title: expr_gmpG_cebpa_wt_Rep1

description: Colony Forming Unit - Granulocyte


title: expr_pregm_cebpa_wt_Rep3

status: Public on May 29 2018

type: SRA

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaløes Vej 5, 4.

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
The reads were mapped to mouse genome (mm9) using STAR (default parameters) (Dobin et al., 2013) and expression levels for non-redundant set of genes (N=21,147) were quantified using featureCounts (Liao et al., 2013). Read counts were normalized using RLE method (Love et al., 2014).
Differential gene expression analysis between preGM WT and KO populations, and between CFU-G and CFU-M populations was performed using DESeq2 (Love et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM.

molecule: total RNA

organism: Mus musculus

source_name: preGM

growth_protocol: Cells sorted from freshly harvested murine bone marrow

extract_protocol:
Total RNA was extracted from LSK, preGMs, GMP, CFU-G, CFU-M, granulocytes and monocytes in biological triplicates, using RNeasy Micro Kit (Qiagen).
RNA was processed for double-stranded cDNA synthesis using the Ovation RNA-Seq System V2 (NuGEN Technologies).  Subsequently the sheared cDNA (fragment size from 150 – 550 bp) was subjected to library preparation using the Ovation Ultralow System V2 (NuGEN Technologies). The indexed cDNA libraries were pooled in equimolar ratios and subjected to 75-cycles sequencing on NextSeq 500 System (Illumina).

tag: genotype

value: wt

tag: tissue

value: bone marrow

tag: cell markers


title: expr_gmp_cebpa_wt_Rep3

source_name: GMP

value: Lin-, Sca-1-, ckit+, CD150-, FcgRII/III+


title: Sample 29: diet14071615_pooled_hypo_1

city: Beijing

first: John

last: Speakman

address: No. 1 West Beichen Road,

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: diet D14071615

data_processing:
All sequencing was carried out using the Illumina NextSeq 500 sequencer.
Paired-end reads were mapped to the Mus musculus genome (GRCm38) using Bowtie 2-2.1.0 with bowtie2-build -f, TopHat-2.0.10, and Samtools-0.1.19 with samtools sort -n ;
Uniquely mapped reads for each gene were counted against the GTF file of GRCm38 provided by Ensembl (release 83) using HTSeq-0.6.1p1 using htseq-count -r name -s reverse;
After read count data were obtained from the TopHat-HTSeq pipeline, counts per million (CPM) value for each gene was calculated by using the R package ‘edgeR’ (version 3.12.0, R version 3.2.2) to normalize the count data by the size of the library of each sample. Genes with the CPM value ≥ 1 in at least one of the 24 diets group were retained (Anders et al., 2013).
Genome_build: GRCm38 provided by Ensembl (release 83)
Supplementary_files_format_and_content: Ninety-six ".count" files for all  the 96 samples containing read count for each gene from the TopHat-HTSeq pipeline; also two ".xls" files for the two tissue types, hypothalamus and white adipose tissue, containing counts per million (CPM) values for genes with the CPM value ≥ 1 in at least one of the 24 diet groups.

source_name: Hypothalamus

growth_protocol: All mice were fed a standard diet with 10% fat and 20% protein (D12450B, Research Diets Ltd) for 2 weeks as the baseline period. Following 2 weeks of baseline monitoring (at age 12 weeks), all mice were randomly allocated to different groups and switched to the experimental diets for 12 weeks. After 12 weeks all mice were sacrificed and dissected.

extract_protocol:
From each diet group, the hypothalami of 8/20 individuals were collected. The left halves of two, and the right halves of another two, were pooled together as one sample, and the same was performed with the other 4 hypothalami, resulting in each diet group having 2 pooled samples of 4 hypothalami (n = 48 samples in total across 24 diets). From each diet group, the sWAT and eWAT of 12/20 individuals were also collected. A small piece from each of six sWAT collections were pooled together as one sample, and the same was performed with the other six eWAT collections. In this way each diet group had one pooled sWAT sample and one pooled eWAT sample (also n = 48 across 24 diets). The total RNA of the hypothalamus and WAT was isolated using the RNeasy Mini Kit (QIAGEN, 74104) according to manufacturer's protocol.
All sequencing was carried out using the Illumina NextSeq 500 sequencer using standard Illumina protocols

treatment_protocol: In total, mice were fed on 4 diet series, each series consisting of 6 different diets (total = 24 diets). In the first two series (Series 1: D14071601–D14071606 and series 2: D14071607 – D14071612) we fixed the level of fat by energy, and varied the protein content. The protein source was casein. The balance was made up by carbohydrate (roughly equal mix of corn starch and maltodextrose). The source of fat was a mix of cocoa butter, coconut oil, menhaden oil, palm oil and sunflower oil. This mix was designed to match the balance of saturated, mono-unsaturated and polyunsaturated fats (ratio 47.5: 36.8: 15.8) and the n-6: n-3 ratio (14.7: 1) in the typical western diet. The proportions of the different fat constituents and hence fatty acid distributions did not change as the total fat content changed. Sucrose and cellulose were both fixed 5% by energy and weight respectively, and all diets were supplemented with a standard vitamin and mineral mix. In the second two series of diets (series 3: D14071613 – D14071618 and series 4: D14071619 – D14071624) we fixed the level of protein by energy and then allowed the fat content to vary.  In these diets the sucrose, cellulose and vitamin and mineral contents were the same as the diets in series 1 and 2. All these diets can be ordered direct from research diets (www.researchdiets.com) using the diet codes provided.

tag: strain

value: Hypothalamus

tag: gender

value: male

tag: age

value: 24 weeks

value: wild type


title: Sample 31: diet14071616_pooled_hypo_1

description: diet D14071616


title: expr_pregm_cebpa_ko_Rep3

value: CEBPA KO


title: expr_gmpM_cebpa_wt_Rep1

description: Colony Forming Unit - Monocyte

source_name: CFU-M

value: Lin- Sca1- cKit+ CD150- CD41- FcgRII/III(hi) CD115+


title: expr_pregm_cebpa_ko_Rep2


title: Sample 27: diet14071614_pooled_hypo_1

description: diet D14071614


title: Sample 26: diet14071613_pooled_hypo_2

description: diet D14071613


title: expr_gmp_cebpa_wt_Rep1


title: expr_pregm_cebpa_wt_Rep2


title: expr_pregm_cebpa_wt_Rep1


title: Sample 25: diet14071613_pooled_hypo_1

description: diet D14071613


title: expr_lsk_cebpa_wt_Rep2

source_name: LSK

value: Lin-, Sca-1+, ckit


title: Sample 24: diet14071612_pooled_hypo_2

description: diet D14071612


title: expr_pregm_cebpa_ko_Rep1


title: expr_lsk_cebpa_wt_Rep1


title: PU1_gmpM_rep1

description: Colony Forming Unit - Monocyte

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 (default parameters)
Enhancers were defined on H3K4me1 histone modification using PARE v0.01 (default parameters)
Peaks were called using macs2. To increase the specificity of the enriched regions, we used a control sample prepared using a control anti-body (‘IgG’ control). Further, Irreproducible Discovery Rate (IDR) was used at a false discovery rate of 0.05 to filter out irreproducible regions between the two replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM. Identical reads are counted once. bedGraph files were converted to bigWig format using bedGraphToBigWig tool.

molecule: genomic DNA

extract_protocol:
Genomic DNA extraction protocol not provided.
Precipitated DNA were mixed with 0-2 ng E. Coli DNA, depending on the amount of ChIP DNA isolated. This mix was amplified using NEB Next ChIP-seq sample prep reagent set 1 (New England Biolabs) according to manufacturer’s protocol.

value: wildtype

tag: chip-antibody

value: Sc-352, Santa Cruz


title: PU1_gmpG_rep2

description: Colony Forming Unit - Granulocyte

source_name: CFU-G

value: Lin- Sca1-cKit+ CD150- CD41- FcgRII/III(hi) CD115-


title: Sample 23: diet14071612_pooled_hypo_1

description: diet D14071612


title: CEBPA_gmpG_rep3

description: Colony Forming Unit - Granulocyte

value: 14AA, Santa Cruz


title: THP-1-HSVC819S-2

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

data_processing:
Reads were trimmed on both ends and discard bases before 1 and after 25
Trimmed reads were aligned to hg38 by using STAR - 2.5.3a
counts were normalized by add 1
fiter was performed with FDR <= 0.05 and fold change >= 2
Genome_build: hg38
Supplementary_files_format_and_content: text files were generated including the differential expression gene lists with FDR <= 0.05 and fold change >= 2

organism: Homo sapiens

growth_protocol: THP-1 monocytes were cultured in RPMI-1640 Medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted by using Qiagen Rneasy kit.
mRNA was purified and library was constructed by using KAPA Stranded mRNA-Seq Kit according to the manufactor's protocol.

treatment_protocol: THP-1 cells were mock-infected or infected with HSV-1UL37WT or HSV-1UL37C819S (MOI = 5) for 4 h.

tag: cell line

tag: cell type

value: Human monocytes

tag: infected with

value: HSV-1UL37C819S virus


title: THP-1-HSVC819S-1


title: THP-1-control-2

value: control (mock-infected)


title: PU1_gmpG_rep1

description: Colony Forming Unit - Granulocyte


title: H3K27ac_monocytes_rep1

source_name: Monocytes

value: Ter119- B220- CD3- NK1.1- CD115+ cKit- CD34- FcgRII/III+ Ly6G- CD11b+

value: ab4729, Abcam


title: H3K27ac_gmpM_rep2

description: Colony Forming Unit - Monocyte

value: bone marrow


title: H3K4me1_monocytes_rep3

value: ab8895, Abcam


title: THP-1-HSV-1

value: HSV-1UL37WT virus


title: CEBPA_gmpG_rep1

description: Colony Forming Unit - Granulocyte


title: H3K27ac_monocytes_rep2


title: H3K27ac_gmpM_rep1

description: Colony Forming Unit - Monocyte


title: CEBPA_gmpG_rep2

description: Colony Forming Unit - Granulocyte


title: THP-1-control-1


title: THP-1-HSV-2


title: H3K27ac_gmpG_rep1

description: Colony Forming Unit - Granulocyte


title: expr_lsk_cebpa_wt_Rep3

value: wt


title: H3K27ac_gmpG_rep2

description: Colony Forming Unit - Granulocyte


title: H3K4me1_monocytes_rep1


title: H3K4me1_monocytes_rep2


title: H3K4me1_gmpM_rep3

description: Colony Forming Unit - Monocyte


title: H3K4me1_gmpM_rep2

description: Colony Forming Unit - Monocyte


title: CEBPA_gmpM_rep1

description: Colony Forming Unit - Monocyte


title: PU1_gmpG_rep3

description: Colony Forming Unit - Granulocyte


title: KGC-A rep2

city: Boston

first: Krushna

middle: C

last: Patra

state: MA

address: 185 Cambridge Street

department: Cancer Center

country: USA

institute: MGH

data_processing:
Reads aligned to mouse genome with tophat version 2.0.8 using mm9 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflinks version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html) with the -G flag to use the mm9 reference annotation to estimate isoform expression and not assemble novel transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: 3D culture of cancer cells_KGC-A

growth_protocol: Murine pancreatic tumor cells were derived from the KGC GEM models. [KRASG12D/+; Rosa26-LSL-rtTALox/+, TetO-GNASR201C, Ptf1a-Cre]. Tumor tissues were collected in ice cold 20 mL DMEM with 1X Antibiotic-Antimycotic. A transection of the tumor tissue was taken for histological verification and the rest was washed twice with 10 mL HBSS and then minced aseptically with a razor blade on a 10-cm dish. The minced tissue was digested in a small flask for 1 hour on a bench-top stirrer with 2.6 U Liberase DH in 10 mL DMEM containing 1X Antibiotic-Antimycotic at 37 °C. 10 mL tissue homogenates were transferred to a 50 mL falcon tube and centrifuged at 1,000 rpm, 5 min, 4 °C. The pellet was then washed with HBSS 2-3 times by centrifugation. A 100 μm strainer was used to removed undigested large tissue debris. The flow-through was centrifuged at 1,200 rpm for 5 minutes, and the pellet was resuspended with full duct media (DMEM:F12, 5 mg/ml Glucose, 1.22 mg/ml nicotinamide, 5 nM 3,3,5-tri-iodo-L-thyronine, 1 μM Dexamethasone, 5 ml/L ITS+, 1X Pen/Strep, 20 ng/ml mouse EGF, 5% NuSerum IV and 25 μg/ml bovine pituitary extract) with Rho-associated protein kinase (ROCK) inhibitor (10 μg/ml)) and plated on irradiated feeder cells. Media was supplemented with 200 ng/ml doxycycline. The frozen cells were thawed on feeder layer with ROCK inhibitor and grown as 3D organoids in matrigel.

