Public on Aug 28 2018

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Reads were mapped on mixed reference of human genome hg19 and lammbda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport
Genome_build: hg19 and lambra genome
Supplementary_files_format_and_content: bedGraph

source_name: lung

growth_protocol: Cultured in MEM+10%FBS

extract_protocol:
Genomic DNA was purified using QIAAmp Mini Kit
Genomic DNA was treated with bisufite using Methyl Easy Gold Kit from Zymo Research, then adaputor tagging was performed with tPBAT protocol.

treatment_protocol: Cells were removed from culture flask with Tripsin-EDTA and collected by centrifugation.

tag: cell line

tag: amount of input library

value: 1.2 fmol

value: fibroblast-like cell

value: lung

value: 16 week embryo


title: Mixed tPBAT Library - 600 amol

value: 600 amol


title: Mixed tPBAT Library - 4.8 fmol

value: 4.8 fmol


title: Mixed tPBAT Library - 300 amol

value: 300 amol


title: rPBAT Library spiked with 20% PhiX control

extract_protocol:
Genomic DNA was purified using QIAAmp Mini Kit
Genomic DNA was treated with bisufite using Methyl Easy Gold Kit from Zymo Research, then adaputor tagging was performed with tPBAT or rPBAT protocol.

tag: pbat protocol

value: rPBAT


title: Mixed tPBAT Library

value: tPBAT


title: Mixed tPBAT Library - 9.6 fmol

value: 9.6 fmol


title: Mixed tPBAT Library - 2.4 fmol

value: 2.4 fmol


title: JS96_TAGGTC_trimmed

city: Cambridge

first: Luyi

address: 415 main st Cambridge

institute: Broad institute

data_processing:
The data was first demultiplexed by the cell barcode sequence and then aligned and counted using Rsubread (1.5.0)  and featureCounts (1.5.0) with mm10 genome annotation. Quality control was performed using scPipe to remove low quality cells.
The distance of the percentage of cells in three DC subtype between sisters were calculated, and used together with the total cell count as the input of Mahalanobis distance for outlier detection. Random permutation on sisters described in Figure 1B were used to get a null distribution and a 0.05 p-value cut-off was used to exclude sisters with different lineage output, leaving us with 98 clones.
Genome_build: mm10
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a clone. For meta data, XXX_fill_sis1/XXX_fill_sis2 represent the fate bias of filler cells in sister wells, which is considered as population control. cDC1_sis1.. E.t.c are cell count of cDCs. The cell counts are normalized using beads so they are not integers.

source_name: hematopoietic stem and progenitor cells

growth_protocol: bone marrow cells were extracted from C57BL/6 mice and cultured at a density of 1.5 x 10^6 in 96-round bottom plates with DC culture medium and 200 ng/ml FLT3L obtained from Dr Jian-Guo Zhang (WEHI).  To generate conditioned medium that can sustain the growth and differentiation of isolated DC progenitors, medium derived from FLT3L cultures after 3.5 days was centrifuged to remove cells, then passed through a 0.22-μm filter, and frozen aliquots stored at -80°C, as described previously. This medium is referred to as DC-conditioned medium (DC-CM).

extract_protocol:
On day 2.5 after culture, each 200 μl cultured well was mixed well, then 100 µL of the contents transferred manually to a separate new well, and given approximately 30-60 minutes to settle. The 96-well plates containing sister wells derived from each single UBC-GFP LSK clone were imaged on a Nikon TiE live cell imaging system. Cells were maintained at 37 °C in a humidified atmosphere and 5% CO2. Images were acquired in DIC and fluorescence using a 4x 0.13NA plan neofluor objective, and GFP filter (FITC, ex 465-495, DM 505, em 515-555). A Z-stack of 150 μm, with interval of 50um was performed and, the best focus plane was automatically selected for analysis using an offline Metamorph software (v 7.8.2.0) licence and method for automatic segmentation and cell count. Cell count script parameters, region size and diameter, were changed per experiment, on the basis of visual inspection of the 100 single cell controls. After imaging, cell cultures were incubated in 37 °C and at 5% CO2 for 4.5 days.
Depending on cell abundance 1 – 10 cells per clone were FACS sorted for RNA sequencing. Transcriptome libraries were generated according to the CEL-Seq protocol with the exception that all column purifications were replaced by magnetic bead purifications using AMPure XP beads (Beckman Coulter A63880). Libraries were sequenced on the Illumina NextSeq500 sequencer using a 75-cycle kit.

treatment_protocol: The isolation and sorting of GFP+ progenitors was performed as described. Briefly, bone marrow from C57BL/6-TG (UBC-GFP) was extracted and cells were enriched for ckit (2B8 conjugated to APC) via magnetic activated cell sorting (MACS) positive selection. The ckit enriched fraction was subsequently stained for Sca-1 (E13 161-7conjugated to Alexa Fluor 594 or Alexa Fluor 680), IL-7R (A7R34-2.2 conjugated to biotin with streptavidin-PECy7) and FLT3 (A2F10 conjugated to Phycoerythrin). Cells with positive expression of GFP, ckit, sca-1 and FLT3, while negative for IL-7R, were deemed MPPs and sorted into FLT3L-DC "filler" cultures as single cells, with 100-cell controls in duplicate. Cells with positive expression of GFP, cKit and Sca-1 were deemed Sca1+cKit+ (SKs). Cells were sorted using the BD Influx, BD FacsARIA W and BD FacsAria L. Single SKs from UBC-GFP mice were deposited in 96 well round bottomed wells pre-seeded with 1.5 x 10^6 total C57BL/6 BM cells (filler cells) cultured in DC culture medium with and additional 200 ng/mL FLT3L 37 °C and at 5% CO2 for 2.5 days.

