title: ASC_Day3

source_name: Pre-adipocytes from liposuction material, cultured, 3 days after adipogenic stimulation (Day 3).

value: Non-proliferating, differentiated for 3 days


title: ASC_Day-2

status: Public on Dec 10 2014

type: SRA

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

library_source: transcriptomic

data_processing:
reads aligned with tophat v2.0.8b with parameter –-b2-very-sensitive,
transcript abundance estimated with cufflinks v2.1.1 with parameter -–GTF-guide
reference gtf with cuffmerge v2.1.1 with parameters -g, -s
diffrential expression analysis with cuffdiff v2.1.1 with parameters -b, -s, -u
csv file created from columns 5,10,14,18,22 from cuffdiff output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value

molecule: total RNA

organism: Homo sapiens

source_name: Pre-adipocytes from liposuction material, cultured, undifferentiated, proliferating, 2 days before adipogenic stimulation.

growth_protocol: Primary ASCs isolated from liposuction material were cultured in T175 flasks under proliferative conditions in high-glucose DMEM (4.5 g/l; Life Technologies-BRL) containing 20% FBS and 2 ng/ml basic fibroblast growth factor (Sigma-Aldrich). Cells at passage 5-7 were used for adipogenic induction. When cells reached confluency, adipogenic differentiation was induced by replacing growth medium with DMEM/F12 containing 10% FBS and by addition of 0.5 µM 1-methyl-3 isobutylxanthine (Dumex Alpharma), 1 µM dexamethasone (Dumex Alpharma), 10 µg/ml insulin (Novo Nordisk) and 100 µM (Dumex Alpharma) indomethacin for up to 9 days.

extract_protocol:
Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

treatment_protocol: Cells were cultured as described under Growth protocol. 10e6 cells were cultured to the indicated stages for total RNA isolation.

tag: cell type

value: Pre-adipocytes

tag: passages

value: Cells in passage 5-7

tag: treatment

value: control

tag: time

value: 2 days before adipogenic stimulation (Day -2)

tag: differentiation state

value: Proliferating, undifferentiated


title: Vitis vinifera Carignan infected by E. necator c-strain 6dpi-rep2

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

country: USA

institute: Joint Genome Institute

description: Leaves were collected at 6 days post inoculation

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Predicted transcriptomes of Erysiphe necator c-strain (JNVN00000000) and V. vinifera (GCA_000003745.2) were combined and used as a reference for mapping PM-infected grape leaves reads.
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal. Only reads with a mapping score greater than 30 were retained
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91. Only reads with a mapping score greater than 30 were retained.
Genome_build: Reads were mapped on E. necator (JNVN00000000) and V. vinifera (GenBank Assembly ID: GCA_000003745.2) predicted transcriptomes. The study focused on E. necator gene expression. Mapping on V. vinifera scaffold was done to limit non-specific mapping of grape reads.  Only counts of uniquely mapped E. necator genes are reported.
Supplementary_files_format_and_content: GEO_En_c-strain_time_course_raw_counts.txt : tab delimited text file, raw read counts determined by mapping the sequencing reads, only E. necator reads.

organism: Vitis vinifera

source_name: Vitis vinifera cv. Carignan leaves inoculated with Erysiphe necator (isolate: c-strain)

growth_protocol: Carignan detach leaves were disinfected with a 3% sodium hypochlorite solution and placed in Petri dishes containing 8 g/L water agar. A portable paint sprayer was used to inoculated leaves with a 1x106 conidia/mL suspension of the C-strain isolate in 0.001% Tween. The leaves were maintained under ambient conditions.

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Leaves were collected at 12 hours, 24 hours, 3 days, and 6 days post inoculation.

tag: biological replicate

tag: tissue

value: Leaves

tag: time point

value: 6 days post inoculation


title: P. chlororaphis 30-84_WT_AB_rep1

status: Public on Dec 11 2014

city: College station

first: Dongping

last: Wang

state: TX

address: Wellborn

institute: TAMU

description: Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

data_processing:
Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.
Filtering and alignment of the SOLiD 4 paired-end data was performed at the UTGSAF using the AB SOLiD BioScope Whole Transcriptome pipeline (v1.3), for whole-transcriptome RNA-seq analysis.
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Mapped reads were visualized using BamView in Artemis 13.2.0 (Rutherford et al. 2000).
The number of reads per kb of transcript per million mapped reads (RPKM) was used to normalize the raw data (Mortazavi et al., 2008), and mean RPKM values were determined for both the wild-type and gacA mutant samples.
Genome_build: NCBI Genome Accession #: PRJNA67533
Supplementary_files_format_and_content: Excel file containing the RPKM values for each gene

organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

source_name: wild type bacterial cells

growth_protocol: Three biological replicates of every strain were started from single colonies located on three separate plates containing AB + 2% CAA and then transferred to 10 ml AB + 2% CAA broth. All cultures were grown at 28˚C with shaking (150 rpm) to an approximate OD600 = 1.2.

extract_protocol:
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing.