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (V2) was used for the construction of sequencing libraries using standard Illumina protocols

treatment_protocol: 3D organoid cultures were grown in 200ng/ml doxycycline.

tag: strain background

tag: genotype/variation

value: KRAS(G12D);GNAS R201C

value: Pancreas

tag: cell type/line

value: pancreatic tumor cells KGC-A

value: 5Day 3D culture


title: KGC-B rep2

source_name: 3D culture of cancer cells_KGC-B

value: pancreatic tumor cells KGC-B


title: KGC-B rep1


title: H3K4me1_gmpM_rep1

description: Colony Forming Unit - Monocyte

value: wildtype

value: Lin- Sca1- cKit+ CD150- CD41- FcgRII/III(hi) CD115+


title: H3K4me1_gmpG_rep3

description: Colony Forming Unit - Granulocyte

value: Lin- Sca1-cKit+ CD150- CD41- FcgRII/III(hi) CD115-


title: DCEXO4

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the Mus musculus transcriptome, using RSEM v1.2.30.
Genome_build: Ensembl genebuild 76 (Mus musculus GRCm38).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

source_name: Bone Marrow derived dendritic cells

growth_protocol: Bone Marrow derived dendritic cells(BMDC) were cultured for 9 days using GMCSF and spliting every 3 days.

extract_protocol:
RNA from cells was obtained using following RNeasy kit protocol from QIAGEN.
Index-tagged cDNA libraries were constructed from total RNA (1 μg) with the NEBNext RNA sample preparation kit. Quality, quantity, and size distribution of the Illumina libraries were determined using the DNA-1000 kit (Agilent Bioanalyzer).
Libraries were sequenced (single-end mode and length of 61 bp) on the IlluminaHiSeq 2500 system using the standard RNA sequencing protocol in the NEBNext kit.

value: Bone Marrow derived dendritic cells

tag: agent

value: exosome


title: H3K4me1_gmpG_rep2

description: Colony Forming Unit - Granulocyte


title: DCEXO1


title: H3K4me1_gmpG_rep1

description: Colony Forming Unit - Granulocyte


title: DC4


title: DCEXO3


title: DCEXO2


title: DC3


title: DC2


title: DC1


title: PU1_GMP_wt_ChIP-seq_rep2

value: Lin-, Sca-1-, ckit+, CD150-, FcgRII/III+

value: Sc-352, Santa Cruz


title: PU1_lsk_wt_ChIP-seq_rep2

value: Lin-, Sca-1+, ckit


title: PU1_preGM_ko_ChIP-seq_rep2

value: CEBPA KO

value: bone marrow


title: PU1_preGM_wt_ChIP-seq_rep1


title: PU1_preGM_ko_ChIP-seq_rep1


title: PU1_GMP_wt_ChIP-seq_rep1


title: PU1_preGM_wt_ChIP-seq_rep2


title: CEBPA_preGM_wt_ChIP-seq_rep2

value: 14AA, Santa Cruz


title: H3K27ac_Granulocytes_wt_ChIP-seq_rep1

source_name: Granulocytes

value: ab4729, Abcam


title: H3K27ac_Granulocytes_wt_ChIP-seq_rep2


title: CEBPA_preGM_wt_ChIP-seq_rep1


title: H3K27ac_GMP_wt_ChIP-seq_rep2


title: PU1_lsk_wt_ChIP-seq_rep1


title: KGC-A rep1

value: KRAS(G12D);GNAS R201C


title: H3K27ac_preGM_wt_ChIP-seq_rep2


title: H3K27ac_GMP_wt_ChIP-seq_rep1


title: H3K27ac_preGM_ko_ChIP-seq_rep1


title: H3K27ac_preGM_ko_ChIP-seq_rep2


title: H3K27ac_preGM_wt_ChIP-seq_rep1


title: H3K27ac_lsk_wt_ChIP-seq_rep2


title: H3K27ac_lsk_wt_ChIP-seq_rep1


title: H3K4me1_GMP_wt_ChIP-seq_rep2

value: ab8895, Abcam


title: H3K4me1_preGM_ko_ChIP-seq_rep2


title: H3K4me1_Granulocytes_wt_ChIP-seq_rep2


title: H3K4me1_Granulocytes_wt_ChIP-seq_rep1


title: H3K4me1_GMP_wt_ChIP-seq_rep1


title: H3K4me1_preGM_ko_ChIP-seq_rep1


title: H3K4me1_preGM_wt_ChIP-seq_rep2


title: H3K4me1_preGM_wt_ChIP-seq_rep1


title: H3K4me1_lsk_wt_ChIP-seq_rep2


title: Emc5-mV-BirA_input

city: Cambridge

first: Jonathan

middle: S

last: Weissman

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

description:
ribosome protected mRNA fragment
yeast_codon_counts.txt

data_processing:
Library strategy: ribosome profiling
base calls were called with Illumina CASAVA software (1.6-1.8)
3' adaptor was trimmed using a custom python script
reads were aligned sequentially first to rRNA, then unaligned reads were aligned to tRNA, then unaligned reads were aligned to a genomic index (sacCer3 for yeast) or to UCSC known gene cDNA sequences (hg19)
expression was quantitated using custom scripts after P-site mapping
Genome_build: sacCer3 and hg19
Supplementary_files_format_and_content: tab delimited file containing gene annotations, count (yeast) and rpkm (HeLa) data

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6. HeLa Cells were cultured in 15 cm plates with Dulbecco modified eagle medium (DMEM) with 10% fetal bovine serum (Gibco) until ~80% confluency.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.  HeLa cells were lysed using 500 µl per polysome lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton x-100, 1 mM DTT, 8% glycerol, 100 µg/ml CHX, 24 U/ml Turbo DNase) per plate using a rubber cell scraper to facilitate lysis.
Footprinting was performed with RNase I (yeast) or MNase (HeLa cells), monosomes were purified on 10-50% sucrose gradients (yeast) or a sucrose cushion (HeLa). For proximity-specific samples, biotinylated ribosomes were purified on streptavidin dynabeads.  RNA was extracted with trizol and protected fragments gel purified.  Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2.  Ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.

treatment_protocol: Yeast cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction then induced with 10 nM biotin.  HeLa cells were treated with 100 ug/ml CHX for 2 min.

tag: strain/cell line

value: emc5::EMC5-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1

tag: lentivirally transduced transgenes


title: Emc5-mV-BirA_pulldown


title: reanalyzed_Ubc6,input

description:
ribosome protected mRNA fragment
originally accessioned as: GSM1495513
yeast_codon_counts.txt

value: his3::pSEC63-BirA-mVenus-UBC6 TA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 leu2delta0


title: reanalyzed_Ssh1,pulldown

description:
ribosome protected mRNA fragment
originally accessioned as: GSM1495512
yeast_codon_counts.txt

value: ssh1::BirA-mVenus-SSH1::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1


title: reanalyzed_Ubc6,pulldown

description:
ribosome protected mRNA fragment
originally accessioned as: GSM1495514
yeast_codon_counts.txt


title: input DNA_Rep2

city: Chicago

first: Sarah

middle: E

last: London

state: IL

address: 940 E 57th Street

institute: University of Chicago

description:
Replciate 2
9_002IUC_pooled_Input_tgu_i81
Input_Rep2

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the taeGut2 using the BWA algorithm (v0.6.1, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7. --- or e.g.: Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: taeGut2
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks

organism: Taeniopygia guttata

source_name: auditory forebrain_input DNA

growth_protocol: Tutored and Isolate P67 males were raised with either 1 adult male + 1 adult female (Tutored) or 2 adult females (Isolate) from P21 onward

extract_protocol:
Aduitory forebrain was rapidly dissected, and frozen. Upon thawing tissue was fixed immediately1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

value: Posthatch day 67

tag: Sex

value: male

tag: experience

value: Tutored & Isolate

value: brain; auditory forebrain

tag: chip antibody


title: RNA Polymerase II ChIP-seq_Isolate_Rep2

description:
Replciate 2
8_002IUC_Isolated_Pol2_tgu_i93
Isolate__PolII_Rep2

source_name: auditory forebrain_RNA Polymerase II ChIP-seq

value: Isolate

tag: tissue

value: PolII


title: H3K27me3_ChIPseq_Tutored_Rep2

description:
Replciate 2
1_002IUC_Tutored_H3K27me3_tgu_i86
Tutored_H3K27me3_Rep2

source_name: auditory forebrain_H3K27me3_ChIPseq

value: Tutored


title: H3K9me3_ChIPseq_Isolate_Rep2

description:
Replciate 2
6_002IUC_Isolated_H3K9me3_tgu_i91
Isolate__H3K9me3_Rep2

source_name: auditory forebrain_H3K9me3_ChIPseq

value: H3K9me3 (Active Motif, #39161)


title: reanalyzed_Ssh1,input

description:
ribosome protected mRNA fragment
originally accessioned as: GSM1495511
yeast_codon_counts.txt

tag: genotype


title: H3K4me1_lsk_wt_ChIP-seq_rep1

value: wildtype

tag: cell markers

value: Lin-, Sca-1+, ckit


title: H3K4me3_ChIPseq_Tutored_Rep2

description:
Replciate 2
AB5_Slondon_TutNew_H3K4me3_A005_r1
Tutored_H3K4me3_Rep2

source_name: auditory forebrain_H3K4me3_ChIPseq

tag: age

value: H3K4me3 (Active Motif, #39159)


title: H3K4me3_ChIPseq_Isolate_Rep2

description:
Replciate 2
AB1_Slondon_IsoNew_H3K4me3_A001_r1
Isolate__H3K4me3_Rep2


title: H3K27me3_ChIPseq_Isolate_Rep2

description:
Replciate 2
2_002IUC_Isolated_H3K27me3_tgu_i87
Isolate__H3K27me3_Rep2


title: H3K9me3_ChIPseq_Tutored_Rep2

description:
Replciate 2
5_002IUC_Tutored_H3K9me3_tgu_i90
Tutored_H3K9me3_Rep2


title: Emc5-mV-BirA_replicate_pulldown


title: PolII_ChIPseq_P32

source_name: auditory forebrain

growth_protocol: Tutored and Isolate P67 males were raised with either 1 adult male + 1 adult female (Tutored) or 2 adult females (Isolate) from P21 onward; P32 males remained in home flight aviaries

value: brain

value: Posthatch day 32

value: Normal

value: PolII (Abcam, #ab5095)


title: RNA Polymerase II ChIP-seq_Isolate_Rep1


title: H3K9me3_ChIPseq_P32


title: input DNA_Tutor_Isolate_pool_Rep1


title: input DNA_P32


title: H3K4me3_ChIPseq_Tutored_Rep1


title: H3K4me3_ChIPseq_P32


title: H3K4me3_ChIPseq_Isolate_Rep1


title: RNA Polymerase II ChIP-seq_Tutored_Rep1


title: H3K27me3_ChIPseq_P32


title: RNA Polymerase II ChIP-seq_Tutored_Rep2

description:
Replciate 2
7_002IUC_Tutored_Pol2_tgu_i92
Tutored_PolII_Rep2


title: H3K27me3_ChIPseq_Isolate_Rep1


title: H3K27me3_ChIPseq_Tutored_Rep1


title: Emc5-mV-BirA_replicate_input

value: emc5::EMC5-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1


title: H3K9me3_ChIPseq_Tutored_Rep1


title: G6 Splenic Macrophages tumor only

status: Public on May 28 2018

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.6.3, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: Spleen

growth_protocol: 6-8 week old female SCID-beige mice were injected intraperitoneally with CD19+ Raji tumor cells. Tumor cells were left to grow for three weeks.