value: hematopoietic stem and progenitor cells

tag: description

value: progenitor cells at day 2.5


title: JS96_AGCCAG_trimmed


title: JS96_GACACG_trimmed


title: JS96_CTAACG_trimmed


title: JS96_GCTTGT_trimmed


title: JS96_AGCCAC_trimmed


title: JS96_ATGTGG_trimmed


title: JS96_TAGGTT_trimmed


title: JS96_GCTTGC_trimmed


title: JS96_AGCCAT_trimmed


title: JS96_CTAACT_trimmed


title: PBMC + #1 abs

city: Kobe

first: Sunao

last: Sugita

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: The Laboratory for Retinal Regeneration

institute: RIKEN Center for Developmental Biology

description: PBMC, collected from a healthy donor + #1 abs, novel T-cell suppressive antibody (another name 20-2b2 antibody, host: Rat)

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.

source_name: PBMC + #1 abs, co-cultured for 48 hr

growth_protocol: PBMC, 2 X 10^6/well + Rat IgG, 100 ng/mL, co-cultured for 48 hr  PBMC, 2 X 10^6/well + #1 abs, 100 ng/mL, co-cultured for 48 hr  PBMC, 2 X 10^6/well + OKT-3, 100 ng/mL, co-cultured for 48 hr

extract_protocol: The total RNA of (1) PBMC + Rat IgG, (2) PBMC + #1 abs, and (3) PBMC + OKT-3 were extracted by High Pure RNA Isolation Kit (Roche) after the cells were incubated for 48 hr.

treatment_protocol: PBMC + Rat IgG, 100 ng/mL  PBMC + #1 abs, 100 ng/mL  PBMC + OKT-3, 100 ng/mL

value: PBMC

tag: disease state

value: healthy


title: PBMC + Rat IgG

description: PBMC, collected from a healthy donor + Rat IgG, isotype control antibody (purified NA/LE Rat IgG2a)

source_name: PBMC + Rat IgG, co-cultured for 48 hr

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.


title: JS96_GCTTGG_trimmed


title: PBMC + OKT-3

description: PBMC , collected from a healthy donor + OKT-3, common T-cell suppressive antibody (host: mouse)

source_name: PBMC + OKT-3, co-cultured for 48 hr


title: JS96_TCACAG_trimmed

value: no cell sorted


title: JS96_CGTGTG_trimmed


title: LF-CD1

description: Gene expression data from hypothalamus following 2 months of diet

value: male

value: hypothalamus

value: 14-15 weeks

value: low-fat (16% kcal/d) diet)