tag: genotype/variation

value: wild type

tag: growth phase

value: logarithm phase

tag: media

value: AB minimal medium + 2% casamino acids (CAA)

tag: strain


title: NipB_BAC_STARRseq_input

city: Vienna

first: Alexander

last: Stark

address: Dr Bohr-Gasse 7

country: Austria

institute: Research Institute for Molecular Pathology (IMP), Vienna Biocenter VBC

description:
plasmid DNA (containing genomic DNA fragments)
PCR amplified Plasmid library

library_source: genomic

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 4 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. We additionally employed redundancy filter to remove clustered reads that could be due to sequence artefacts. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments), and merged these fragments from the two replicates. Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of STARR-seq and input. We performed hypergeometric tests to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: focused BAC library (in STARR-seq vector)

extract_protocol: Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) was isolated, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector. To construct the dCP STARR-seq vector, the sequence between BglII and FseI from the pGL3-Promoter backbone (Promega; cat. no. E1751) was replaced with the Drosophila Synthetic Core Promoter (DSCP), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal. The hkCP STARR-seq vector is identical to the dCP STARR-seq vector except we replaced the DSCP with the RpS12 core promoter. The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.

tag: genotype

value: y; cn bw sp - sequenced strain (Adams et al. 2000)

tag: experimental procedure

value: STARR-Seq


title: eEF1delta_BAC_STARRseq_input


title: DSCP_BAC_STARRseq_input


title: X16_BAC_STARRseq_input


title: RpS12_BAC_STARRseq_input


title: eve_BAC_STARRseq_input


title: pnr_BAC_STARRseq_input


title: evelong_BAC_STARRseq_input


title: evelong_BAC_S2_STARRseq

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)

source_name: S2 cells

value: S2 cells


title: pnr_BAC_S2_STARRseq


title: NipB_BAC_S2_STARRseq


title: hsp70_BAC_S2_STARRseq


title: RpS12_BAC_S2_STARRseq


title: eEF1delta_BAC_S2_STARRseq


title: pnr_STARRseq_input

source_name: whole genome library (in STARR-seq vector)


title: M5385_uninvolved

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Sequenced reads were aligned to the reference genome NCBI build 37 using TopHat version 1.3.3. We only used uniquely mapped reads with less than 3 mismatches.
We constructed a dataset-dependent transcriptome (see the linked article for detail), and the expression level of each gene was obtained by counting the number of reads. Reads mapped to multiple exons in a gene were counted only once. The gtf file showed the chromosome coordinates for each gene identifier in the ReadCount_42samples file.
Genome_build: genome NCBI build 37
Supplementary_files_format_and_content: data matrix (ReadCount_42samples.txt) containing read counts and gtf file showing the chromosome coordinates for each gene identifier in the ReadCount_42samples.txt file

source_name: skin

extract_protocol:
RNA was prepared from the frozen biopsies using the Qiagen Allprep kit. Skin punch biopsies were trimmed of visible subcutaneous fat and visible blood was removed by blotting on saline-soaked gauze.  Biopsies were then snap frozen in liquid nitrogen and stored at -80 deg C.  For RNA isolation, frozen skin biopsy samples were wrapped in an aluminum foil pouch pre-frozen in liquid nitrogen, placed in a prechilled steel mortar, and crushed with a hammer. The pulverized frozen tissue was quickly transferred into a 1.5-ml microcentrifuge containing 1 ml of the Allprep buffer and glass grinding beads. The tube was vigorously agitated on a Vortex mixer for 5 minutes to complete the extraction process. From this point on the sample was processed exactly as described in the kit manual. RNA quality and quantity were checked using an Agilent Bioanalyzer.
Libraries for high throughput sequencing were prepared using the Illumina mRNA-Seq kit. Briefly, the process involved isolating polyadenylated RNA, fragmentation by heating at 90°C, random-primed cDNA preparation, ligation of adaptors, and size selection on an agarose gel. A gel slice corresponding to approximately 120 bp insert was isolated, and the DNA was extracted and amplified by 15 cycles of PCR using the adaptor primers. The gel purified final product was checked for quality and quantity on an Agilent Bioanalyzer. The library thus prepared was sequenced one sample per lane in an 8-lane flow cell on the Illumina Genome Analyzer IIx. The raw sequencing output of the 80-base single read sequencing was 2000-3000 Mb per lane corresponding to 25-37.5 million reads.

tag: tissue type

value: Uninvolved skin


title: 6490_psoriatic

value: psoriatic skin


title: DSCP_BAC_S2_STARRseq


title: CASP499_psoriatic


title: M5050_normal

value: normal skin


title: M4618_normal


title: X16_STARRseq_input


title: M8492_uninvolved


title: M8470_uninvolved


title: eEF1delta_STARRseq_input


title: pnr_S2_STARRseq

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
pnr_S2.peaks.txt


title: M8755_uninvolved


title: eve_BAC_S2_STARRseq


title: NipB_S2_STARRseq_rep1


title: NipB_S2_STARRseq_rep2

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
NipB_S2_rep2.peaks.txt


title: M9081_uninvolved


title: M8815_uninvolved


title: X16_S2_STARRseq_rep2

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
X16_S2_rep2.peaks.txt


title: X16_S2_STARRseq_rep1


title: X16_BAC_S2_STARRseq


title: eEF1delta_S2_STARRseq_rep2


title: M9132_uninvolved


title: M8554_uninvolved


title: M8487_uninvolved


title: eEF1delta_S2_STARRseq_rep1

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
eEF1delta_S2_rep1.peaks.txt


title: NipB_STARRseq_input


title: hkCP_OSC_STARRseq_rep2

description:
PCR amplified cDNA (STARR-seq transcript)
library strategy: STARR-Seq

