title: 28a

city: Santiago

first: Francisco

middle: A

last: Cubillos

address: Obispo Manuel Umaña 050, Edificio de Alimentos, Estación Central

department: Departamento de Ciencia y Tecnología de los Alimentos

country: Chile

institute: Universidad de Santiago de Chile

data_processing:
Only reads with Phred > 30 were used based on BGI pipeline for  filtering and verified using the Fastqc software
reads were aligned to hybrid genomes from the parental strains using rsem
Specific alles were filtered using the ASE option from RSEM
Genome_build: reference strain S288c
Supplementary_files_format_and_content: bam and matrix txt files were generated using rsem, count_mat.txt files contain read count data.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Samples were grown in YPD media up to OD between 0,8-1

extract_protocol:
RNA was extracted utilising the E.Z.N.A. Total RNA Kit I (OMEGA) according to the supplier’s instructions. RNA samples were then treated with DNase I (Promega) to remove genomic DNA traces and total RNA was recovered using the GeneJET RNA Cleanup and Concentration Micro Kit (Thermo Scientific). RNA integrity was confirmed using a Fragment Analyzer.
The RNA-seq libraries were constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina).

tag: strain

value: WE x SA F1 hybrid

value: WE x SA


title: 24e

status: Public on May 21 2016

type: SRA

library_source: transcriptomic

molecule: total RNA

value: WA x WE F1 hybrid

tag: genotype

value: WA x WE


title: 7161_311

city: Leiden

first: Nicolas

last: Davin

address: Darwingweg 4

department: Botany

country: Netherlands

institute: Naturalis

data_processing:
Low read quality filtering using Trimmomatic v0.0.3 (Illumina TruSeq adapters were filtered out, the first nine bases were removed, sliding window over four bases with quality threshold of Phred>20 was applied corresponding to base call accuracy>99%, only reads in pairs and with a minimum length of 45bp were retained)
Read mapping to the TAIR10 Arabisopsis thaliana genome using TopHat v2.0.8 (using default parameters)
Genome_build: Arabidopsis thaliana TAIR v10
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each samples and statistical differentially expression for each pairwise comparison

organism: Arabidopsis thaliana

source_name: Herbaceous stem soc1ful

growth_protocol: 16h light per day, 20C

extract_protocol: Total RNA was isolated from stems and leaves using EZNA Plant RNA Kit (Omega Bio-tek, VWR international) including DNAse I treatment on column (Qiagen, Netherlands) according to the manufacturers’ instructions. Poly A+ RNA purification and strand-specific cDNA library preparation for Illumina Hiseq 2000 were performed by Leiden Genome Technology Center (Leiden, the Netherlands) as described in Parkhomchuk et al. (2009).

treatment_protocol: Sample were flash frozen in liquid nitrogen and concerved at -80C until extraction

tag: tissue type

value: Stem

tag: ecotype


title: 24c


title: 5DAP_C

city: Delhi

first: Manu

last: Agarwal

address: Chatra Marg, North campus

department: Department of Botany

country: India

institute: University of Delhi

description: paired end, illumina HiSeq platform

data_processing:
Paired end reads were quality filtered and pooled together to construct an assembly using Trinity at 25 K-mer.
Transcripts were quantified with the help of RSEM. Transcripts having less then 1 read count in all the libraries were removed.
Assembly were further annotated for functional characterisation using FastAnnotator
Differentially expressed transcript were identifed using edgeR.
Genome_build: n/a
Supplementary_files_format_and_content: Tab delimited text file
Supplementary_files_format_and_content: Assembly.fa: Assembly sequence
Supplementary_files_format_and_content: Assembly_Annotation: Assembly annotation

organism: Brassica juncea

source_name: Silique

growth_protocol: B. juncea plants were grown in field conditions in the month of october and self pollinated at the time of flowering initation.

extract_protocol:
Total RNA was extracted from stressed as well as control siliques using Qiagen’s plant RNA extraction kit as per the manufacturer’s protocol.
RNA-seq libraries were prepared utilizing TruSeq RNA sample preparation kit v2 (Illumina Inc., USA) as per the manufacturer’s protocol

treatment_protocol: Self-pollinated branches (5,10,15,20,25 and 30 DAP) were excised and placed in a beaker filled with water and subjected to cold treatment at 4°C for 6 h and 12 h followed by immediate harvesting. Self-pollinated branches placed in water under field conditions served as control.

tag: developmental stage

value: 5DAP silique

tag: stress duration

value: Control


title: 28d


title: 28e


title: 7157_307


title: Col-0 24 hours 100 uM MG132 4

city: Cold Spring Harbor

first: Nicholas

last: Gladman

state: NY

address: 1 Bungtown Rd

department: ARS

country: USA

institute: USDA

description: this sample includes a technical replicate

data_processing:
Quality control (trimming of raw reads) was performed with Trimmomatic using the default parameters
Alignment was performed through Tophat-Bowtie 2 against the TAIR 10 genome using the Ensemble 2013 Arabidopsis.gtf file for annotations.  Parameters: -i 30 -I 5000 --min-segment-intron 30 --max-segment-intron 5000 --min-coverage-intron 30 --max-coverage-intron 5000 --no-convert-bam --b2-very-sensitive
Read counts were generated through HTSeq using TAIR10 .gtf file for annotations. Parameters:  -m intersection-nonempty -t exon -s no
Differential expression analysis was performed via the edgeR package (negative binomial normalization) using the Col-0 No treatment as the control comparison. Analysis was run as described in manual example using calcNormFactors and GLM dispersion options.
Genome_build: TAIR10

source_name: 5 DAG Arabidopsis seedling

growth_protocol: Seedlings were sterilized with 50% bleach and stratified for 2 days at 4 degrees C in the dark, then grown in liquid culture (1/2 MS salts, 1% Sucrose) under constant light at ~22 degrees C in 12-well plates.

extract_protocol:
Seedlings were pressed between paper towels to remove excess liquid and frozen immediately in liquid nitrogen, then pulverized and total RNA isolation was performed using Trizol Reagent.  mRNA was isolated via the TruSeq RNA library sample preparation kit v2 (Illumina).
TruSeq RNA library sample preparation kit v2 (Illumina).  This was performed by the University of Wisconsin-Madison Gene Expression Center (http://www.biotech.wisc.edu/services/gec).

treatment_protocol: After 5 days growth, fresh media was swapped out and either 0 or 100 uM or MG132 was added to each well.  Incubation time was either 3 or 24 hours for MG132-treated samples.  No-treatment samples were harvested immediately at the 5 day mark.

tag: treatment

value: 24 hours 100 uM MG132


title: Col-0 24 hours 100 uM MG132 3


title: 7154_430

source_name: leaf WT

value: Leaf

value: WT


title: 22b

value: NA x WA F1 hybrid

value: NA x WA


title: Col-0 3 hours 100 uM MG132 3

value: 3 hours 100 uM MG132


title: 24a


title: Col-0 3 hours 100 uM MG132 4


title: 7151_412


title: Col-0 No Treatment 4

value: No MG132


title: 22c


title: 22a


title: 7148_409


title: 7152_428

source_name: Cambium stem WT


title: rpn10-1 No Treatment 1


title: 20d

value: NA x WE F1 hybrid

value: NA x WE


title: 7149_410


title: Col-0 No Treatment 3


title: 20c


title: rpn12a-1 No Treatment 1


title: 7146_407


title: 7153_429

source_name: Herbaceous stem WT


title: 16c

value: WA x SA F1 hybrid

value: WA x SA


title: 20a


title: 7150_411


title: 7147_408


title: Col-0 24 hours 100 uM MG132 2


title: Col-0 24 hours 100 uM MG132 1


title: Col-0 3 hours 100 uM MG132 2


title: Col-0 3 hours 100 uM MG132 1


title: 16a


title: 16b


title: Col-0 No Treatment 2


title: BMPC2 fq

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

description: CD19- CD138+ plasma cells were purified by fluorescence activated cell sorting from bone marrow apsirates

data_processing:
FastQ Groomer
TopHat for gapped read mapping
Partek Genomics Suite v6.6 for generation of RPKM values
Genome_build: Ensembl_R72 reference human genome
Supplementary_files_format_and_content: Excel file of RPKM values for each sample

organism: Homo sapiens

source_name: bone marrow plasma cells

growth_protocol: primary ex vivo

extract_protocol:
Qiagen Rneasy Micro Kit
Clontech Smart Seq; barcodes: CCCGGACC-llpc4; GCAACGC-llpc1; GGTCCTC-llpc2; TACAGAC-llpc3

tag: tissue

value: bone marrow

tag: markers


title: BMPC3 fq


title: 12d

value: NA x SA F1 hybrid

value: NA x SA


title: Col-0 No Treatment 1


title: rpn12a-1 No Treatment 2


title: 12a


title: BMPC1 fq


title: In vitro CIS-/- NK cells rep2

status: Public on May 20 2016

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least two libraries.
Counts were converted to log2 counts per million, quantile normalised and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.01 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each gene in each library.

