title: INPkyA

city: West Haven

first: Kalle

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were aligned to the Homo Sapiens reference genome (hg19) using using the ultra-fast short DNA sequence aligner Bowtie2
Two biological samples were sequenced at Yale Center for Genome Analysis using Illumina Genome Analyzer II platform. For each sample at least 35 million reads were acquired and basic quality parameters checked with FASTQC. Sequence reads were aligned to the human reference genome (hg19) using DNA sequence aligner Bowtie2 with option “very-sensitive” producing 66-72% uniquely aligning reads. Further filtering of the alignments was done using Samtools (view -b -q 1). Peak calling was done using MACS2 protocol (Liu T 2014, Methods in Molecular biology XXX), specifying following options: fixed fragment length 146 bp recommended by MACS2 author (--nomodel --extsize 146) and p value 1e10-4. From the resulting MACS2 peaks only the peaks outside ENCODE blacklist regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz) were kept.
Further filtering of the alignments was done using Samtools (view -b -q 1).
Peak calling was done using MACS2.0, specifying following options: fixed fragment length 146 bp (--nomodel --extsize 146) and p value 1e10-4.
From the resulting MACS2 peaks the peaks inside ENCODE blacklist regions were removed
Genome_build: GRCh37.69
Supplementary_files_format_and_content: COahrABpe4q1s_peaks.narrowPeakfilt.txt is a text file that contains the normal decidualization media condition AHR ChIP-Seq peak coordinates after MACS2 run and filtering
Supplementary_files_format_and_content: KYahrABpe4q1s_peaks.narrowPeakfilt.txt is a text file that contains the kynurenine treatment AHR ChIP-Seq peak coordinates after MACS2 run and filtering

source_name: decidual stromal cells

growth_protocol: Human endometrial stromal fibroblasts (ESF) (T HESC, ATCC CRL-4003) were grown with DMEM (Sigma-Aldrich, D2906), supplemented with 10% charcoal stripped calf-serum (Hyclone), 1% antibiotic/antimycotic (ABAM; Gibco), 1nM sodium pyruvate (Gibco), 0.1% Insulin-Transferrin-Selenium (ITS premix, BD Biosciences), and 0.12% sodium bicarbonate. Cells were in vitro decidualized for 2 days by addition of 0.5 mM 8-Br-cAMP (Sigma) and 0.5 μM of synthetic progestin medroxyprogesterone acetate (MPA) in DMEM supplemented with 2% charcoal-stripped calf-serum. For ChIP-seq cells were further treated with AHR activator L-kynurenine (100 µM) (n=2) or normal decidualization media (n=2) for additional one hour.

extract_protocol:
Cells were harvested, resuspended and chemically cross-linked in suspension by the addition of 1% fresh formaldehyde with 9 minutes incubation at room temperature on a rotator. Cross-linking was quenched and cells were harvested by centrifugation and washed twice in cold PBS. Nuclei were extracted and sonication was performed using a Misonix S4000 sonicator.  Fragment size between 200bp and 600bp was obtained and confirmed by gel electrophoresis and Bionalyzer.
DNA library preparation and high-throughput sequencing were performed on an Illumina Genome Analyzer II following the protocol recommended by Illumina with a 75bp readleght at the Yale Center for Genome Analysis.

treatment_protocol: 2 days in vitro decidualized endometrial stromal fibroblast (ATCC: CRL-4003) plus one hour 100 µM L-kynurenine treatment

value: ATCC CRL-4003

value: L-kynurenine

tag: chip antibody


title: AHRcoB

status: Public on Jun 01 2019

type: SRA

middle: T

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

treatment_protocol: 2 days in vitro decidualized endometrial stromal fibroblast (ATCC: CRL-4003) grown in culture

tag: cell line

tag: treatment

value: control

value: Ah Receptor Antibody (H-211):sc-5579 (Santa Cruz, CA)


title: MEL624 control cells, replicate A [m6A MeRIP-Seq]

city: Mexico City

first: David

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

description:
MEL624-Cont-m6A-A
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-Cont-avg.bw
hg38-MEL624-m6A-Cont-avg.bw

library_source: transcriptomic

data_processing:
library strategy: m6A MeRIP-Seq
Reads were aligned against hg38 genome assembly with hisat 2.0.4 using the following parameters: --no-unal --rna-strandness R
sam files were sorted and converted to bam with samtools v1.7. Reads with QS < 10 were excluded
Normalized bigWig files were generated from bam files with bamCoverage from the deepTools suite v3.0.2 with the following parameters: -bs 20 --normalizeUsing BPM --skipNAs. Reads that overlap with the blacklisted regions from ENCODE project were excluded
Average bigWig files for the biological replicates were generated using the bigwigCompare program from the deepTools suite v3.0.2
Read counts for the RNAseq inputs were calculated with featureCounts from the Rsubread package v1.22.3 in a R 3.3.3 environment
The read count table was analyzed with edgeR v3.12.1 in a R 3.3.3 environment and log2 TPM measurements were generated. After calculating normalization factors and estimating dispersion, DEG genes between KOs and Control cells were calculated using glm modeling with a FDR < 1e-5. A final list of DEG shared between KO1 and KO2 was generated using in-house scripts
Genome_build: hg38, ensebml genes 93 annotation
Supplementary_files_format_and_content: bigwig files depicting average normalized read coverage, tab-delimited txt with log2 TPM information from RNAseq inputs as calculated by edgeR

molecule: total RNA

source_name: MEL624 control cells

growth_protocol: MEL624 cells were grown in standard DMEM media supplemented with 10% FBS and pen/strep in a 37C CO2 incubator

extract_protocol:
Total RNA was extracted from ~20 million cells with Trizol, following manufacturer instructions. 200ug of total RNA were subjected to two rounds of mRNA purification using the magnetic mRNA isolation kit from NEB (#S1550S)
Illumina sequencing libraries were prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina from NEB (#E7760), following manufacture's instructions

tag: cellosaurus cell line identifier

tag: cell type

value: Human melanoma cell line

tag: genotype/variation

value: Wild type + Random sgRNA

tag: rip antibody

value: m6A antibody


title: AHRcoA


title: INPkyB


title: D14 MODY1-2

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome using tophat-2.0.14
Raw counts were calculated using HtSeq-count
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, raw htseq counts for each sample, edgeR output

molecule: polyA RNA

extract_protocol:
RNA was harvested from cells using the PrepEase RNA Spin Kit (Affymetrix)
mRNA was first isolated with poly dT beads from 1-10µg of total RNA. RNA-seq libraries were prepared using the NEXTflex Rapid Directional RNA-SEQ Kit (dUTP-Based) v2 as per manufacturer's direction.

tag: genotype

value: HNF4A p.Ile271fs

tag: family identifier

tag: gender

value: male


title: INPcoA


title: 6dKYN_2

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
Transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: DSC24hKYN_DSC24hTCDD_DSC6dKYN_DSC6dTCDD_HTseqcounts_TPMs.txt is a tab limited text file that contains the HTseq read counts and transcripts per million (TPM) values for the samples reported in this submission

extract_protocol:
Cell cultures were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy Mini or Midi RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100 µM L-kynurenine or 10 nM TCDD  (2,3,7,8-Tetrachlorodibenzo-p-dioxin) for 24 hours or 6 days

value: 8 days in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture

value: 100 µM L-kynurenine

tag: time


title: INPcoB


title: 24hTCDD_2

value: 3 days in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture

value: 10 nM TCDD


title: AHRkyB


title: AHRkyA


title: 24hTCDD_3


title: 6dTCDD_2


title: 24hTCDD_1


title: 24hKYN_3


title: 24hKYN_2


title: 24hKYN_1


title: Cortex2.CCKVLANXX.SM2_052318p4_H9

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
scRNA-seq
full-length
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

organism: Mus musculus

source_name: Cortex

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

tag: Sex

value: Male

tag: age

value: one month

tag: strain

tag: library construction


title: Cortex2.CCKVLANXX.SM2_052318p4_H6


title: Cortex2.CCKVLANXX.SM2_052318p4_H5


title: Cortex2.CCKVLANXX.SM2_052318p4_H3


title: Cortex2.CCKVLANXX.SM2_052318p4_H7


title: Cortex2.CCKVLANXX.SM2_052318p4_H1


title: Cortex2.CCKVLANXX.SM2_052318p4_H2


title: Cortex2.CCKVLANXX.SM2_052318p4_H8


title: Cortex2.CCKVLANXX.SM2_052318p4_H12


title: Cortex2.CCKVLANXX.SM2_052318p4_G8


title: Cortex2.CCKVLANXX.SM2_052318p4_H11


title: Cortex2.CCKVLANXX.SM2_052318p4_G9


title: Cortex2.CCKVLANXX.SM2_052318p4_H10


title: Cortex2.CCKVLANXX.SM2_052318p4_G7


title: Cortex2.CCKVLANXX.SM2_052318p4_G5


title: Cortex2.CCKVLANXX.SM2_052318p4_G2


title: Cortex2.CCKVLANXX.SM2_052318p4_G4


title: Cortex2.CCKVLANXX.SM2_052318p4_G6


title: Cortex2.CCKVLANXX.SM2_052318p4_G3


title: Axin- vs Axin+

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description:
polarity(+)
251486841828_1_3

hyb_protocol: Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: Animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.

treatment_protocol: Tamoxifen (Sigma) was injected intraperitoneally into mice either as single dose or on three consecutive days (4 mg/25 g bodyweight, diluted in 200 µl corn oil) at the indicated time points to deplete Rspo3 expression

value: Axin-

value: epithelial cells

tag: cell sorting

value: td Tomato negative

value: Axin+

value: td Tomato positive


title: Cortex2.CCKVLANXX.SM2_052318p4_H4


title: Axin+ vs Axin-

description:
polarity(-)
251486841828_1_4


title: 5410 D vs. 6866 D

description:
polarity(+)
251486841825_1_1

value: colon cells

value: colon distal

value: Rspo3 KO

value: colon


title: 6869 D vs. 5428 D

description:
polarity(-)
251486841825_1_2


title: Monocyte Ly6Chigh from WT mice

first: Pawel

last: Durek

institute: Deutsches Rheuma-Forschungszentrum

description:
Chip1_MoLy6highWT
Each chip was generated with total RNA, pooled from several mice.

hyb_protocol: 15 µg cRNA was hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 645 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidic station 450 with HWS kit.

scan_protocol: Chips were scanned using the Affymetrix GeneChip scanner 3000 7G, and the raw data were generated with the Affymetrix Expression Console software v 1.2.1.