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 4 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. We additionally employed redundancy filter to remove clustered reads that could be due to sequence artefacts. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments), and merged these fragments from the two replicates. Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of STARR-seq and input. We performed hypergeometric tests to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Processed data files represent data from both replicates.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

molecule: polyA RNA

source_name: OSC cells_hkCP

value: OSC cells


title: M7912_uninvolved


title: hkCP_S2_STARRseq_input

description:
PCR amplified Plasmid library
library strategy: STARR-Seq


title: hkCP_OSC_STARRseq_rep1


title: M7838_uninvolved


title: M5130_uninvolved


title: M5219_uninvolved


title: hkCP_S2_STARRseq_rep1

source_name: S2 cells_hkCP


title: hkCP_S2_STARRseq_rep2


title: M5997_psoriatic


title: M8771_uninvolved


title: M7305_uninvolved


title: Dahl Salt Resistant rats (Dahl R)

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

data_processing:
Image analysis and base calling was performed using Solexa pipeline V1.8 (Off-Line Base Caller software, version 1.8)
Short reads (pass Solexa CHASTITY quality filter) were aligned to Rat reference genome (UCSC build RN4) and Rat transcriptome (Ensembl 63) using Tophat software (version 1.3.1).
The gene expression level (FPKM value) and significant changes in gene expression was then calculated using Cufflinks software (version 1.0.3).
Genome_build: Rat reference genome (UCSC build RN4) and Rat transcriptome (Ensembl 63)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample with low and high confidence…

organism: Rattus norvegicus

source_name: Dahl Salt Resistant rats (Dahl R)

growth_protocol: All rats born on the same day were selected and weaned at 30 days of age.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The rRNA depleted total RNA was reverse transcribed, fragmented, and 3’ end repaired, after adding a “dA” base to the 3’ end, the Illumina adapter was ligated to the double strand cDNA. The adpter ligated library was then amplified using Illumina’s proprietary amplification primers. Final product was purified by PAGE gel. ~200-300 bp fragments were selected at the gel size fractionation step. The final size of the library was confirmed by Agilent 2100 Bioanalyzer using DNA 1000 Kit.

treatment_protocol: After weaning all rats were fed with Low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).

tag: age

value: 54 days old

tag: diet

value: Low-salt (0.3%) diet

value: Kidney


title: Dahl Salt Sensitive rats (Dahl S)

source_name: Dahl Salt Sensitive rats (Dahl S)

value: 53 days old


title: Spontaneously hypertensive rat (SHR)

source_name: Spontaneously hypertensive rat (SHR)

value: 55 days old


title: M7264_uninvolved


title: M7807_uninvolved


title: M5064_normal


title: M6346_uninvolved


title: M8483_uninvolved


title: M8481_uninvolved


title: M4992_normal


title: M856_uninvolved


title: M4247_psoriatic


title: M4271_uninvolved


title: M6844_uninvolved


title: M3822_psoriatic


title: M3023_psoriatic


title: M4124_normal


title: M953_psoriatic


title: M9048_normal


title: M9037_normal


title: M8704_uninvolved


title: M4390_uninvolved


title: dCP_OSC_STARRseq_input

description:
plasmid DNA (containing genomic DNA fragments)
library strategy: STARR-Seq


title: Spleen_Input DNA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Basecalls performed using CASAVA version 1.4
alignment using bowtie 0.12 using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

organism: Mus musculus

source_name: Spleen red pulp macrophages

extract_protocol:
Chromatin was eluted from the beads, then treated with RNase (Roche) for 30 min at 37°c and with Proteinase K (NEB) for 2 hrs at 37°c. Reverse cross-linking was performed at 65°c overnight. DNA was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter) at 2.3x ratio. Sequential steps of end-repair, A-base addition, adapter-ligation and amplification were performed, with DNA purification with SPRI beads after each step. Following the amplification step, DNA concentration was measured, and equivalent amounts of barcoded ChIPed DNA from each sample were pooled together. An additional size-selection step was performed
Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
Nat Protoc. 2013 Mar;8(3):539-54. doi: 10.1038/nprot.2013.023. PMID: 23429716

value: Spleen

tag: cell type

value: Spleen red pulp macrophages

tag: chip antibody


title: M8485_uninvolved


title: dCP_OSC_STARRseq_rep2

source_name: OSC cells_dCP


title: Neutrophils_Input DNA

source_name: Neutrophils

value: Bone marrow

value: Neutrophils


title: dCP_S2_STARRseq_input


title: M9036_normal


title: monocyte_Input DNA

source_name: Monocytes

value: Monocytes


title: M7832_uninvolved


title: peritoneal_mac_Input DNA

source_name: Peritoneal cavity macrophages

value: Peritoneal cavity

value: Peritoneal cavity macrophages


title: Lung_input DNA

source_name: Lung macrophages

value: Lung

value: Lung macrophages


title: SI_Input DNA

source_name: Small intestine macrophages

value: Small intestine

value: Small intestine macrophages


title: E12_SHHCRE-28G

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing:
Quantified with Cufflinks v2.1.1, using the -u, -b, and -G options.
Genome_build: Ensembl 65
Supplementary_files_format_and_content: Tab-delimited text file including FPKM values. Gene-level results were reported.