extract_protocol:
Cells were sorted directly into 750ul of Trizol LS (Invitrogen).  The volume was adjusted to 1ml with PBS and extraction was performed according to instructions provided by the manufacturer. After ribogreen quantification and quality control of Agilent BioAnalyzer, total RNA underwent amplification using the SMART-seq V4 (Clonetech) ultra low input RNA kit for sequencing. For 2-10 ng of total RNA, 12 cycles of amplification were performed. For lesser amount (0.13 to2 ng), 13 cycles of amplification were performed.
10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 38.5 million paired reads were generated per sample and the percent of mRNA bases was over 77% on average.

treatment_protocol: After 3 weeks of tumor growth, mice received 1928z 30e6 CAR T cells.

tag: strain

value: SCID-beige

tag: tumor bearing

value: yes

tag: car treated

value: no


title: G6 Splenic Ly6Cint monocytes tumor only


title: G6 Splenic Ly6Chi monocytes tumor only


title: G6 Splenic DCs tumor only


title: G6 Peritoneal Monocytes  tumor only

source_name: Peritoneum


title: G6 Peritoneal Resident Macrophages  tumor only


title: G6 Peritoneal DCs tumor only


title: G5 Splenic Ly6Cint monocytes tumor only


title: G5 Splenic Macrophages tumor only


title: H3K9me3_ChIPseq_Isolate_Rep1

value: Posthatch day 67

value: male


title: G5 Peritoneal Monocytes  tumor only


title: G5 Splenic DCs tumor only


title: G5 Splenic Ly6Chi monocytes tumor only


title: G5 Peritoneal Resident Macrophages  tumor only


title: G4 Splenic DCs tumor only


title: G4 Splenic Macrophages tumor only


title: G5 Peritoneal DCs tumor only


title: G5 Peritoneal Ly6Chi Macrophages  tumor only


title: G4 Splenic Ly6Chi monocytes tumor only


title: G4 Peritoneal Monocytes  tumor only


title: G4 Peritoneal Resident Macrophages  tumor only


title: G6 Peritoneal Ly6Chi Macrophages  tumor only


title: G4 Peritoneal Ly6Chi Macrophages  tumor only


title: G4 Peritoneal DCs tumor only


title: HSC_5FU_Treated_WT_A3

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: WT HSCs were sorted from BM of 5FU treated mice

data_processing:
Adapter trimming with Trimmomatic
Alignment against Ensembl 77 cDNA with Bowtie (v 1.1.1, parameters: -q -p 6 -a -m 100 --minins 0 --maxins 5000 --fr --sam --chunkmbs 200)
Transcript quantification with BitSeq (v 1.12.0)
Transcripts collapsed per gene and biological replicate in R
Statistical analysis and variance-stablizing transformation with DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file with normalized expression estimates per gene (Ensembl ID)

source_name: Bone marrow HSCs

extract_protocol:
100 cells of the respective cell type were sorted into 4µl of lysis buffer containing 3.8µl of 0.2% Triton X-100 and 0.2µl of RNase inhibitor. Cells were stored at -80°C until cDNA synthesis.
cDNA and libraries were generated according to the Smart-seq2 protocol as published recently (Picelli et al. 2015).

treatment_protocol: see Methods Section

tag: cell type

value: HSC

tag: treatment

value: WT

tag: flowcell


title: HSC_5FU_Treated_WT_A2


title: HSC_Untreated_WT_D3

description: WT HSCs were sorted from BM


title: HSC_5FU_Treated_KO_A8

description: MEK1 deficient HSCs were sorted from BM of 5FU treated mice

value: KO


title: HSC_Untreated_WT_D2

description: WT HSCs were sorted from BM


title: HSC_Untreated_WT_D1

description: WT HSCs were sorted from BM


title: HSC_Untreated_KO_D4

description: MEK1 deficient HSCs were sorted from BM


title: HSC_5FU_Treated_WT_A4


title: HSC_5FU_Treated_KO_A6


title: HSC_Untreated_KO_D6

description: MEK1 deficient HSCs were sorted from BM


title: HSC_5FU_Treated_WT_D4


title: HSC_Untreated_KO_D5

description: MEK1 deficient HSCs were sorted from BM


title: G3 Splenic Ly6Cint monocytes CRS


title: G3 Splenic Macrophages CRS


title: G3 Splenic Ly6Chi monocytes CRS


title: G4 Splenic Ly6Cint monocytes tumor only


title: G3 Splenic DCs CRS


title: G3 Peritoneal Resident Macrophages CRS


title: G3 Peritoneal Monocytes CRS


title: G3 Peritoneal Ly6Chi Macrophages CRS


title: G3 Peritoneal DCs CRS


title: G2 Splenic Macrophages CRS


title: HSC_5FU_Treated_KO_A5


title: G2 Peritoneal Resident Macrophages CRS


title: G2 Splenic Ly6Cint monocytes CRS


title: G1 Splenic Macrophages CRS


title: G2 Peritoneal Monocytes CRS


title: G2 Splenic DCs CRS


title: ore15-2_2

type: RNA

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

hyb_protocol: Microarray chips were hybridized using Agilent’s Gene Expression Hybridization Kit and washed with Agilent’s Gene Expression Wash Buffer Kit.

scan_protocol: An Agilent SureScan Microarray Scanner

data_processing:
Scanned images were analyzed and quantified using Agilent Feature Extraction software (version 11.5). Log2 intensities of the probes were first normalized using quantile normalization. Applicable cutoffs for reliable signals in probes were determined by Gaussian curve fitting (Signal ≥ 5.818)
Probes targeting multiple genes were ignored and data was analyzed based on gene expression, not on transcript expression (see Series supplementary files: Processed_data_AGI-Gene-based_data.txt, agilent_array_elements-2010-12-20.txt, README.txt)

organism: Arabidopsis thaliana

source_name: ore15-2, 4 DAE

label_protocol: Total RNA was amplified and labeled using Agilent's one-color Low Input Quick Amp Labeling kit

growth_protocol: Arabidopsis were grown on the soil for 13 days in 16:8 light-dark (LD) cycle

extract_protocol: Total RNA was isolated using WelprepTM Total RNA Isolation Reagent

treatment_protocol: Plants were harvested at 5 h after light-on.

tag: genotype/variation

value: 3 or 4th leaves


title: G2 Splenic Ly6Chi monocytes CRS


title: ore15-1D_2

source_name: ore15-1D, 4 DAE


title: Col_1

source_name: Col, 4 DAE

value: wild type


title: G2 Peritoneal DCs CRS


title: ore15-2_1


title: G1 Splenic Ly6Chi monocytes CRS


title: ore15-1D_1


title: Col_2


title: G1 Splenic DCs CRS


title: 87.5 mg/kg ceritinib, 1

city: Seoul

first: Kyoung-Ho

last: Pyo

address: 50 Yonseiro

department: Avison Biomedical Research Center

institute: Severance Hospital, Yonsei University College of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: H3122 tumor

label_protocol: Total RNA was amplified and purified using Target Amp-Nano Labeling Kit for Illumina Expression Bead Chip (EPICENTRE) to yield biotinylated cRNA according to the manufacturer’s instructions

extract_protocol: Total RNA was extracted using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol

tag: agent

value: 87.5 mg/kg ceritinib

tag: cell line


title: 87.5 mg/kg ceritinib, 2


title: 100 mg/kg ceritinib, 2

value: 100 mg/kg ceritinib


title: 100 mg/kg ceritinib, 3


title: 100 mg/kg ceritinib, 1


title: G2 Peritoneal Ly6Chi Macrophages CRS


title: 75 mg/kg ceritinib, 3

value: 75 mg/kg ceritinib


title: rnp-2(tm4058)_expt_2

first: Martin

last: Newman

address: 185 Cambridge St, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to WS235 whole genome using STAR
The number of reads that span unspliced introns (IEJ) and spliced junctions (EEJ) were count using samtools, then normalized by library size.
Genome_build: ws235
Supplementary_files_format_and_content:
EJ = the number of normalized RPM for reads that span unspliced introns (near both the 5' splice donor and 3' splice acceptor sites).
EEJ = the number of normalized RPM for reads that span *spliced* junctions.

organism: Caenorhabditis elegans

growth_protocol: All C. elegans strains were grown at 20oC unless otherwise indicated (Brenner 1974).

extract_protocol:
RNA was isolated from embryos using Trizol according to manufacturer's protocol.  Small RNA fraction was isolated by excision from a 15% TBE / Urea PAGE gel.
Standard Illumina-based protocol for library generation from small RNA.

treatment_protocol: Embryos were isolated from adult C. elegans using standard alkaline / hypochlorite treatment.

tag: strain background

value: embryos

tag: molecule subtype

value: purified small RNA


title: Control, 1

value: Control


title: 75 mg/kg ceritinib, 1


title: 75 mg/kg ceritinib, 2


title: 87.5 mg/kg ceritinib, 3


title: rnp-2(mg582)_expt_2


title: Control, 2


title: rnp-3(ok1424)_expt_1


title: rnp-2(mg582)_expt_1


title: G1 Splenic Ly6Cint monocytes CRS


title: wildtype_N2_expt_1


title: G1 Peritoneal Resident Macrophages CRS


title: G1 Peritoneal DCs CRS


title: 75 mg/kg ceritinib, 4


title: CRTC3 BKO-SVF-Fsk

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

data_processing:
MiSeq Generation of fastq files
tophat2 alignment
cuffdiff alignment
Genome_build: mm10
Supplementary_files_format_and_content: .diff file from cuffdiff comparing all four samples. Sample name is in the 'description' field.

source_name: Primary SVF cells from brown fat

extract_protocol:
total RNA extracted with Qiagen Rneasy kit
polyA RNA isolated and library prepared with NEBnext Ultra kit

treatment_protocol: Stock FSK (Forskolin) is added to cultures to a final concentration of 10 uM (micro molar).