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, Joachim R. Grün) with the BioRetis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMed ID: 19265543). CEL file chip data were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Resulting data were uploaded into the BioRetis database. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All single chips were compared to all other single chips. The following parameters of absolute and comparative analyses were included in the BioRetis database: expression heights (Signals), call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR), call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Normally calculated t-tests of log Signals and SLRs could not be used here in one vs. one chip analyses. Therefore, for each present transcript, the significance of differential expression between two arrays was only obtained with a non-parametrically calculated Change call (one-sided Wilcoxon's signed rank test after Tukey-Biweight reduction of outliers, calculated by GCOS with all 11 oligo pairs on that chip), i.e., a transcript was called significant if the Change call was D/MD or I/MI, respectively. Significantly differentially expressed genes were filtered using both default parameter sets of filter criteria and further reduced with fold change (FC) and Signal height or differences and HPCDA-Volcano-Plots as explained in DOI: 10.13140/RG.2.1.2547.5923. Filter parameters are a combination of four different queries. They were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing analysis beginning with first 3 letters SGU and click on Next. Click on Chose an existing parameterset and select JRG_Increase for increased or JRG_Decrease for decreased probesets, respectively, and click on Fill. At the bottom of the site check the box named * use Bonferroni correction and click on Search only to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each, were analyzed in BioRetis with all possible 3 vs. 3 chips comparisons (one direction).

label: Biotin

source_name: Chip1: Ly6Chigh monocytes from control littermate mice

label_protocol: Labeling of total RNA was performed using the GeneChip 3' IVT Expression Kit from Affymetrix according to the manufacturer's instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, biotinylated cRNA was transcribed, and fragmented.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: WT or miR-146a-/- mouse spleen were treated for 4 min with RBC and ACT red blood cell lysis buffer, respectively. Splenic CD11b+ cells were isolated using the CD11b Microbeads (Miltenyi Biotec). Then, the Ly6C antibody staining was performed according to the manufacturer’s instructions. Cells were FACS sorted on a BD FACSAria Cell Sorting System (BD Biosciences) with >97% purity. To obtain sufficient mRNA amount, cells of several mice were pooled.

tag: strain/background

value: monocytes from spleen

tag: flow cytometric cell sorting

tag: genotype of sorted cells

value: WT


title: Monocyte Ly6Clow from WT mice

description:
Chip2_MoLy6lowWT
Each chip was generated with total RNA, pooled from several mice.

source_name: Chip2: Ly6Clow monocytes from control littermate mice


title: Cortex2.CCKVLANXX.SM2_052318p4_G1


title: Monocyte Ly6Chigh from miR-146a-/- KO mice

description:
Chip3_MoLy6high_miR146aKO
Each chip was generated with total RNA, pooled from several mice.

source_name: Chip3: Ly6Chigh monocytes from miR-146a-/- KO mice


title: Monocyte Ly6Clow from miR-146a-/- KO mice

description:
Chip4_MoLy6low_miR146aKO
Each chip was generated with total RNA, pooled from several mice.