source_name: E12.5 Shh bladder epithelium

extract_protocol:
Total RNA was isolated from cells using the RNeasy Micro Kit (Qiagen).  Briefly,  FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer).   The cells were quickly frozen on dry-ice and allowed to thaw on ice.  After the cells were thawed, 50ul of SDS-lysis buffer (50mMTric-HCL pH 7.4/0.05%SDS) was added, the cells were vortexed and an equal volume of 70% ETOH was added.  The cells were voxtexed,  placed on a Qiagen column and centrifuged for 1min at 10,000rpm.  The column was washed by adding 350ul of RW1 and centrifuged for 1min at 10,000rpm.  The extracted RNA was then subject to a 15min on-column DNAse digest following the manufacture's protocol.  After DNase digestion, the column was rinsed with a series of washes including: 350ul of RW1, 500ul RPE and 500ul of 80% ETOH.  After the washes, the column was centrifuged at 10,000 rpm for 5min to ensure the removal of residual ETOH.  The RNA was eluted by adding 16ul of RNAse-free H20 and incubated at room temperature for 2min.  The Qiagen column was placed into a 1.5ml eppendorf tube and centrifuged at 10,000 rpm for 1min to collect the RNA.
2ng total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN #7102).  The libraries were prepared with the Nextera DNA Sample Preparation kit (Illumina Technologies).  50 ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme), incubating at 55C for 5 min.  Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research).   The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle 98C for 30 s (one cycle), 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min.  The purified DNA was captured on an Illumina flow cell for cluster generation.  Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Whole E12 embryos were placed in PBS.  GFP fluorescence was determined directly using a dissecting microscope.  For each GFP positive embryo, the urogenital sinus including hindgut, was completely removed.  The hindgut and lower urethral section of the urogenital sinus were pinched off, resulting with the upper sinus containing mostly primitive bladder.  The piece of urogenital sinus collected was torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37C for no more than 25min.  After incubation, all samples were kept on ice.  One volume of ice-cold DMEM/F12  plus 10% FBS was added to the sample and spun down at 4C for  5min at 3000 rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then sorted to separate GFP+ cells from tdTomato+ cells.

tag: component sampled

value: epithelial layer of primitive bladder

tag: theiler stage

tag: Sex

value: unknown

tag: pooled sample

value: yes

tag: pool size

value: 5 embryos


title: dCP_S2_STARRseq_rep2

source_name: S2 cells_dCP

value: S2 cells


title: dCP_S2_STARRseq_rep1


title: Microglia_Input DNA

source_name: Brain microglia

tag: tissue

value: Brain

value: Brain microglia


title: E12_SHHCRE-22G

value: 6 embryos


title: LI_Input DNA

source_name: Large intestine macrophages

value: Large intestine

value: Large intestine macrophages


title: E18_KRT5_4G

source_name: E18 Krt5 urothelium of bladder

treatment_protocol: Whole E17/E18 embryos were placed in PBS. GFP fluorescence was determined directly using a dissecting microscope. For each GFP positive embryo, the bladder was removed at the bladder neck.  The bladder was cut in half and incubated in 20mM EDTA/PBS for 20min at 37C.  It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500uL of 0.25% trypsin, with vigorous vortexing and trituration at 37C for no more than 25min.  After incubation, all samples were kept on ice.  One volume of ice-cold DMEM/F12  plus 10% FBS was added to the sample and spun down at 4C for 5min at 3000rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then sorted to separate GFP+ cells from tdTomato+ cells.

value: basal cell layer of bladder urothelium

value: 3 embryos


title: P5_UP2Cre_7G

source_name: P5 Upk2 urothelium of bladder

treatment_protocol: Neonatal mice were euthanized and placed in PBS. The bladder was removed at the bladder neck for all embryos or pups and cut in half.  GFP fluorescence was determined directly using a dissecting microscope.  For each GFP positive bladder, it was incubated in 20mM EDTA/PBS for 20min at 37C. It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500uL of 0.25% trypsin, with vigorous vortexing and trituration at 37C for no more than 25min.  After incubuation, all samples were kept on ice.  One volume of ice-cold DMEM/F12  plus 10% FBS was added to the sample and spun down at 4C for 5min at 3000 rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then sorted to separate GFP+ cells from tdTomato+ cells.

value: urothelium of bladder

value: 7 embryos


title: E17_5UP2Cre

source_name: E17 Upk2 urothelium of bladder

treatment_protocol: Whole E17 embryos were placed in PBS.  The bladder was removed at the bladder neck for all embryos or pups and cut in half.  GFP fluorescence was determined directly using a dissecting microscope.  For each GFP positive bladder, it was incubated in 20mM EDTA/PBS for 20min at 37C.  It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500ul of 0.25% trypsin, with vigorous vortexing and trituration at 37C for no more than 25min.  After incubuation all samples were kept on ice.  One volume of ice-cold DMEM/F12  plus 10% FBS was added to the sample and spun down at 4C for 5 min at 3000 rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then sorted to separate GFP+ cells from tdTomato+ cells.

value: 4 embryos


title: E17SHH_17G

source_name: E17 Shh urothelium of bladder

treatment_protocol: Whole E17/E18 embryos were placed in PBS.  GFP fluorescence was determined directly using a dissecting microscope.  For each GFP positive embryo the bladder was removed at the bladder neck.  The bladder was cut in half and incubated in 20mM EDTA/PBS for 20min at 37C.  It was transferred to fresh DMEM/F12 medium in a petri dish and the urothelium was peeled off the basal lamina, torn and placed in 500uL of 0.25% trypsin, with vigorous vortexing and trituration at 37C for no more than 25min.  After isolation, the samples were kept on ice.  One volume of ice-cold DMEM/F12  plus 10% FBS was added to the sample and spun down at 4C for 5min at 3000 rpm.  The media was removed and the pellet resuspended in fresh ice-cold DMEM/F12 medium.  It was passed through a 35um nylon mesh filter and then sorted to separate GFP+ cells from tdTomato+ cells