value: CRTC3 BKO mice

value: differentiated Primary brown fat SVF cells

value: 2 hours FSK treatment


title: CRTC3 BKO-SVF-con

treatment_protocol: untreated

value: Untreated


title: G1 Peritoneal Monocytes CRS

value: SCID-beige

value: yes


title: wildtype_N2_expt_2


title: G1 Peritoneal Ly6Chi Macrophages CRS


title: WT-SVF-con

value: Wild-type mice


title: WT-SVF-Fsk


title: H3122-LR_3

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

tag: phenotype

value: ceritinib-resistant


title: Humanized mouse liver, fenofibrate treatment, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: G283_H09_m_hLiver_203.CEL (feno)

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

label: biotin

source_name: Liver from a chimeric mouse with a humanized liver, after 4 days fenofibrate treatment

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The animal study was carried out in PXB mice (genotype: cDNA-uPA+/wt/SCID, uPA+/wt; B6;129SvEv-Plau, SCID; C.B-17/Icr-scid/scid Jcl) at PhoenixBio Co. Ltd. Briefly, cryopreserved human hepatocytes from a 2-year-old Hispanic girl were purchased from BD Biosciences (Woburn, MA, USA). After thawing, the hepatocytes were transplanted into hemizygous 2- to 4-week-old cDNA-uPA/SCID mice via the spleen under anesthesia. . A full description of the generation of these mice can be found elsewhere [PMID: 26536627]. Six male mice between 12-18 weeks of age were used for the study.

extract_protocol: Total RNA was prepared from liver using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0)

treatment_protocol: Fenofibrate was dissolved in 0.5% hydroxypropyl methylcellulose (Shinestu Kagaku Kogyo, Japan) and administered orally to the mice at a dose of 300 mg/kg once per day for 4 days with a disposable plastic sonde (Fuchigami Kikai Co., Kyoto, Japan). Three mice received fenofibrate and three mice received the control treatment with vehicle only.

value: PXB (chimeric mouse, with more than 70% of the liver replaced with normal human hepatocytes)

tag: Sex

value: male

tag: treated with

value: Fenofibrate (300 mg/kg, dissolved in 0.5% hydroxypropyl methylcellulose)


title: H3122-LR_2


title: Selenium deficient proerythroblasts, replicate 3

city: State College

first: K. Sandeep

last: Prabhu

state: Pennsylvania

address: 115 Henning Building, University Park

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

description: Proerythroblasts sorted from spleen of selenium deficient mice treated with phenylhydrazine.

hyb_protocol: Labeled samples were hybridized to Mouse Transcriptpme 1.0 microarrays, and were washed and stained as recommended by the manufacturer.

scan_protocol: Arrays were scanned with an Affymetrix GCS3000 Scanner.

data_processing: The data were processed with Affymetrix Expression Console Software using default settings.

source_name: mouse spleen day3 post phenylhydrazine treatment

label_protocol: Samples were labeled with the Affymetrix GeneChip WT Pico Reagent Kit according to the manufacturer's instruction. 5ng of total RNA was used as input.

growth_protocol: Sorted primary cells from mouse spleen.

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

treatment_protocol: Mice were kept on selenium deficient or adequate diet for three months prior phenylhydrazine treatment and cell sorting.

tag: gender

tag: tissue

value: spleen

value: proerythroblasts


title: Selenium deficient basophilic erythroblasts, replicate 2

description: Basophilic erythroblasts sorted from spleen of selenium deficient mice treated with phenylhydrazine.

value: basophilic erythroblasts


title: Selenium deficient basophilic erythroblasts, replicate 1


title: Selenium deficient basophilic erythroblasts, replicate 3


title: H3122-LR_1


title: Selenium adequate proerythroblasts, replicate 3

description: Proerythroblasts sorted from spleen of selenium adequate mice treated with phenylhydrazine.


title: H3122-WT_3

value: control


title: Selenium deficient proerythroblasts, replicate 2


title: Selenium adequate proerythroblasts, replicate 2


title: Humanized mouse liver, control treatment, replicate 3

description: G283_G09_m_hLiver_103.CEL (veh)

source_name: Liver from a chimeric mouse with a humanized liver, after 4 days control treatment

value: cDNA-uPA+/wt/SCID, uPA+/wt; B6;129SvEv-Plau, SCID; C.B-17/Icr-scid/scid Jcl

value: vehicle only (0.5% hydroxypropyl methylcellulose)


title: Selenium adequate proerythroblasts, replicate 1


title: Humanized mouse liver, fenofibrate treatment, replicate 1

description: G283_H05_m_hLiver_201_3.CEL (feno)

value: Liver from a chimeric mouse with a humanized liver


title: Humanized mouse liver, control treatment, replicate 2

description: G283_G07_m_hLiver_102.CEL (veh)


title: Selenium deficient proerythroblasts, replicate 1


title: Female C57/B7 Day 5 Tofacitinib mouse9

status: Public on May 27 2018

first: Jane

middle: E.

last: Cerise

address: 1150 St. Nicholas Avenue

institute: Columbia University

description: Gene expression from dorsal skin from C57/B6 mice treated with tofacitinib for 4 days

hyb_protocol: Arrays used were Affymetrix mouse 430 2.0, hybridized at the CUMC microarray facility

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000.

data_processing: The data were analyzed with Bioconductor/R and were GCRMA normalized.

source_name: Dorsal skin from C57/B6 micetreated topically with Tofacitinib for 4 days

label_protocol: The Ovation RNA Amplification kit (Nugen) was used to generate amplified cDNA for microarray analysis.

extract_protocol: Whole skin biopsies were flash frozen in liquid nitrogen and stored in -80*C. Samples were then homogenized and extraced using Qiagen RNAeasy micro kit.

treatment_protocol: Skin biopsies were taken from C57/B6 females, 8.5 week of age on day 0 (pre treatment) and then treated daily with topical application of vehicle alone (DMSO), Ruxolitinib and Tofacitinib. On day 5, mice were sacrified and a second whole skin biopsy was taken from treated skin.

tag: mouse

tag: time

value: Tofa

value: skin


title: Humanized mouse liver, fenofibrate treatment, replicate 2

description: G283_H07_m_hLiver_202.CEL (feno)

tag: strain


title: Selenium adequate basophilic erythroblasts, replicate 2

description: Basophilic erythroblasts sorted from spleen of selenium adequate mice treated with phenylhydrazine.


title: Selenium adequate basophilic erythroblasts, replicate 1


title: H3122-WT_1


title: Selenium adequate basophilic erythroblasts, replicate 3


title: H3122-WT_2


title: Humanized mouse liver, control treatment, replicate 1

description: G283_G05_m_hLiver_101.CEL (veh)


title: Female C57/B7 Day 5 Tofacitinib mouse7

description: Gene expression from dorsal skin from C57/B6 mice treated with ruxolitinib for 4 days


title: Female C57/B7 Day 5 Ruxolitinib mouse6

source_name: Dorsal skin from C57/B6 micetreated topically with Ruxolitinib for 4 days

value: Ruxo


title: Female C57/B7 Day 5 Tofacitinib mouse8

description: Gene expression from dorsal skin from C57/B6 mice treated with tofalitinib for 4 days


title: Female C57/B7 Day 5 Ruxolitinib mouse4


title: Female C57/B7 Day 5 DMSO mouse3

description: Gene expression from dorsal skin from C57/B6 micetreated topically with DMSO for 4 days

source_name: Dorsal skin from C57/B6 micetreated topically with DMSO for 4 days

value: DMSO


title: HEK293T_MLL3_W383L_KI_R1

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Cells with MLL3 W383L mutation

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cell medium was composed as follows: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

value: Kidney cell line

tag: passages

value: Low passages (6-10)

value: MLL3 W383L mutation


title: HEK293T_MLL3_W383L_KI_R2

description: Cells with MLL3 W383L mutation

tag: cell type


title: Female C57/B7 Day 0 8.5 weeks mouse6

description: Gene expression from dorsal skin from C57/B6 mice at 8.5 weeks

source_name: Dorsal skin from C57/B6 mice at 8.5 weeks

tag: treatment

value: baseline


title: Female C57/B7 Day 0 8.5 weeks mouse4


title: HEK293T_MLL3_WT_KI_R2

description: Cells with wild type MLL3

value: wild type MLL3


title: Female C57/B7 Day 0 8.5 weeks mouse7


title: Female C57/B7 Day 0 8.5 weeks mouse9


title: HEK293T_MLL3_G368V_KI_R1

description: Cells with MLL3 G368V mutation

value: MLL3 G368V mutation


title: HEK293T_MLL3_WT_KI_R1

description: Cells with wild type MLL3


title: Female C57/B7 Day 0 8.5 weeks mouse5


title: Female C57/B7 Day 5 DMSO mouse2


title: HEK293T_MLL3_G368V_KI_R2

description: Cells with MLL3 G368V mutation


title: Female C57/B7 Day 0 8.5 weeks mouse8


title: HEK293T_MLL3_KO_Clone2_R2

description: Cells with MLL3 depletion

value: MLL3 depletion


title: HEK293T_MLL3_WT_R1

description: Cells with wild type MLL3


title: HEK293T_MLL3_WT_R2

description: Cells with wild type MLL3


title: HEK293T_MLL3_KO_Clone2_R1

description: Cells with MLL3 depletion


title: HEK293T_MLL3_KO_Clone1_R1

description: Cells with MLL3 depletion


title: Input_MLL3_W383L

description: Cells with MLL3 W383L mutation

tag: chip antibody

value: H3K27me3 (homemade)


title: Input_MLL3_G368V

description: Cells with MLL3 G368V mutation

tag: genotype/variation


title: Input_HEK293T_MLL3_WT

description: Cells with wild type MLL3


title: H3K27me3_HEK293T_MLL3_W383L_KI

description: Cells with MLL3 W383L mutation


title: mog-2(ok1221)_expt_1

value: embryos

value: purified small RNA


title: H3K27me3_HEK293T_MLL3_G368V_KI

description: Cells with MLL3 G368V mutation


title: H3K27me3_HEK293T_MLL3_WT

description: Cells with wild type MLL3


title: H3K27me3_CAL51_MLL3_KO_GSK126

description: Cells with MLL3 deletion and treated with GSK126

value: breast cancer cell

tag: drug treatment

value: MLL3 deletion


title: Female C57/B7 Day 0 8.5 weeks mouse3


title: Female C57/B7 Day 0 8.5 weeks mouse2


title: H3K27me3_CAL51_MLL3_KO

description: Cells with MLL3 deletion

tag: cell line


title: Female C57/B7 Day 0 8.5 weeks mouse1


title: H3K27me3_CAL51_MLL3_WT

description: Cells with wild type MLL3


title: HEK293T_MLL3_KO_Clone1_R2

description: Cells with MLL3 depletion


title: Input_CAL51_UTX_KO

description: cells with UTX deletion

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

tag: sample type


title: H3K4me1_CAL51_MLL3_WT

description: normal cells

value: H3K4me1 (homemade)


title: UTX_CAL51_UTX_WT

description: normal cells

value: UTX (homemade)


title: Input_CAL51_MLL3_KO

description: cells with MLL3 deletion


title: MLL3_CAL51_MLL3_Exon8_KO

description: cells with MLL3 deletion

value: MLL3_MR (homemade)