organism: Mus musculus

source_name: spleen, bone marrow and blood

extract_protocol:
Murine natural killer cells were harvested from various organs (spleen, bone marrow, blood) and single-cell suspensions prepared by forcing of organs through 70 μM sieves. NK cells were purified using anti-CD49b (DX5) Microbeads (Miltenyi Biotec) according to manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen, bone marrow and blood

tag: cell type

value: Nature Killer cells

tag: culture

value: in vitro

value: CIS-/-


title: In vitro wild type NK cells rep2

value: wild type


title: In vitro CIS-/- NK cells rep1


title: Angus #4, hour 2

status: Public on May 23 2016

city: Burlington

first: David

last: Kerr

state: VT

address: 570 Main Street

department: Animal and Veterinary Sciences

institute: University of Vermont

data_processing:
Illumina Casava 1.7 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the UMD v. 3.1 bovine genome. Only reads with a median q score above 20 were considered for mapping.
Genome_build: UMD 3.1/bosTau6
Supplementary_files_format_and_content: tab-delimited text files incude raw reads mapping to genomic location.

organism: Bos taurus

source_name: Bovine dermal fibroblasts, Angus, 2 hrs post LPS

growth_protocol: Fibroblasts were grown in DMEM supplemented with 5% fetal bovine serum, 1X ITS, and 1X Pen/Strep antibiotic in a T75 culture flask and then challenged in a 6-well plate.

extract_protocol:
mRNA was collected following challenge with the 5 Prime RNA PerfectPure Extraction Kit. Cell lyaste from duplicate wells were pooled prior to RNA extraction.
Massively Parallel sequencing library preparation was performed in accordance to the Illumina TruSeq RNA Sample Prep LT version 2 (RS-122-2001/2002). Breifly, each sample was Poly-A enriched for mRNA followed by a reverse transcription step with SuperScript II (Invitrogen) to convert mRNA to cDNA, then fragmented, end repaired, and adenylated. Illumina indexed adaptors, which contain a universal PCR primer and flow cell binding site, were ligated onto each sample. Each index sequence was unique for the purpose of labelling each sample with its own sequence for individualization and demultiplexing purposes. An Illumina specific PCR master mix was used to perform PCR enrichment/amplification for a predetermined number of cycles using a standard PCR cycle titration in order to keep the number of cycles to a minimum and reduce potential for duplicate sequences in the final data. Generally, 6-10 cycles were required. The enriched PCR product is cleaned using AMPure Beads (Beckman Coulter) and the resulting product is quantified using a Qubit Spectrofluorometer and Aligent Bioanalyzer 2100 High sensitivity DNA chip.

treatment_protocol: Cells were treated with 100ng/ml of LPS (Sigma, St. Louis, MO)

tag: breed

value: Angus

value: dermal fibroblasts

value: lipopolysaccharide (LPS)

tag: hours post lps


title: BMPC4 fq


title: Ex vivo wild type NK cells rep2

value: ex vivo


title: Ex vivo CIS-/- NK cells rep1


title: Ex vivo CIS-/- NK cells rep2


title: Tet2_3aDKO CMS Bisulfite-Seq

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

description: 2 technical replicates of biological replicate 1

library_source: genomic

data_processing:
use BSMAP-2.87 to align bisulfite-treated sequencing reads to the mouse genome mm9 of bisulfite treated data
use MACS to identify the peaks of CMS
Genome_build: mm9
Supplementary_files_format_and_content: BED files include chromosome, start, end, -log(q-value).The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.

molecule: genomic DNA

source_name: Hematopoietic stem cells (HSC)

growth_protocol: secondary transplanted mouse HSCs

extract_protocol:
DNA extraction bu Purelink extraction kit
Bisulfite treated DNA are immunoprecipitation for CMS with anti-CMS serum, then the pull-downed DNA are made into library with IlluminaTruSeq DNA sample preparation kit

treatment_protocol: Tet2 KO and Tet2_3a DKO whole bone marrow are transplanted into lethally irradiated recipient mouse, LSK CD48- CD150+ HSCs are isolated from secondary transplanted mouse

value: Tet2 and Dnmt3a double knockout Hematopoietic stem cell

tag: cell surface marker

value: Lin- ckit+Sca1+ CD48- CD150+


title: 12b


title: Tet2_Dnmt3aDKO r1 Bisulfite-Seq

description: technical replicate of biological replicate 1

data_processing:
use BSMAP-2.87 to align bisulfite-treated sequencing reads to the mouse genome mm9 of bisulfite treated data
use moabs to compute the methylation ratio of single base level
Genome_build: mm9
Supplementary_files_format_and_content: chromosome, start, end, methylation ratio, total reads, methylated reads, strand, next nucletide of cytosine, plus_strand, total reads from plus strand, methylated reads from plus strand, minus strand, total reads from minus strand, methylated reads from minus strand

extract_protocol:
DNA extraction by Purelink extraction kit
bisulfite treated DNA was made into library with Illumina TruSeq DNA sample preparation kit


title: Frozen.5K

status: Public on May 22 2016

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Library strategy: ATAC-seq
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie version1.1.1 with the default parameters
reads per million normalized bigWig files were generated using the GenomicRanges R/Bioconductor package and UCSC tool bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: reads per million normalized bigWig

source_name: CD19+ B cells

extract_protocol:
The indicated number of naïve B cells (CD19+IgD+CD3-CD27-Mtg-CD24+CD38-) were sorted by FACS
Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg.  Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C.  DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

tag: facs sorting markers

value: B cells

value: blood


title: Tet2KO r1  Bisulfite-Seq

value: Tet2 knockout Hematopoietic stem cell


title: Tet2KO CMS Bisulfite-Seq


title: Tet2KO r2 Bisulfite-Seq

description: technical replicate of biological replicate 2


title: Wild-type Villus Input DNA

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
Villus_INPUT_DNA
Villus_INPUT

data_processing:
Alignment: ChIP-seq:bowtie. RNA-seq: Tophat, version 2.0.6
ChIP-Seq - peak calling: SICER, version 1.1
RNA-Seq - normalized and differential expression: Cufflinks, version 2.0.1; default setting; Cuffdiff was used with default settings and FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq Tag Density bigwig file for visualizing aligned sequence tags
RNA-Seq: Differential expression table, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Control ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
RNA-Seq: Differential expression tables, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Eed-del Villus, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.

source_name: Control mouse intestinal stem cells

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated, but not immunoprecipitated.
The ChIPseq DNA Sample Prep Kit (Illumina) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.

treatment_protocol: Not injected with tamoxifen.

tag: strain background

value: B6;129 mixed

tag: genotype/variation

value: Wild-Type

value: Adult Epitheial cells; proximal 1/3 of intestine


title: Wild-type Lgr5+ ISC H3K27me3 ChIP-Seq rep 1

description:
ISC_H3K27me3_ChIP-seq
Lgr5_H3K27me3_ChIP

extract_protocol:
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ChIPseq DNA Sample Prep Kit (Illumina) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.

value: Eed+/+; Lgr5-EGFP-IRES-CREERT2

value: Adult intestinal stem cell; proximal 1/3 of intestine

tag: chip antibody

value: H3K27me3 antibody (07-449, Millipore)


title: Eed-null Villus RNA-seq biological rep 2

description:
Eed-del_Villus_2
347_EED_KO_Villus_RNAseq

source_name: Eed-del Villus cells

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Epithelium was frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: EedF/F; Villin-CRE


title: Eed-null Villus RNA-seq biological rep 3

description:
Eed-del_Villus_3
355_EED_KO_Villus_RNAseq


title: Tet2_Dnmt3aDKO r2 Bisulfite-Seq

tag: strain


title: In vitro wild type NK cells rep1

value: spleen, bone marrow and blood

value: Nature Killer cells

value: in vitro

tag: genotype

value: wild type


title: Eed-null Villus RNA-seq biological rep 1

description:
Eed-del_Villus_1
343_EED_KO_Villus_RNAseq


title: Wild-type Lgr5+ ISC Input DNA

description:
ISC_INPUT_DNA
Lgr5_INPUT

source_name: Control mouse villus cells

extract_protocol:
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated, but not immunoprecipitated.
The ChIPseq DNA Sample Prep Kit (Illumina) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.


title: Wild-type Villus RNA-seq biological rep 3

description:
Control_VC_3
357_Control_Villus_RNAseq

value: EedF/F; Cre-


title: Wild-type Villus RNA-seq biological rep 1

description:
Control_VC_1
345_Control_Villus_RNAseq


title: Tet2_3aDKO r1 RNAseq

data_processing:
RNA-sequencing reads were mapped to mm9 using TopHat 2.0.10 pipleline.
Genome_build: mm9
Supplementary_files_format_and_content: TXT files include gene name, chromosome, start, end, FPKM of Gene.