value: no


title: E17SHH_14G


title: E17SHH_16G


title: 13157_CM6G


title: dCP_OSC_STARRseq_rep1

value: OSC cells


title: PodS - 5002

city: Clemson

first: Scott

middle: L

last: Pratt

state: SC

address: 138 Poole Ag Center

institute: Clemson University

description: microRNA

data_processing:
The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). The extracted sequencing reads were stored in the raw data file.
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis.
Briefly, unmappable reads (e.g., impure sequences) were removed and remaining sequences between 15 and 32 nt were grouped by unique sequences. Sequences were mapped against reported miRNA (miRbase version 17.0: http://www.mirbase.org/index.shtml), species’ genomes, and other RNA databases (e.g., RFam, repase, mRNA) and were classified into categories (as noted defined in the processed data file).
Genome_build: UCSC Genome Browser assembly ID: bosTau7
Supplementary_files_format_and_content: counts

organism: Bos taurus

source_name: Ejaculated spermatozoa

extract_protocol:
Total RNA enriched for microRNA was isolated from sperm using a modified protocol for Ambion's mirVana microRNA Isolation kit (reference will be provided upon publication).
Using Illumina Truseq Small RNA Preparation Kit, according to manufacturer's protocols.

tag: breed

value: Angus

value: spermatozoa


title: 13156_CM4G

value: epithelial layer of primitive bladder

value: unknown


title: RNA-Seq CAST copy enhancer_KO

status: Public on Dec 09 2014

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

data_processing:
RNA-seq data were mapped using Novoalign.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped reads for RNA-seq and ChIP-seq are provided as bed files. ChIP-seq and RNA-seq data were only used to generate browser tracks and we did not perform any further analysis.

source_name: mouse embryonic stem cell

growth_protocol: The F123 cells were cultured as described previously (Selvaraj et al. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nature Biotechnology 2013)

extract_protocol: Libraries were prepared according to Illumina's instruction or cited literatures.

value: The distal Sox2 enhancer on the CAST allele was deleted.

value: mouse embryonic stem cell


title: RNA-Seq both copy enhancer_KO

value: The distal Sox2 enhancers on both 129 and CAST allele were deleted.


title: DKO1

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

data_processing:
reads were aligned to mm10 plus extended splice junctions using novoalign (2.08.01). Up to 50 alignments were reported and adapter sequences were trimmed by novoalign.
splice junction alignments were converted back to genomic space using the USeq (8.8.7) SamTranscriptomeParser application (default settings).
the final alignment files were used in the USeq (8.8.7) DefinedRegionDifferentialSeq application to generate counts per gene, variance stabilized counts, FPKM values and to determine differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files contain raw read counts, normalized counts and FPKM values for each sample

source_name: CD4+ T cells,  miR-155 and miR-146a double knock out

extract_protocol:
Total RNA extracted with Qiagen miRNeasy kit
Illumina TruSeq Stranded w/ Ribozero

tag: genotype/variation

tag: cell population

value: CD4+ T cells


title: ChIP-Seq H3K4me3 F123

data_processing:
For ChIP-Seq, first 36 bases of each read were used for mapping with bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped reads for RNA-seq and ChIP-seq are provided as bed files. ChIP-seq and RNA-seq data were only used to generate browser tracks and we did not perform any further analysis.

tag: strain

tag: antibody

value: H3K4me3 (Abcam ab8580)


title: RNA-Seq 129 copy enhancer_KO

value: The distal Sox2 enhancer on the 129 allele was deleted.


title: ChIP-Seq H3K27ac F123

value: H3K27ac (Abcam ab4729)


title: 146KO3

source_name: CD4+ T cells,  miR-146a knock out


title: DKO2


title: RNA-Seq wildtype F123


title: ChIP-Seq H3K27ac J1


title: Kupffer_Input DNA

source_name: Kupffer cells

value: Liver

value: Kupffer cells


title: 146KO2


title: 146KO1


title: 155KO1

source_name: CD4+ T cells,  miR-155 knock out


title: WT2

source_name: CD4+ T cells, WT

value: wild type


title: WT3


title: KO2-non-Tfh

source_name: CD4+CXCR5-PD1- non Tfh cells, miR-155 knock out

value: CD4+CXCR5-PD1- non Tfh cells


title: KO2-Tfh

source_name: CD4+CXCR5+PD1+ Tfh cells, miR-155 knock out

value: CD4+CXCR5+PD1+ Tfh cells


title: WT1


title: KO1-non-Tfh


title: WT1-non-Tfh

source_name: CD4+CXCR5-PD1- non Tfh cells, WT


title: KO1-Tfh


title: WT2-non-Tfh


title: WT1-Tfh

source_name: CD4+CXCR5+PD1+ Tfh cells, WT


title: DKO3


title: WT2-Tfh


title: Tc-zen1 Naïve3

city: Leiden

first: Chris

last: Jacobs

state: Zuid-Holland

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: paired-end experiment (R1,R2)

data_processing:
Adapter sequences were trimmed, sequences of quality 20 or lower were trimmed, bases below a quality of 3 from the 3'end were trimmed and we discarded reads shorter than 20bp all using CLC Genomics Workbench 6.
Sequences were mapped using CLC Genomics Workbench 6, 2 mismatches to the reference genome were allowed, seedlength was set to 28, mismatch quality to 100.
Minimum paired distance set to 180
Maximum paired distance set to 300
Genome_build: Tcas_3.0
Supplementary_files_format_and_content: The mapping results as output from CLC Genomics Workbench 6, expression data and all other available information is included in supplied data tables.