title: JS96_CTAACC_trimmed


title: JS96_GACACT_trimmed


title: JS96_ATGTGC_trimmed


title: JS96_GACACC_trimmed


title: JS96_TCACAT_trimmed


title: JS96_CGTGTT_trimmed


title: JS96_CGTGTC_trimmed


title: JS96_TCACAC_trimmed


title: JS96_ACGACT_trimmed


title: JS96_TGATGT_trimmed


title: JS96_CATCAG_trimmed


title: JS96_TGATGG_trimmed


title: JS96_GTCGTG_trimmed


title: JS96_ACGACA_trimmed


title: JS96_GTCGTT_trimmed


title: JS96_ACGACG_trimmed


title: JS96_TGATGA_trimmed


title: JS96_CATCAA_trimmed


title: JS96_GTCGTA_trimmed


title: JS96_CATCAT_trimmed


title: JS96_TGATGC_trimmed


title: JS96_ACGACC_trimmed


title: JS96_CATCAC_trimmed


title: JS96_GTCGTC_trimmed


title: JS91_TAGGTG_trimmed


title: JS91_AGCCAG_trimmed


title: JS96_ATGTGT_trimmed


title: JS91_GCTTGG_trimmed


title: JS91_TAGGTT_trimmed


title: JS91_GCTTGT_trimmed


title: JS91_AGCCAT_trimmed


title: JS91_CTAACT_trimmed


title: JS91_TAGGTC_trimmed


title: JS91_AGCCAC_trimmed


title: JS91_CTAACC_trimmed


title: JS91_GCTTGC_trimmed


title: JS91_CGTGTG_trimmed


title: JS91_GACACG_trimmed


title: JS91_CGTGTT_trimmed


title: JS91_ATGTGC_trimmed


title: JS91_GACACC_trimmed


title: JS91_CGTGTC_trimmed


title: JS91_ATGTGT_trimmed


title: JS91_TCACAT_trimmed


title: JS91_GACACT_trimmed


title: JS91_TCACAC_trimmed


title: JS91_GTCGTG_trimmed


title: JS91_CATCAG_trimmed


title: JS91_CTAACG_trimmed


title: JS91_TGATGT_trimmed


title: JS91_ACGACT_trimmed


title: JS91_GTCGTT_trimmed


title: JS91_CATCAT_trimmed


title: JS91_TGATGA_trimmed


title: JS91_ACGACA_trimmed


title: JS91_GTCGTA_trimmed


title: JS91_CATCAA_trimmed


title: JS91_ATGTGG_trimmed


title: JS91_TCACAG_trimmed


title: JS91_TGATGG_trimmed


title: JS91_ACGACC_trimmed


title: JS91_ACGACG_trimmed


title: JS91_TGATGC_trimmed


title: JS91_GTCGTC_trimmed


title: D9JS27_BC39_R2


title: JS91_CATCAC_trimmed


title: D9JS27_BC34_R2


title: D9JS27_BC35_R2


title: D9JS27_BC32_R2


title: D9JS27_BC36_R2


title: D9JS27_BC33_R2


title: D9JS27_BC38_R2


title: D9JS27_BC30_R2


title: D9JS27_BC29_R2


title: D9JS27_BC28_R2


title: D9JS27_BC31_R2


title: D9JS27_BC27_R2


title: D9JS27_BC26_R2


title: D9JS27_BC24_R2


title: D9JS27_BC23_R2


title: D9JS27_BC25_R2


title: D9JS27_BC21_R2


title: D9JS27_BC22_R2


title: D9JS27_BC20_R2


title: D9JS27_BC37_R2


title: D9JS27_BC16_R2


title: D9JS27_BC19_R2


title: D9JS27_BC15_R2


title: D9JS27_BC17_R2


title: D9JS27_BC18_R2


title: D9JS27_BC14_R2


title: D9JS27_BC13_R2


title: D9JS27_BC12_R2


title: D9JS27_BC8_R2


title: D9JS27_BC11_R2


title: D9JS27_BC9_R2


title: D9JS27_BC6_R2


title: D9JS27_BC7_R2


title: D9JS27_BC2_R2


title: D9JS27_BC3_R2


title: D9JS27_BC4_R2


title: D9JS27_BC5_R2


title: D9JS27_BC1_R2


title: D9JS27_BC10_R2


title: JEK15-525

city: Bloomington

first: Xilin

last: Li

state: Indiana

address: 2719 E 10th street Rm230

institute: Indiana University

data_processing:
Base-calling was done bcl2fastq v2.20.0.422.
Trimming was done by Trimmomatic (v0.32) with the following parameters: ILLUMINACLIP:adapters.fa:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:16
Custom perl script was used to remove very short potential adapter sequence from the ends of the reads (would remove max 10 bps and min 2 bps) and the remaining read had to be 17 bps or larger
Fastx_clipper (v0.0.13.2) -l 17 -v -M 1 was used for removing the adapters.
Reads were mapped to mouse repetitive elements RepeatMasker version open-4.0.5.
Alignment was performed with Tophat (v2.1.1) with the following parameters: --b2-very-sensitive --read-edit-dist 2 --max-multihits 100.
The summary table was prepared from the read mapping data to known features (repeats and gene features) using custom perl scripts.
Genome_build: mm10
Supplementary_files_format_and_content: excel spread sheet including the raw counts of each gene for each sample

source_name: Liver from mice fed high fat diet

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and total RNA was isolated using mirVana™ RNA Isolation Kit (AM1560). Illumina TruSeq® Stranded Total RNA Library Prep kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Liver

value: 21-22 weeks


title: JEK15-520

source_name: Liver from mice fed control diet

tag: age


title: JEK15-519


title: JEK15-521


title: mouse_Sample2_RNA_seq

first: Eric

middle: Jan

last: Foss

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample2

data_processing:
trim reads (DNA)
filter based on CpG content (DNA)
alignment with bowtie2 (DNA)
alignment with gsnap (RNA)
measure coverage with bedtools genomeCoverageBed (RNA)
normalize to total counts (RNA)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt files with raw and normalized counts

source_name: brain

extract_protocol:
dissect brains from CRE-plus and cre-minus mice
Rubicon Genomics ThruPLEX DNA-seq kit (DNA); Illumina TruSeq DNA LT Sample Prep Kit (RNA)
single end (RNA); paired end (RNA)

value: brain

tag: mice

value: CRE-plus

tag: genotype

value: Xist-delta/MeCP2-GFP-Xist2lox females with Nestin-Cre transgene


title: H3K27Ac -DHT ChIP-seq (duplicate of GSM1249447)

city: Los Angeles

first: Yu

middle: (Phoebe)

last: Guo

state: California

address: 1450 Biggy Street, NRT 6514

institute: Univ. of Southern California

data_processing:
Illumina Casava 1.8.2 software used for basecalling
ChIP-seq sequence reads were alligned to the UCSC human genome assembly HG19 using bowtie 2 (H3K27Ac), Illumina eland pipeline (TCF7L2), BWA Input DNA
ChIP-seq peaks were called using Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) with the following settings for H3K27Ac: 250bp fragments, alpha-value=0.0001, FDR=0.001, histone modification analysis.  For TCF7L2: 150 bp fragments, alpha-value=0.001, FDR=0.001
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peak files in gff format

source_name: prostate cancer cell line LNCaP

growth_protocol: Cells were grown in RPMI with charcoal-stripped serum and collected when 80% confluent

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: LNCaP

tag: passage


title: mouse_Sample7_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample7

value: cre-minus

value: Xist-delta/MeCP2-GFP-Xist2lox females without Nestin-Cre transgene


title: JEK15-526


title: JEK15-522


title: mouse_Bedalov3_DNA_methylation

description:
DNA cut with LpnPI
Bedalov-3

data_processing:
Library strategy: LpnPI DNA methylation profiling
trim reads (DNA)
filter based on CpG content (DNA)
alignment with bowtie2 (DNA)
alignment with gsnap (RNA)
measure coverage with bedtools genomeCoverageBed (RNA)
normalize to total counts (RNA)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt files with raw and normalized counts