source_name: Chip4: Ly6Clow monocytes from miR-146a-/- KO mice


title: Cortex2.CCKVLANXX.SM2_052318p4_G12


title: Cortex2.CCKVLANXX.SM2_052318p4_G10


title: Cortex2.CCKVLANXX.SM2_052318p4_F9


title: Cortex2.CCKVLANXX.SM2_052318p4_F5


title: Cortex2.CCKVLANXX.SM2_052318p4_F8


title: Cortex2.CCKVLANXX.SM2_052318p4_F3


title: Cortex2.CCKVLANXX.SM2_052318p4_F6


title: Cortex2.CCKVLANXX.SM2_052318p4_F7


title: Cortex2.CCKVLANXX.SM2_052318p4_F4


title: Cortex2.CCKVLANXX.SM2_052318p4_F12


title: Cortex2.CCKVLANXX.SM2_052318p4_G11


title: Cortex2.CCKVLANXX.SM2_052318p4_F11


title: Cortex2.CCKVLANXX.SM2_052318p4_E9


title: Cortex2.CCKVLANXX.SM2_052318p4_E7


title: Cortex2.CCKVLANXX.SM2_052318p4_F10


title: Cortex2.CCKVLANXX.SM2_052318p4_E5


title: Cortex2.CCKVLANXX.SM2_052318p4_E4


title: Cortex2.CCKVLANXX.SM2_052318p4_E8


title: Cortex2.CCKVLANXX.SM2_052318p4_F1


title: Cortex2.CCKVLANXX.SM2_052318p4_F2


title: Cortex2.CCKVLANXX.SM2_052318p4_E1


title: Cortex2.CCKVLANXX.SM2_052318p4_E2


title: Cortex2.CCKVLANXX.SM2_052318p4_E3


title: Cortex2.CCKVLANXX.SM2_052318p4_E12


title: Cortex2.CCKVLANXX.SM2_052318p4_D9


title: Cortex2.CCKVLANXX.SM2_052318p4_E11


title: Cortex2.CCKVLANXX.SM2_052318p4_E6


title: Cortex2.CCKVLANXX.SM2_052318p4_E10


title: Cortex2.CCKVLANXX.SM2_052318p4_D8


title: Cortex2.CCKVLANXX.SM2_052318p4_D6


title: Cortex2.CCKVLANXX.SM2_052318p4_D5


title: Cortex2.CCKVLANXX.SM2_052318p4_D2


title: Cortex2.CCKVLANXX.SM2_052318p4_D4


title: Cortex2.CCKVLANXX.SM2_052318p4_D11


title: Cortex2.CCKVLANXX.SM2_052318p4_D3


title: Cortex2.CCKVLANXX.SM2_052318p4_D10


title: Cortex2.CCKVLANXX.SM2_052318p4_D1


title: Cortex2.CCKVLANXX.SM2_052318p4_C9


title: Cortex2.CCKVLANXX.SM2_052318p4_D7


title: Cortex2.CCKVLANXX.SM2_052318p4_C8


title: Cortex2.CCKVLANXX.SM2_052318p4_D12


title: Cortex2.CCKVLANXX.SM2_052318p4_C7


title: Cortex2.CCKVLANXX.SM2_052318p4_C6


title: Cortex2.CCKVLANXX.SM2_052318p4_C4


title: Cortex2.CCKVLANXX.SM2_052318p4_C5


title: Cortex2.CCKVLANXX.SM2_052318p4_C1


title: Cortex2.CCKVLANXX.SM2_052318p4_C11


title: Cortex2.CCKVLANXX.SM2_052318p4_C3


title: Cortex2.CCKVLANXX.SM2_052318p4_C10


title: Cortex2.CCKVLANXX.SM2_052318p4_B9


title: Cortex2.CCKVLANXX.SM2_052318p4_B8


title: Cortex2.CCKVLANXX.SM2_052318p4_B6


title: Cortex2.CCKVLANXX.SM2_052318p4_C12


title: Cortex2.CCKVLANXX.SM2_052318p4_C2


title: Cortex2.CCKVLANXX.SM2_052318p4_B5


title: Cortex2.CCKVLANXX.SM2_052318p4_B7


title: Cortex2.CCKVLANXX.SM2_052318p4_B4


title: Cortex2.CCKVLANXX.SM2_052318p4_B3


title: 6dKYN_1

value: 8 days in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture

tag: cell line

tag: treatment


title: Cortex2.CCKVLANXX.SM2_052318p4_B2


title: Cortex2.CCKVLANXX.SM2_052318p4_B1


title: Cortex2.CCKVLANXX.SM2_052318p4_B12


title: Cortex2.CCKVLANXX.SM2_052318p4_A4


title: Cortex2.CCKVLANXX.SM2_052318p4_A9


title: Cortex2.CCKVLANXX.SM2_052318p4_B10


title: Cortex2.CCKVLANXX.SM2_052318p4_A8


title: Cortex2.CCKVLANXX.SM2_052318p4_A6


title: Cortex2.CCKVLANXX.SM2_052318p4_A5


title: Cortex2.CCKVLANXX.SM2_052318p4_A7


title: Cortex2.CCKVLANXX.SM2_052318p4_A2


title: Cortex2.CCKVLANXX.SM2_052318p4_A12


title: Cortex2.CCKVLANXX.SM2_052318p4_A1


title: Cortex2.CCKVLANXX.SM2_052318p4_A3


title: Cortex2.CCKVLANXX.SM2_052318p3_H9


title: Cortex2.CCKVLANXX.SM2_052318p3_H5


title: Cortex2.CCKVLANXX.SM2_052318p3_H4


title: Cortex2.CCKVLANXX.SM2_052318p3_H7


title: Cortex2.CCKVLANXX.SM2_052318p3_H3


title: Cortex2.CCKVLANXX.SM2_052318p4_A11


title: Cortex2.CCKVLANXX.SM2_052318p3_H8


title: Cortex2.CCKVLANXX.SM2_052318p3_H2


title: Cortex2.CCKVLANXX.SM2_052318p3_H6


title: Cortex2.CCKVLANXX.SM2_052318p3_H11


title: Cortex2.CCKVLANXX.SM2_052318p3_H10


title: Cortex2.CCKVLANXX.SM2_052318p4_A10


title: Cortex2.CCKVLANXX.SM2_052318p3_H1


title: Cortex2.CCKVLANXX.SM2_052318p3_H12


title: Cortex2.CCKVLANXX.SM2_052318p3_G8


title: Cortex2.CCKVLANXX.SM2_052318p3_G9


title: Cortex2.CCKVLANXX.SM2_052318p3_G6


title: Cortex2.CCKVLANXX.SM2_052318p3_G5


title: Cortex2.CCKVLANXX.SM2_052318p4_B11


title: Cortex2.CCKVLANXX.SM2_052318p3_G4


title: Cortex2.CCKVLANXX.SM2_052318p3_G10


title: Cortex2.CCKVLANXX.SM2_052318p3_G2


title: Cortex2.CCKVLANXX.SM2_052318p3_G12


title: Cortex2.CCKVLANXX.SM2_052318p3_G11


title: Cortex2.CCKVLANXX.SM2_052318p3_G1


title: Cortex2.CCKVLANXX.SM2_052318p3_F8


title: Cortex2.CCKVLANXX.SM2_052318p3_G7


title: Cortex2.CCKVLANXX.SM2_052318p3_F5


title: Cortex2.CCKVLANXX.SM2_052318p3_F2


title: Cortex2.CCKVLANXX.SM2_052318p3_F3


title: Cortex2.CCKVLANXX.SM2_052318p3_F12


title: Cortex2.CCKVLANXX.SM2_052318p3_F1


title: Cortex2.CCKVLANXX.SM2_052318p3_F11


title: Cortex2.CCKVLANXX.SM2_052318p3_F7


title: Cortex2.CCKVLANXX.SM2_052318p3_F4


title: Cortex2.CCKVLANXX.SM2_052318p3_E8


title: Cortex2.CCKVLANXX.SM2_052318p3_E9


title: Cortex2.CCKVLANXX.SM2_052318p3_E7


title: Cortex2.CCKVLANXX.SM2_052318p3_G3


title: Cortex2.CCKVLANXX.SM2_052318p3_E6


title: Cortex2.CCKVLANXX.SM2_052318p3_E5


title: Cortex2.CCKVLANXX.SM2_052318p3_F10


title: Cortex2.CCKVLANXX.SM2_052318p3_E4


title: Cortex2.CCKVLANXX.SM2_052318p3_E2


title: Cortex2.CCKVLANXX.SM2_052318p3_E1


title: Cortex2.CCKVLANXX.SM2_052318p3_F9


title: Cortex2.CCKVLANXX.SM2_052318p3_E12


title: Cortex2.CCKVLANXX.SM2_052318p3_E10


title: Cortex2.CCKVLANXX.SM2_052318p3_D9


title: Cortex2.CCKVLANXX.SM2_052318p3_E11


title: Cortex2.CCKVLANXX.SM2_052318p3_F6


title: Cortex2.CCKVLANXX.SM2_052318p3_D8


title: Cortex2.CCKVLANXX.SM2_052318p3_D7


title: 6dTCDD_1

tag: cell type


title: Cortex2.CCKVLANXX.SM2_052318p3_D2


title: Cortex2.CCKVLANXX.SM2_052318p3_D3


title: Cortex2.CCKVLANXX.SM2_052318p3_D12


title: Cortex2.CCKVLANXX.SM2_052318p3_D1


title: Cortex2.CCKVLANXX.SM2_052318p3_D11


title: Cortex2.CCKVLANXX.SM2_052318p3_D10


title: Cortex2.CCKVLANXX.SM2_052318p3_D5


title: Cortex2.CCKVLANXX.SM2_052318p3_E3


title: Cortex2.CCKVLANXX.SM2_052318p3_C9


title: Cortex2.CCKVLANXX.SM2_052318p3_C8


title: Cortex2.CCKVLANXX.SM2_052318p3_C5


title: Cortex2.CCKVLANXX.SM2_052318p3_C6


title: Cortex2.CCKVLANXX.SM2_052318p3_C7


title: Cortex2.CCKVLANXX.SM2_052318p3_C12


title: Cortex2.CCKVLANXX.SM2_052318p3_C1


title: Cortex2.CCKVLANXX.SM2_052318p3_D6


title: Cortex2.CCKVLANXX.SM2_052318p3_C3


title: Cortex2.CCKVLANXX.SM2_052318p3_C11


title: Cortex2.CCKVLANXX.SM2_052318p3_C10


title: Cortex2.CCKVLANXX.SM2_052318p3_B8


title: Cortex2.CCKVLANXX.SM2_052318p3_B5


title: Cortex2.CCKVLANXX.SM2_052318p3_B6


title: Cortex2.CCKVLANXX.SM2_052318p3_B3


title: Cortex2.CCKVLANXX.SM2_052318p3_B4


title: Cortex2.CCKVLANXX.SM2_052318p3_D4


title: Cortex2.CCKVLANXX.SM2_052318p3_B7


title: Cortex2.CCKVLANXX.SM2_052318p3_B1


title: Cortex2.CCKVLANXX.SM2_052318p3_B12


title: Cortex2.CCKVLANXX.SM2_052318p3_B2


title: Cortex2.CCKVLANXX.SM2_052318p3_B11


title: Cortex2.CCKVLANXX.SM2_052318p3_A8


title: Cortex2.CCKVLANXX.SM2_052318p3_A9


title: Cortex2.CCKVLANXX.SM2_052318p3_B10


title: Cortex2.CCKVLANXX.SM2_052318p3_C4


title: Cortex2.CCKVLANXX.SM2_052318p3_C2


title: Cortex2.CCKVLANXX.SM2_052318p3_A5


title: Cortex2.CCKVLANXX.SM2_052318p3_A7


title: Cortex2.CCKVLANXX.SM2_052318p3_A6


title: Cortex2.CCKVLANXX.SM2_052318p3_A1


title: Cortex2.CCKVLANXX.SM2_052318p3_A4


title: Cortex2.CCKVLANXX.SM2_052318p3_A3


title: Cortex2.CCKVLANXX.SM2_052318p3_B9


title: Cortex2.CCKVLANXX.SM2_052318p3_A12


title: Cortex2.CCKVLANXX.SM2_052318p2_H9


title: Cortex2.CCKVLANXX.SM2_052318p3_A10


title: Cortex2.CCKVLANXX.SM2_052318p3_A2


title: Cortex2.CCKVLANXX.SM2_052318p2_H7


title: Cortex2.CCKVLANXX.SM2_052318p2_H6


title: Cortex2.CCKVLANXX.SM2_052318p2_H5


title: Cortex2.CCKVLANXX.SM2_052318p2_H4


title: Cortex2.CCKVLANXX.SM2_052318p2_H3


title: Cortex2.CCKVLANXX.SM2_052318p2_H8


title: Cortex2.CCKVLANXX.SM2_052318p2_H12


title: Cortex2.CCKVLANXX.SM2_052318p2_H1


title: Cortex2.CCKVLANXX.SM2_052318p2_H11


title: Cortex2.CCKVLANXX.SM2_052318p2_H10


title: Cortex2.CCKVLANXX.SM2_052318p2_G9


title: Cortex2.CCKVLANXX.SM2_052318p2_G6


title: Cortex2.CCKVLANXX.SM2_052318p2_G4


title: Cortex2.CCKVLANXX.SM2_052318p2_G7


title: Cortex2.CCKVLANXX.SM2_052318p3_A11


title: Cortex2.CCKVLANXX.SM2_052318p2_G3


title: Cortex2.CCKVLANXX.SM2_052318p2_G12


title: Cortex2.CCKVLANXX.SM2_052318p2_F9


title: Cortex2.CCKVLANXX.SM2_052318p2_G1


title: Cortex2.CCKVLANXX.SM2_052318p2_F8


title: Cortex2.CCKVLANXX.SM2_052318p2_F4


title: Cortex2.CCKVLANXX.SM2_052318p2_F5


title: Cortex2.CCKVLANXX.SM2_052318p2_G11


title: Cortex2.CCKVLANXX.SM2_052318p2_G5


title: Cortex2.CCKVLANXX.SM2_052318p2_F7


title: Cortex2.CCKVLANXX.SM2_052318p2_F1


title: Cortex2.CCKVLANXX.SM2_052318p2_F11


title: Cortex2.CCKVLANXX.SM2_052318p2_F3


title: Cortex2.CCKVLANXX.SM2_052318p2_G8


title: Cortex2.CCKVLANXX.SM2_052318p2_F12


title: Cortex2.CCKVLANXX.SM2_052318p2_F10


title: Cortex2.CCKVLANXX.SM2_052318p2_E8


title: Cortex2.CCKVLANXX.SM2_052318p2_E7


title: Cortex2.CCKVLANXX.SM2_052318p2_E6


title: Cortex2.CCKVLANXX.SM2_052318p2_E5


title: Cortex2.CCKVLANXX.SM2_052318p2_E4


title: Cortex2.CCKVLANXX.SM2_052318p2_G2


title: Cortex2.CCKVLANXX.SM2_052318p2_G10


title: Cortex2.CCKVLANXX.SM2_052318p2_E3


title: Cortex2.CCKVLANXX.SM2_052318p2_E9


title: Cortex2.CCKVLANXX.SM2_052318p2_F6


title: Cortex2.CCKVLANXX.SM2_052318p2_E1


title: Cortex2.CCKVLANXX.SM2_052318p2_D8


title: Cortex2.CCKVLANXX.SM2_052318p2_E10


title: Cortex2.CCKVLANXX.SM2_052318p2_E11


title: Cortex2.CCKVLANXX.SM2_052318p2_F2


title: Cortex2.CCKVLANXX.SM2_052318p2_D9


title: Cortex2.CCKVLANXX.SM2_052318p2_E12


title: Cortex2.CCKVLANXX.SM2_052318p2_D7


title: Cortex2.CCKVLANXX.SM2_052318p2_D5


title: Cortex2.CCKVLANXX.SM2_052318p2_D6


title: Cortex2.CCKVLANXX.SM2_052318p2_D2


title: Cortex2.CCKVLANXX.SM2_052318p2_D3


title: Cortex2.CCKVLANXX.SM2_052318p2_D11


title: Cortex2.CCKVLANXX.SM2_052318p2_D10


title: Cortex2.CCKVLANXX.SM2_052318p2_D12


title: Cortex2.CCKVLANXX.SM2_052318p2_C8


title: Cortex2.CCKVLANXX.SM2_052318p2_C7


title: Cortex2.CCKVLANXX.SM2_052318p2_E2


title: Cortex2.CCKVLANXX.SM2_052318p2_C6


title: Cortex2.CCKVLANXX.SM2_052318p2_C9


title: Cortex2.CCKVLANXX.SM2_052318p2_C5


title: Cortex2.CCKVLANXX.SM2_052318p2_C4


title: Cortex2.CCKVLANXX.SM2_052318p2_C3


title: Cortex2.CCKVLANXX.SM2_052318p2_C2


title: Cortex2.CCKVLANXX.SM2_052318p2_C1


title: Cortex2.CCKVLANXX.SM2_052318p2_C11


title: Cortex2.CCKVLANXX.SM2_052318p2_D4


title: Cortex2.CCKVLANXX.SM2_052318p2_B9


title: Cortex2.CCKVLANXX.SM2_052318p2_D1


title: Cortex2.CCKVLANXX.SM2_052318p2_B6


title: Cortex2.CCKVLANXX.SM2_052318p2_B7


title: Cortex2.CCKVLANXX.SM2_052318p2_B8


title: Cortex2.CCKVLANXX.SM2_052318p2_C10


title: Cortex2.CCKVLANXX.SM2_052318p2_B1


title: Cortex2.CCKVLANXX.SM2_052318p2_B4


title: Cortex2.CCKVLANXX.SM2_052318p2_B10


title: Cortex2.CCKVLANXX.SM2_052318p2_A9


title: Cortex2.CCKVLANXX.SM2_052318p2_A7


title: Cortex2.CCKVLANXX.SM2_052318p2_A6


title: Cortex2.CCKVLANXX.SM2_052318p2_A5


title: Cortex2.CCKVLANXX.SM2_052318p2_A4


title: Cortex2.CCKVLANXX.SM2_052318p2_A3


title: Cortex2.CCKVLANXX.SM2_052318p2_A2


title: Cortex2.CCKVLANXX.SM2_052318p2_B12


title: Cortex2.CCKVLANXX.SM2_052318p2_C12


title: Cortex2.CCKVLANXX.SM2_052318p2_A8


title: Cortex2.CCKVLANXX.SM2_052318p2_A12


title: Cortex2.CCKVLANXX.SM2_052318p2_A10


title: Cortex2.CCKVLANXX.SM2_052318p2_A11


title: Cortex2.CCKVLANXX.SM2_052318p2_A1


title: Cortex2.CCKVLANXX.SM2_052318p1_H7


title: Cortex2.CCKVLANXX.SM2_052318p1_H8


title: Cortex2.CCKVLANXX.SM2_052318p1_H9


title: Cortex2.CCKVLANXX.SM2_052318p1_H4


title: Cortex2.CCKVLANXX.SM2_052318p1_H5


title: Cortex2.CCKVLANXX.SM2_052318p1_H6


title: Cortex2.CCKVLANXX.SM2_052318p1_H3


title: Cortex2.CCKVLANXX.SM2_052318p2_B5


title: Cortex2.CCKVLANXX.SM2_052318p1_H2


title: Cortex2.CCKVLANXX.SM2_052318p2_B2


title: Cortex2.CCKVLANXX.SM2_052318p2_B3


title: Cortex2.CCKVLANXX.SM2_052318p1_H1


title: Cortex2.CCKVLANXX.SM2_052318p1_H12


title: Cortex2.CCKVLANXX.SM2_052318p2_B11


title: Cortex2.CCKVLANXX.SM2_052318p1_H11


title: Cortex2.CCKVLANXX.SM2_052318p1_G9


title: Cortex2.CCKVLANXX.SM2_052318p1_G8


title: Cortex2.CCKVLANXX.SM2_052318p1_G5


title: Cortex2.CCKVLANXX.SM2_052318p1_G7


title: Cortex2.CCKVLANXX.SM2_052318p1_G6


title: Cortex2.CCKVLANXX.SM2_052318p1_G4


title: Cortex2.CCKVLANXX.SM2_052318p1_G3


title: Cortex2.CCKVLANXX.SM2_052318p1_G2


title: Cortex2.CCKVLANXX.SM2_052318p1_G1


title: Cortex2.CCKVLANXX.SM2_052318p1_G10


title: Cortex2.CCKVLANXX.SM2_052318p1_G11


title: Cortex2.CCKVLANXX.SM2_052318p1_G12


title: Cortex2.CCKVLANXX.SM2_052318p2_H2


title: Cortex2.CCKVLANXX.SM2_052318p1_H10


title: Cortex2.CCKVLANXX.SM2_052318p1_F8


title: Cortex2.CCKVLANXX.SM2_052318p1_F5


title: Cortex2.CCKVLANXX.SM2_052318p1_E2


title: Cortex2.CCKVLANXX.SM2_052318p1_E8


title: Cortex2.CCKVLANXX.SM2_052318p1_E5


title: Cortex2.CCKVLANXX.SM2_052318p1_F6


title: Cortex2.CCKVLANXX.SM2_052318p1_F2


title: Cortex2.CCKVLANXX.SM2_052318p1_F1


title: Cortex2.CCKVLANXX.SM2_052318p1_E11


title: Cortex2.CCKVLANXX.SM2_052318p1_F3


title: Cortex2.CCKVLANXX.SM2_052318p1_E9


title: Cortex2.CCKVLANXX.SM2_052318p1_F12


title: Cortex2.CCKVLANXX.SM2_052318p1_F7


title: Cortex2.CCKVLANXX.SM2_052318p1_F4


title: Cortex2.CCKVLANXX.SM2_052318p1_F10


title: Cortex2.CCKVLANXX.SM2_052318p1_E6


title: Cortex2.CCKVLANXX.SM2_052318p1_F11


title: Cortex2.CCKVLANXX.SM2_052318p1_E3


title: Cortex2.CCKVLANXX.SM2_052318p1_D8