title: CAL51_MLL3_Exon8_KO_Rep1

description: cells with MLL3 deletion


title: CAL51_MLL3_Exon8_WT_Rep1

description: normal cells


title: Input_CAL51_MLL3_WT

description: normal cells


title: UTX_CAL51_UTX_KO

description: cells with UTX deletion


title: H3K4me1_CAL51_MLL3_KO

description: cells with MLL3 deletion


title: CAL51_MLL3_Exon8_KO_Rep2

description: cells with MLL3 deletion


title: Input_CAL51_MLL3_Exon8_KO

description: cells with MLL3 deletion


title: 293T-W383L-KI-Rep2

description: MLL3-W383L knockin cells

value: Kidney cell


title: 293T-WT-Rep1

description: normal cells

value: WT


title: 293T-WT-Rep2

description: normal cells


title: 293T-W383L-KI-Rep1

description: MLL3-W383L knockin cells


title: 293T-G368V-KI-Rep1

description: MLL3-G368V knockin cells


title: 293T-G368V-KI-Rep2

description: MLL3-G368V knockin cells


title: Input_CAL51_UTX_WT

description: cells with MLL3 deletion


title: UTX_CAL51_BAP1_WT_R2

description: Cells with wild type BAP1

value: wild type BAP1


title: UTX_CAL51_BAP1_WT_R1

description: Cells with wild type BAP1

value: Low passages (6-10)


title: UTX_CAL51_BAP1_KO_R2

description: Cells with BAP1 deletion

value: BAP1 deletion


title: Suz12_CAL51_BAP1_KO

description: Cells with BAP1 deletion


title: Suz12_CAL51_BAP1_WT

description: Cells with wild type BAP1


title: UTX_CAL51_BAP1_KO_R1

description: Cells with BAP1 deletion


title: MLL3_CAL51_BAP1_WT_R2

description: Cells with wild type BAP1


title: MLL3_CAL51_BAP1_KO_R2

description: Cells with BAP1 deletion


title: MCF7_shBAP1_2_R2

description: Cells treated with BAP1 shRNA-2

value: BAP1 shRNA-2


title: MCF7_shLuciferase_R2

description: Cells treated with luciferase shRNA

value: luciferase shRNA


title: Input_CAL51_BAP1_WT R4

description: Cells with wild type BAP1

tag: antibody


title: MCF7_shBAP1_2_R1

description: Cells treated with BAP1 shRNA-2


title: MCF7_shBAP1_1_R1

description: Cells treated with BAP1 shRNA-1

value: BAP1 shRNA-1


title: MCF7_shBAP1_1_R2

description: Cells treated with BAP1 shRNA-1


title: Input_CAL51_BAP1_WT R3

description: Cells with wild type BAP1


title: Input_CAL51_BAP1_KO R4

description: Cells with BAP1 deletion


title: Input_CAL51_BAP1_KO R3

description: Cells with BAP1 deletion


title: Input_CAL51_BAP1_KO R2

description: Cells with BAP1 deletion


title: MCF7_shLuciferase_R1

description: Cells treated with luciferase shRNA


title: Input_CAL51

description: Normal cells


title: HEK293T_BAP1_WT

description: Cells with wild type BAP1

value: Kidney cell line


title: HEK293T_BAP1_KO_Clone53_R1

description: Cells with BAP1 deletion


title: MLL3_CAL51_BAP1_WT_R1

description: Cells with wild type BAP1


title: HEK293T_BAP1_KO_Clone46_R1

description: Cells with BAP1 deletion


title: H3K4me3_CAL51_BAP1_WT

description: Cells with wild type BAP1

value: H3K4me3 (homemade)


title: H3K4me1_CAL51_BAP1_WT

description: Cells with wild type BAP1


title: H3K4me3_CAL51_BAP1_KO

description: Cells with BAP1 deletion


title: H3K4me1_CAL51_BAP1_KO

description: Cells with BAP1 deletion


title: H3K27me3_CAL51_UTX_WT

description: Cells with wild type BAP1

value: H3K27me3 (CST)


title: H3K27me3_CAL51_UTX_KO

description: Cells with BAP1 deletion


title: H3K27me3_CAL51_BAP1_WT_R2

description: Cells with wild type BAP1


title: Input_CAL51_BAP1_WT R1

description: Cells with wild type BAP1


title: Input_CAL51_BAP1_WT R2

description: Cells with wild type BAP1


title: H3K27me3_CAL51_BAP1_WT_R1

description: Cells with wild type BAP1


title: Input_CAL51_BAP1_KO R1

description: Cells with BAP1 deletion


title: H2AUb_CAL51_BAP1_KO_R2

description: Cells with BAP1 deletion

value: H2AK119Ub (CST)


title: H3K27me3_CAL51_BAP1_KO_R2

description: Cells with BAP1 deletion

value: breast cancer cell


title: H2AUb_CAL51_BAP1_WT_R1

description: Cells with wild type BAP1


title: H3K27me3_CAL51_BAP1_KO_R1

description: Cells with BAP1 deletion


title: H2AUb_CAL51_BAP1_WT_R2

description: Cells with wild type BAP1


title: CAL51_UTX_KO_R1

description: Cells with UTX deletion

value: UTX deletion


title: H2AUb_CAL51_BAP1_KO_R1

description: Cells with BAP1 deletion


title: CAL51_UTX_WT_R1

description: Cells with wild type UTX

value: wild type UTX


title: CAL51_UTX_KO_R2

description: Cells with UTX deletion


title: CAL51_Pol II

description: Normal cells

value: CAL51_Pol II

value: Pol II (CST)


title: H3K4me3_jizi.rep1

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to oryza sativa(MSU7.0) using bwa mem or tophat2 to map  with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, macs 1.3 was used to identify read enriched regions(peaks). For RNA-Seq, HTSeq-count was used to count the RNA-seq alignment files.
Genome_build: MSU 7.0
Supplementary_files_format_and_content: In ChIP-Seq, peak files was provided; In RNA-Seq, read counts for genes(MSU7.0) was provided.

organism: Oryza sativa

growth_protocol: The rice seeds were germinated in sterilized water, and were then placed in soil in an experimental field of the Institute of Plant Physiology and Ecology (Shanghai, China) under natural growing conditions during kharif season of 2013. Panicles were harvested.

extract_protocol:
Harvested samples were either frozen in liquid nitrogen for re-sequencing and RNA sequencing. or directly vacuum-infiltrated with formaldehyde cross-linking solution for ChIP assay. ChIP assay was performed with the antibody against H3 trimethyl-Lys 4 (Abcam, Cat. ab8580), H3 monomethyl-Lys 4 (Millipore,07-436), H3 trimethyl-Lys 27 (Upstate, USA, Cat. 07–449), H3 acetyl-Lys 27 (Upstate, USA, Cat. 07–360) and H3 trimethyl-Lys 36 (Abcam, Cat. ab9050).
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China). Libraries were sequenced on the HiSeq 2500 (Illumina) to produce 51 bp single reads for rice ChIP-seq, and 101 bp paired reads for  re-sequencing and RNA sequencing.

tag: ecotype

value: Japonica cultivar, JZ1560

value: young panicle

value: H3K4me3 (Abcam, Cat. ab8580)


title: CAL51_MLL3_WT_R1

description: Cells with wild type MLL3

value: Low passages (6-10)

value: wild type MLL3


title: CAL51_MLL3_WT_R2

description: Cells with wild type MLL3


title: H3K4me3_jizi.rep2


title: H3K4me1_jizi.rep2

value: H3K4me1 (Millipore, Cat. 07–436)


title: CAL51_MLL3_KO_Clone3_R2

description: Cells with MLL3 deletion Clone3

value: MLL3 deletion Clone3


title: H3K4me1_jizi.rep1


title: H3K36me3_jizi.rep1

value: H3K36me3 (Abcam, Cat. ab9050)


title: H3K27me3_jizi.rep3

value: H3K27me3 (Millipore, Cat. 07–449)


title: H3K27me3_jizi.rep2


title: CAL51_UTX_WT_R2

description: Cells with wild type UTX


title: CAL51_MLL3_KO_Clone1_R2

description: Cells with MLL3 deletion Clone1

value: MLL3 deletion Clone1


title: CAL51_MLL3_KO_Clone2_R1

description: Cells with MLL3 deletion Clone2

value: MLL3 deletion Clone2


title: H3K27ac_jizi.rep1

value: H3K27ac (Millipore, Cat. 07–360)


title: CAL51_H3K4me3

description: Normal cells

value: breast cancer cell

value: H3K4me3 (homemade)


title: CAL51_MLL3_KO_Clone1_R1

description: Cells with MLL3 deletion Clone1


title: CAL51_H3K4me1

description: Normal cells

value: H3K4me1 (homemade)


title: H3K27me3_input_jizi.rep1


title: H3K27me3_jizi.rep1


title: H3K4me1_huanghuazhan.rep2

value: Indica cultivar, HHZ


title: H3K4me3_huanghuazhan.rep1


title: CAL51_BAP1_WT_R2

description: Cells with wild type BAP1

value: wild type BAP1


title: CAL51_H3K27Ac

description: Normal cells

value: H3K27Ac (CST)


title: CAL51_BAP1_KO_R2

description: Cells with BAP1 deletion

value: BAP1 deletion


title: CAL51_MLL3_KO_Clone3_R1

description: Cells with MLL3 deletion Clone3


title: H3K36me3_huanghuazhan.rep1

value: young panicle


title: H3K4me1_huanghuazhan.rep1


title: CAL51_BAP1_WT_R1

description: Cells with wild type BAP1

value: Low passages (6-10)


title: H3K27me3_input_huanghuazhan.rep1


title: CAL51_BAP1_KO_R1

description: Cells with BAP1 deletion


title: CAL51_MLL3_KO_Clone2_R2

description: Cells with MLL3 deletion Clone2


title: H3K27me3_huanghuazhan.rep3


title: BAP1_NTD_CAL51_BAP1_WT

description: Cells with wild type BAP1

value: BAP1_NTD (homemade)


title: BAP1_NTD_CAL51_BAP1_KO

description: Cells with BAP1 deletion


title: reseq_huanghuazhan

description: Re-Sequencing

organism: Oryza sativa Indica Group

source_name: young panicle

extract_protocol:
Harvested samples were either frozen in liquid nitrogen for re-sequencing and RNA sequencing. or directly vacuum-infiltrated with formaldehyde cross-linking solution for ChIP assay.  For rice samples, ChIP assay was performed with the antibody against H3 trimethyl-Lys 4 (Abcam, Cat. ab8580), H3 monomethyl-Lys 4 (Millipore,07-436), H3 trimethyl-Lys 27 (Upstate, USA, Cat. 07–449), H3 acetyl-Lys 27 (Upstate, USA, Cat. 07–360) and H3 trimethyl-Lys 36 (Abcam, Cat. ab9050)
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China). Libraries were sequenced on the HiSeq 2500 (Illumina) to produce 51 bp single reads for rice ChIP-seq, and 101 bp paired reads for  re-sequencing and RNA sequencing.

tag: cultivar

value: HHZ


title: H3K27me3_huanghuazhan.rep2


title: H3K27me3_huanghuazhan.rep1


title: BAP1_FL_CAL51_BAP1_WT_R2

description: Cells with wild type BAP1

value: BAP1_FL (homemade)


title: RNA-seq_jizi

organism: Oryza sativa Japonica Group


title: BAP1_FL_CAL51_BAP1_WT_R1

description: Cells with wild type BAP1


title: BAP1_FL_CAL51_BAP1_KO_R2

description: Cells with BAP1 deletion


title: H3K27ac_huanghuazhan.rep2


title: BAP1_FL_CAL51_BAP1_KO_R1

description: Cells with BAP1 deletion


title: H3K27ac_huanghuazhan.rep1


title: reseq_jizi

description: Re-Sequencing


title: H3K27me3_wheat_50G

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Triticum aestivum(refseqv1.0)  using bwa.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, macs 1.3 was used to identify reads enriched regions(peaks).
Genome_build: Triticum aestivum (refseqv1.0)
Supplementary_files_format_and_content: In ChIP-Seq, peak files was provided.