extract_protocol:
RNA extraction by Qiagen Rneasy micro kit
Followed the manufacturer protocol of Illumia TruSeq RNA Library Preparation kit

value: Tet2 and Dnmt3a double knockout Hematopoietic stem cell


title: Tet2KO r2 RNAseq

value: Lin- ckit+Sca1+ CD48- CD150+


title: Tet2KO r1 RNAseq


title: Tet2_3aDKO r2 RNAseq


title: Ex vivo wild type NK cells rep1

value: ex vivo


title: Wild-type Villus RNA-seq biological rep 2

description:
Control_VC_2
350_Control_Villus_RNAseq


title: Wild-type Ent-Pro H3K4me2 ChIP-seq

data_processing:
Alignment: ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ChIP-Seq - peak calling: SICER, version 1.1
RNA-Seq - normalized and differential expression: Cufflinks, version 2.0.1; default setting; Cuffdiff was used with default settings and FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags (Tag Density bigwig format)
Supplementary_files_format_and_content: RNA-Seq: Differential expression table, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Control ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
Supplementary_files_format_and_content: RNA-Seq: Differential expression tables, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Eed-del Villus, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.

source_name: Ent-Pro H3K4me2

extract_protocol:
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K4me2 antibody overnight (07-030, Millipore) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

tag: injected with

value: 1mg Tamoxifen for 5 consecutive days

tag: tissue/cell type source

value: Crypts; proximal 1/3 small intestines

value: Control mouse enterocyte progenitor cells

value: H3K4me2 antibody (07-030, Millipore)


title: Wild-type Sec-Pro H3K27me3 ChIP-seq

source_name: Sec-Pro H3K27me3

extract_protocol:
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 100 umol/kg DBZ (notch inhibitor) at 0 hours, again at 12 hours, and sacrificed at 38 hours.

value: B6;129 mixed

value: Control mouse secretory progenitor cells


title: Wild-type Villus H3K27me3 ChIP-Seq rep 1

description:
Villus_H3K27me3_ChIP-seq
Villus_H3K27me3_ChIP

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ChIPseq DNA Sample Prep Kit (Illumina) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.

value: Eed+/+; Villin-CRE

value: Adult Epitheial cells; proximal 1/3 of intestine


title: Wild-type Villus Pol2 ChIP-Seq rep 2

source_name: Villus Pol2 ChIP-Seq

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug Pol2 antibody overnight (SC-899, Santa Cruz) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Eed+/+; CRE-

value: Adult Epithelium; proximal 1/3 of intestine

value: Control mouse villus cells

value: Pol2 antibody (SC-899, Santa Cruz)


title: shCamta1A-3

city: Heidelberg

first: Carlos

last: Bas Orth

address: Im Neuenheimer Feld 307

department: Anatomy and Cell Biology

country: Germany

institute: Ruprecht-Karls-University Heidelberg

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using TopHat v1.4.1 with default parameters
The aligned read files (accepted_hits.bam) were name sorted and transformed to SAM files with SAMtools v0.1.19
The sorted files were passed to HTSeq-count v0.6.1 to get the raw counts with parameter -s no
Differential expression was analyzed with the likelihood ratio test using DESeq2 v1.4.5 in R 3.1.1
Genome_build: mm9

source_name: hippocampus, CAMTA1 knock-down sample, infected with anti-CAMTA1 shRNA sequence A

extract_protocol:
rAAV-shRNA infected regions of hippocampal tissue were identified by mCherry fluorescence, dissected under a fluorescence microscope, and stored in RNAlater (Ambion). Total RNA was isolated using a QIAGEN RNeasy kit with additional on-column DNase I digestion according to the manufacturer's instructions.
Non-strand-specific RNA-seq libraries were prepared from 1.5 µg of each total RNA sample with the NEBNext RNA Library Prep Kit for Illumina, polyA mRNA was selected for the library construction.

treatment_protocol: non-targeting control shRNA, anti-Camta1 shRNA A, or anti-Camta1 shRNA B was delivered to the dorsal hippocampus of 8-week old mice by stereotaxic injection of recombinant adeno-associated viruses (rAAV). Brain tissue was isolated 3 weeks after virus injection.

tag: Sex

value: male

value: brain


title: shCamta1A-2

description: CAMTA1 knock-down sample, infected with anti-CAMTA1 shRNA sequence A


title: shCamta1A-1


title: shCamta1B-2

source_name: hippocampus, CAMTA1 knock-down sample, infected with anti-CAMTA1 shRNA sequence B


title: shCamta1B-1

description: CAMTA1 knock-down sample, infected with anti-CAMTA1 shRNA sequence B


title: shCamta1B-3


title: Wild-type Ent-Pro H3K27me3 ChIP-seq

source_name: Ent-Pro H3K27me3

value: H3K27me3 antibody (07-449, Millipore)


title: shControl-3

source_name: hippocampus, control sample, infected with non-targeting control shRNA


title: Wild-type Villus Pol2 ChIP-Seq rep 1


title: Wild-type Villus H3K27me3 ChIP-Seq rep 3

source_name: Villus H3K27me3 ChIP-Seq

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus H3K4me3 ChIP-Seq

description:
Villus_H3K4me3_ChIP-seq
Villus_H3K4me3_ChIP

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Villus cell pallet was digested with MNase (Sigma N3755) and dialised against RIPA buffer. The digested chromatin was incubated with 5ug of H3K4me3 antibody overnight (Abcam ab8580) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Eed+/+; Cre-

value: H3K4me3 antibody (Abcam ab8580)


title: shControl-2

description: control sample, infected with non-targeting control shRNA


title: Wild-type Villus H3K27me3 ChIP-Seq rep 2


title: Wild-type Lgr5+ ISC H3K27me3 ChIP-Seq rep 2

source_name: Lgr5+ve ISC H3K27me3 ChIP-Seq

extract_protocol:
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Eed+/+; Lgr5-EGFP-IRES-CREERT2

value: Crypts; proximal 1/3 of small intestine


title: shControl-1


title: Wild-type Lgr5+ ISC RNA-seq biological rep 2

description:
Control_ISC_2
1304_Control_Lgr5_RNAseq

extract_protocol:
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry.
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Adult intestinal stem cell; proximal 1/3 of intestine


title: Wild-type Lgr5+ ISC RNA-seq biological rep 3

description:
Control_ISC_3
367_Control_Lgr5_RNAseq


title: sh3 DHT 1 ERG

first: Thomas

last: Westerling

address: 450 Brookline Ave

institute: Dana Farber Cancer institute

description: ChIP DNA

data_processing:
BWA version 0.7.4-r385,  aln parameters -q 5 -l 32 -k 2 -t 4
MACS2 version 2.1.0.20140616,  callpeak --SPMR -B -q 0.01 --keep-dup 1
cat , all AR ChIPseq summit files
bedtools v2.20.1 slop -b 200, all AR ChIPseq summit files
bedtools v2.20.1 merge -d 1 -c 4  union AR ChIPseq summit file
Qlucore Omics Explorerer 3.1(19) - Generating summary Matrix file using union AR ChIPseq Peakfile, counting reads falling withing Peak features, Normalization according to Omics Explorer
Genome_build: hg19
Supplementary_files_format_and_content: raw data, pass filter Illumina NextSeq500 fastq files. Summit files, bed format Macs2 output, ChIPseq summits

source_name: cell line VCaP

growth_protocol: DMEM, Charcol Dextran stripped FBS for hormone depletion(2days), Doxycycline for shRNA construct induction (5days)

extract_protocol:
ChIP protocol - Purification using Magio beads
Kapa HTP library preparation kit on a Sciclone NGS workstation using MagBio beads

treatment_protocol: 24h ligand as indicated for each sample

tag: shRNA

value: PRMT5 sh3

value: ERG

tag: treatment

value: DHT

tag: cell line

value: VCaP


title: Wild-type Sec-Pro H3K4me2 ChIP-seq

source_name: Sec-Pro H3K4me2

value: B6;129 mixed

value: 100 umol/kg DBZ (notch inhibitor) at 0 hours, again at 12 hours

value: Crypts; proximal 1/3 small intestines

tag: cell type

value: Control mouse secretory progenitor cells

value: H3K4me2 antibody (07-030, Millipore)


title: sh2 DHT 2 ERG

description: ChIP DNA

value: PRMT5 sh2


title: sh1 DHT 2 ERG

description: ChIP DNA

value: PRMT5 sh1


title: sh3 DHT 2 ERG

description: ChIP DNA


title: sh2 DHT 1 ERG

description: ChIP DNA


title: sh1 DHT 1 ERG

description: ChIP DNA


title: NTC DHT 1 ERG

description: ChIP DNA

value: PRMT5 NTC


title: sh2 DHT 3 AR

description: ChIP DNA

value: AR


title: sh3 DHT 3 AR

description: ChIP DNA


title: sh1 DHT 2 AR

description: ChIP DNA


title: NTC DHT 2 AR

description: ChIP DNA


title: sh3 DHT 2 AR

description: ChIP DNA


title: sh2 DHT 2 AR

description: ChIP DNA


title: sh2 R1881 2 AR

description: ChIP DNA


title: NTC DHT 3 AR

description: ChIP DNA


title: sh1 DHT 3 AR

description: ChIP DNA


title: Wild-type Lgr5+ ISC RNA-seq biological rep 1

description:
Control_ISC_1
1363_Control_Lgr5_RNAseq


title: NTC DHT 2 ERG

description: ChIP DNA


title: sh2 R1881 1 AR

description: ChIP DNA


title: sh2 DHT 1 AR

description: ChIP DNA


title: NTC DHT 1 AR

description: ChIP DNA


title: NTC R1881 1 AR

description: ChIP DNA


title: sh3 DHT 1 AR

description: ChIP DNA


title: SLNCR1 cons rep2

first: Carl

last: Novina

department: Cancer Immunology

institute: Dana-Farber Cancer Institute

description: processed data file: SLNCR1cons_vs_vector.deseq.txt

data_processing:
Read alignment to the hg19 reference genome/transcriptome was performed with STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15).
Raw sequence files converted to base-calls by the sequencer software
Sequencing reads aligning to unique exons are summed within each gene locus. Counting is performed by featureCounts software (http://bioinformatics.oxfordjournals.org/content/30/7/923.full.pdf). Reads located in regions where genomic features overlap are ignored since they cannot be definitively assigned to a single transcript.
Read-count normalization is performed by DESeq software (http://genomebiology.com/2010/11/10/R106/).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including GeneID, BaseMean(Average), BaseMean Replicate1, BaseMean Relicate2, fold change, Log2 fold change, p-value and adjusted p-value. For these DESEq output files, Basemean A refers to vector only while Basemean B refers to expression of either SLNCR1, SLNCR1 delta cons or SLNCR1 cons (as denoted in the file title).