title: Cortex2.CCKVLANXX.SM2_052318p1_D6


title: Cortex2.CCKVLANXX.SM2_052318p1_D7


title: Cortex2.CCKVLANXX.SM2_052318p1_E7


title: Cortex2.CCKVLANXX.SM2_052318p1_E10


title: Cortex2.CCKVLANXX.SM2_052318p1_D9


title: Cortex2.CCKVLANXX.SM2_052318p1_F9


title: Cortex2.CCKVLANXX.SM2_052318p1_D5


title: Cortex2.CCKVLANXX.SM2_052318p1_E4


title: Cortex2.CCKVLANXX.SM2_052318p1_E1


title: Cortex2.CCKVLANXX.SM2_052318p1_D4


title: Cortex2.CCKVLANXX.SM2_052318p1_E12


title: Cortex2.CCKVLANXX.SM2_052318p1_D2


title: Cortex2.CCKVLANXX.SM2_052318p1_D3


title: Cortex2.CCKVLANXX.SM2_052318p1_D1


title: Cortex2.CCKVLANXX.SM2_052318p1_C7


title: Cortex2.CCKVLANXX.SM2_052318p1_C3


title: Cortex2.CCKVLANXX.SM2_052318p1_C4


title: Cortex2.CCKVLANXX.SM2_052318p1_D12


title: Cortex2.CCKVLANXX.SM2_052318p1_C1


title: Cortex2.CCKVLANXX.SM2_052318p1_C10


title: Cortex2.CCKVLANXX.SM2_052318p1_B9


title: Cortex2.CCKVLANXX.SM2_052318p1_C11


title: Cortex2.CCKVLANXX.SM2_052318p1_C5


title: Cortex2.CCKVLANXX.SM2_052318p1_B7


title: Cortex2.CCKVLANXX.SM2_052318p1_C6


title: Cortex2.CCKVLANXX.SM2_052318p1_D11


title: Cortex2.CCKVLANXX.SM2_052318p1_B8


title: Cortex2.CCKVLANXX.SM2_052318p1_D10


title: Cortex2.CCKVLANXX.SM2_052318p1_C12


title: Cortex2.CCKVLANXX.SM2_052318p1_B4


title: Cortex2.CCKVLANXX.SM2_052318p1_B5


title: Cortex2.CCKVLANXX.SM2_052318p1_C2


title: Cortex2.CCKVLANXX.SM2_052318p1_C8


title: Cortex2.CCKVLANXX.SM2_052318p1_B6


title: Cortex2.CCKVLANXX.SM2_052318p1_B3


title: Cortex2.CCKVLANXX.SM2_052318p1_B1


title: Cortex2.CCKVLANXX.SM2_052318p1_B12


title: Cortex2.CCKVLANXX.SM2_052318p1_B11


title: Cortex2.CCKVLANXX.SM2_052318p1_B10


title: Cortex2.CCKVLANXX.SM2_052318p1_A8


title: Cortex2.CCKVLANXX.SM2_052318p1_A6


title: Cortex2.CCKVLANXX.SM2_052318p1_A7


title: Cortex2.CCKVLANXX.SM2_052318p1_A4


title: Cortex2.CCKVLANXX.SM2_052318p1_A3


title: Cortex2.CCKVLANXX.SM2_052318p1_A2


title: Cortex2.CCKVLANXX.SM2_052318p1_A5


title: Cortex2.CCKVLANXX.SM2_052318p1_A12


title: Cortex2.CCKVLANXX.SM2_052318p1_A1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H6

description:
scRNA-seq
3'-end
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

value: sci-RNA-seq


title: Cortex2.CCKVLANXX.SM2_052318p1_A10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H4


title: Cortex2.CCKVLANXX.SM2_052318p1_A11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H3


title: Cortex2.CCKVLANXX.SM2_052318p1_B2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H5


title: Cortex2.CCKVLANXX.SM2_052318p1_C9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G6


title: Cortex2.CCKVLANXX.SM2_052318p1_A9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_H7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F6


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E6


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_G9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_F9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D6


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_D12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C6


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_E11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B7


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B6


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B1


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B10


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B11


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_B8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A5


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A4


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_C2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A6


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A2


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A12


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A11


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H7


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H6


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H4


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H3


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A9


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H12


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G9


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A7


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G8


title: Cortex2.CCKVLANXX.052318-SciSeq-p3_A3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G7


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G6


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F9


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F6


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F7


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F8


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G11


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F4


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_H11


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F11


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G4


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E8


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E9


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E4


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E12


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E11


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F12


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D9


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_G12


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D8


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_F1


title: Ost_hIRF8WT_Day4_1

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

data_processing:
Convert from BCL and demultiplex using Casava 1.8.4 or bcl2fastq 2.17.1
Map to mm10 using Tophat 2.1.0
Calculate RPKM using Partek GS 6.6
ANOVA comparisons on Log2 RPKM (with 0.1 offse) using Partek GS 6.6
PCA plots of RPKM values using Partek GS 6.6
Normalized BigWig files using deepTools bamCoverage
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

source_name: cultured BMM

extract_protocol:
RNAeasy extraction of total RNA was performed according to the manufacturer's (Qiagen) instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMMs from Irf8-/- and Irf8+/+ mice were cultured in the presence of MCSF and RANKL for 8 days to generate terminally differentiated osteoclasts. For transduction studies, BMMs from Irf8-/- mice were transduced with hIRF8WT, hIRF8G388S, or hIRF8379-389, followed by treatment with MCSF and RANKL for 8 days to generate terminally differentiated osteoclasts.

value: Osteoclast

tag: time point


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D7


title: Ost_hIRF8WT_Day4_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E7


title: Ost_hIRF8WT_Day4_3


title: Mac_mock_Untreated_2

value: BM derived Macrophage

value: mock

tag: agent

value: Untreated


title: Mac_mock_Untreated_1

tag: genotype


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D6

value: Male

value: one month


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D4


title: Mac_mock_IFNg+LPS-8hr_1

value: IFNg+LPS


title: Mac_mock_IFNg+LPS-8hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D3


title: Mac_mock_IFNg+LPS-4hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D12


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D2


title: Mac_mock_IFNg+LPS-1hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_E6


title: Mac_mock_IFNg_1

value: IFNg


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C9


title: Mac_hIRF8WT_Untreated_2


title: Mac_hIRF8WT_Untreated_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C8


title: Mac_hIRF8WT_IFNg+LPS-8hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_D11


title: Mac_mock_IFNg_2


title: Mac_hIRF8WT_IFNg+LPS-8hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C6


title: Mac_hIRF8WT_IFNg+LPS-4hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C7


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C4


title: Mac_mock_IFNg+LPS-4hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C2


title: Mac_hIRF8WT_IFNg+LPS-1hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C1


title: Mac_hIRF8WT_IFNg_2


title: Mac_hIRF8WT_IFNg_1


title: Mac_hIRF8WT_IFNg+LPS-1hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C12


title: Mac_hIRF8G388S_Untreated_2


title: Mac_hIRF8G388S_Untreated_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B9


title: Mac_hIRF8G388S_IFNg+LPS-4hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B8


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B7


title: Mac_hIRF8G388S_IFNg+LPS-8hr_1


title: Mac_hIRF8G388S_IFNg+LPS-4hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B6


title: Mac_hIRF8G388S_IFNg+LPS-1hr_2


title: Mac_hIRF8WT_IFNg+LPS-4hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B4


title: Mac_hIRF8G388S_IFNg+LPS-1hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B12


title: Mac_hIRF8G388S_IFNg_1


title: Mac_hIRF8G388S_IFNg_2


title: Mac_hIRF8379-389_IFNg+LPS-8hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B1


title: Mac_hIRF8379-389_Untreated_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_C11


title: Mac_hIRF8379-389_IFNg+LPS-8hr_1


title: Mac_hIRF8379-389_IFNg+LPS-4hr_2


title: Mac_hIRF8G388S_IFNg+LPS-8hr_2


title: Mac_hIRF8379-389_Untreated_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A9


title: Mac_hIRF8379-389_IFNg+LPS-4hr_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A7


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B5


title: Mac_hIRF8379-389_IFNg+LPS-1hr_2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A8


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A6


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A5


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A4


title: Mac_hIRF8379-389_IFNg_1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A3


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A2


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B11


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_B10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A12


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A1


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A10


title: Cortex2.CCKVLANXX.052318-SciSeq-p2_A11


title: Cortex2.CCJ15ANXX.SM2_052318p4_H9


title: Cortex2.CCJ15ANXX.SM2_052318p4_H8


title: Mac_hIRF8379-389_IFNg+LPS-1hr_1


title: Mac_hIRF8379-389_IFNg_2


title: Cortex2.CCJ15ANXX.SM2_052318p4_H7


title: Cortex2.CCJ15ANXX.SM2_052318p4_H6


title: Cortex2.CCJ15ANXX.SM2_052318p4_H5


title: Cortex2.CCJ15ANXX.SM2_052318p4_H4


title: Cortex2.CCJ15ANXX.SM2_052318p4_H1


title: Cortex2.CCJ15ANXX.SM2_052318p4_H2


title: Cortex2.CCJ15ANXX.SM2_052318p4_H3


title: Cortex2.CCJ15ANXX.SM2_052318p4_H12


title: Cortex2.CCJ15ANXX.SM2_052318p4_H11


title: EA10047_314655_HUGENE-1_0-ST-V1_HU.FB.72HR.MEDIA#1

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix HG U133 Plus version 2 arrays.

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

data_processing: Expression data are normalized using RMA algorithm, then scaled so that the 2% trimmed mean is 150.

label: biotin

source_name: synovium

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

growth_protocol: Fibroblasts (RA-32) were plated on day 1 at 50,000 cells per well in 24-well plates in 10% FBS containing media. Cells were serum-starved on day 2 by changing to 1% FBS-containing media.

extract_protocol: RNA was extracted using the Qiagen RNeasy Micro Kit.

treatment_protocol: Cells were stimulated with TNF (1 ng/mL) or TNF (1 ng/mL) + IL-17A (1 ng/mL) or IL-17A (1ng/mL) on day 3 for 0, 1, 2, 4 , 8, 12, 18, 24 and 72 hours.

tag: replicate

value: MEDIA


title: Cortex2.CCJ15ANXX.SM2_052318p4_H10


title: EA10047_314654_HUGENE-1_0-ST-V1_HU.FB.24HR.TNF+IL17#2


title: EA10047_314659_HUGENE-1_0-ST-V1_HU.FB.72HR.TNF+IL17#1


title: EA10047_314660_HUGENE-1_0-ST-V1_HU.FB.72HR.TNF+IL17#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_G9


title: EA10047_314656_HUGENE-1_0-ST-V1_HU.FB.72HR.MEDIA#2


title: EA10047_314651_HUGENE-1_0-ST-V1_HU.FB.24HR.IL17#1


title: EA10047_314658_HUGENE-1_0-ST-V1_HU.FB.72HR.TNF#2

value: TNF


title: EA10047_314648_HUGENE-1_0-ST-V1_HU.FB.24HR.MEDIA#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_G8


title: EA10047_314649_HUGENE-1_0-ST-V1_HU.FB.24HR.TNF#1


title: EA10047_314645_HUGENE-1_0-ST-V1_HU.FB.18HR.TNF+IL17#1


title: EA10047_314653_HUGENE-1_0-ST-V1_HU.FB.24HR.TNF+IL17#1


title: EA10047_314647_HUGENE-1_0-ST-V1_HU.FB.24HR.MEDIA#1


title: EA10047_314644_HUGENE-1_0-ST-V1_HU.FB.18HR.IL17#2


title: EA10047_314652_HUGENE-1_0-ST-V1_HU.FB.24HR.IL17#2


title: EA10047_314646_HUGENE-1_0-ST-V1_HU.FB.18HR.TNF+IL17#2


title: EA10047_314643_HUGENE-1_0-ST-V1_HU.FB.18HR.IL17#1


title: EA10047_314650_HUGENE-1_0-ST-V1_HU.FB.24HR.TNF#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_G6


title: EA10047_314657_HUGENE-1_0-ST-V1_HU.FB.72HR.TNF#1


title: EA10047_314641_HUGENE-1_0-ST-V1_HU.FB.18HR.TNF#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_G5


title: EA10047_314640_HUGENE-1_0-ST-V1_HU.FB.18HR.MEDIA#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_G4


title: EA10047_314642_HUGENE-1_0-ST-V1_HU.FB.18HR.TNF#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_G3


title: EA10047_314639_HUGENE-1_0-ST-V1_HU.FB.18HR.MEDIA#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_G2