organism: Triticum aestivum

source_name: seedling

growth_protocol: The seeds of bread wheat were sterilized by 30% H2O2 for 10 min followed by 5 times washes with distilled water. The sterilized seeds were germinated in water for 3 days at 22 °C. Germinated seeds with residual endosperm were transferred to soil. After 9 days in long-day conditions, the ground and underground parts were harvested.

extract_protocol:
Harvested samples were directly vacuum-infiltrated with formaldehyde cross-linking solution for ChIP assay. ChIP assay was performed with the antibodies against H3 trimethyl-Lys 27 (Upstate, USA, Cat. 07-449) and H3 trimethyl-Lys 4 (Abcam, Cat. ab8580) for wheat.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China). The DSN kit from Illumina was used for DSN library normalization. Libraries were sequenced on the HiSeq 3000 (Illumina) to produce 151 bp paired reads for wheat.

value: Chinese Spring

value: seedling

value: H3K27me3 (Millipore, Cat. 07-449)


title: H3K4me3_wheat_DSN

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to oryza sativa(MSU7.0) using bwa mem or tophat2 to map  with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, macs 1.3 was used to identify reads enriched regions(peaks).
Genome_build: Triticum aestivum (refseqv1.0)
Supplementary_files_format_and_content: In ChIP-Seq, peak files was provided

value: H3K4me3 (Abcam, Cat. ab8580)


title: H3K4me3_wheat_50G

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to oryza sativa(MSU7.0) using bwa mem or tophat2 to map  with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, macs 1.3 was used to identify reads enriched regions(peaks).
Genome_build: Triticum aestivum (refseqv1.0)
Supplementary_files_format_and_content: In ChIP-Seq, peak files was provided.


title: F265

status: Public on May 26 2018

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description: Cecum_Germ-free C57BL/6J WT_High Fat Diet + B. wadsworthia + L. rhamnosus

hyb_protocol: Samples were hybridized to SurePrint G3 mouse GE v2 8x60K (G4858A-074809) arrays and scanned by G2565CA Scanner System (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the  Agilent DNA Microarray Scanner (G2505C) using one color scan setting for  1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye  channel is set to Green and Green PMT is set to 100%).

data_processing: Image analyses and raw signal intensities were  quantified by Feature Extraction Software v10.7.3.1 (Agilent Technologies)  according to the GE1_107_Sep09 protocol.

source_name: Coecum, HFD + B.wad + L.rhamn

label_protocol: Labelling of total RNA (100ng) was performed with the  One-Color Low Input Quick Amp Labelling kit (Agilent Technologies).

extract_protocol: Total RNA was prepared from total tissue of caecum tip by using the column-based RNeasy® Micro Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with RNA integrity number (RIN) greater than 9 were selected for further analysis.

treatment_protocol: Germ-free mice with either control diet (CD) or high fat diet (HFD). Germ-free mice were then colonized with a microbiota called altered Scheduler flora. Three weeks after, the mice were either colonized with B. wadsworthia and either treated or not treated with L. rhamnosus.

value: Cecum

value: male

tag: age

value: 5 weeks old

value: Germ-free C57BL/6J WT


title: A240

description: Cecum_Germ-free C57BL/6J WT_Control Diet

source_name: Coecum, CD

tag: gender

value: Control Diet


title: D255

description: Cecum_Germ-free C57BL/6J WT_High Fat Diet + L. rhamnosus

source_name: Coecum, HFD + L.rhamn

tag: tissue

value: High Fat Diet + L. rhamnosus


title: CAL51_MLL3_Exon8_WT_Rep2

description: normal cells

value: breast cancer cell


title: E262

description: Cecum_Germ-free C57BL/6J WT_High Fat Diet + B. wadsworthia

source_name: Coecum, HFD + B.wad

value: High Fat Diet + B. wadsworthia


title: B245

description: Cecum_Germ-free C57BL/6J WT_Control Diet + L. rhamnosus

source_name: Coecum, CD + B.wad

value: Control Diet + L. rhamnosus


title: C253

description: Cecum_Germ-free C57BL/6J WT_High Fat Diet

source_name: Coecum, HFD

value: High Fat Diet


title: D256


title: F263

value: High Fat Diet + B. wadsworthia + L. rhamnosus


title: A241


title: F267


title: C251


title: B247

source_name: Coecum, CD + L.rhamn


title: D257


title: F266


title: A239


title: E261


title: A238


title: B248


title: B244


title: A242


title: B246


title: H3K27me3_CAL51_MLL3_KO_DMSO

description: Cells  with MLL3 deletion and treated with DMSO

value: Low passages (6-10)

value: H3K27me3 (homemade)

value: DMSO

value: MLL3 deletion


title: E260


title: E259


title: C250


title: D254


title: C249


title: F264


title: MLL3_CAL51_BAP1_KO_R1

description: Cells with BAP1 deletion

value: MLL3_MR (homemade)

value: BAP1 deletion


title: RNA-Seq of human GSC infected Mock-3

city: Suzhou

first: feng

last: ma

state: Jiangsu

address: 218 Xinghu Street, B5-527

department: Suzhou Institute of Systems Medicine

institute: CAMS

data_processing:
bcl2fastq(v 2.17) software was used to base-calling
trimmomatic was used to remove illumina sequencing adapters within raw reads of every sample, trim low quality bases of both read ends
clean reads were mapped to human hg38 reference genome with STAR
DESeq2 was used to identify DEGs (p<=0.05, FC>=2) based on raw reads counts.
Genome_build: human hg38
Supplementary_files_format_and_content: xls files include reads counts for each Sample

source_name: From specimen #4121

growth_protocol: Glioma stem cells derived from specimen 4121 were seeded in 6-well plate at a density of 1×106/well and cultured in Neurobasal complete media (Gibco) supplemented with 1× B27 without vitamin A (Gibco), 2 mM L-glutamine (MACGENE), 1 mM sodium pyruvate (MACGENE), 10 ng/ml basic fibroblast growth factor (FGF; R&D Systems), and 10 ng/ml epidermal growth factor (EGF; R&D Systems).

extract_protocol:
The total cellular RNA was extracted at 48 hours post infection with PureLink RNA minikit (Life Technology). RNA concentration was quantified using a Qubit 2.0 Fluorometer (Thermo Fisher). The quality of extracted RNA was evaluated using an Agilent Technology 2100 Bioanalyzer.
RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s guideline.

treatment_protocol: After being seeded in the 6-well plate, cells were infected with ZIKV at an MOI of 1 for 48h.

value: Glioma stem cells

tag: culture

value: in vitro

tag: infection


title: VATTR_rep3_372

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: VAT (epididymal)

growth_protocol: Live cells were sorted by flow cytometry from the spleen and visceral adipose (epididymal) tissue of mice.

extract_protocol:
Spleen were mechanically dissociated and visceral adipose tissue were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ CD25+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

tag: strain

tag: Sex

value: male

tag: age (months)

value: VAT (epididymal)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: VATTR_rep3_368