growth_protocol: A375 cells were maintained in DMEM plus 10% FBS.

extract_protocol:
Cells were harvested 48 hours post-transfection RNA was isolated using Trizol® (Life Technologies) and Qiagen RNeasy Mini Kit and treated with DNase.
RNA was selected using NEBNext® PolyA mRNA Magnetic Isolation Module and libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: Cells were transfected with pcDNA3.1(-) empty vector control, or vector expressing SLNCR1, SLNCR1 delta conserved, or SLNCR1 conserved 24 hours post-seeding using Lipofectamine 2000 (Invitrogen).

tag: tissue

value: skin

tag: disease

value: malignant melanoma


title: scrambled control rep1

data_processing:
Read alignment to the hg19 reference genome/transcriptome was performed with STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15).
Raw sequence files converted to base-calls by the sequencer software
Sequencing reads aligning to unique exons are summed within each gene locus. Counting is performed by featureCounts software (http://bioinformatics.oxfordjournals.org/content/30/7/923.full.pdf). Reads located in regions where genomic features overlap are ignored since they cannot be definitively assigned to a single transcript.
Read-count normalization is performed by DESeq software (http://genomebiology.com/2010/11/10/R106/).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including GeneID, BaseMean(Average), BaseMean Replicate1, BaseMean Relicate2, fold change, Log2 fold change, p-value and adjusted p-value.  For these DESeq output files, BasemeanA refers to WM1976 cells transfected with a scrambled siRNA control, while BasemeanB refers the cells transfected with an siRNA targeting SLNCR1.

growth_protocol: WM1976 cells were maintained in DMEM plus 10% FBS.

extract_protocol:
Cells were harvested 48 hours post-transfection RNA was isolated using Trizol® (Life Technologies) and Qiagen RNeasy Mini Kit and treated with DNase.
RNA was selected using NEBNext® PolyA mRNA Magnetic Isolation Module and libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: Cells were transfected with scrambled siRNA control, or siRNA targeting SLNCR1 24 hours post-seeding using RNAiMAX (Invitrogen)


title: SLNCR1 delta cons rep2

description: processed data file: SLNCR1deltacons_vs_vector.deseq.txt


title: siRNA SLNCR1 rep1


title: Endothelial_CD31_pos_WT3

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description: Cell population isolated by flow cytometry using indicated markers from animals with indicated genotypes

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Tumor bearing lungs from K-rasG12D/+; miR-143/145+/+ mouse

growth_protocol: RNA was extracted from cell populations isolated in vivo from tumor-bearing lungs and subjected to flow cytometry with indicated surface markers

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.

treatment_protocol: No treatment

value: Lung endothelial cells (CD31+)


title: scrambled control rep2


title: sh1 R1881 2 AR

description: ChIP DNA


title: NTC R1881 2 AR

description: ChIP DNA


title: SLNCR1 rep2

description: processed data file: SLNCR1_vs_vector.deseq.txt


title: vector rep2


title: SLNCR1 rep1


title: vector rep1


title: SLNCR1 cons rep1


title: Pusa Ruby Control 2

city: Kolkata

first: Pallob

last: Kundu

state: West Bengal

address: P 1/12 CIT Scheme VIIM

department: Division of Plant Biology

institute: Bose Institute

description:
Samples collected about 72 hours post infection
small RNA

data_processing:
Cutadapt was used to trim the adapter sequence from the fastq read sequences. sickle-master was used to pick reads above quality score of 30 and minimum read length of 18 bases. Reads of length greater than 25 nt were discarded.
The resulting reads were used to BLAST against known miRNAs from tfgd and other known plant miRNAs from mirbase. Reads with greater than 98% identity and alignment length greater than 18 were taken for further processing
Only the read alignment against the miRNA from the plant closest to sly was considered, for those reads aligning to multiple plant miRNAs other than sly. miRNA count was considered based on the number of reads aligning with the miRNA.
The process was repeated for all the samples.
DEseq was performed on the read counts, to find the differentially expressed miRNAs between the infected and control samples.
Genome_build: tfgd and mirbase
Supplementary_files_format_and_content: .txt files, representing the small RNA sequences with their corresponding read counts

organism: Solanum lycopersicum

source_name: Leaf tissue

growth_protocol: Tomato plants were grown under controlled environment, at 25ºC temperature. Prior to the infection  plants were kept in a humid chamber for 24 hours. Alternaria fungus was grown on Potato Dextrose Agar plate, collected by scraping, homogenized, suspended in MES buffer  and colony forming units (CFU) were counted.

extract_protocol:
Three Trizol (Invitrogen) extracted RNA for the samples “Control 1, Control 2 and Infected 1” were used.  For one sample “Infected 2”Agilent Plant RNA Isolation kit (#5188-2780) was used for RNA extraction.  RNA purity was tested using Nanodrop 1000(Agilent Technologies).Integrity of RNA was assessed using Bioanalyzer 2100 (Agilent Technologies) on a RNA 6000 Nanochip. The QC criteria to pass the RNA quality on Bioanalyzer is RIN>7.The samples were found to be suitable for small RNA sequencing. For infected samples, only the infection zone tissues were collected.
Small RNA libraries for sequencing were constructed according to the IlluminaTruSeq Small RNA library protocol outlined in “TruSeq Small RNA Sample Preparation Guide” (Part # 15004197; Rev. A; Nov 2010). 1ug (microgram) of total RNA was used as the starting material. Briefly, 3’ adaptors were ligated to the specific 3’OH group of small RNA followed by 5’ adaptor ligation. The ligated products were reverse transcribed with Superscript II Reverse transcriptase by priming with Reverse transcriptase primers. The cDNA was enriched by 11cycles of PCR and cleaned using Polyacrylamide gel. The library was size selected in the range of 140 – 190 bp followed by overnight gel elution and salt precipitation using glycogen, 3M Sodium Acetate and absolute ethanol. The precipitate was re-suspended in resuspension buffer. The prepared library was quantified using Nanodrop and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent).The spread observed indicated an insert size of 22-70bp which is representative of smRNA fraction. Based on this observed Bioanalyzer profile they were decided to be suitable for sequencing.

treatment_protocol: Mock inoculation was done with the buffer (MES) in which Alternaria spore forming units were suspended. Plants were infected with a solution (~1000000 CFU/ml) of  Alternaria using droplet inoculation method (~10 microlitre drop on  leaves).

value: leaf

tag: cultivar

value: Pusa Ruby

tag: infection status

value: Mock infected

tag: tissue appearance

value: Normal


title: Pusa Ruby Infected 1_mRNA

description: Samples collected about 72 hours post infection

data_processing:
SeqQC_V2.2 was used for base calling, reads with > 20 phred score were considered.
Tophat-2.0.7 and Cufflinks-2.0.1 tools were used for spliced alignment and estimation of transcript abundance.
cuffdiff was used to find the Significant differential gene expression result of control vs infected
Genome_build: Tomato genome (Sol Genomics Network)
Supplementary_files_format_and_content: .txt files, representing the identified genes with raw read counts.

growth_protocol: Tomato plants were grown under controlled environment, at 25°C temperature. Prior to the infection  plants were kept in a humid chamber for 24 hours. Alternaria fungus was grown on Potato Dextrose Agar plate, collected by scraping, homogenized, suspended in MES buffer  and colony forming units (CFU) were counted.

extract_protocol:
Total RNA from leaf tissues were prepared using TRIZOL reagent and standard protocol. For infected samples, only the infection zone tissues were collected.
Transcriptome library for sequencing was constructed according to the Illumina TruSeq RNA library protocol outlined in “TruSeq RNA Sample Preparation Guide” (Part # 15008136; Rev. A; Nov 2010). Briefly, the mRNA from 1ug of Total RNA purified using Oligo dT beads was fragmented for 4 minutes at elevated temperature (94°C) in the presence of divalent cations and reverse transcribed with Superscript II Reverse transcriptase by priming with Random Hexamers. Second strand cDNA was synthesized in the presence of DNA Polymerase I and RnaseH. The cDNA was cleaned up using Agencourt Ampure XP SPRI beads (Beckman Coulter). Illumina Adapters were ligated to the cDNA molecules after end repair and addition of “A”- base. SPRI cleanup was performed after ligation. The library was amplified using 11 cycles of PCR for enrichment of adapter ligated fragments. The prepared library was quantified using Nanodrop and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent).