title: Cortex2.CCJ15ANXX.SM2_052318p4_G1


title: Cortex2.CCJ15ANXX.SM2_052318p4_G12


title: EA10047_314637_HUGENE-1_0-ST-V1_HU.FB.12HR.TNF+IL17#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_G7


title: Cortex2.CCJ15ANXX.SM2_052318p4_G10


title: Cortex2.CCJ15ANXX.SM2_052318p4_F9


title: Cortex2.CCJ15ANXX.SM2_052318p4_F8


title: Cortex2.CCJ15ANXX.SM2_052318p4_G11


title: Cortex2.CCJ15ANXX.SM2_052318p4_F3


title: Cortex2.CCJ15ANXX.SM2_052318p4_F5


title: Cortex2.CCJ15ANXX.SM2_052318p4_F7


title: Cortex2.CCJ15ANXX.SM2_052318p4_F6


title: Cortex2.CCJ15ANXX.SM2_052318p4_F4


title: Cortex2.CCJ15ANXX.SM2_052318p4_F2


title: Cortex2.CCJ15ANXX.SM2_052318p4_F1


title: Cortex2.CCJ15ANXX.SM2_052318p4_F12


title: EA10047_314636_HUGENE-1_0-ST-V1_HU.FB.12HR.IL17#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_F11


title: EA10047_314631_HUGENE-1_0-ST-V1_HU.FB.8HR.TNF+IL17#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_F10


title: EA10047_314638_HUGENE-1_0-ST-V1_HU.FB.12HR.TNF+IL17#2


title: EA10047_314632_HUGENE-1_0-ST-V1_HU.FB.8HR.TNF+IL17#2


title: EA10047_314635_HUGENE-1_0-ST-V1_HU.FB.12HR.IL17#1


title: EA10047_314630_HUGENE-1_0-ST-V1_HU.FB.8HR.IL17#2


title: EA10047_314629_HUGENE-1_0-ST-V1_HU.FB.8HR.IL17#1


title: EA10047_314633_HUGENE-1_0-ST-V1_HU.FB.12HR.TNF#1


title: EA10047_314634_HUGENE-1_0-ST-V1_HU.FB.12HR.TNF#2


title: EA10047_314627_HUGENE-1_0-ST-V1_HU.FB.8HR.TNF#1


title: EA10047_314628_HUGENE-1_0-ST-V1_HU.FB.8HR.TNF#2


title: EA10047_314626_HUGENE-1_0-ST-V1_HU.FB.8HR.MEDIA#2


title: EA10047_314621_HUGENE-1_0-ST-V1_HU.FB.4HR.IL17#1


title: EA10047_314619_HUGENE-1_0-ST-V1_HU.FB.4HR.TNF#1


title: EA10047_314622_HUGENE-1_0-ST-V1_HU.FB.4HR.IL17#2


title: EA10047_314620_HUGENE-1_0-ST-V1_HU.FB.4HR.TNF#2


title: EA10047_314623_HUGENE-1_0-ST-V1_HU.FB.4HR.TNF+IL17#1


title: EA10047_314625_HUGENE-1_0-ST-V1_HU.FB.8HR.MEDIA#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_E8


title: Cortex2.CCJ15ANXX.SM2_052318p4_E7


title: Cortex2.CCJ15ANXX.SM2_052318p4_E9


title: EA10047_314624_HUGENE-1_0-ST-V1_HU.FB.4HR.TNF+IL17#2


title: Mac_mock_IFNg+LPS-1hr_2


title: Cortex2.CCJ15ANXX.SM2_052318p4_E6


title: Cortex2.CCJ15ANXX.SM2_052318p4_E5


title: Cortex2.CCJ15ANXX.SM2_052318p4_E4


title: EA10047_314616_HUGENE-1_0-ST-V1_HU.FB.2HR.TNF+IL17#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_E3


title: EA10047_314615_HUGENE-1_0-ST-V1_HU.FB.2HR.TNF+IL17#1


title: EA10047_314618_HUGENE-1_0-ST-V1_HU.FB.4HR.MEDIA#2


title: EA10047_314614_HUGENE-1_0-ST-V1_HU.FB.2HR.IL17#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_E2


title: Cortex2.CCJ15ANXX.SM2_052318p4_E1


title: EA10047_314613_HUGENE-1_0-ST-V1_HU.FB.2HR.IL17#1


title: EA10047_314617_HUGENE-1_0-ST-V1_HU.FB.4HR.MEDIA#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_E12


title: Cortex2.CCJ15ANXX.SM2_052318p4_D8


title: Cortex2.CCJ15ANXX.SM2_052318p4_D7


title: Cortex2.CCJ15ANXX.SM2_052318p4_D9


title: EA10047_314611_HUGENE-1_0-ST-V1_HU.FB.2HR.TNF#1


title: Cortex2.CCJ15ANXX.SM2_052318p4_D5


title: Cortex2.CCJ15ANXX.SM2_052318p4_E11


title: Cortex2.CCJ15ANXX.SM2_052318p4_D6


title: Cortex2.CCJ15ANXX.SM2_052318p4_E10


title: EA10047_314612_HUGENE-1_0-ST-V1_HU.FB.2HR.TNF#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_D3


title: Cortex2.CCJ15ANXX.SM2_052318p4_D1


title: Cortex2.CCJ15ANXX.SM2_052318p4_D2


title: EA10047_314609_HUGENE-1_0-ST-V1_HU.FB.1HR.TNF+IL17#1


title: EA10047_314610_HUGENE-1_0-ST-V1_HU.FB.1HR.TNF+IL17#2


title: EA10047_314608_HUGENE-1_0-ST-V1_HU.FB.1HR.IL17#2


title: EA10047_314606_HUGENE-1_0-ST-V1_HU.FB.1HR.TNF#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_D4


title: EA10047_314607_HUGENE-1_0-ST-V1_HU.FB.1HR.IL17#1


title: EA10047_314601_HUGENE-1_0-ST-V1_HU.FB.0HR.UNTREATED#1

value: UNTREATED


title: EA10047_314602_HUGENE-1_0-ST-V1_HU.FB.0HR.UNTREATED#2


title: EA10047_314604_HUGENE-1_0-ST-V1_HU.FB.1HR.MEDIA#2


title: Cortex2.CCJ15ANXX.SM2_052318p4_D10


title: E14.5 Adam19KO CNCCs

city: Kyoto

first: Atsuko

last: Sehara-Fujisawa

state: 京都府

address: Department of Growth Regulation,, Institute for Frontier Medical Sciences, Kyoto Univ.,

country: Japan

institute: Inst. for Frontier Life and Med. Sci., Kyoto University

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST(Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000TG.

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA16 implemented in the GeneSpring 12.6.

source_name: E14.5 embryonic hearts

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) were used according to Affymetrix protocol.

extract_protocol: Total RNA was extracted with RNeasy micro Plus Kit(Qiagen).

treatment_protocol: Dissected hearts were digested with 0.2% collagenase type 2 (Worthington) by gentle pipetting. Dissociated cells were resuspended with 5% heat-inactivated fetal bovine serum (FBS) in DMEM-high glucose (Gibco) and filtrated through 35μm cell strainer caps(BD Pharmingen). tdTomato+ cells were sorted as CNCCs using FACS.

tag: strain background

tag: genotype/variation

value: Adam19-/-; Wnt1-Cre; R26tdTomato/+

tag: developmental stage

tag: tissue

value: embryonic hearts

value: Cardiac Neural Crest Cells (CNCCs)


title: EA10047_314605_HUGENE-1_0-ST-V1_HU.FB.1HR.TNF#1

tag: time


title: Cortex2.CCJ15ANXX.SM2_052318p4_D12

tag: Sex

tag: age

tag: strain

tag: library construction


title: E14.5 WT CNCCs

value: Adam19+/+; Wnt1-Cre; R26tdTomato/+


title: Cortex2.CCJ15ANXX.SM2_052318p4_C9


title: Cortex2.CCJ15ANXX.SM2_052318p4_C8


title: Cortex2.CCJ15ANXX.SM2_052318p4_C6


title: Cortex2.CCJ15ANXX.SM2_052318p4_C7


title: Cortex2.CCJ15ANXX.SM2_052318p4_D11


title: Cortex2.CCJ15ANXX.SM2_052318p4_C3


title: Cortex2.CCJ15ANXX.SM2_052318p4_C2


title: Cortex2.CCJ15ANXX.SM2_052318p4_C4


title: SM6p2 Non-treated rep 2

city: Randwick

first: Klaartje

last: Somers

address: High Street gate 9

country: Australia

institute: Children's Cancer Institute, Lowy Cancer Research Centre, UNSW

hyb_protocol: Hybridisation was performed according to the Illumina Whole Genome Gene Expression Direct Hybridization Assay protocol. 750 ng of cRNA was hybridised for 16h at 58°C rocking at speed 5.

scan_protocol: Arrays were scanned on Illumina BeadArray Reader as outlined in the Illumina Whole-Genome Gene Expression Direct Hybridisation Assay protocol.

data_processing: The data were normalized using quantile normalization within the beadarray and limma package in R

source_name: SM6p2 cell line

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Part Number AMIL1791). 200 ng of total RNA was labelled according to the standard protocol.

growth_protocol: PER-485, SM6p2 and SM6p3 cells were cultured in RPMI supplemented with 20% fetal bovine serum, 1% Non-essential Amino Acid Mix (100x) and 1% 100mM Sodium Pyruvate Solution (100x)

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: PER-485, SM6p2 and SM6p3 cells were seeded at 1.6x105 cells/ml in RPMI 1640 with supplements for 48h in a 5% CO2 37°C incubator

value: leukaemia cell line


title: SM6p3 Non-treated rep 1

source_name: SM6p3 cell line


title: PER-485 Non-treated rep 3

source_name: PER-485 cell line


title: SM6p2 Non-treated rep 3


title: SM6p2 Non-treated rep 1


title: Cortex2.CCJ15ANXX.SM2_052318p4_C1


title: SM6p3 Non-treated rep 2


title: Cortex2.CCJ15ANXX.SM2_052318p4_C5


title: PER-485 Non-treated rep 1


title: Cortex2.CCJ15ANXX.SM2_052318p4_C11


title: Cortex2.CCJ15ANXX.SM2_052318p4_C10


title: Cortex2.CCJ15ANXX.SM2_052318p4_B9


title: Cortex2.CCJ15ANXX.SM2_052318p4_B8


title: PER-485 3h CCI-006 rep 3

scan_protocol: Arrays were scanned on Illumina BeadArray Reader as outlined in the Illumina Whole-Genome Gene Expression Direct Hybridisation Assay protocol

growth_protocol: PER-485 cells were cultured in RPMI supplemented with 20% fetal bovine serum, 1% Non-essential Amino Acid Mix (100x) and 1% 100mM Sodium Pyruvate Solution (100x)

treatment_protocol: PER-485 cells (seeded at 1.6x105 cells/ml in RPMI 1640 with supplements) were treated for 3h in a 5% CO2 37°C incubator with 5 μM CCI-006 (in DMSO) or corresponding amount of vehicle (DMSO)


title: Cortex2.CCJ15ANXX.SM2_052318p4_C12


title: Cortex2.CCJ15ANXX.SM2_052318p4_B7


title: PER-485 3h CCI-006 rep 1


title: PER-485 3h CCI-006 rep 2


title: Cortex2.CCJ15ANXX.SM2_052318p4_B5


title: Cortex2.CCJ15ANXX.SM2_052318p4_B4


title: Cortex2.CCJ15ANXX.SM2_052318p4_B6


title: Cortex2.CCJ15ANXX.SM2_052318p4_B3


title: PER-485 Non-treated rep 2


title: PER-485 3h DMSO rep 1


title: Cortex2.CCJ15ANXX.SM2_052318p4_B2


title: HepaRG_D10_2

city: les mureaux

first: Karim

last: Fekir

address: 22 rue paul doumer

country: France

institute: Inserm

description:
Gene expression of committed HepaRG (10 days of culture)
KF017

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (profile Agilent G3-GX-1color).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE_1-107_sep09_ssSurogates and Grid: 028004_D_F_20110325. Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 100% of the values in at least one condition  had a detected flag (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which 100% of the values in at least one condition were within the range of interest (i.e. 20-100th percentile).