title: VATTR_rep3_359


title: RNA-Seq of human GSC infected ZIKV-3

tag: cell type

value: ZIKV


title: VATTR_rep3_371

tag: sample type


title: RNA-Seq of human GSC infected Mock-1


title: VATTR_rep3_373


title: VATTR_rep3_366


title: VATTR_rep3_358


title: VATTR_rep3_363


title: VATTR_rep3_367


title: RNA-Seq of human GSC infected Mock-2


title: VATTR_rep3_355


title: VATTR_rep3_357


title: VATTR_rep3_360


title: VATTR_rep3_370


title: RNA-Seq of human GSC infected ZIKV-2


title: VATTR_rep3_369


title: RNA-Seq of human GSC infected ZIKV-1


title: VATTR_rep3_349


title: VATTR_rep3_348


title: VATTR_rep3_351


title: VATTR_rep3_354


title: VATTR_rep3_352


title: VATTR_rep3_350


title: VATTR_rep3_365


title: VATTR_rep3_347


title: VATTR_rep3_364


title: VATTR_rep3_356


title: VATTR_rep3_346


title: VATTR_rep3_344


title: VATTR_rep3_340


title: VATTR_rep3_335


title: VATTR_rep3_328


title: VATTR_rep3_327


title: VATTR_rep3_326


title: VATTR_rep3_321


title: VATTR_rep3_324


title: VATTR_rep3_320


title: VATTR_rep3_345


title: VATTR_rep3_319


title: VATTR_rep3_332


title: VATTR_rep3_341


title: VATTR_rep3_343


title: VATTR_rep3_339


title: VATTR_rep3_333


title: VATTR_rep3_323


title: VATTR_rep3_342


title: VATTR_rep3_338


title: VATTR_rep3_336


title: VATTR_rep3_330


title: VATTR_rep3_334


title: VATTR_rep3_325


title: VATTR_rep3_318


title: VATTR_rep3_308


title: VATTR_rep3_309


title: VATTR_rep3_313


title: VATTR_rep3_312


title: VATTR_rep3_307


title: VATTR_rep3_306


title: VATTR_rep3_304


title: VATTR_rep3_303


title: VATTR_rep3_305


title: VATTR_rep3_296


title: VATTR_rep3_293


title: VATTR_rep3_298


title: VATTR_rep3_300


title: VATTR_rep3_299


title: VATTR_rep3_301


title: VATTR_rep3_291


title: VATTR_rep3_289


title: VATTR_rep3_294


title: VATTR_rep3_285


title: VATTR_rep3_295


title: VATTR_rep3_284


title: VATTR_rep3_290


title: VATTR_rep3_292


title: VATTR_rep3_282


title: VATTR_rep3_283


title: VATTR_rep3_288


title: VATTR_rep3_278


title: VATTR_rep3_275


title: VATTR_rep3_273


title: VATTR_rep3_276


title: VATTR_rep3_279


title: VATTR_rep3_271


title: VATTR_rep3_270


title: VATTR_rep3_302


title: VATTR_rep3_269


title: VATTR_rep3_267


title: VATTR_rep3_286


title: VATTR_rep3_281


title: VATTR_rep3_264


title: VATTR_rep3_262


title: VATTR_rep3_263


title: VATTR_rep3_256


title: VATTR_rep3_257


title: VATTR_rep3_251


title: VATTR_rep3_254


title: VATTR_rep3_252


title: VATTR_rep3_249


title: VATTR_rep3_243


title: VATTR_rep3_247


title: VATTR_rep3_242


title: VATTR_rep3_238


title: VATTR_rep3_244


title: VATTR_rep3_239


title: VATTR_rep3_240


title: VATTR_rep3_241


title: VATTR_rep3_237


title: VATTR_rep3_236


title: VATTR_rep3_265


title: VATTR_rep3_234


title: VATTR_rep3_232


title: VATTR_rep3_233


title: VATTR_rep3_261


title: VATTR_rep3_230


title: VATTR_rep3_260


title: VATTR_rep3_258


title: VATTR_rep3_228


title: VATTR_rep3_229


title: VATTR_rep3_250


title: VATTR_rep3_227


title: VATTR_rep3_253


title: VATTR_rep3_226


title: VATTR_rep3_248


title: VATTR_rep3_224


title: VATTR_rep3_221


title: VATTR_rep3_220


title: VATTR_rep3_216


title: VATTR_rep3_215


title: VATTR_rep3_214


title: VATTR_rep3_217


title: VATTR_rep3_210


title: VATTR_rep3_213


title: VATTR_rep3_209


title: VATTR_rep3_208


title: VATTR_rep3_207


title: VATTR_rep3_206


title: VATTR_rep3_200


title: VATTR_rep3_201


title: VATTR_rep3_199


title: VATTR_rep3_203


title: VATTR_rep3_204


title: VATTR_rep3_225


title: VATTR_rep3_223


title: VATTR_rep3_205


title: VATTR_rep3_194


title: VATTR_rep3_195


title: VATTR_rep3_196


title: VATTR_rep3_222


title: VATTR_rep3_198


title: VATTR_rep3_197


title: VATTR_rep3_192


title: VATTR_rep3_218


title: VATTR_rep3_190


title: VATTR_rep3_191


title: VATTR_rep3_188


title: VATTR_rep3_185


title: VATTR_rep3_189


title: VATTR_rep3_184


title: VATTR_rep3_183


title: VATTR_rep3_186


title: VATTR_rep3_182


title: VATTR_rep3_179


title: VATTR_rep3_178


title: VATTR_rep3_177


title: VATTR_rep3_171


title: VATTR_rep3_174


title: VATTR_rep3_172


title: VATTR_rep3_169


title: VATTR_rep3_175


title: VATTR_rep3_193


title: VATTR_rep3_167


title: VATTR_rep3_165


title: VATTR_rep3_164


title: VATTR_rep3_176


title: VATTR_rep3_163


title: VATTR_rep3_162


title: VATTR_rep3_157


title: VATTR_rep3_156


title: VATTR_rep3_158


title: VATTR_rep3_166


title: VATTR_rep3_154


title: VATTR_rep3_155


title: VATTR_rep3_151


title: VATTR_rep3_152


title: VATTR_rep3_149


title: VATTR_rep3_153


title: VATTR_rep3_187


title: VATTR_rep3_147


title: VATTR_rep3_144


title: VATTR_rep3_146


title: VATTR_rep3_143


title: VATTR_rep3_140


title: VATTR_rep3_135


title: VATTR_rep3_129


title: VATTR_rep3_139


title: VATTR_rep3_138


title: VATTR_rep3_127


title: VATTR_rep3_125


title: VATTR_rep3_160


title: VATTR_rep3_124


title: VATTR_rep3_121


title: VATTR_rep3_120


title: VATTR_rep3_137


title: VATTR_rep3_134


title: VATTR_rep3_132


title: VATTR_rep3_133


title: VATTR_rep3_116


title: VATTR_rep3_145


title: VATTR_rep3_112


title: VATTR_rep3_131


title: VATTR_rep3_126


title: VATTR_rep3_108


title: VATTR_rep3_118


title: VATTR_rep3_110


title: VATTR_rep3_119


title: VATTR_rep3_114


title: VATTR_rep3_115


title: VATTR_rep3_142


title: VATTR_rep3_122


title: VATTR_rep3_107


title: VATTR_rep3_98


title: VATTR_rep3_106


title: VATTR_rep3_103


title: VATTR_rep3_117


title: VATTR_rep3_105


title: VATTR_rep3_99


title: VATTR_rep3_102


title: VATTR_rep3_96


title: VATTR_rep3_101


title: VATTR_rep3_92


title: VATTR_rep3_95


title: VATTR_rep3_93


title: VATTR_rep3_100


title: VATTR_rep3_91


title: VATTR_rep3_94


title: VATTR_rep3_113


title: VATTR_rep3_104


title: VATTR_rep3_97


title: VATTR_rep3_111


title: VATTR_rep3_85


title: VATTR_rep3_82


title: VATTR_rep3_79


title: VATTR_rep3_89


title: VATTR_rep3_78


title: VATTR_rep3_86


title: VATTR_rep3_74


title: VATTR_rep3_73


title: VATTR_rep3_81


title: VATTR_rep3_71


title: VATTR_rep3_75


title: VATTR_rep3_77


title: VATTR_rep3_72


title: VATTR_rep3_68


title: VATTR_rep3_69


title: VATTR_rep3_70


title: VATTR_rep3_67


title: VATTR_rep3_66


title: VATTR_rep3_90


title: VATTR_rep3_62


title: VATTR_rep3_61


title: VATTR_rep3_63


title: VATTR_rep3_60


title: VATTR_rep3_84


title: VATTR_rep3_55


title: VATTR_rep3_57


title: VATTR_rep3_58


title: VATTR_rep3_54


title: VATTR_rep3_87


title: VATTR_rep3_56


title: VATTR_rep3_53


title: VATTR_rep3_51


title: VATTR_rep3_76


title: VATTR_rep3_50


title: VATTR_rep3_52


title: VATTR_rep3_48


title: VATTR_rep3_46


title: VATTR_rep3_47


title: VATTR_rep3_40


title: VATTR_rep3_38


title: VATTR_rep3_36


title: VATTR_rep3_42


title: VATTR_rep3_44


title: VATTR_rep3_41


title: VATTR_rep3_45


title: VATTR_rep3_43


title: VATTR_rep3_35


title: VATTR_rep3_34


title: VATTR_rep3_39


title: VATTR_rep3_28


title: VATTR_rep3_33


title: VATTR_rep3_31


title: VATTR_rep3_27


title: VATTR_rep3_30


title: VATTR_rep3_25


title: VATTR_rep3_26


title: VATTR_rep3_22


title: VATTR_rep3_24


title: VATTR_rep3_18


title: VATTR_rep3_20


title: VATTR_rep3_23


title: VATTR_rep3_16


title: VATTR_rep3_19


title: VATTR_rep3_15


title: VATTR_rep3_17


title: VATTR_rep3_14


title: VATTR_rep3_11


title: VATTR_rep3_5


title: VATTR_rep3_7


title: VATTR_rep3_10


title: VATTR_rep3_12


title: VATTR_rep3_2


title: VATTR_rep2_368


title: VATTR_rep2_369


title: VATTR_rep3_9


title: VATTR_rep3_3


title: VATTR_rep2_370


title: VATTR_rep2_371


title: VATTR_rep3_13


title: VATTR_rep3_8


title: VATTR_rep2_367


title: VATTR_rep2_366


title: VATTR_rep2_361


title: VATTR_rep2_363


title: VATTR_rep2_364


title: VATTR_rep2_357


title: VATTR_rep2_359


title: VATTR_rep2_360


title: VATTR_rep2_355


title: VATTR_rep2_354


title: VATTR_rep2_353


title: VATTR_rep2_350


title: VATTR_rep2_351


title: VATTR_rep2_348


title: VATTR_rep2_346


title: VATTR_rep2_343


title: VATTR_rep2_341


title: VATTR_rep2_339


title: VATTR_rep2_365


title: VATTR_rep2_336


title: VATTR_rep2_340


title: VATTR_rep2_334


title: VATTR_rep2_342


title: VATTR_rep2_338


title: VATTR_rep2_337


title: VATTR_rep2_335


title: VATTR_rep2_333


title: VATTR_rep2_330


title: VATTR_rep2_332


title: VATTR_rep2_327


title: VATTR_rep2_325


title: VATTR_rep2_323


title: VATTR_rep2_326


title: VATTR_rep2_321


title: VATTR_rep2_328


title: VATTR_rep2_322


title: VATTR_rep2_349


title: VATTR_rep2_318


title: VATTR_rep2_320


title: VATTR_rep2_319


title: VATTR_rep2_317


title: VATTR_rep2_345


title: VATTR_rep2_316


title: VATTR_rep2_315


title: VATTR_rep2_314


title: VATTR_rep2_329


title: VATTR_rep2_311


title: VATTR_rep2_310


title: VATTR_rep2_313


title: VATTR_rep2_306


title: VATTR_rep2_312


title: VATTR_rep3_4


title: VATTR_rep2_307


title: VATTR_rep2_309


title: VATTR_rep2_303


title: VATTR_rep2_305


title: VATTR_rep2_304


title: VATTR_rep2_295


title: VATTR_rep2_302


title: VATTR_rep2_294


title: VATTR_rep2_293


title: VATTR_rep2_296


title: VATTR_rep2_297


title: VATTR_rep2_300


title: VATTR_rep2_289


title: VATTR_rep2_292


title: VATTR_rep2_291


title: VATTR_rep2_288


title: VATTR_rep2_287


title: VATTR_rep2_286


title: VATTR_rep2_299


title: VATTR_rep2_284


title: VATTR_rep2_283


title: VATTR_rep2_277


title: VATTR_rep2_274


title: VATTR_rep2_281


title: VATTR_rep2_280


title: VATTR_rep2_278


title: VATTR_rep2_279


title: VATTR_rep2_285


title: VATTR_rep2_275


title: VATTR_rep2_272


title: VATTR_rep2_270


title: VATTR_rep2_271


title: VATTR_rep2_267


title: VATTR_rep2_266


title: VATTR_rep2_298


title: VATTR_rep2_264


title: VATTR_rep2_263


title: VATTR_rep2_269


title: VATTR_rep2_260


title: VATTR_rep2_259


title: VATTR_rep2_256


title: VATTR_rep2_253


title: VATTR_rep2_276


title: VATTR_rep2_251


title: VATTR_rep2_273


title: VATTR_rep2_301


title: VATTR_rep2_248


title: VATTR_rep2_249


title: VATTR_rep2_245


title: VATTR_rep2_247


title: VATTR_rep2_246


title: VATTR_rep2_243


title: VATTR_rep2_268


title: VATTR_rep2_237


title: VATTR_rep2_239


title: VATTR_rep2_235


title: VATTR_rep2_238


title: VATTR_rep2_236


title: VATTR_rep2_255


title: VATTR_rep2_262


title: VATTR_rep2_232


title: VATTR_rep2_254


title: VATTR_rep2_231