organism: Tribolium castaneum

source_name: eggs, Naïve

growth_protocol: Eggs were kept at 30°C before and after treatment. Control eggs were generated by parental RNAi using a non-Tribolium dsRNA sequence, serosa-less eggs were generated by parental RNAi with dsRNA of the Tczen1 gene.

extract_protocol:
Eggs were pooled in groups of approximately 300, these were rinsed in bleech to remove the chorion after which they were washed with water. Total RNA of eggs was extracted using trizol extraction (Invitrogen) after which the RNA was purified and DNA digested on column with the RNeasy kit (Qiagen).
Library was constructed by the ZFscreens sequencing company, Leiden, the Netherlands.

treatment_protocol: Eggs were untreated (Naive), pricked with a sterile needle (Sterile) or pricked with a needle dipped in a concentrated mixture of E.coli and M.luteus (Septic).

value: eggs

tag: replicate


title: Tc-zen1 Septic1

description: paired-end experiment (R1,R2)

source_name: eggs, Septic


title: Control Sterile3

description: paired-end experiment (R1,R2)

source_name: eggs, Sterile

value: Control


title: Tc-zen1 Septic2

description: paired-end experiment (R1,R2)


title: Tc-zen1 Sterile1

description: paired-end experiment (R1,R2)


title: Control Septic3

description: paired-end experiment (R1,R2)


title: Control Septic1

description: paired-end experiment (R1,R2)


title: Tc-zen1 Sterile3

description: paired-end experiment (R1,R2)


title: Tc-zen1 Naïve2

description: paired-end experiment (R1,R2)


title: Tc-zen1 Naïve1

description: paired-end experiment (R1,R2)


title: Control Septic2

description: paired-end experiment (R1,R2)


title: Tc-zen1 Sterile2

description: paired-end experiment (R1,R2)


title: 155KO3


title: Control Sterile2

description: paired-end experiment (R1,R2)


title: Wildtype Septic3

description: paired-end experiment (R1,R2)

value: Wildtype


title: Control Naïve1

description: paired-end experiment (R1,R2)


title: Wildtype Septic2

description: paired-end experiment (R1,R2)


title: Control Sterile1

description: paired-end experiment (R1,R2)


title: T2

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

country: China

institute: Tongji University

data_processing:
Basecalls performed by strandard Illumina basecalling software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using tophat v2.0.4 with parameters --bowtie1 --solexa1.3-quals -p 12 --no-coverage-search --library-type fr-unstranded --segment-length 24 –no-novel-juncs
Fragments Per Kilobase of transcript per Million mapped reads(FPKM) were caculated by using Cufflinks v2.0.0 with parameters -p 12 -N
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample; Each file contain columns of tracking_id,gene_id,FPKM,FPKM_status,etc.

source_name: 2nd generation iPS cells

extract_protocol:
Embryos were removed, flash frozen on dry ice, and 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: cell line


title: 32 rep1


title: Wildtype Septic1

description: paired-end experiment (R1,R2)


title: Wildtype Sterile3

description: paired-end experiment (R1,R2)


title: Wildtype Sterile2

description: paired-end experiment (R1,R2)


title: S8


title: 32 rep2


title: Control Naïve3

description: paired-end experiment (R1,R2)


title: Wildtype Naïve2

description: paired-end experiment (R1,R2)


title: Wildtype Sterile1

description: paired-end experiment (R1,R2)


title: Control Naïve2

description: paired-end experiment (R1,R2)


title: Wildtype Naïve3

description: paired-end experiment (R1,R2)


title: R1 rep1

source_name: ES cells


title: R1 rep2


title: 16-6 rep1


title: 155KO2


title: WT_S2_2.0_minus_TEX

status: Public on Dec 08 2014

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description: WT HCD

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping  (READemption 0.3.0)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: NC_002505.1, NC_002506.1 and  NC_001133.9, NC_001134.8, NC_001135.5, NC_001136.10, NC_001137.3, NC_001138.5, NC_001139.9, NC_001140.6, NC_001141.2, NC_001142.9, NC_001143.9, NC_001144.5, NC_001145.3, NC_001146.8, NC_001147.6, NC_001148.4, NC_001224.1
Supplementary_files_format_and_content: wiggle

organism: Vibrio cholerae

source_name: wild typ_-TEX_OD=2.0

growth_protocol: V. cholerae was grown aerobically in LB  at 37°C and samples were collected at OD600=0.1 and 2.0

extract_protocol:
Trizol Reagent followed by Dnase I treatment
The cDNA libraries were constructed as previously described (Dugar et al. 2013). For Illumina sequencing (HiSeq) of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a HiSeq 2000 machine (Illumina) in single-read mode and 100 cycles.