title: mouse_Bedalov2_DNA_methylation

description:
DNA cut with LpnPI
Bedalov-2


title: JEK15-528


title: mouse_Sample8_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample8


title: mouse_Sample4_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample4


title: mouse_Sample3_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample3


title: mouse_Sample6_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample6


title: mouse_Sample1_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample1


title: mouse_Bedalov5_DNA_methylation

description:
DNA cut with LpnPI
Bedalov-5


title: H3K27Ac +DHT ChIP-seq (duplicate of GSM1249448)

growth_protocol: Cells were grown in RPMI with charcoal-stripped serum, and stimulated with 10nM DHT for 4hr before collection (collected when 80% confluent)


title: JEK15-523


title: mouse_Sample5_RNA_seq

description:
RNA seq
transcript_data_8_nestin_CRE_mice_080918_1.txt
Sample5


title: mouse_Bedalov1_DNA_methylation

description:
DNA cut with LpnPI
Bedalov-1


title: mouse_Bedalov4_DNA_methylation

description:
DNA cut with LpnPI
Bedalov-4


title: 1_ChIP_OPC_Chd7_1

city: Paris

first: Carlos

last: Parras

address: 47 bd de l'hopital batiment ICM

country: France

institute: ICM

description: Chd7 ChIP in OPCs

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Data were filtered using SAMtools and PCR-derived duplicates removed by using PICARD MarkDuplicates
peaks were called using MACS (Model-based Analysis of ChIP-Seq)with options: keep-dup all, nolambda, broad, nomodel, extsize 75 -q 0.01 and filtered according to the following criteria: (i) length>=100bp and (ii) p-value<=5%
Genome_build: mm10
Supplementary_files_format_and_content: broadpeaks files with in this order: chrom, chromStart, chromEnd, peak name, score, signalValue, pValue, qValue

source_name: O4+ cells

growth_protocol: in vivo Magnetic-activated cell sorting of O4+ cells from P7 WT mouse cortices using anti-O4 antibodies

extract_protocol:
Lysates were clarified from sonicated nuclei and Chd7-DNA and Chd8-DNA complexes were isolated with O4 antibody.
The ChIP-seq libraries were prepared using TruSeq ChIP library preparation kit (Illumina ip-202-1012)

value: Cortex and Corpus callosum

value: Postnatal day 7

value: Anti-Chd7 (Cell Signaling; 6505)


title: Mouse_Healthy1_002

city: La Jolla

first: Catherine

last: Hedrick

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute for Allergy and Immunology

description:
processed data file:
Zhu_SC-10X_mouse_annotation.txt
Zhu_SC-10X_mouse_raw-counts.txt

data_processing:
Reads from single-cell RNA-seq were aligned and collapsed into unique molecular identifier (UMI) counts using 10x genomics’s cell-ranger software (version 1.3.0)
Counts were normalized across libraries with the aggregate function from cellranger for human and mouse separately
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab delimited files include counts and annotations for each sample

source_name: Cluster#C cells

extract_protocol:
Single-cell RNA-seq using 10X genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol (Zheng et. al., 2017).
Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol
Libraries were sequenced on HiSeq2500 platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles.

treatment_protocol: human hNeP cells were FACS sorted from healthy donor's fresh bone marrow.  Mouse Cluster#C cells were FACS sorted from healthy mice fresh BM as well as B16F10 melanoma tumor-bearing mice fresh BM.

tag: subject #

value: Mouse #1

tag: mouse status

value: healthy

value: bone marrow

tag: cell type surface markers

value: Lin- CD117+ Ly6A/E- Siglec F- FcεRIα- CD16/32+ Ly6B+ CD162lo CD48lo Ly6Clo CD115-

value: Cluster#C cells


title: Mouse_Tumor1_002

value: Mouse #4

value: B16F10 melanoma tumor-bearing mice


title: dE3

city: Hangzhou

first: Zhong-Min

last: Dai

state: Zhejiang

address: 16 Xuelin Street, Xiasha

institute: Hangzhou Normal University

description:
processed data file:
gene_counts.txt
gene_expression.txt
transcript_counts.txt
transcript_expression.txt
SG-2028-caCat_L2_323323

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 whole genome using bowtie2 v2.3.2.
Transcripts Per Million (TPM) and Fragments Per Kilobase Million (FPKM) were calculated using a protocol from Wagner et al., Theory in Biosciences, 2012 and Trapnell et al., Nature Biotechnology, 2010, respectively.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: txt files include TPM and FPKM values for each Sample

source_name: Nestin-Cre mediated Ctnnb1 Ex3 deletion (gain of function, dE3)

extract_protocol:
Spinal cord were removed, immersed in RNAstore solution (CWBiotech) and stored in -80oC, and RNA was harvested using Trizol reagent (Sangon).
VAHTS™ mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: embryonic day 13.5

value: Spinal cord


title: Mouse_Healthy2_002

value: Mouse #2

tag: tissue

tag: cell type


title: Mouse_Tumor3_002

value: Mouse #6


title: WT

description:
processed data file:
gene_counts.txt
gene_expression.txt
transcript_counts.txt
transcript_expression.txt
SG-2028-WT_L2_324324

source_name: wild type (WT)

value: wild type


title: Mouse_Tumor2_002

value: Mouse #5


title: Mouse_Healthy3_001

value: Mouse #3


title: Mouse_Healthy3_002


title: cKO

description:
processed data file:
gene_counts.txt
gene_expression.txt
transcript_counts.txt
transcript_expression.txt
SG-2028-koCKO_L3_312312

source_name: Ex2-6 deletion (loss of function, cKO)