title: VATTR_rep2_234


title: VATTR_rep2_230


title: VATTR_rep2_252


title: VATTR_rep2_229


title: VATTR_rep2_227


title: VATTR_rep2_226


title: VATTR_rep2_228


title: VATTR_rep2_224


title: VATTR_rep2_225


title: VATTR_rep2_219


title: VATTR_rep2_223


title: VATTR_rep2_221


title: VATTR_rep2_240


title: VATTR_rep2_216


title: VATTR_rep2_220


title: VATTR_rep2_242


title: VATTR_rep2_241


title: VATTR_rep2_215


title: VATTR_rep2_214


title: VATTR_rep2_233


title: VATTR_rep2_212


title: VATTR_rep2_210


title: VATTR_rep2_207


title: VATTR_rep2_209


title: VATTR_rep2_208


title: VATTR_rep2_206


title: VATTR_rep2_205


title: VATTR_rep2_202


title: VATTR_rep2_204


title: VATTR_rep2_201


title: VATTR_rep2_200


title: VATTR_rep2_198


title: VATTR_rep2_197


title: VATTR_rep2_218


title: VATTR_rep2_194


title: VATTR_rep2_217


title: VATTR_rep2_193


title: VATTR_rep2_191


title: VATTR_rep2_183


title: VATTR_rep2_176


title: VATTR_rep2_178


title: VATTR_rep2_187


title: VATTR_rep2_185


title: VATTR_rep2_182


title: VATTR_rep2_181


title: VATTR_rep2_184


title: VATTR_rep2_188


title: VATTR_rep2_180


title: VATTR_rep2_189


title: VATTR_rep2_190


title: VATTR_rep2_173


title: VATTR_rep2_171


title: VATTR_rep2_172


title: VATTR_rep2_169


title: VATTR_rep2_164


title: VATTR_rep2_165


title: VATTR_rep2_174


title: VATTR_rep2_163


title: VATTR_rep2_162


title: VATTR_rep2_166


title: VATTR_rep2_196


title: VATTR_rep2_203


title: VATTR_rep2_168


title: VATTR_rep2_161


title: VATTR_rep2_192


title: VATTR_rep2_160


title: VATTR_rep2_170


title: VATTR_rep2_167


title: VATTR_rep2_159


title: VATTR_rep2_153


title: VATTR_rep2_152


title: VATTR_rep2_154


title: VATTR_rep2_158


title: VATTR_rep2_151


title: VATTR_rep2_142


title: VATTR_rep2_148


title: VATTR_rep2_140


title: VATTR_rep2_144


title: VATTR_rep2_139


title: VATTR_rep2_156


title: VATTR_rep2_145


title: VATTR_rep2_150


title: VATTR_rep2_143


title: VATTR_rep2_146


title: VATTR_rep2_135


title: VATTR_rep2_133


title: VATTR_rep2_136


title: VATTR_rep2_132


title: VATTR_rep2_134


title: VATTR_rep2_131


title: VATTR_rep2_130


title: VATTR_rep2_128


title: VATTR_rep2_126


title: VATTR_rep2_155


title: VATTR_rep2_125


title: VATTR_rep2_141


title: VATTR_rep2_138


title: VATTR_rep2_124


title: VATTR_rep2_118


title: VATTR_rep2_120


title: VATTR_rep2_114


title: VATTR_rep2_115


title: VATTR_rep2_113


title: VATTR_rep2_111


title: VATTR_rep2_116


title: VATTR_rep2_117


title: VATTR_rep2_108


title: VATTR_rep2_106


title: VATTR_rep2_110


title: VATTR_rep2_109


title: VATTR_rep2_112


title: VATTR_rep2_103


title: VATTR_rep2_102


title: VATTR_rep2_105


title: VATTR_rep2_107


title: VATTR_rep2_101


title: VATTR_rep2_100


title: VATTR_rep2_99


title: VATTR_rep2_104


title: VATTR_rep2_98


title: VATTR_rep2_97


title: VATTR_rep2_96


title: VATTR_rep2_95


title: VATTR_rep2_127


title: VATTR_rep2_121


title: VATTR_rep2_94


title: VATTR_rep2_93


title: VATTR_rep2_90


title: VATTR_rep2_91


title: VATTR_rep2_86


title: VATTR_rep2_82


title: VATTR_rep2_81


title: VATTR_rep2_83


title: VATTR_rep2_92


title: VATTR_rep2_84


title: VATTR_rep2_78


title: VATTR_rep2_73


title: VATTR_rep2_74


title: VATTR_rep2_72


title: VATTR_rep2_76


title: VATTR_rep2_75


title: VATTR_rep2_71


title: VATTR_rep2_69


title: VATTR_rep2_68


title: VATTR_rep2_67


title: VATTR_rep2_77


title: VATTR_rep2_64


title: VATTR_rep2_63


title: VATTR_rep2_62


title: VATTR_rep2_66


title: VATTR_rep2_85


title: VATTR_rep2_59


title: VATTR_rep2_58


title: VATTR_rep2_61


title: VATTR_rep2_60


title: VATTR_rep2_88


title: VATTR_rep2_57


title: VATTR_rep2_56


title: VATTR_rep2_89


title: VATTR_rep2_52


title: VATTR_rep2_51


title: VATTR_rep2_55


title: VATTR_rep2_80


title: VATTR_rep2_50


title: VATTR_rep2_54


title: VATTR_rep2_49


title: VATTR_rep2_48


title: VATTR_rep2_47


title: VATTR_rep2_43


title: VATTR_rep2_46


title: VATTR_rep2_39


title: VATTR_rep2_41


title: VATTR_rep2_45


title: VATTR_rep2_44


title: VATTR_rep2_42


title: VATTR_rep2_40


title: VATTR_rep2_34


title: VATTR_rep2_37


title: VATTR_rep2_36


title: VATTR_rep2_33


title: VATTR_rep2_38


title: VATTR_rep2_31


title: VATTR_rep2_35


title: VATTR_rep2_30


title: VATTR_rep2_53


title: VATTR_rep2_29


title: VATTR_rep2_28


title: VATTR_rep2_24


title: VATTR_rep2_25


title: VATTR_rep2_27


title: VATTR_rep2_32


title: VATTR_rep2_21


title: VATTR_rep2_26


title: VATTR_rep2_18


title: VATTR_rep2_19


title: VATTR_rep2_22


title: VATTR_rep2_17


title: VATTR_rep2_20


title: VATTR_rep2_16


title: VATTR_rep2_23


title: VATTR_rep2_15


title: VATTR_rep2_14


title: VATTR_rep2_11


title: VATTR_rep2_13


title: VATTR_rep2_12


title: VATTR_rep2_5


title: VATTR_rep2_7


title: VATTR_rep2_8


title: VATTR_rep2_4


title: VATTR_rep2_1


title: VATTR_rep2_2


title: ColonTR_1109

growth_protocol: Live cells were sorted by flow cytometry from the spleen and colon lamina propria of mice (carrying a Foxp3 reporter gene).

extract_protocol:
Spleen were mechanically dissociated and colon were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

value: B6 Foxp3-Ires-Gfp


title: ColonTR_1112


title: ColonTR_1110


title: VATTR_rep2_3


title: ColonTR_1106


title: ColonTR_1103


title: ColonTR_1108


title: ColonTR_1102


title: ColonTR_1104


title: ColonTR_1094


title: ColonTR_1095


title: ColonTR_1097


title: ColonTR_1098


title: ColonTR_1090


title: ColonTR_1091


title: ColonTR_1086


title: ColonTR_1081


title: ColonTR_1085


title: ColonTR_1079


title: ColonTR_1078


title: ColonTR_1080


title: ColonTR_1084


title: ColonTR_1077


title: ColonTR_1075


title: ColonTR_1074


title: ColonTR_1072


title: ColonTR_1069


title: ColonTR_1073


title: ColonTR_1065


title: ColonTR_1067


title: ColonTR_1068


title: ColonTR_1066


title: ColonTR_1064


title: ColonTR_1061


title: ColonTR_1059


title: ColonTR_1053


title: ColonTR_1092


title: ColonTR_1096


title: ColonTR_1056


title: ColonTR_1052


title: ColonTR_1048


title: ColonTR_1057


title: ColonTR_1045


title: ColonTR_1046


title: ColonTR_1040


title: ColonTR_1037


title: ColonTR_1050


title: ColonTR_1035


title: ColonTR_1030


title: ColonTR_1032


title: ColonTR_1033


title: ColonTR_1029


title: ColonTR_1027


title: ColonTR_1028


title: ColonTR_1023


title: ColonTR_1025


title: ColonTR_1020


title: ColonTR_1017


title: ColonTR_1015


title: ColonTR_1013


title: ColonTR_1009


title: ColonTR_1011


title: ColonTR_1005


title: ColonTR_1006


title: ColonTR_1007


title: ColonTR_1003


title: ColonTR_995


title: ColonTR_997


title: ColonTR_1002


title: ColonTR_987


title: ColonTR_991


title: ColonTR_989


title: ColonTR_1022


title: ColonTR_983


title: ColonTR_980


title: ColonTR_978


title: ColonTR_993


title: ColonTR_976


title: ColonTR_1008


title: ColonTR_975


title: ColonTR_972


title: ColonTR_971


title: ColonTR_970


title: ColonTR_968


title: ColonTR_967


title: ColonTR_964


title: ColonTR_963


title: ColonTR_1001


title: ColonTR_961


title: ColonTR_994


title: ColonTR_958


title: ColonTR_954


title: ColonTR_960


title: ColonTR_992


title: ColonTR_953


title: ColonTR_950


title: ColonTR_949


title: ColonTR_940


title: ColonTR_938


title: ColonTR_937


title: ColonTR_943


title: ColonTR_939


title: ColonTR_946


title: ColonTR_924


title: ColonTR_934


title: ColonTR_921


title: ColonTR_918


title: ColonTR_923


title: ColonTR_922


title: ColonTR_912


title: ColonTR_905


title: ColonTR_908


title: ColonTR_907


title: ColonTR_901


title: ColonTR_944


title: ColonTR_902


title: ColonTR_898


title: ColonTR_894


title: ColonTR_889


title: ColonTR_935


title: ColonTR_892


title: ColonTR_887


title: ColonTR_883


title: ColonTR_885


title: ColonTR_886


title: ColonTR_928


title: ColonTR_880


title: ColonTR_872


title: ColonTR_873


title: ColonTR_871


title: ColonTR_915


title: ColonTR_870


title: ColonTR_909


title: ColonTR_868


title: ColonTR_904


title: ColonTR_867


title: ColonTR_900


title: ColonTR_865


title: ColonTR_866


title: ColonTR_864


title: ColonTR_863


title: ColonTR_893


title: ColonTR_859


title: ColonTR_858


title: ColonTR_857


title: ColonTR_860


title: ColonTR_855


title: ColonTR_881


title: ColonTR_856


title: ColonTR_854


title: ColonTR_851


title: ColonTR_847


title: ColonTR_846


title: ColonTR_842


title: ColonTR_840


title: ColonTR_838


title: ColonTR_839


title: ColonTR_831


title: ColonTR_826


title: ColonTR_828


title: ColonTR_827


title: ColonTR_824


title: ColonTR_821


title: ColonTR_819


title: ColonTR_823


title: ColonTR_820


title: ColonTR_869


title: ColonTR_818


title: ColonTR_853


title: ColonTR_817


title: ColonTR_849


title: ColonTR_844


title: ColonTR_809


title: ColonTR_843


title: ColonTR_810


title: ColonTR_813


title: ColonTR_806


title: ColonTR_811


title: ColonTR_841


title: ColonTR_830


title: ColonTR_799


title: ColonTR_797


title: ColonTR_804


title: ColonTR_795


title: ColonTR_794


title: ColonTR_793


title: ColonTR_783


title: ColonTR_791


title: ColonTR_785


title: ColonTR_786


title: ColonTR_779


title: ColonTR_778


title: ColonTR_789


title: ColonTR_777


title: ColonTR_781


title: ColonTR_770


title: ColonTR_805


title: ColonTR_775


title: ColonTR_808


title: ColonTR_767


title: ColonTR_771


title: ColonTR_769


title: ColonTR_762


title: ColonTR_776


title: ColonTR_798


title: ColonTR_773


title: ColonTR_760


title: ColonTR_768


title: ColonTR_755


title: ColonTR_759


title: ColonTR_757


title: ColonTR_752


title: ColonTR_751


title: ColonTR_754


title: ColonTR_747


title: ColonTR_739


title: ColonTR_746


title: ColonTR_749


title: ColonTR_744


title: ColonTR_745


title: ColonTR_750


title: ColonTR_737


title: ColonTR_738


title: ColonTR_729


title: ColonTR_728


title: ColonTR_736


title: ColonTR_725


title: ColonTR_722


title: ColonTR_726


title: ColonTR_715


title: ColonTR_716


title: ColonTR_714


title: ColonTR_835


title: ColonTR_720


title: ColonTR_710


title: ColonTR_711


title: ColonTR_708


title: ColonTR_713


title: ColonTR_707


title: ColonTR_703


title: ColonTR_698


title: ColonTR_727


title: ColonTR_701


title: ColonTR_697


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