treatment_protocol: When indicated samples were treated with Terminator Exonucleae (TEX; epicentre)

tag: strain background

tag: tex

value: minus TEX

tag: od600 at collection


title: WT_S2_0.1_plus_TEX

description: WT LCD

source_name: wild typ_+TEX_OD=0.1

value: plus TEX


title: WT_S1_2.0_minus_TEX

description: WT HCD


title: WT_S2_0.1_minus_TEX

description: WT LCD

source_name: wild typ_-TEX_OD=0.1


title: WT_S2_2.0_plus_TEX

description: WT HCD

source_name: wild typ_+TEX_OD=2.0


title: WT_S1_2.0_plus_TEX

description: WT HCD


title: WT_S1_0.1_plus_TEX

description: WT LCD


title: WT_S1_0.1_minus_TEX

description: WT LCD


title: Wildtype Naïve1

description: paired-end experiment (R1,R2)


title: D47E_S2_2.0_plus_TEX

description: D47E HCD

value: locked low cell density QS-mutant


title: 16-6 rep2


title: D47E_S2_2.0_minus_TEX

description: D47E HCD


title: D47E_S2_0.1_minus_TEX

description: D47E LCD


title: D47E_S1_2.0_plus_TEX

description: D47E HCD


title: D47E_S2_0.1_plus_TEX

description: D47E LCD


title: D47E_S1_0.1_minus_TEX

description: D47E LCD


title: WT_LSK_4 RRBS 2

city: Houston

first: Margaret

last: Goodell

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description:
technical replicate 2 biological replicate of WT LSK cells derived from primary transplant control 3
MG40858_GATCAG.SE.newmeth.txt

data_processing:
Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.74 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 --ct-snp=no-action. For paired-end experiment, the first 29 bases of read1 files were extracted with fastx tool kit to match read length single-end experiments.
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, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, 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 progenitors

growth_protocol: Dnmt3aKO HSCs were transplanted into lethally irradiated recipients. When the mice became moribund, they were diagnosed with hematopoietic malignancies, and whole bone marrow samples were harvested from mice diagnosed with AML and MDS and thymus samples were harvested from mice diagnosed with T-ALL. WT HSCs were transplanted into lethally irradiated recipients, then stem and progenitor cells (lin-Sca1+cKit+) were sorted from bone marrow and CD4/CD8 double positive T cells from thymus of healthy mice as controls

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. Alternatively, the KO3a_TALL_2b library was bisulfite converted with Zymo EZ DNA Methylation-Gold kit.

tag: cell type

value: Bone marrow progenitors

tag: cell surface marker

tag: genotype

value: Mx1-Cre+; Dnmt3a+/+


title: KO3a_MDS_4 RRBS 4

description:
technical replicate 4 biological replicate 4 of MDS disease
MG40758_TGACCA.SE.newmeth.txt

source_name: Bone marrow cells

value: Bone marrow cells


title: AreaX_Singing_WCE

city: Cambridge

first: Andreas

middle: R

last: Pfenning

state: MA

address: Computer Science and Artificial Intelligence Laboratory

department: CSAIL

institute: Massachusetts Institute of Technology

data_processing:
The reads from the sequencing experiment were transformed into BFQ format and then aligned to the zebra finch genome taeGut3.2.4.74 (Taeniopygia_guttata.taeGut3.2.4, ENSEMBL version 74, http://www.ensembl.org/) using MAQ v0.7.1 with default parameters (http://maq.sourceforge.net/).
The files were then transformed into SAM format, reads that did not uniquely map to the genome were removed, and read number statistics was calculated using SAMTools v1.1
MACS2 was also used to build log-likelihood files of signal compared to noise for pooled Area X samples and pooled RA samples with parameter “-m logLR -p 0.0001”
To minimize the Area X bias at the peak calling level, peaks were called independently for pooled Area X and pooled RA samples. BEDTools (9) was used to take the union of these peaks, at 500 bp resolution. Peaks were called using MACS v2.1 (https://github.com/taoliu/MACS/) with parameters “-g 1e9 -p 1e-2 --nomodel --shiftsize 73 -B –SPMR --keep-dup all”. To only keep the highest quality peaks, where quantitative differences could be measured, we used a stringent p-value threshold of 1E-5.
Once peaks were called, we used the read counts within peaks to determine differential H3K27ac activity between Area X and RA. HT-Seq v0.6.1 (http://www-huber.embl.de/users/anders/HTSeq/) was used to count the number of reads that overlapped each peak (parameter “-m union”).
Genome_build: Taeniopygia_guttata-3.2.4
Supplementary_files_format_and_content: The bigwig files were generated using MACS2; RAX_readCounts file contains the genomic coordiantes based on peak calling and the read counts per sample

organism: Taeniopygia guttata

source_name: Laser Captured Brain Tissue

extract_protocol:
We dissected whole song nuclei using a different approach. A razor was used to cut off part of the brainstem to create a flat surface with the forebrain, and the back of the brain (cerebellum region) was mounted against a thin plexiglass wall with Vetbond 3M tissue adhesive, placed on the surface of a Stoelting tissue slicer (Cat# 51415). Then 400 μm coronal thick sections were cut, and the sections placed in cold (4o C, on ice) PBS with a proteinase inhibitor cocktail (Roche USA Cat #11697498001, Indianapolis, IN) in a petri dish. The Petri dish with the sections was then placed under a dissecting microscope (Olympus MVX10), and song nuclei quickly dissected (within 5-15 min) with fine scissors and forceps (Fine Science Tools USA, Foster City, CA). The dissected song nuclei were placed in separate eppendorf tubes, frozen on dry ice, and stored at -80oC until further use. Punched samples from Area X or RA were pooled from six birds, resulting in 3 biological replicate groups for each behavioral condition.
These pooled brain samples were dounced in 1% formaldehyde PBS buffer and kept at room temperature for 15 minutes, washed twice with cold PBS, then lysed in 200 μL lysis buffer (1% SDS, 10 mM EDTA, and 50 mM Tris pH 8.1). The crosslinked material was sonicated with a Bioruptor (Diagenode, Denville, NJ, USA) with 30 seconds on/off cycles to an average size range of 200-400 bp as visualized by agarose gel electrophoresis. Sonicated supernatants were diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCL, pH 8.1, 167 mM NaCl) before immunoprecipitation. 6 μL of antibody (anti histone H3K27ac, Abcam Cat #Ab4729, Cambridge, MA, USA) was first incubated with 100 μL of Dynabeads Protein G (Invitrogen Cat. #10004D, Grand Island, NY, USA) for 4 hours at 4° C, then the antibody conjugate was added to 2 mL of lysate for overnight IP. Standard TruSeq adapters were ligated for library preparation using the NEB Library Preparation Kit (NEB 6240S and NEB E7335s, Ipswich, MA, USA) and 50 bp single-end sequencing was performed at the Duke Sequencing and Analysis Core Resource on a Hi-Seq 2000 machine at 30 million reads per sample.