title: 109_3E

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: RNA-seq

data_processing:
SOLiD 5500 deep sequencer run (single, 50 nt) was performed with single index to generate color-space data in XSQ format.
XSQ files were subjected to generation of the color-space CSFASTA/QUAL read sequence files using Life Technologies XSQTools software package. The TopHat-Cufflinks pipeline with the Bowtie backend aligner was used to align the color space read data to the Xla_9.1 Xenpus reference gonome sequence to generate BAM files.
Cufflinks processed RNA-seq BAM files to generate normalized amounts of mRNA expression based on the Xla_9.1 annotation.
Genome_build: Xla_9.1 (Xenbase release 9.1)
Supplementary_files_format_and_content: Microsoft Excel xlsx spreadsheets including normalized relative intensity of mRNA expression
Supplementary_files_format_and_content: FPKM

source_name: X. lavis embryo (stage 10.5; pool of five embryos)

growth_protocol: Eggs from two clutches (labeled D and E) of female X. laevis were fertilized in vitro and embryos staged according to Nieuwkoop and Faber (1994).

extract_protocol:
Each dish was harvested at gastrula stage 10.5 in 5-embryo aliquots. Replicates were taken from two different clutches (D & E), and 5 replicates were analyzed within each clutch (10 replicates total). Each five embryo pool was homogenized in 200 μL of TriPure (Roche).  Total RNA was DNAse treated, LiCl precipitated, and 100 ng was reverse transcribed into cDNA using Ovation RNA Amplification System V2 (NuGEN).
Total RNA was subjected to cDNA synthesis using the Ovation RNA Amplification System V2 kit (NuGEN). Deep sequencing libraries were generated from the cDNA using the ABI SOLiD 5500 Fragment Library Core Kit (Life Technologies).

tag: exposure


title: KD-CKX1 5.8_59_rep3

city: Olomouc

first: Petr

last: Vojta

address: Hnevotinska 5

institute: Palacky University

data_processing:
The reads were mapped to the reference genome of Hordeum vulgare (Hordeum_082214v1.30) by STAR aligner (STAR_2.4.2a)
Reads quantification was processed by subread-1.5.2 against GTF/GFF file (Hordeum_vulgare.082214v1.30.gtf)
Normalized counts were obtained by DESeq2 normalization
Genome_build: Hordeum_082214v1.30
Supplementary_files_format_and_content: DESeq2 normalized counts

source_name: whole spike

extract_protocol:
3 µg of total RNA from each sample, extracted with RNAqueous kit (Thermo Fischer Scientific, Waltham, USA) and treated with TURBO DNA-free kit (Thermo Fischer Scientific, Waltham, USA) was used for cDNA library preparation by Illumina® TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, Madison, USA).
cDNA library was prepared by Illumina® TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, Madison, USA)

tag: cultivar

value: Golden Promise

value: whole spike

value: BBCH scale - stage 59

value: KD-CKX1 line


title: Pretreated-6h [EA12035_255971_MOGENE-1_0-ST-V1_4.6HPREIFN]

city: Sapporo

first: Rui

last: Kamada

address: N10 W8, Kita-ku

department: Department of Chemistry, Faculty of Science

institute: Hokkaido University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: We obtained Microarray data (Affymetrix) from EA, A Quintiles Company. GeneSpring software was used for finding up/down regulated genes from the data (CHP files).

source_name: Bone-marrow derived macrophages

label_protocol: Affymetrix protocol

growth_protocol: Bone-marrow derived macrophages derived from H3.3-HA knockin mice were routinly generated by 10% of L-cell conditioned media in DMEM supplemented with 10% FBS

extract_protocol: RNA was harvested from bone-marrow derived macrophages using Trizol reagent.

treatment_protocol: Differentiated macrophages were treated with Interferon-gamma.

tag: cells

value: Bone-marrow derived macrophages

tag: group

value: Pretreated

tag: time point

value: H3.3-HA knock-in


title: Pretreated-3h [EA12035_260029_MOGENE-1_0-ST-V1_4.3HPREIFN]


title: Pretreated-3h [EA12035_260033_MOGENE-1_0-ST-V1_8.3HPREIFN]


title: Naïve-3h [EA12035_260028_MOGENE-1_0-ST-V1_3.3HNAIVE]

value: Naïve


title: Naïve-3h [EA12035_260032_MOGENE-1_0-ST-V1_7.3HNAIVE]


title: Naïve-0h [EA12035_260026_MOGENE-1_0-ST-V1_1.0HNAIVE]


title: Pretreated-0h [EA12035_255969_MOGENE-1_0-ST-V1_2.0HPREIFN]


title: Naïve-0h [EA12035_260030_MOGENE-1_0-ST-V1_5.0HNAIVE]


title: Pretreated-0h [EA12035_260027_MOGENE-1_0-ST-V1_2.0HPREIFN]


title: Naïve-6h [EA12035_255974_MOGENE-1_0-ST-V1_7.6HNAIVE]


title: Naïve-6h [EA12035_255970_MOGENE-1_0-ST-V1_3.6HNAIVE]


title: Mouse_Tumor3_001

value: bone marrow

value: Lin- CD117+ Ly6A/E- Siglec F- FcεRIα- CD16/32+ Ly6B+ CD162lo CD48lo Ly6Clo CD115-

value: Cluster#C cells


title: Pretreated-0h [EA12035_255973_MOGENE-1_0-ST-V1_6.0HPREIFN]


title: Mouse_Healthy2_001

value: healthy


title: Naïve-0h [EA12035_255972_MOGENE-1_0-ST-V1_5.0HNAIVE]


title: Pretreated-0h [EA12035_260031_MOGENE-1_0-ST-V1_6.0HPREIFN]