treatment_protocol: Mock inoculation was done with the buffer (MES) in which Alternaria spore forming units were suspended. Plants were infected with a solution (~1000000 CFU/ml) of  Alternaria using droplet inoculation method (~10 microlitre drop on leaves).

value: Alternaria infected

value: Chlorotic/slightly blight


title: Pusa Ruby Control 1


title: Pusa Ruby Infected 2


title: Pusa Ruby Infected 1


title: siRNA SLNCR1 rep2


title: mBM_LECT2_5d

city: Ningbo

first: Zhang

last: Hao

address: Fenghua Road No. 818

country: China

institute: NINGBO UNIVERSITY

data_processing:
By base calling, the original image data produced by the sequencer is transferred into sequences, which are defined as "raw reads"(or "raw data") and saved as ".fastq" files. As the raw reads may contain low quality reads and or adaptor sequences, preprocessing is necessary before starting further analysis. Normally, data cleaning (or data filtering) is performed to obtain "clean reads" (or "clean data") for further analysis.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample. The related information of gene is also provided (Coverage, Symbol, Description and so on).
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
Screening of differentially expressed genes (DEGs) between two samples. This analysis includes the screening of genes that are differentially expressed among samples, and GO functional enrichment analysis and KEGG pathway enrichment analysis for these DEGs. Referring to "The significance of digital gene expression profiles[4]", we have developed a strict algorithm to identify differentially expressed genes between two samples.
Genome_build: mm8
Supplementary_files_format_and_content: The GeneDiffExp files include GeneID, Gene_length, Expression and RPKM values between samples.

source_name: Bone marrow cells

extract_protocol:
The bone marrow cells were flushed out from femur, tibia, pelvis, and humerous in PBS. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.

treatment_protocol: Recombinant LECT2 was subcutaneously injected at a dose of 300 μg/kg body weight (once a day for 0, 3, or 5 days) in mice.

tag: age

value: 6-8 weeks

value: 300 μg/kg bw Recombinant LECT2  once a day for 5 days

value: Bone marrow cells


title: sh1 DHT 1 AR

description: ChIP DNA

value: DHT

value: VCaP


title: mBM_LECT2_3d

value: 300 μg/kg bw Recombinant LECT2  once a day for 3 days


title: Pusa Ruby Control 1_mRNA


title: mBM_LECT2_0d


title: nfstse90m0h2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: molecule: Bru-labeled RNA

data_processing:
Library strategy: Bru-Seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
NCBI RefSeq isoforms were condensed to create gene meta-transcripts (Paulsen et al., Methods, 2014). The number of reads falling on a given region of these meta-transcripts were counted and normalized by the size of the meta-transcript and by the size of the library (i.e. the RPKM method, Chepelev et al., Nucleic Acids Research, 2009).
Genome_build: hg19
Supplementary_files_format_and_content: gene expression (as BED 6 with 3 custom columns).  The columns of the BED files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder, not used); (6) strand; (7) hits count; (8) density – count/length; (9) RPKM - count/(length/1E3)/(mapped read count/1E6). Hits count is calculated by summing the base coverages and divided by the read length (as opposed to counting reads directly) and thus are not necessarily integer values.  RPKM is calculated for the first 30 kb of genes over 30 kb long and for the entire gene where genes are less than or equal to 30 kb long.

source_name: Foreskin fibroblasts (HF1)

growth_protocol: HF1 cells were grown as monolayers in MEM supplied with 10% fetal bovine serum and antibiotics (Invitrogen) at 37C.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads. After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Cells were grown in serum-free media for 48 h at 37C.  Where indicated, serum (FBS) was then added to conditioned media to a final concentration of 10%. Cells were then incubated in conditioned media with 2 mM bromouridine (BrU) at 37C for 30 min.

tag: time between serum addition and rna extraction

value: 120 min

tag: time between bru labeling and rna extraction

value: 30 min

tag: labeling agent

value: Bromouridine (Bru)


title: nfstse60m0h2

description: molecule: Bru-labeled RNA

value: 90 min


title: SLNCR1 delta cons rep1

value: skin

value: malignant melanoma


title: nfstse30m0h2

description: molecule: Bru-labeled RNA

value: 60 min


title: nfst0h2

description: molecule: Bru-labeled RNA


title: DDX3X CLIP 4

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: protocol: CLIP-Seq

data_processing:
Illumina single ended reads were trimmed of adapter using Cutadapt,
aligned using Burrows-Wheeler Aligner (BWA 0.5.5)
coverage was obtained by summarizing coverage of aligned bases with quality score greater than 15 at each position of the reference genome
peaks were called for coverage over 10x and those present in control IgG sample were removed
Genome_build: hg19
Supplementary_files_format_and_content: txt file for abundance measurements for targeted regions

source_name: HEK293T cells

growth_protocol: HEK293T cellswere grown in Dulbecco’s Modified Eagle’s Serum,  DMEM,  supplemented with 10% fetal bovine serum, FBS and 1% Pen-Strep (100 U/ml penicillin, 100 µg/ml streptomycin. Cells were incubated at 37 °C and with a 5% CO2 concentration.

extract_protocol:
Ptotein lysis was performed in cold Nonidet P-40 buffer for 10 min on ice followed by addition of a 1:100 volume of RQ1 DNase (Promega). After DNAse treatment, RNAse I was added (0.0–2 U) and samples were incubated for 4 min at 37 °C.
After RNA extraction, library was prepared using Nextflex Small RNA Sequencing Kit and Sequencing was performed on an Illumina HiSeq 2000 using TruSeq SBS v3 reagents according to the manufacturer’s instructions

treatment_protocol: Cells were seeded in 10 cm dish and harvested 24 hr later to obtain protein extracts. No additional treatments were done

value: neuronal

tag: clip antibody

value: anti-DDX3X monoclonal (clone 2253C5a)

tag: antibody manufacturer

value: Santa Cruz Biotechnologies

tag: antibody catalog number

tag: protein immunoprecipitated


title: WT DDX3X Ribo-seq

description: Protocol: Ribo-Seq

data_processing:
Library strategy: Ribo-Seq
Illumina single ended reads were trimmed of adapter using Cutadapt,
aligned using Burrows-Wheeler Aligner (BWA 0.5.5)
coverage was obtained by summarizing coverage of aligned bases with quality score greater than 15 at each position of the reference genome
peaks were called on coverage
Genome_build: hg19
Supplementary_files_format_and_content: txt file for abundance measurements

extract_protocol:
RNA was extracted from sedimented polysomal fraction using miRNeasy kit (Qiagen)
RNA library was performed as done by: Ingolia, N.T., Brar, G.A., Rouskin, S., McGeachy, A.M., and Weissman, J.S. (2012).  Nat Protoc 7, 1534-1550. Sequencing was performed on an Illumina HiSeq 2000 using TruSeq SBS v3 reagents according to the manufacturer’s instructions.

treatment_protocol: HEK293T cells were transfected with either empty vector or FLAG-tagged DDX3X constructs for 24 h. After transfection, cells were pre-treated with harringtonine (2 μg/ml for 90 seconds, LKT Laboratories, cat. no. H0169) followed by addition of cycloheximide (100 μg/ml, Sigma/Aldrich).

value: Neuronal

tag: transfection construct

value: cells transiently transfected with WT DDX3X expressing vector

tag: over-expression product

value: FLAG-tagged WT DDX3X


title: DDX3X CLIP 3

description: protocol: CLIP-Seq

tag: cell line


title: IgG

description: protocol: CLIP-Seq

tag: cell type

value: mouse IgG


title: vector control Ribo-seq

description: Protocol: Ribo-Seq

value: cells transiently transfected with empty pCDNA3.1 vector

value: none (control)


title: G325E Ribo-seq

description: Protocol: Ribo-Seq

value: cells transiently transfected with DDX3X-G325E expressing vector

value: FLAG-tagged DDX3X G325E


title: DDX3X siRNA RNA-seq

data_processing:
Illumina single ended reads were trimmed of adapter using Cutadapt,
aligned using Burrows-Wheeler Aligner (BWA 0.5.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

growth_protocol: HEK293T cells were grown in Dulbecco’s Modified Eagle’s Serum,  DMEM,  supplemented with 10% fetal bovine serum, FBS and 1% Pen-Strep (100 U/ml penicillin, 100 µg/ml streptomycin. Cells were incubated at 37 °C and with a 5% CO2 concentration.

extract_protocol:
RNA was extracted using RNAeasy kit (Qiagen)
RNA sequencing libraries were prepared using approximately 1 µg total RNA using TruSeq RNA Sample Prep v2 kits according to the manufacturer’s instructions (Illumina, San Diego, CA.). Sequencing was performed on an Illumina HiSeq 2000 using TruSeq SBS v3 reagents according to the manufacturer’s instructions.