source_name: HepaRG, day10

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop (Thermo Fischer Scientific, Waltham, MA).  amplification yield was 3.05 ± 0.98 µg cRNA and specific activity was 12.25 ± 3.28 pmol Cy3 per µg cRNA.

extract_protocol: RNA extractions were performed with RNeasy mini kit (Qiagen)  following the manufacturer's recommendations. RNA was qualified using a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA).

treatment_protocol:
hESC (WA09, WiCell) were maintained on irradiated mouse embryonic fibroblast feeder cells, in DMEM/F12 medium supplemented with 20% knockout serum replacement, 1mM L-glutamine, 1% non essential amino acids, 0.1 mM beta-mercaptoethanol, and 4 ng/ml bFGF.
SP: HepaRG were cultured in William's E medium with reduced fetal bovine serum (2%), insulin (1µg/ml), and hydrocortisone hemisuccinate (1 μM) for 5 days, then cells were sorting by flow cytometry using a BD FACSAria IIITM
Sphere: HepaRG were cultured in William's E medium with reduced fetal bovine serum (2%), insulin (1µg/ml), and hydrocortisone hemisuccinate (1 μM) for 5 days, then they were cultured in DMEM/F12 medium supplemented with 20% knockout serum replacement, 1mM L-glutamine, 1% non essential amino acids, 0.1 mM β-mercaptoethanol, and 4 ng/ml bFGF in ultra-low attachment plate for 5 more days.
HepaRG-D4 were cultured in William's E medium supplemented with fetal bovine serum (10%), insulin (5µg/ml), and hydrocortisone hemisuccinate (50 μM) during 4 days after seeding.
HepaRG-D10 were cultured in William's E medium supplemented with fetal bovine serum (10%), insulin (5µg/ml), and hydrocortisone hemisuccinate (50 μM) during 10 days after seeding.

tag: origin cell line

value: HepaRG

tag: differentiation stage

value: more differentiated (day10)

value: committed HepaRG (10 days of culture)


title: HepaRG_D10_1

description:
Gene expression of committed HepaRG (10 days of culture)
KF016


title: Cortex2.CCJ15ANXX.SM2_052318p4_B1


title: HepaRG_D10_3

description:
Gene expression of committed HepaRG (10 days of culture)
KF018


title: PER-485 3h DMSO rep 3

tag: cell line


title: Cortex2.CCJ15ANXX.SM2_052318p4_B12


title: PER-485 3h DMSO rep 2


title: Cortex2.CCJ15ANXX.SM2_052318p4_B11


title: HepaRG_D4_3

description:
Gene expression of HepaRG-progenitors (4 days of culture)
KF014

source_name: HepaRG, day4

value: Progenitors (day4)

tag: cell type

value: HepaRG-progenitors (4 days of culture)


title: Cortex2.CCJ15ANXX.SM2_052318p4_B10

value: Male


title: Cortex2.CCJ15ANXX.SM2_052318p4_A9

value: one month


title: Cortex2.CCJ15ANXX.SM2_052318p4_A8


title: Sphere_4

description:
Gene expression of Sphere-forming cells
KF011

source_name: Sphere-forming cells

value: Stem/progenitors (day10)

value: Sphere-forming cells


title: Sphere_1

description:
Gene expression of Sphere-forming cells
KF008


title: Cortex2.CCJ15ANXX.SM2_052318p4_A7


title: HepaRG_D4_1

description:
Gene expression of HepaRG-progenitors (4 days of culture)
KF012


title: HepaRG_D4_4

description:
Gene expression of HepaRG-progenitors (4 days of culture)
KF015


title: Cortex2.CCJ15ANXX.SM2_052318p4_A6


title: Cortex2.CCJ15ANXX.SM2_052318p4_A5


title: SP_4

description:
Gene expression of Side Population
KF007

source_name: Side population

value: Stem/progenitors

value: Side Population


title: HepaRG_D4_2

description:
Gene expression of HepaRG-progenitors (4 days of culture)
KF013


title: Mouse-liver-development-W6.fq

city: Beijing

first: Tongqing

last: Gong

address: Life Science Park Road 38#

country: China

institute: National Center for Protein Sciences (Beijing)

data_processing:
Illumina HiSeq 4000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mus musculus GRCm38.p2 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
FastQC from Simon Andrews et al.(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)  were used to provide a simple way to do some quality control checks on raw sequence data
Fractions Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mihaela Pertea et al., Nature Protocols,2016.
Genome_build: Mus musculus GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: liver

growth_protocol: The aging by "embryonic days" relate to in the female presence of a vaginal plug indicating that the mating occurred.(https://embryology.med.unsw.edu.au/embryology/index.php/Mouse_Timeline_Detailed#Timed_Pregnancy)

extract_protocol:
Flash tissue frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina SBS regent (Hiseq 4000 SBS KIT) was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: development stage

value: Postnatal weeks 6


title: SP_3

description:
Gene expression of Side Population
KF006


title: SP_2

description:
Gene expression of Side Population
KF005


title: Mouse-liver-development-W8.fq

value: Postnatal weeks 8


title: Cortex2.CCJ15ANXX.SM2_052318p4_A4

description:
scRNA-seq
full-length
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv


title: Cortex2.CCJ15ANXX.SM2_052318p4_A3


title: SP_1

description:
Gene expression of Side Population
KF004


title: Sphere_3

description:
Gene expression of Sphere-forming cells
KF010


title: hESC_1

description:
Gene expression of hESC
KF001

source_name: hESC, H9

value: hESC


title: hESC_3

description:
Gene expression of hESC
KF003


title: hESC_2

description:
Gene expression of hESC
KF002


title: Mouse-liver-development-W3.fq

value: Postnatal weeks 3


title: Cortex2.CCJ15ANXX.SM2_052318p4_A1

source_name: Cortex


title: Cortex2.CCJ15ANXX.SM2_052318p4_A2


title: Mouse-liver-development-D5.fq

value: Postnatal days 5


title: Sphere_2

description:
Gene expression of Sphere-forming cells
KF09

value: HepaRG


title: Cortex2.CCJ15ANXX.SM2_052318p4_A12


title: Mouse-liver-development-W1.fq

value: Postnatal weeks 1


title: Mouse-liver-development-D3.fq

value: Postnatal days 3


title: Cortex2.CCJ15ANXX.SM2_052318p4_A11


title: Mouse-liver-development-E17.5.fq

value: Embryonic days 17.5


title: Mouse-liver-development-D1.fq

value: Postnatal days 1


title: Cortex2.CCJ15ANXX.SM2_052318p3_H9

value: Male


title: Cortex2.CCJ15ANXX.SM2_052318p4_A10

value: one month


title: Mouse-liver-development-E18.5.fq

value: Embryonic days 18.5


title: Mouse-liver-development-E16.5.fq

value: Embryonic days 16.5


title: Mouse-liver-development-W2.fq

value: Postnatal weeks 2


title: Mouse-liver-development-E14.5.fq

value: Embryonic days 14.5


title: Cortex2.CCJ15ANXX.SM2_052318p3_H3


title: Cortex2.CCJ15ANXX.SM2_052318p3_H4


title: Mouse-liver-development-E12.5.fq

value: liver

value: Embryonic days 12.5


title: Cortex2.CCJ15ANXX.SM2_052318p3_H7


title: Cortex2.CCJ15ANXX.SM2_052318p3_H6


title: Mouse-liver-development-E15.5.fq

value: Embryonic days 15.5


title: Mouse-liver-development-E13.5.fq

value: Embryonic days 13.5


title: RNA-seq PhenDC3 rep3

city: Montpellier

first: Marcel

last: Mechali

address: 141, Rue de la Cardonille

department: Replication and Genome Dynamics

institute: Institute of Human Genetics, CNRS

description: analysis of gene expression pattern

data_processing:
Illumina Casava1.7 software used for basecalling.
Read mapping using Bowtie2 version 2.2.5
Sequenced reads was first filtered by Illumina Purity Filter and trimmed with sickle software (version 1.2) keeping a minimum read length of 30 nucleotides. If an overrepresented sequence (adapter) is identified in quality reports after trimming: the adapters sequences are removed using cutadapt software (version 1.9.1)
For origin mapping (SNS-seq) we applied a procedure using two peak calling programs with complementary properties to identify origins. MACS2 (version 2.1.0, parameters: callpeak, -t 60, -m 10 30, p-value 1e-5, band-width 500, effective genome size 2.3e-9) identifies well-delimited peaks, whereas SICER (Zang et al. 2009, parameters: redundancy threshold 1, window size 200pb, fragment size 500, effective genome fraction 0.83 and gap size 600) returns wider regions enriched in reads.
For transcription analysis (RNA-seq) TopHat software (version 2.1.1) was used for splice junction mapping with Bowtie2 (version 2.2.9) for reads mapping. Reads counting on gene was done using HTSeq-count (version 0.6.1p1). Data were normalized to the relative log expression implemented in edgeR (version 3.16.5), and the statistical analysis to identify differentially expressed genes was performed using DESeq2 (version 1.14.1)
Genome_build: mm10
Supplementary_files_format_and_content: BED, BigWig, TXT, XLS

source_name: Embryonic Stem Cells

growth_protocol: Cells were grown on gelatin-coated dishes in GMEM medium supplemented with 2mM Glutamine, 0.05mM 2-Mercaptoethanol,  1000 units/ml LIF and 10% Foetal Bovine Serum (FBS).

extract_protocol:
Total genomic DNA was extracted with DNAzol (Invitrogen, ref. 10503027), obtained DNA was fractionated according to the size by sucrose gradient. Nascent DNA was precipitated from fractions containing DNA fragments of 0.5 to 2 kb in size. DNA fragments contaminating NS were eliminated by λ-Exo digestion. DNA fragments were phosphorylated by T4 polynucleotide kinase and digested overnight with 150 U of λ-Exo to eliminate contaminating DNA fragments.  DNA phosphorylation and overnight λ-Exo digestion was repeated twice. A third λ−Exo digestion (100 units) was performed for 2 h at 37°C after the second round of overnight digestion. Controls for each nascent strand purification were prepared by treating a half of NS-containing DNA with 0,1 ug/ul RNase A and 100 mU/ul T2 in pH 5.2 for 2 h at 37°C in order to remove RNA primers prior to the λ-Exo digestion. Total RNA was extracted using the RNeasy Mini Kit (Qiagen; cat 74104) according to the manufacturer protocol
DNA Libraries wrere constructed using Illumina TruSeq ChIP Sample Prep Set A (ref 15034288) , RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturer’s protocols. Libraries were validated using the Fragment Analyzer system with the Standard Sensitivity NGS Fragment Analysis Kit (maker).

treatment_protocol: Asynchronous CGR8 cells were treated with either 0,5% DMSO (Control) or 10 μM PhenDC (experiment) for 48h.