title: Mouse_Tumor1_001

value: Mouse #4

value: B16F10 melanoma tumor-bearing mice


title: Mouse_Healthy1_001

value: Mouse #1


title: mTEChi_ATAC_11

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: mTEChi_ATAC_merged_q_10_signal_mapq_10_treat_pileup.bw, TEC_ATAC_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_ATAC_MAPQ_10_peaks_minus_blacklist.bb

data_processing:
QC was performed using FastQC and Trimmomatic
RNA-seq reads were aligned using HISAT (version 0.1.6) and ChIP-seq peaks were pre-aligned using BWA (version 0.5.9) and Stampy (--bamkeepgoodreads)
Single cell RNA-seq outliers were identified using robust PCA on alignment proportion, ERCC92 spike-in proportion, number of detectable genes, proportion of reads mapping to protein-coding genes, proportion of mitochondrial transcripts, proportion of ribosomal transcripts, 3’ to 5’ coverage bias, transcriptomic variance, cell-to-mean correlation, the proportion of the library accounted for by the top 500 transcripts and GC content. Cells passing QC are listed in the associated counts matrix (WT_unadj.counts.gz).
RNA-seq reads were assigned to genes using HTSeq (intersection non-empty)
ChIP-seq and ATAC-seq bigWig profiles and peak-calls were generated using MACS2 on deduplicated BAM files with MAPQ >10
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include counts for RNA-seq samples, bigWig files show ChIP/input signal and bigBed files show peak calls for ChIP-seq samples

source_name: mTEChi

extract_protocol:
Thymic lobes were cleaned from fatty tissues and incubated with Liberase and DNaseI (Roche Diagnostics; 200μg/ml and 30μg/ml, respectively; 45min, 37ºC) to obtain a cell suspension which was subsequently filtered through a nylon mesh (100micro pore size, Sefar Nitex) to remove debris. TEC were sorted and then RNA was either isolated from single cells using the SMART-seq2 protocol. TEC for ChIP-seq and ATAC-seq were treated as detailed in Žuklys S et al. Nature Immunology 2016:17(10):1206-1215
RNA-seq libraries were prepared using the appropriate Illumina kit for SMART-seq2 or HiSeq2500 (ChIP-seq). Nextera adapters were used for single cell RNA-seq, ATAC-seq and ChIP-seq.

treatment_protocol: ChIP antibodies were (histone modification, company, cat #): H3K4me3, Diagenode, C15410003; H3K27me3, Millipore, 07-449; H3K4me1, Abcam, ab8895; H3K9ac, Abcam, ab4441; H3K4ac, Millipore, 07-539; H3K9me3, Millipore, 05-1242; H3K27ac, Abcam, ab4729.

tag: strain

value: wild-type

tag: sample type

value: ATAC

value: mTEChi


title: WT_3_H4

description:
WT_unadj.counts.gz
WT_3_H4

tag: genotype


title: WT_3_H9

description:
WT_unadj.counts.gz
WT_3_H9


title: cTEC_ATAC_08

description: cTEC_ATAC_08_q_10_signal_mapq_10_treat_pileup.bw, TEC_ATAC_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_ATAC_MAPQ_10_peaks_minus_blacklist.bb

source_name: cTEC

value: cTEC


title: mTEClo_ATAC_10

description: mTEClo_ATAC_merged_q_10_signal_mapq_10_treat_pileup.bw, TEC_ATAC_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_ATAC_MAPQ_10_peaks_minus_blacklist.bb

source_name: mTEClo

value: mTEClo


title: mTEClo_ATAC_09


title: WT_3_H8

description:
WT_unadj.counts.gz
WT_3_H8


title: WT_3_H6

description:
WT_unadj.counts.gz
WT_3_H6


title: WT_3_H3

description:
WT_unadj.counts.gz
WT_3_H3


title: Naïve-0h [EA12035_255968_MOGENE-1_0-ST-V1_1.0HNAIVE]


title: WT_3_H2

description:
WT_unadj.counts.gz
WT_3_H2


title: Mouse_Tumor2_001

value: Mouse #5


title: WT_3_H12

description:
WT_unadj.counts.gz
WT_3_H12


title: WT_3_G9

description:
WT_unadj.counts.gz
WT_3_G9


title: WT_3_H10

description:
WT_unadj.counts.gz
WT_3_H10


title: WT_3_G7

description:
WT_unadj.counts.gz
WT_3_G7


title: WT_3_H1

description:
WT_unadj.counts.gz
WT_3_H1


title: WT_3_H11

description:
WT_unadj.counts.gz
WT_3_H11


title: WT_3_G8

description:
WT_unadj.counts.gz
WT_3_G8


title: mTEChi_ATAC_12


title: WT_3_G6

description:
WT_unadj.counts.gz
WT_3_G6


title: WT_3_H5

description:
WT_unadj.counts.gz
WT_3_H5


title: WT_3_G3

description:
WT_unadj.counts.gz
WT_3_G3


title: WT_3_G4

description:
WT_unadj.counts.gz
WT_3_G4


title: WT_3_G12

description:
WT_unadj.counts.gz
WT_3_G12


title: WT_3_G2

description:
WT_unadj.counts.gz
WT_3_G2


title: WT_3_G11

description:
WT_unadj.counts.gz
WT_3_G11


title: WT_3_G10

description:
WT_unadj.counts.gz
WT_3_G10


title: WT_3_F4

description:
WT_unadj.counts.gz
WT_3_F4


title: WT_3_F7

description:
WT_unadj.counts.gz
WT_3_F7


title: WT_3_F6

description:
WT_unadj.counts.gz
WT_3_F6


title: WT_3_F5

description:
WT_unadj.counts.gz
WT_3_F5


title: WT_3_F2

description:
WT_unadj.counts.gz
WT_3_F2


title: WT_3_F3

description:
WT_unadj.counts.gz
WT_3_F3


title: WT_3_G1

description:
WT_unadj.counts.gz
WT_3_G1


title: WT_3_F8

description:
WT_unadj.counts.gz
WT_3_F8


title: WT_3_F9

description:
WT_unadj.counts.gz
WT_3_F9


title: Pretreated-6h [EA12035_255975_MOGENE-1_0-ST-V1_8.6HPREIFN]