treatment_protocol: For knockdown experiments, HEK293T cells were treated with control or DDX3X siRNA oligos for 48 h. For overexpression experiments, cells were transfected with 5 µg of GFP alone, or GFP-DDX3X variants for 32 h followed by collection of GFP-positive cell population by flow-cytometry (FACS LSR II D, BD Biosciences)cells were transfected with plasmids from 30 h

value: cells transfected with DDX3X siRNA for 48 hr


title: DDX3X CLIP 2

description: protocol: CLIP-Seq


title: control siRNA RNA-seq

value: cells transfected with control siRNA for 48 hr


title: GFP- WT DDX3X RN-Aseq

value: cells transiently transfected with GFP WT DDX3X expressing plasmid

tag: sorting parameter

value: sorted by flow cytometry for GFP+ population

value: GFP-WT DDX3X


title: GFP-control RNA-seq

value: cells transiently transfected with GFP expressing plasmid

value: GFP


title: WT3a_FLT3 1 WGBS

status: Public on May 19 2016

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: Biological replicate 1 of FLT3-ITD leukemia for WGBS. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation

data_processing:
Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.74 using the following parameters: -v 10 -g 2 -w 5 -p 8 -x 1000 -R -S 42; Duplicate reads were removed by picard tools. Cytosine methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z -g -m 5 --ct-snp=no-action. Note that when a sample was run on more than one lane of the same flow cell, the fastq files have been concatenated accordingly.
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus (strands combined), number of total C counts on this locus (strands combined), number of total C+T counts on this locus (strands combined), number of total G counts on this locus of reverse strand (value is NA), number of total G+A counts on this locus of reverse strand (value is NA), lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

source_name: Bone marrow

growth_protocol: Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Thymus or whole bone marrow cells from each genotype were collected from transplant recipients.

extract_protocol:
Extract DNA using Qiagen Allprep Mini kit.
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were bisulfite converted with Qiagen Epitect kit.

value: Leukemic cells

tag: cell surface marker

tag: genotype

tag: strain


title: nfstse0m0h2

description: molecule: Bru-labeled RNA

value: 30 min

value: Bromouridine (Bru)


title: KO3a/FLT3-ITD GFPOE rep2 Total Input ChIP-seq

description: Biological replicate 2 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Total Input DNA.

data_processing:
Raw reads were quality trimmed (Trimgalore) and uniquely mapped to the mm9 reference genome using Bowtie2. Peak calling was performed with MACS 2.0.1 (2.0.10.20131216) with parameters (-t –c –f BAMPE). One tag from each unique position was examined to eliminate peaks generated by clonal amplification. We retained Fli1 ChIP-seq peaks meeting the following criteria: (1) MACS q-value < 0.01, (2) > 10% overlap with reference DNAse hotspot regions. Enrichment for the FLI1 motif was verified by the AME function in MEME. Peaks among conditions or replicates were consolidated by selecting a representative peak if the summits were separated by a distance < 11-bp (size of the enriched FLI1 motif MA0475.1 published in the JASPAR CORE database).
Enrichment of Fli1 was compared with Danpos 2.2.2. Briefly, Experiments were input subtracted and quantile normalized to an antibody-matched reference sample (GSM552233) processed by the identical workflow. The signal was quantified in 10-bp step sizes and written out in wiggle file format. Wiggle files have been converted to bigWig.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files (BED5 format) contain the locations of the peak summits, the 5th column representing the -log10pvalue. The bigWig files were created from Danpos2 wiggle files. More information may be found in the Macs2 and Danpos2 documentation.

growth_protocol: Dnmt3a knock-out FLT3-ITD bulk tumors were harvested, transduced with MSCV-Dnmt3a-GFP (or MSCV-IRES-GFP), and re-transplanted into a tertiary host. ChIP was performed from bulk tumors when the mice developed T-ALL again.

extract_protocol:
2 million cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was terminated by addition of 0.125M glycine and washed with ice-cold PBS containing protease inhibitor cocktail (PIC, Roche). Samples were sonicated to 200-500bp fragments for 8 cycles at 5 minutes each (Biorupter, Diagenode). Sheared chromatin were incubated with FLI1 antibody (ab15289;Abcam) and Protein A (Dynabeads, Invitrogen). Chromatin were reverse crosslinked at 68°C for 3 hours at mixed in Elution buffer (1M Tris pH 7.5, 0.5M EDTA, 5M NaCl, 10% SDS, Proteinase K) at 1100rpm. DNA was purified by MiniElute PCR Purification Kit (Qiagen) and eluted in 22μL EB buffer.
Purified DNA was used to generate libraries with the ThruPLEX-FD preparation kit (Rubicon)

tag: chip antibody


title: WT_GFP 1 WGBS

description: Biological replicate 1 of CD4/CD8 double positive thymocytes from WT GFP control for WGBS

source_name: Thymus

value: Murine thymus derived CD4/CD8 double positive T cells


title: KO3a/FLT3-ITD GFPOE rep2 Fli1 ChIP-seq

description: Biological replicate 2 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Fli1-enriched DNA.

value: Abcam ab15289


title: KO3a/FLT3-ITD GFPOE rep1 Total Input ChIP-seq

description: Biological replicate 1 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Total Input DNA.


title: KO3a_FLT3 2 WGBS

description: Biological replicate 2 of Dnmt3aKO/FLT3-ITD leukemia for WGBS. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: DDX3X CLIP 1

description: protocol: CLIP-Seq

value: neuronal

value: anti-DDX3X monoclonal (clone 2253C5a)

value: Santa Cruz Biotechnologies


title: GFP- DDX3X T275M mutant RNA-seq

value: Neuronal

value: cells transiently transfected with GFP DDX3X T275M expressing plasmid

value: GFP-DDX3X T275M


title: KO3a/FLT3-ITD 3aOE rep2 Total Input ChIP-seq

description: Biological replicate 2 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Total Input DNA.


title: KO3a/FLT3-ITD GFPOE rep1 Fli1 ChIP-seq

description: Biological replicate 1 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Fli1-enriched DNA.


title: KO3a/FLT3-ITD 3aOE rep1 Fli1 ChIP-seq

description: Biological replicate 1 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Fli1-enriched DNA.


title: KO3a/FLT3-ITD 3aOE rep1 Total Input ChIP-seq

description: Biological replicate 1 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Total Input DNA.


title: KO3a/FLT3-ITD 3aOE rep2 Fli1 ChIP-seq

description: Biological replicate 2 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Fli1-enriched DNA.


title: GFP- DDX3X G302V mutant RNA-seq

value: cells transiently transfected with GFP DDX3X G302V expressing plasmid

value: GFP-DDX3X G302V


title: WT3a FLT3-ITD 2 H3K4me1 ChIP-seq

description: Biological replicate 2 of FLT3-ITD leukemia for ChIP-seq, H3K4me1-enriched DNA.

data_processing:
Raw reads were quality trimmed (Trimgalore) and uniquely mapped to the mm9 reference genome using Bowtie2. Peak calling was performed with MACS 2.0.1 (2.0.10.20131216) with parameters (-t –c –f BAMPE). One tag from each unique position was examined to eliminate peaks generated by clonal amplification. We retained those H3K4me1 and H3K27ac ChIP-seq peaks meeting the following criteria: (1) MACS fold-change > 3 and q-value < 0.01, (2) > 10% overlap with reference DNAse hotspot regions.
Chromatin marks were compared with Danpos 2.2.2. Briefly, the experiments were input background-subtracted and normalized to 10,000,000 reads. The signal was quantified in 10-bp step sizes and written out in wiggle file format. Wiggle files have been converted to bigWig.
Genome_build: mm9
Supplementary_files_format_and_content: The narrowPeak are BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. Definition of some specific columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. The bigWig files were created from Danpos2 wiggle files. More information may be found in the Macs2 and Danpos2 documentation.

extract_protocol:
2 million FACS-sorted cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was terminated by addition of 0.125M glycine and washed with ice-cold PBS containing protease inhibitor cocktail (PIC, Roche). Samples were sonicated to 200-500bp fragments for 8 cycles at 5 minutes each (Biorupter, Diagenode). Sheared chromatin were incubated with antibodies and Protein A (Dynabeads, Invitrogen). Antibodies used were against H3K27ac (ab4729; Abcam), H3K4me1 (ab8895; Abcam). Chromatin were reverse crosslinked at 68°C for 3 hours at mixed in Elution buffer (1M Tris pH 7.5, 0.5M EDTA, 5M NaCl, 10% SDS, Proteinase K) at 1100rpm. DNA was purified by MiniElute PCR Purification Kit (Qiagen) and eluted in 22μL EB buffer.
Purified DNA was used to generate libraries with the ThruPLEX-FD preparation kit (Rubicon)

value: Abcam ab8895


title: WT3a FLT3-ITD 2 H3K27ac ChIP-seq

description: Biological replicate 2 of FLT3-ITD leukemia for ChIP-seq, H3K27ac-enriched DNA.