tag: treatment

value: 10 μM PhenDC

value: Embryonic Stem Cells


title: Cortex2.CCJ15ANXX.SM2_052318p3_H1


title: Cortex2.CCJ15ANXX.SM2_052318p3_H2


title: Cortex2.CCJ15ANXX.SM2_052318p3_H12


title: RNA-seq PhenDC3 rep1

description: analysis of gene expression pattern


title: RNA-seq  Ctrl  rep3

description: analysis of gene expression pattern

value: 0.5% DMSO


title: Cortex2.CCJ15ANXX.SM2_052318p3_H11


title: Cortex2.CCJ15ANXX.SM2_052318p3_H10


title: RNA-seq  Ctrl  rep1

description: analysis of gene expression pattern


title: Cortex2.CCJ15ANXX.SM2_052318p3_H8


title: Cortex2.CCJ15ANXX.SM2_052318p3_G9


title: Cortex2.CCJ15ANXX.SM2_052318p3_H5


title: RNA-seq PhenDC3 rep2

description: analysis of gene expression pattern


title: Cortex2.CCJ15ANXX.SM2_052318p3_G7


title: Cortex2.CCJ15ANXX.SM2_052318p3_G6


title: RNAse-treated SNS-seq PhenDC3 sample

description: genome-wide origin mapping

data_processing:
Library strategy: SNS-seq
Illumina Casava1.7 software used for basecalling.
Read mapping using Bowtie2 version 2.2.5
Sequenced reads was first filtered by Illumina Purity Filter and trimmed with sickle software (version 1.2) keeping a minimum read length of 30 nucleotides. If an overrepresented sequence (adapter) is identified in quality reports after trimming: the adapters sequences are removed using cutadapt software (version 1.9.1)
For origin mapping (SNS-seq) we applied a procedure using two peak calling programs with complementary properties to identify origins. MACS2 (version 2.1.0, parameters: callpeak, -t 60, -m 10 30, p-value 1e-5, band-width 500, effective genome size 2.3e-9) identifies well-delimited peaks, whereas SICER (Zang et al. 2009, parameters: redundancy threshold 1, window size 200pb, fragment size 500, effective genome fraction 0.83 and gap size 600) returns wider regions enriched in reads.
For transcription analysis (RNA-seq) TopHat software (version 2.1.1) was used for splice junction mapping with Bowtie2 (version 2.2.9) for reads mapping. Reads counting on gene was done using HTSeq-count (version 0.6.1p1). Data were normalized to the relative log expression implemented in edgeR (version 3.16.5), and the statistical analysis to identify differentially expressed genes was performed using DESeq2 (version 1.14.1)
Genome_build: mm10
Supplementary_files_format_and_content: BED, BigWig, TXT, XLS


title: SNS-seq PhenDC3 rep1

description: genome-wide origin mapping


title: Cortex2.CCJ15ANXX.SM2_052318p3_G5


title: RNAse-treated SNS-seq Ctrl sample

description: genome-wide origin mapping


title: Cortex2.CCJ15ANXX.SM2_052318p3_G3


title: SNS-seq  Ctrl  rep1

description: genome-wide origin mapping


title: Cortex2.CCJ15ANXX.SM2_052318p3_G2


title: BT_2cell.2

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

description: Zar-/+ polar body transfer 2cell embryos

data_processing:
Illumina Casava1.7 software used for basecalling.
Low quality base and adapters were removed by cutadapt v1.11
Sequenced reads were mapped to mm9 using HISAT2 version 2.1.0 with default parameters
Gene expressions were calculated by cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: 2-cell embyro

value: polar body transfer 2 cell embryo


title: SNS-seq  Ctrl rep2

description: genome-wide origin mapping


title: Cortex2.CCJ15ANXX.SM2_052318p3_G1


title: BT_2cell.1


title: RNA-seq  Ctrl rep2

description: analysis of gene expression pattern


title: Cortex2.CCJ15ANXX.SM2_052318p3_G11


title: L-PT_2cell.3

description: Zar-/+ late pronuclear transfer 2cell embryos

value: late pronuclear transfer 2 cell embryo


title: Cortex2.CCJ15ANXX.SM2_052318p3_G4


title: L-PT_2cell.2


title: Cortex2.CCJ15ANXX.SM2_052318p3_G10


title: Cortex2.CCJ15ANXX.SM2_052318p3_G12


title: Cortex2.CCJ15ANXX.SM2_052318p3_G8


title: L-PT_2cell.1


title: Cortex2.CCJ15ANXX.SM2_052318p3_F9


title: E-PT_2cell.3

description: Zar-/+ early pronuclear transfer 2cell embryos

value: early pronuclear transfer 2 cell embryo


title: Cortex2.CCJ15ANXX.SM2_052318p3_F8

value: Male


title: E-PT_2cell.2


title: Cortex2.CCJ15ANXX.SM2_052318p3_F7

value: one month


title: SNS-seq  Ctrl  rep3

description: genome-wide origin mapping


title: SNS-seq PhenDC3 rep2

description: genome-wide origin mapping


title: ST_2cell.2

description: Zar-/+ spindle transfer 2 cell embryos

tag: genotype/variatiion

value: spindle transfer 2 cell embryo


title: E-PT_2cell.1


title: Cortex2.CCJ15ANXX.SM2_052318p3_F5


title: Cortex2.CCJ15ANXX.SM2_052318p3_F4


title: ST_2cell.1

description: Zar-/+ spindle transfer 2 cell embryos


title: EA10047_314603_HUGENE-1_0-ST-V1_HU.FB.1HR.MEDIA#1

tag: replicate

value: MEDIA


title: Zar1_zygote.3

description: Zar-/- zygotes

tag: strain background

value: ICR

value: zygotes


title: Zar1_zygote.2

description: Zar-/- zygotes

tag: genotype/variation


title: Cortex2.CCJ15ANXX.SM2_052318p3_F3


title: Cortex2.CCJ15ANXX.SM2_052318p3_F2


title: Cortex2.CCJ15ANXX.SM2_052318p3_F1


title: WT_zygote.3

description: wild type zygotes

value: wild type

tag: developmental stage


title: Cortex2.CCJ15ANXX.SM2_052318p3_F12


title: Cortex2.CCJ15ANXX.SM2_052318p3_F11


title: WT_zygote.1

description: wild type zygotes

tag: tissue


title: WT_zygote.2

description: wild type zygotes


title: Zar1_MII.4

description: Zar-/- MII oocytes

value: MII oocytes

value: oocytes


title: Zar1_MII.3

description: Zar-/- MII oocytes


title: Zar1_MII.2

description: Zar-/- MII oocytes


title: Cortex2.CCJ15ANXX.SM2_052318p3_E7


title: Zar1_MII.1

description: Zar-/- MII oocytes

value: oocyteso


title: Cortex2.CCJ15ANXX.SM2_052318p3_E6


title: Cortex2.CCJ15ANXX.SM2_052318p3_F6


title: Cortex2.CCJ15ANXX.SM2_052318p3_E4


title: WT_MII.2

description: wild type MII oocytes


title: WT_MII.3

description: wild type MII oocytes


title: Cortex2.CCJ15ANXX.SM2_052318p3_E3


title: Cortex2.CCJ15ANXX.SM2_052318p3_E2


title: Zar1_zygote.1

description: Zar-/- zygotes


title: Cortex2.CCJ15ANXX.SM2_052318p3_E1


title: Dgcr8WT_rep3

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

state: CA

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

description: UTP prepared RNAseq library

data_processing:
Reads were mapped to the mouse genome (mm10) using Tophat version 2.0.12.
Mapped reads were counted that overlapped annotated exons or introns using Refseq gene annotation. In this counting step, intronic regions were reduced by 10nt at start and end
Exonic and intronic reads were normalized separately for sample size using DESeq (Anders and Huber, 2010)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain normalized read counts for exonic or intronic regions of Refseq genes. Additionally the sum of nucleotides considered as exonic or intronic per gene is indicated.

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo  Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β-  mercaptoethanol.

extract_protocol:
Total RNA was extracted with Trizol (Life Technologies)
Strand-specific mRNA sequencing libraries  from purified polyadenylated RNA were prepared using the UTP method. Muliplexing barcode sequences were incorporated during the PCR amplification.

value: mouse embryonic stem cells

tag: experimental series

value: Dgcr8 knockout series


title: Dgcr8WT_rep1

description: UTP prepared RNAseq library


title: Dgcr8WT_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_E5

tag: Sex


title: WT_MII.1

description: wild type MII oocytes


title: Cortex2.CCJ15ANXX.SM2_052318p3_E11

tag: age


title: Cortex2.CCJ15ANXX.SM2_052318p3_F10

tag: strain


title: Cortex2.CCJ15ANXX.SM2_052318p3_E10

tag: library construction


title: Cortex2.CCJ15ANXX.SM2_052318p3_E9


title: Cortex2.CCJ15ANXX.SM2_052318p3_E8


title: Cortex2.CCJ15ANXX.SM2_052318p3_D9


title: DicerWT_rep2

description: UTP prepared RNAseq library

value: TFC

value: Dicer knockout series


title: Dgcr8KO_rep1

description: UTP prepared RNAseq library


title: DicerWT_rep1

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_D7


title: DicerWT_rep3

description: UTP prepared RNAseq library


title: DicerKO_rep3

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_D6


title: Cortex2.CCJ15ANXX.SM2_052318p3_D8


title: Cortex2.CCJ15ANXX.SM2_052318p3_D5


title: Cortex2.CCJ15ANXX.SM2_052318p3_D4


title: DicerKO_rep1

description: UTP prepared RNAseq library


title: Dgcr8KO_rep3

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_E12


title: Wild type no KLA treatment replicate 2

city: La Jolla

first: Christopher

middle: K

last: Glass

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions. mRNA-Seq results were trimmed to remove A-stretches originating from the library preparation. Each sequence tag returned by the Illumina Pipeline was aligned to the mm10 assembly using ELAND allowing up to 2 mismatches. Only tags that mapped uniquely to the genome were considered for further analysis. Peak finding and downstream analysis was performed using HOMER, a software suite created for analysis of high-throughput sequencing data (Heinz et al., 2010). Detailed instructions for analysis can be found at http://homer.salk.edu/homer/.
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: Wild type no KLA treatment

growth_protocol: Primary BMDM cells were isolated from male 6 to 8-week-old C57Bl/6 mice (Charles River Laboratories). BMDMs were obtained by PBS flush of femurs and tibias, red blood cells lysed, and remaining cells plated in RPMI 1640 supplemented with 20% fetal bovine serum (FBS, Gibco, cat. 12657-029), 30% L-cell conditioned medium, 100 U/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine. Cells were seeded in non-tissue culture treated Optilux Petri dishes (BD Biosciences), incubated at 37 °C in a 5% CO2 atmosphere for 7 days.

extract_protocol:
RNA was extracted from treated BMDMs using the Direct-Zol kit from Zymo Research.
Libraries were prepared from 2 biological replicates per condition. RNA-Seq libraries were prepared as previously described (Kaikkonen et al., 2013). Sequencing libraries were prepared using magnetic beads similar to described previously using barcoded adapters (NextFlex, Bioo Scientific) (Garber et al., 2012).

treatment_protocol: Cells were treated with 100 µM KLA (699500, Avanti Polar Lipids) in growth media for noted times.

value: vehicle

tag: time

value: bone marrow derived macrophages (BMDMs)


title: DicerKO_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_D3


title: Cortex2.CCJ15ANXX.SM2_052318p3_D1


title: Cortex2.CCJ15ANXX.SM2_052318p3_D2


title: Cortex2.CCJ15ANXX.SM2_052318p3_D12


title: Wild type KLA treatment 6h replicate 2

source_name: Wild type KLA treatment 6h

value: KLA


title: Wild type KLA treatment 24h replicate 2

source_name: Wild type KLA treatment 24h


title: Wild type KLA treatment 24h replicate 1


title: Cortex2.CCJ15ANXX.SM2_052318p3_D10

value: Male


title: Wild type KLA treatment 6h replicate 1


title: Dgcr8KO_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_C9

value: one month


title: Wild type KLA treatment 1h replicate 2

source_name: Wild type KLA treatment 1h


title: Cortex2.CCJ15ANXX.SM2_052318p3_C8


title: Cortex2.CCJ15ANXX.SM2_052318p3_C7


title: Wild type KLA treatment 1h replicate 1


title: Phlpp1 Knockout no KLA treatmeat replicate 1

source_name: Phlpp1 Knockout no KLA treatmeat


title: Phlpp1 Knockout no KLA treatment replicate 2

source_name: Phlpp1 Knockout no KLA treatment


title: Cortex2.CCJ15ANXX.SM2_052318p3_C5


title: Phlpp1 Knockout KLA treatment 6h replicate 1

source_name: Phlpp1 Knockout KLA treatment 6h


title: Cortex2.CCJ15ANXX.SM2_052318p3_C3


title: Phlpp1 Knockout KLA treatment 24h replicate 2

source_name: Phlpp1 Knockout KLA treatment 24h


title: Wild type no KLA treatmeat replicate 1

source_name: Wild type no KLA treatmeat


title: Phlpp1 Knockout KLA treatment 24h replicate 1


title: Cortex2.CCJ15ANXX.SM2_052318p3_C4


title: Cortex2.CCJ15ANXX.SM2_052318p3_C12


title: Cortex2.CCJ15ANXX.SM2_052318p3_C2


title: Cortex2.CCJ15ANXX.SM2_052318p3_C1


title: Cortex2.CCJ15ANXX.SM2_052318p3_D11


title: Phlpp1 Knockout KLA treatment 1h replicate 1

source_name: Phlpp1 Knockout KLA treatment 1h


title: Cortex2.CCJ15ANXX.SM2_052318p3_B9


title: Cortex2.CCJ15ANXX.SM2_052318p3_C10


title: Cortex2.CCJ15ANXX.SM2_052318p3_C11


title: Cortex2.CCJ15ANXX.SM2_052318p3_B8


title: Cortex2.CCJ15ANXX.SM2_052318p3_B7


title: Cortex2.CCJ15ANXX.SM2_052318p3_C6


title: Cortex2.CCJ15ANXX.SM2_052318p3_B6


title: Phlpp1 Knockout KLA treatment 6h replicate 2


title: TTFHAgo2_-dox96h_+2.5dox48h_smallRNA_rep2

description: total small RNA

data_processing:
Sequencing adaptors (AGATCGGAAGAGCGGTT) were removed using cutadapt and reads >=15nt were retained. Read were collapsed tracking the number of identical sequences.
Collapsed reads were mapped to the mouse genome (mm10) appended with tandem repeat sequences using Bowtie version 1.0.1 allowing up to two mismatches.  Multimapping reads were assigned randomly to genome. To recover 3' tRNA fragments, nonmapping reads were trimmed for CCA and remapped allowing up to one mismatch.
For miRNA read counts, uncollapsed reads from the two biological replicates were combined to detect reads with Ago loss.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file contains uncollapsed miRNA read counts.