value: Bone-marrow derived macrophages


title: WT_3_F11

description:
WT_unadj.counts.gz
WT_3_F11


title: WT_3_F10

description:
WT_unadj.counts.gz
WT_3_F10


title: WT_3_G5

description:
WT_unadj.counts.gz
WT_3_G5


title: WT_3_F12

description:
WT_unadj.counts.gz
WT_3_F12


title: WT_3_E8

description:
WT_unadj.counts.gz
WT_3_E8


title: WT_3_E4

description:
WT_unadj.counts.gz
WT_3_E4


title: WT_3_F1

description:
WT_unadj.counts.gz
WT_3_F1


title: WT_3_E2

description:
WT_unadj.counts.gz
WT_3_E2


title: WT_3_E5

description:
WT_unadj.counts.gz
WT_3_E5


title: WT_3_E10

description:
WT_unadj.counts.gz
WT_3_E10


title: WT_3_E11

description:
WT_unadj.counts.gz
WT_3_E11


title: WT_3_E12

description:
WT_unadj.counts.gz
WT_3_E12


title: WT_3_E1

description:
WT_unadj.counts.gz
WT_3_E1


title: WT_3_D9

description:
WT_unadj.counts.gz
WT_3_D9


title: WT_3_D8

description:
WT_unadj.counts.gz
WT_3_D8


title: WT_3_D7

description:
WT_unadj.counts.gz
WT_3_D7


title: WT_3_D4

description:
WT_unadj.counts.gz
WT_3_D4


title: WT_3_D11

description:
WT_unadj.counts.gz
WT_3_D11


title: WT_3_D2

description:
WT_unadj.counts.gz
WT_3_D2


title: WT_3_D5

description:
WT_unadj.counts.gz
WT_3_D5


title: WT_3_D3

description:
WT_unadj.counts.gz
WT_3_D3


title: WT_3_D12

description:
WT_unadj.counts.gz
WT_3_D12


title: WT_3_D10

description:
WT_unadj.counts.gz
WT_3_D10


title: WT_3_D1

description:
WT_unadj.counts.gz
WT_3_D1


title: WT_3_E7

description:
WT_unadj.counts.gz
WT_3_E7


title: WT_3_C7

description:
WT_unadj.counts.gz
WT_3_C7


title: WT_3_E6

description:
WT_unadj.counts.gz
WT_3_E6


title: WT_3_C9

description:
WT_unadj.counts.gz
WT_3_C9


title: WT_3_C6

description:
WT_unadj.counts.gz
WT_3_C6


title: WT_3_C5

description:
WT_unadj.counts.gz
WT_3_C5


title: WT_3_E9

description:
WT_unadj.counts.gz
WT_3_E9


title: WT_3_C8

description:
WT_unadj.counts.gz
WT_3_C8


title: WT_3_E3

description:
WT_unadj.counts.gz
WT_3_E3


title: WT_3_C4

description:
WT_unadj.counts.gz
WT_3_C4


title: WT_3_C2

description:
WT_unadj.counts.gz
WT_3_C2


title: WT_3_C3

description:
WT_unadj.counts.gz
WT_3_C3


title: WT_3_C12

description:
WT_unadj.counts.gz
WT_3_C12


title: WT_3_C1

description:
WT_unadj.counts.gz
WT_3_C1


title: WT_3_C10

description:
WT_unadj.counts.gz
WT_3_C10


title: WT_3_C11

description:
WT_unadj.counts.gz
WT_3_C11


title: WT_3_D6

description:
WT_unadj.counts.gz
WT_3_D6


title: WT_3_B9

description:
WT_unadj.counts.gz
WT_3_B9


title: WT_3_B8

description:
WT_unadj.counts.gz
WT_3_B8


title: WT_3_B7

description:
WT_unadj.counts.gz
WT_3_B7


title: WT_3_B6

description:
WT_unadj.counts.gz
WT_3_B6


title: WT_3_B3

description:
WT_unadj.counts.gz
WT_3_B3


title: WT_3_B5

description:
WT_unadj.counts.gz
WT_3_B5


title: WT_3_B4

description:
WT_unadj.counts.gz
WT_3_B4


title: WT_3_B12

description:
WT_unadj.counts.gz
WT_3_B12


title: WT_3_B2

description:
WT_unadj.counts.gz
WT_3_B2


title: WT_3_B11

description:
WT_unadj.counts.gz
WT_3_B11


title: WT_3_B10

description:
WT_unadj.counts.gz
WT_3_B10


title: WT_3_A9

description:
WT_unadj.counts.gz
WT_3_A9


title: WT_3_A8

description:
WT_unadj.counts.gz
WT_3_A8


title: WT_3_A7

description:
WT_unadj.counts.gz
WT_3_A7


title: WT_3_A6

description:
WT_unadj.counts.gz
WT_3_A6


title: WT_3_A2

description:
WT_unadj.counts.gz
WT_3_A2


title: WT_3_A4

description:
WT_unadj.counts.gz
WT_3_A4


title: WT_3_A3

description:
WT_unadj.counts.gz
WT_3_A3


title: WT_3_A11

description:
WT_unadj.counts.gz
WT_3_A11


title: WT_3_A10

description:
WT_unadj.counts.gz
WT_3_A10


title: WT_3_A12

description:
WT_unadj.counts.gz
WT_3_A12


title: WT_3_A1

description:
WT_unadj.counts.gz
WT_3_A1


title: WT_2_H9

description:
WT_unadj.counts.gz
WT_2_H9


title: WT_2_H8

description:
WT_unadj.counts.gz
WT_2_H8


title: WT_2_H7

description:
WT_unadj.counts.gz
WT_2_H7


title: WT_2_H5

description:
WT_unadj.counts.gz
WT_2_H5


title: WT_2_H2

description:
WT_unadj.counts.gz
WT_2_H2


title: WT_2_H4

description:
WT_unadj.counts.gz
WT_2_H4


title: WT_2_H12

description:
WT_unadj.counts.gz
WT_2_H12


title: WT_2_H11

description:
WT_unadj.counts.gz
WT_2_H11


title: WT_2_H10

description:
WT_unadj.counts.gz
WT_2_H10


title: WT_3_A5

description:
WT_unadj.counts.gz
WT_3_A5


title: WT_2_G8

description:
WT_unadj.counts.gz
WT_2_G8


title: WT_2_H1

description:
WT_unadj.counts.gz
WT_2_H1


title: WT_2_G7

description:
WT_unadj.counts.gz
WT_2_G7


title: WT_3_B1

description:
WT_unadj.counts.gz
WT_3_B1


title: WT_2_G4

description:
WT_unadj.counts.gz
WT_2_G4


title: WT_2_G5

description:
WT_unadj.counts.gz
WT_2_G5


title: WT_2_G3

description:
WT_unadj.counts.gz
WT_2_G3


title: WT_2_G12

description:
WT_unadj.counts.gz
WT_2_G12


title: WT_2_G1

description:
WT_unadj.counts.gz
WT_2_G1


title: WT_2_G10

description:
WT_unadj.counts.gz
WT_2_G10


title: WT_2_F9

description:
WT_unadj.counts.gz
WT_2_F9


title: WT_2_F8

description:
WT_unadj.counts.gz
WT_2_F8


title: WT_2_F7

description:
WT_unadj.counts.gz
WT_2_F7


title: WT_2_H6

description:
WT_unadj.counts.gz
WT_2_H6


title: WT_2_H3

description:
WT_unadj.counts.gz
WT_2_H3


title: WT_2_F3

description:
WT_unadj.counts.gz
WT_2_F3


title: WT_2_F5

description:
WT_unadj.counts.gz
WT_2_F5


title: WT_2_F2

description:
WT_unadj.counts.gz
WT_2_F2


title: WT_2_F10

description:
WT_unadj.counts.gz
WT_2_F10


title: WT_2_F12

description:
WT_unadj.counts.gz
WT_2_F12


title: WT_2_F1

description:
WT_unadj.counts.gz
WT_2_F1


title: WT_2_F11

description:
WT_unadj.counts.gz
WT_2_F11


title: WT_2_G6

description:
WT_unadj.counts.gz
WT_2_G6


title: WT_2_E7

description:
WT_unadj.counts.gz
WT_2_E7


title: WT_2_E3

description:
WT_unadj.counts.gz
WT_2_E3


title: WT_2_E4

description:
WT_unadj.counts.gz
WT_2_E4


title: WT_2_E9

description:
WT_unadj.counts.gz
WT_2_E9


title: WT_2_E5

description:
WT_unadj.counts.gz
WT_2_E5


title: WT_2_G11

description:
WT_unadj.counts.gz
WT_2_G11


title: WT_2_E11

description:
WT_unadj.counts.gz
WT_2_E11


title: WT_2_E2

description:
WT_unadj.counts.gz
WT_2_E2


title: WT_2_F6

description:
WT_unadj.counts.gz
WT_2_F6


title: WT_2_D8

description:
WT_unadj.counts.gz
WT_2_D8


title: WT_2_E10

description:
WT_unadj.counts.gz
WT_2_E10


title: WT_2_D9

description:
WT_unadj.counts.gz
WT_2_D9


title: WT_2_E1

description:
WT_unadj.counts.gz
WT_2_E1


title: WT_2_E12

description:
WT_unadj.counts.gz
WT_2_E12


title: WT_2_F4

description:
WT_unadj.counts.gz
WT_2_F4


title: WT_2_D7

description:
WT_unadj.counts.gz
WT_2_D7


title: WT_2_D6

description:
WT_unadj.counts.gz
WT_2_D6


title: WT_2_D5

description:
WT_unadj.counts.gz
WT_2_D5


title: WT_2_D4

description:
WT_unadj.counts.gz
WT_2_D4


title: WT_2_D3

description:
WT_unadj.counts.gz
WT_2_D3


title: WT_2_D2

description:
WT_unadj.counts.gz
WT_2_D2


title: WT_3_H7

description:
WT_unadj.counts.gz
WT_3_H7


title: WT_2_D11

description:
WT_unadj.counts.gz
WT_2_D11


title: WT_2_E8

description:
WT_unadj.counts.gz
WT_2_E8


title: WT_2_D12

description:
WT_unadj.counts.gz
WT_2_D12


title: WT_2_E6

description:
WT_unadj.counts.gz
WT_2_E6