value: Abcam ab4729


title: WT_GFP 2 WGBS

description: Biological replicate 2 of CD4/CD8 double positive thymocytes from WT GFP control for WGBS


title: KO3a/FLT3-ITD 3aOE 3 RRBS

description: Biological replicate 3 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for RRBS

data_processing:
Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.73 in RRBS mode using the following parameters: -g 1 -w 5 -D C-CGG -p 8 -R -s 12 -S 42 -u; methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z -g -m 5 -u --ct-snp=no-action
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus (strands combined), number of total C counts on this locus (strands combined), number of total C+T counts on this locus (strands combined), number of total G counts on this locus of reverse strand (value is NA), number of total G+A counts on this locus of reverse strand (value is NA), lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

growth_protocol: Bulk or Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Whole bone marrow cells from each genotype were collected from transplant recipients.

tag: tissue

value: bone marrow


title: KO3a/FLT3-ITD 3 H3K27ac ChIP-seq

description: Biological replicate 3 of DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, H3K27ac-enriched DNA.


title: KO3a/FLT3-ITD 1 ChIP-seq Total Input

description: Biological replicate 1 of DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Input DNA.


title: WT3a FLT3-ITD 2 ChIP-seq Total Input

description: Biological replicate 2 of FLT3-ITD leukemia for ChIP-seq, Input DNA.


title: KO3a/FLT3-ITD 3 ChIP-seq Total Input

description: Biological replicate 3 of DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, Input DNA.


title: sh1 R1881 1 AR

description: ChIP DNA

tag: shRNA

value: PRMT5 sh1

value: AR

tag: treatment

value: VCaP


title: KO3a/FLT3-ITD 3aOE 1 RRBS

description: Biological replicate 1 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for RRBS

value: Leukemic cells


title: KO3a/FLT3-ITD GFPOE 2 RRBS

description: Biological replicate 2 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for RRBS


title: KO3a/FLT3-ITD GFPOE 1 RRBS

description: Biological replicate 1 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for RRBS


title: KO3a/FLT3-ITD 3aOE 2 RRBS

description: Biological replicate 2 of tertiary transplant Dnmt3a-overexpressing DNMT3aKO/FLT3-ITD leukemia for RRBS


title: WT3a_KIFLT3_3 RRBS

description: Biological replicate 1 of FLT3-ITD leukemia RRBS. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation

value: Pre-leukemic cells


title: KO3a/FLT3-ITD 1 H3K4me1 ChIP-seq

description: Biological replicate 1 of DNMT3aKO/FLT3-ITD leukemia for ChIP-seq, H3K4me1-enriched DNA.


title: WT3a_KIFLT3_2 RRBS

description: Biological replicate 2 of FLT3-ITD leukemia RRBS. Donor whole bone marrow cells were subjected to to retroviral transduction and transplantation


title: WT3a_KIFLT3_3 RNA-seq

description: Biological replicate 3 of heterozygous knockin Flt3-ITD pre-leukemic bone marrow cells

data_processing:
Reads were aligned with Tophat 2.0.10 to both refseq transcriptome and mm9 genome using parameters: -p 12 --library-type fr-unstranded --read-realign-edit-dist 0 --min-anchor-length 6 --microexon-search --transcriptome-index=mm9_refseq. The refseq transcriptome gtf file was obtained from the Illumina iGenomes collection (archive-2013-03-06-15-01-24) as recommended by the software developers. The gtf file was revised with novel, mouse hematopoietic lincRNA transcripts published in (doi: 10.1016/j.stem.2015.02.002).
Transcript quantification of Refseq genes and mouse hematopoetic lincRNAs was assessed by Cufflinks / Cuffdiff 2.2.1 using parameters: -b -M -p 12 -u
Genome_build: mm9
Supplementary_files_format_and_content: cufflinks.gene.counts.txt and cufflinks.transcript.counts.txt are tab separated matrices of raw gene and transcript counts, respectively. Columns names match the given Sample names in this SubSeries. The genes_plus_linc.gtf file was used for gene and transcript quantification.

growth_protocol: For the FLT3-ITD retroviral model, Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Freshly sorted donor-derived mouse thymus and bone marrow cells (CD4+CD8+) from each genotype were collected from transplant recipients. For the Flt3-ITD knock-in model, bulk bone marrow cells were collected.

extract_protocol:
Extract RNA using Qiagen Allprep DNA/RNA mini kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection


title: HET3a_KIFLT3_3 RRBS

description: Biological replicate 2 of Dnmt3aKO/FLT3-ITD leukemia. Donor whole bone marrow cells were subjected to retroviral transduction and transplantation


title: WT3a_KIFLT3_2 RNA-seq

description: Biological replicate 2 of heterozygous knockin Flt3-ITD pre-leukemic bone marrow cells


title: HET3a_KIFLT3_2 RRBS


title: WT3a_KIFLT3_1 RNA-seq

description: Biological replicate 1 of heterozygous knockin Flt3-ITD pre-leukemic bone marrow cells


title: HET3a_KIFLT3_1 RRBS

description: Biological replicate 1 of Dnmt3aKO/FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: HET3a_KIFLT3_2 RNA-seq

description: Biological replicate 2 of heterozygous Dnmt3aKO / heterozygous knockin Flt3-ITD leukemia


title: KO3a_KIFLT3_1 RNA-seq

description: Biological replicate 1 of Dnmt3aKO / heterozygous knockin Flt3-ITD leukemia


title: KO3a_FLT3_4 RNA-seq

description: Biological replicate 4 of Dnmt3aKO/FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: WT3a_KIFLT3_1 RRBS

description: Biological replicate 1 of heterozygous knockin Flt3-ITD leukemia for RRBS


title: HET3a_KIFLT3_1 RNA-seq

description: Biological replicate 1 of heterozygous Dnmt3aKO / heterozygous knockin Flt3-ITD leukemia


title: KO3a_FLT3_3 RNA-seq

description: Biological replicate 3 of Dnmt3aKO/FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: KO3a/FLT3-ITD GFPOE 3 RRBS

description: Biological replicate 3 of tertiary transplant GFP-overexpressing DNMT3aKO/FLT3-ITD leukemia for RRBS


title: PLB_E12_Hoxa13het-Hoxd13KO_Hoxd13VP

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: Proximal limb mouse E12.5  Hoxa13het-Hoxd13KO_Hoxd13 viewpoint

data_processing:
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the mm10 (GRCm38) mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters “-n 2 --best -strata -m 5”. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
4C figures were made using a running mean algorithm with a window size of eleven fragments and normalized to the same total intensity, over the chr2: 71,000,000-78,000,000 coordinates, such as to see only changes in contacts distribution and to minimize PCR complexity bias in each samples.
Genome_build: mm10
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph), one per viewpoint, per tissue

source_name: Forelimb and Hindlimbs

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 limbs either from wild type, Hoxa13het- Hoxd13KO or Hoxa13d13-dKO mutant embryos were dissected, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 8 distal or proximal limbs were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing.
Hoxd13_inverse_forward:AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAAAATCCTAGACCTGGTCAT
Hoxd13_inverse_reverse:CAAGCAGAAGACGGCATACGAGGCCGATGGTGCTGTATAG
Hoxd11_inverse_forward:AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGCATACTTCCTCAGAAGAGGC
Hoxd11_inverse_reverse:CAAGCAGAAGACGGCATACGACTAGGAAAATTCCTAATTTCAG

tag: age

tag: tissues

value: Proximal fore- and hindlimb


title: DLB_E12_Hoxa13d13-dKO_Hoxd13VP

description: Distal limb mouse E12.5 Hoxa13d13-dKO_Hoxd13 viewpoint

value: Distal fore- and hindlimb


title: DLB_E12_Hoxa13het-Hoxd13KO_Hoxd11VP

description: Distal limb mouse E12.5  Hoxa13het-Hoxd13KO_Hoxd11 viewpoint


title: DLB_E12_Hoxa13het-Hoxd13KO_Hoxd13VP

description: Distal limb mouse E12.5  Hoxa13het-Hoxd13KO_Hoxd13 viewpoint


title: PLB_E12_Hoxa13het-Hoxd13KO_Hoxd11VP

description: Proximal limb mouse E12.5 Hoxa13het-Hoxd13KO_Hoxd11 viewpoint


title: PLB_E12_Hoxa13d13-dKO_Hoxd11VP

description: Proximal limb mouse E12.5 Hoxa13d13-dKO_Hoxd11 viewpoint


title: PFL_E12_WT_Hoxd13VP

description: Proximal forelimb mouse E12.5 WT_Hoxd13 viewpoint

source_name: Forelimb

value: Proximal forelimb

value: wild type


title: PFL_E12_WT_Hoxd11VP

description: Proximal forelimb mouse E12.5 WT_Hoxd11 viewpoint


title: DFL_E12_WT_Hoxd11VP

description: Distal forelimb mouse E12.5 WT_Hoxd11 viewpoint

value: Distal forelimb


title: DFL_E12_WT_Hoxd13VP

description: Distal forelimb mouse E12.5 WT_Hoxd13 viewpoint


title: PFL_E12_Hoxa13d13-dKO_RNAseq_rep1

description: Proximal forelimb mouse E12.5 Hoxa13d13-dKO_RNAseq

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10) genome or a manually- engineered version of the genome, accounting for the Lacz and Neomycin cassettes insertion in Hoxd13 and Hoxa13 respectively. The RNA-seq data were aligned against their respective genomes using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and bedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualization and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10 or customized mm10 genome
Supplementary_files_format_and_content: bedGraph of the forward or reverse strand RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 limbs either from wild type or Hoxa13d13-dKO mutant embryos were used for RNA extraction. Samples were stored in RNAlater at -80°C. The distal or proximal portion of the forelimbs from individual embryos was processed using the RNeasy micro kit (Qiagen) according to manufacturer instructions. On-column DNase I treatment was performed during 20min at room temperature to ensure pure, DNA-free RNA extraction.
A total of 100 ng of pure total RNA was amplified following standard Illumina procedure for polyA-selected RNA. RNA sequencing (RNA-seq) libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on a HiSeq 2500 machine, as single-end, 100 base pairs (bp) reads. The preparation of libraries and sequencing were performed by the genomic platform of the University of Geneva.