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β-mercaptoethanol.

extract_protocol:
Total RNA was extracted with Trizol (Life Technologies)
5’-phosphate independent cloning was accomplished using a circularization based protocol adapted from  (Churchman and Weissman, 2011).  (3' adapter sequence: AGATCGGAAGAGCGGTTCAGCAGGAATGCCGA)

treatment_protocol: TT-FHAgo2 clonal cell lines were propagated in 0.1μg/mL doxycycline (Sigma). For induction to wildtype Ago2 levels, cells were induced with 2.5 μg/mL of doxycycline. For Ago2 loss timecourse, cells were induced to wildtype levels with 2.5 μg/mL doxycycline for 48 hrs then media was replaced with  media without doxycycline. RNA was collected 24,48 and 96 hours after doxycycline removal. For the Ago2 rescue series, cells propagated in 0.1μg/mL doxycycline were cultured without 0.1μg/mL doxycycline for 96 hours then media with either 0.1μg/mL or 2.5 μg/mL doxycycline was added for 48hours before RNA was extracted.

value: without Dox for 96h, then 2.5 μg/mL Dox for 48h

tag: protocol

value: 5'-end independent

value: Ago2 rescue series


title: TTFHAgo2_-dox96h_smallRNA_rep2

description: total small RNA

tag: cell line

value: without Dox for 96h


title: TTFHAgo2_-dox96h_+0.1dox48h_smallRNA_rep1

description: total small RNA

tag: cell type

value: without Dox for 96h, then 0.1 μg/mL Dox for 48h


title: TTFHAgo2_-dox96h_smallRNA_rep1

description: total small RNA


title: TTFHAgo2_+dox48h-dox96h_smallRNA_rep1

description: total small RNA

value: 2.5 μg/mL Dox for 48h, then without Dox for 96h

value: Ago2 loss time course


title: TTFHAgo2_+dox48h-dox96h_smallRNA_rep2

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_B5


title: TTFHAgo2_-dox96h_+0.1dox48h_smallRNA_rep2

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_B4


title: Cortex2.CCJ15ANXX.SM2_052318p3_B3


title: TTFHAgo2_+dox48h-dox48h_smallRNA_rep2

description: total small RNA

value: 2.5 μg/mL Dox for 48h, then without Dox for 48h


title: Phlpp1 Knockout KLA treatment 1h replicate 2


title: Cortex2.CCJ15ANXX.SM2_052318p3_B1


title: TTFHAgo2_+dox48h-dox48h_smallRNA_rep1

description: total small RNA

value: mouse embryonic stem cells


title: Cortex2.CCJ15ANXX.SM2_052318p3_B10


title: TTFHAgo2_+dox48h-dox24h_smallRNA_rep2

description: total small RNA

value: 2.5 μg/mL Dox for 48h, then without Dox for 24h


title: TTFHAgo2_-dox96h_+2.5dox48h_smallRNA_rep1

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_B11


title: Cortex2.CCJ15ANXX.SM2_052318p3_B12


title: TTFHAgo2_+dox48h_smallRNA_rep2

description: total small RNA

value: 2.5 μg/mL Dox for 48h


title: TTFHAgo2_+dox48h_smallRNA_rep1

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_A8


title: TTFHAgo2_+dox48h-dox24h_smallRNA_rep1

description: total small RNA


title: E7_smallRNA_rep1

description: total small RNA

value: Ago mutant genetic series


title: Cortex2.CCJ15ANXX.SM2_052318p3_A7


title: E7_smallRNA_rep2

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_A6


title: B9_smallRNA_rep2

description: total small RNA


title: B9_smallRNA_rep1

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_A4


title: Cortex2.CCJ15ANXX.SM2_052318p3_A5


title: Cortex2.CCJ15ANXX.SM2_052318p3_A3


title: AB2.2_smallRNA_rep1

description: total small RNA


title: AB2.2_smallRNA_rep2

description: total small RNA


title: Cortex2.CCJ15ANXX.SM2_052318p3_A2


title: TTFHAgo2_-dox96h_+2.5dox48h_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_A1


title: Cortex2.CCJ15ANXX.SM2_052318p3_A12


title: TTFHAgo2_-dox96h_+2.5dox48h_rep1

description: UTP prepared RNAseq library


title: TTFHAgo2_-dox96h_+0.1dox48h_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_B2


title: Cortex2.CCJ15ANXX.SM2_052318p3_A11


title: TTFHAgo2_-dox96h_+0.1dox48h_rep1

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_A10


title: Cortex2.CCJ15ANXX.SM2_052318p2_H9


title: TTFHAgo2_-dox96h_rep1

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p3_A9


title: TTFHAgo2_-dox96h_rep2

description: UTP prepared RNAseq library


title: TTFHAgo2_+dox48h-dox96h_rep2

description: UTP prepared RNAseq library


title: TTFHAgo2_+dox48h-dox96h_rep1

description: UTP prepared RNAseq library


title: TTFHAgo2_+dox48h-dox48h_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_H6


title: Cortex2.CCJ15ANXX.SM2_052318p2_H8


title: TTFHAgo2_+dox48h-dox48h_rep1

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_H7


title: TTFHAgo2_+dox48h-dox24h_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_H2


title: Cortex2.CCJ15ANXX.SM2_052318p2_H4


title: Cortex2.CCJ15ANXX.SM2_052318p2_H5


title: Cortex2.CCJ15ANXX.SM2_052318p2_H3


title: TTFHAgo2_+dox48h_rep1

description: UTP prepared RNAseq library


title: C86

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_H1


title: C62

description: UTP prepared RNAseq library


title: E7_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_H10


title: E7_rep3

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_H11


title: TTFHAgo2_+dox48h_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_G9


title: Cortex2.CCJ15ANXX.SM2_052318p2_G8


title: B9_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_G7


title: B9_rep1

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_G6


title: E7_rep1

description: UTP prepared RNAseq library


title: AB2.2_rep2

description: UTP prepared RNAseq library


title: Cortex2.CCJ15ANXX.SM2_052318p2_G5


title: Cortex2.CCJ15ANXX.SM2_052318p2_G4


title: AB2.2_rep1

description: UTP prepared RNAseq library


title: TTFHAgo2_+dox48h-dox24h_rep1

description: UTP prepared RNAseq library


title: C86_WCE

description: Whole Cell Extracts

data_processing:
Reads were mapped to the mouse genome (mm10) appended with tandem repeat sequences using Bowtie version 1.0.1 allowing up to two mismatches.
Before peaks were called using MACS2, mapped bamfiles were downsampled using Picard tools to match total read counts. BigWig file were generated from MACS2 pileup bedgraph output using UCSC tools.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated from MACS2 pileup bedgraph output using UCSC tools.

extract_protocol:
Lysates were clarified from sonicated nuclei and bound DNA fragments were isolated with antibody.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: antibody


title: C86_Pol2_ChIP

description: ChIP

value: Mouse monoclonal RNAPII-CTD abcam ab817


title: Cortex2.CCJ15ANXX.SM2_052318p2_G2


title: Cortex2.CCJ15ANXX.SM2_052318p2_G3


title: Cortex2.CCJ15ANXX.SM2_052318p2_H12


title: Cortex2.CCJ15ANXX.SM2_052318p2_G12


title: C86_H3K27me3_ChIP

description: ChIP

value: Mouse monoclonal H3K27me3 abcam ab6002


title: Cortex2.CCJ15ANXX.SM2_052318p2_G1


title: C86_H3K27ac_ChIP

description: ChIP

value: Rabbit polyclonal H3H27ac abcam ab4729


title: Cortex2.CCJ15ANXX.SM2_052318p2_G11

value: Male


title: C62_WCE

description: Whole Cell Extracts


title: Cortex2.CCJ15ANXX.SM2_052318p2_G10

value: one month


title: Cortex2.CCJ15ANXX.SM2_052318p2_F9


title: C62_H3K9me3_ChIP

description: ChIP

value: Rabbit polyclonal H3K9me3 abcam ab8898


title: C62_H3K27me3_ChIP

description: ChIP


title: C62_Pol2_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_F8


title: Cortex2.CCJ15ANXX.SM2_052318p2_F7


title: C62_H3K27ac_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_F5


title: E7_Pol2_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_F4


title: E7_H3K9me3_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_F3


title: E7_H3K27ac_ChIP

description: ChIP


title: B9_WCE

description: Whole Cell Extracts


title: C86_H3K9me3_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_F1


title: B9_Pol2_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_F12


title: E7_H3K27me3_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_E9


title: Cortex2.CCJ15ANXX.SM2_052318p2_E8


title: Cortex2.CCJ15ANXX.SM2_052318p2_F11


title: Cortex2.CCJ15ANXX.SM2_052318p2_F10


title: B9_H3K27ac_ChIP

description: ChIP


title: Cortex2.CCJ15ANXX.SM2_052318p2_E6


title: Cortex2.CCJ15ANXX.SM2_052318p2_E7


title: 4h_Long_B

first: Andrew

last: McCulloch

address: 9500 Gilman Dr

department: Bioengineering

data_processing:
Quality scores of each sample were analyzed with FastQC.
The final 6 bases of each read were trimmed off of the 3' end of reads using FastX-Toolkit.
Reads were mapped to UCSC mm9 with TopHat v1.4.1.
Gene abundance and differential expression were calculated using Cufflinks v2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: Data was summarized in an .xlsx file, which lists the RPKM value for each sample, plus the fold change and p-value between each stretch condition and control.

source_name: Neonatal cardiac myocytes

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy mini kit.
Libraries were prepared according to TruSeq RNA Sample Prep Kit v2. The first step was to purify the poly-A–containing mRNA molecules using poly-T oligo-attached magnetic beads. The mRNA was then fragmented into 120–210 bp pieces by incubating at 94 °C for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random hexamers. Second strand cDNA synthesis utilized DNA Polymerase I and RNase H. These fragments then went through an end repair process to blunt the ends. A single “A” base was added to the 3' end of the fragment, and then indexed adapters were ligated to the ends. Each adapter had a 7 bp sequence that was unique to one of the fifteen samples. The products were purified and amplified with PCR. This cDNA was quantified using an Agilent Technologies 2100 Bioanalyzer and then subjected to high-throughput sequencing by Illumina HiSeq 2000.

treatment_protocol: Static, biaxial stretch was applied to PDMS with attached cardiac myocytes for up to 4 hours. Stretch magnitude was 14% in the primary stretch axis and 3.6% in the orthogonal axis.