title: DFL_E12_Hoxa13d13-dKO_RNAseq_rep1

description: Distal forelimb mouse E12.5 Hoxa13d13-dKO_RNAseq


title: DFL_E12_WT_RNAseq_rep1

description: Distal forelimb mouse E12.5 WT_RNAseq


title: PFL_E12_WT_RNAseq_rep1

description: Proximal forelimb mouse E12.5 WT_RNAseq


title: DFL_E12_WT_H3K27me3_rep1

description: Distal forelimb mouse E12.5 WT_H3K27me3 ChIPseq

data_processing:
Illumina Casava1.8.2 software used for basecalling.Replicate data set was concatenated together.
Demultiplexed ChIP-seq reads were mapped onto the GRCm38 (mm10) using Bowtie (Galaxy Tool Version 1.1.2) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al., 2014). Both unmapped regions containing adaptors and contamination, and PCR duplicates were removed from mapped reads.
These analyses were performed on the public server of the Galaxy Project (https://usegalaxy.org/) (Hillman-Jackson et al., 2012).
By using bamCompare (Galaxy Tool Version 1.5.9.1.0) from the Galaxy deepTools webserver (http://deeptools.ie-freiburg.mpg.de/), ChIP and input data were normalized and compared to compute the log2 of the number of reads ratio (Ramirez et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input.

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 forelimbs from wild type mice were used for ChIP-seq. Samples were fixed in 1% formaldehyde/PBS for 18 minutes at room temperature, washed at least three times with cold PBS containing protease inhibitor and stored at -80°C. Pools of ten pairs of wild type proximal or distal forelimbs were used for each experiment. The samples were treated with lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl and protease inhibitor) for 10 min on ice, followed by RIPA buffer (TE with 140 mM NaCl, 0.1% deoxycholate, 0.1% SDS, 1% TritonX-100 and protease inhibitor) and fragmented to a range of 200-500 bp by a Biorupter sonication device (Diagenode). PierceTM Protein A/G magnetic beads (88803, Thermo Scientific) were conjugated with each antibody in blocking buffer (PBS, 0.5% Tween20, 0.5% BSA and protease inhibitor) for 4 hrs at 4°C and washed with blocking buffer. Chromatin was incubated with the prepared protein A/G beads overnight at 4°C with rotation. 3 µg of H3K27ac (ab4729, Abcam) and 3 µg of H3K27me3 (07-449, Millipore) were used for each immunoprecipitation. Samples were washed 6 times with RIPA buffer, twice with RIPA/500 mM NaCl buffer, twice with LiCl wash buffer (TE, 250 mM LiCl, 0.5% NP-40 and 0.5% deoxycholate) and twice with TE, followed by eluted in direct elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl and 0.1% SDS). Cross-links were reversed overnight at 65°C and ChIPed DNA was treated with RNase A and proteinase K, and purified by phenol chloroform extraction.
For ChIP-seq, at least 5 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

tag: antibody


title: E11.0_T2_3524

city: Beijing

first: Xianlong

last: Li

address: 5, Yiheyuan Rd., Haidian District

department: Biodynamic Optical Imaging Center, College of Life Sciences

institute: Peking University

data_processing:
remove Illumina adaptor sequences, primer UP1, primer UP2 and 3’ ployA sequences using cutadapt (ver 1.6)
sequence alignment to the mouse genome (mm9) and spiked-in sequences using tophat (v2.0.12)
Cufflinks (v2.2.1) was used to estimate the expression level of each detected gene as fragment per kilobase of transcript per million fragments mapped (FPKM) value
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking (cufflinks output)

source_name: AGM

extract_protocol:
E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T1 CD201-: CD31+CD45-CD41lowc-Kit+CD201low/-, T2 pre-HSCs: CD31+CD45+c-Kit+CD201high, T2 CD41low: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+; bonemarrow: Adult HSC: ESLAM(CD45+ EPCR+ CD48- CD150+).
FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol.

value: T2 pre-HSCs


title: E11.0_T2_3522


title: E11.0_T2_3523


title: E11.0_T2_3525


title: PLB_E12_Hoxa13d13-dKO_Hoxd13VP

description: Proximal limb mouse E12.5 Hoxa13d13-dKO_Hoxd13 viewpoint


title: E11.0_T2_3517


title: E11.0_T2_3521


title: E11.0_T2_3514


title: E11.0_T2_3520


title: DLB_E12_Hoxa13d13-dKO_Hoxd11VP

description: Distal limb mouse E12.5 Hoxa13d13-dKO_Hoxd11 viewpoint


title: E11.0_T2_3510


title: E11.0_T2_3516


title: E11.0_T2_3512


title: E11.0_T2_3511


title: E11.0_T2_3505


title: E11.0_T2_3504


title: E11.0_T2_3503


title: E11.0_T2_3501


title: E11.0_T2_3502


title: E11.0_T1CD201neg_3626


title: E11.0_T1CD201neg_3627


title: E11.0_T2_3506


title: E11.0_T1CD201neg_3622


title: E11.0_T1CD201neg_3621


title: E11.0_T1CD201neg_3620


title: E11.0_T2_3509


title: E11.0_T2_3507


title: E11.0_T1CD201neg_3614


title: E11.0_T2_3508


title: E11.0_T1CD201neg_3615


title: E11.0_T1CD201neg_3616


title: E11.0_T1CD201neg_3609


title: E11.0_T1CD201neg_3610


title: E11.0_T1CD201neg_3611


title: E11.0_T1CD201neg_3605


title: E11.0_T1CD201neg_3608


title: E11.0_T1CD201neg_3617


title: E11.0_T1CD201neg_3604


title: E11.0_T1CD201neg_3619


title: E11.0_T1CD201neg_3602


title: E11.0_T1CD201neg_3625


title: Adult_HSC_3740

source_name: bonemarrow

value: Haematopoietic stem cells


title: E11.0_T1CD201neg_3612


title: E11.0_T1CD201neg_3607


title: Adult_HSC_3739


title: Adult_HSC_3738


title: Adult_HSC_3736


title: Adult_HSC_3737


title: Adult_HSC_3735


title: Adult_HSC_3734


title: Adult_HSC_3733


title: Adult_HSC_3731


title: Adult_HSC_3726


title: Adult_HSC_3727


title: Adult_HSC_3728


title: Adult_HSC_3725


title: Adult_HSC_3730


title: Adult_HSC_3729


title: Adult_HSC_3724


title: Adult_HSC_3723


title: Adult_HSC_3722


title: Adult_HSC_3721


title: Adult_HSC_3720


title: Adult_HSC_3719


title: Adult_HSC_3713


title: Adult_HSC_3718


title: Adult_HSC_3711


title: Adult_HSC_3712


title: Adult_HSC_3732


title: Adult_HSC_3717


title: Adult_HSC_3714


title: Adult_HSC_3709


title: E14.5_FL_3319

molecule: polyA RNA

source_name: fetal liver (FL)

value: E14 HSCs


title: E14.5_FL_3311


title: E14.5_FL_3314


title: E14.5_FL_3312


title: E14.5_FL_3316


title: E11.0_T2_3519


title: E14.5_FL_3305


title: E14.5_FL_3306


title: E14.5_FL_3310


title: E14.5_FL_3308


title: E14.5_FL_3304


title: E14.5_FL_3307


title: E14.5_FL_3309


title: Adult_HSC_3710


title: E14.5_FL_3303


title: E12.5_FL_3127

value: E12 HSCs


title: E14.5_FL_3301


title: E12.5_FL_3128


title: E14.5_FL_3315


title: E12.5_FL_3129


title: E14.5_FL_3302


title: E12.5_FL_3121


title: E12.5_FL_3118


title: E12.5_FL_3125


title: E12.5_FL_3115


title: E12.5_FL_3119


title: E12.5_FL_3116


title: E12.5_FL_3114


title: E12.5_FL_3112


title: E12.5_FL_3111


title: E12.5_FL_3110


title: E12.5_FL_3113


title: E12.5_FL_3105


title: E12.5_FL_3108


title: E12.5_FL_3106


title: E12.5_FL_3107


title: E12.5_FL_3126


title: E11.0_T2_2718

value: Type2 pre-HSCs


title: E11.0_T2_2716


title: E11.0_T2_2719


title: E12.5_FL_3103


title: E11.0_T2_2712


title: E11.0_T2_2709


title: E11.0_T2_2705


title: E12.5_FL_3123


title: E11.0_T2_2713