treatment_protocol: Adult male zebra finches were isolated in sound attenuated chambers, and their brains were excised after light onset and 1-2 hr. of either silence (n=18) or singing (n=18).

value: brain

tag: tissue region

value: Area X

tag: condition

value: 2hr singing

tag: chip antibody

value: Whole Cell Extract


title: WT_LSK_4 RRBS 1

description:
technical replicate 1 biological replicate of WT LSK cells derived from primary transplant control 3
MG40858_GATCAG.SE.newmeth.txt


title: RA_Singing_WCE

tag: tissue

value: RA


title: KO3a_MDS_3 RRBS 4

description:
technical replicate 4 biological replicate 3 of MDS disease
MG40757_TTAGGC.SE.newmeth.txt


title: KO3a_MDS_4 RRBS 2

description:
technical replicate 2 biological replicate 4 of MDS disease
MG40758_TGACCA.SE.newmeth.txt


title: KO3a_MDS_4 RRBS 1

description:
technical replicate 1 biological replicate 4 of MDS disease
MG40758_TGACCA.SE.newmeth.txt


title: RA_Silent_WCE

value: silent


title: KO3a_MDS_4 RRBS 3

description:
technical replicate 3 biological replicate 4 of MDS disease
MG40758_TGACCA.SE.newmeth.txt


title: KO3a_MDS_3 RRBS 2

description:
technical replicate 2 biological replicate 3 of MDS disease
MG40757_TTAGGC.SE.newmeth.txt


title: KO3a_MDS_3 RRBS 3

description:
technical replicate 3 biological replicate 3 of MDS disease
MG40757_TTAGGC.SE.newmeth.txt


title: D47E_S1_2.0_minus_TEX

description: D47E HCD


title: RA_Singing_H3K27ac

value: anti histone H3K27ac (Abcam, Catalog# Ab4729, Lot#s GR132150-3 and GR81163-1)


title: D47E_S1_0.1_plus_TEX

description: D47E LCD


title: AreaX_Singing_H3K27ac


title: AreaX_Silent_H3K27ac


title: WT_LSK_4 RRBS 3

description:
technical replicate 3 biological replicate of WT LSK cells derived from primary transplant control 3
MG40858_GATCAG.SE.newmeth.txt


title: RA_Silent_H3K27ac


title: KO3a_TALL_3 RRBS 4

description:
technical replicate 4 biological replicate 3 of T-ALL disease
MG40761_CAGATC.SE.newmeth.txt

source_name: Leukemic cells

value: Leukemic cells


title: QS-AN_sRNA

city: Wu Han

first: Yan-ni

last: Fang

address: shizi mountain street

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, abandon seqences small than 18 nt, and masked for low-complexity or low-quality sequence, then mapped to ref2 database using soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap

organism: Citrus reticulata

source_name: seedless mutant 'Qianyang seedless' anther

growth_protocol: grown under field conditions

extract_protocol:
Total RNA was isolated from all of the samples using modified trizol method according to Liu et al.,Journal of Huazhong Agricultural University,2006
Small RNA sequencing was carried out using Illumina sequencing technology by the Beijing Genomics institute (BGI). Firstly, RNAs of 18-30 nt long were isolated by size fraction with 15% Tris-borate-EDTA urea polyacrylamide gel. Subsequently, they were ligated to 5' and 3' RNA adaptors (Illumina) by T4 RNA ligase. After that, the adapter-ligated RNA molecules were reverse-transcribed into cDNA by Super Script III using a primer specific to the 3’ adapter, followed by PCR amplification with two primers that annealed to the ends of the adapters. These PCR products constituted the sequencing library.

value: anther

tag: developmental

value: blooming flowers


title: KO3a_MDS_3 RRBS 1

description:
technical replicate 1 biological replicate 3 of MDS disease
MG40757_TTAGGC.SE.newmeth.txt


title: EG-AN_sRNA

source_name: seedy 'Egan No.1' anther


title: QS-SF_sRNA

source_name: seedless mutant 'Qianyang seedless' flowers

value: green bud flowers

value: 2.5-3.5 mm flowers


title: WT_LSK_4 RRBS 4

description:
technical replicate 4 biological replicate of WT LSK cells derived from primary transplant control 3
MG40858_GATCAG.SE.newmeth.txt


title: EG-SF_sRNA

source_name: seedy 'Egan No.1' flowers


title: Ponkan_degradome

source_name: squaring and blooming flowers

value: mixed sample of green bud flowers and anther


title: AreaX_Silent_WCE


title: Male Pupae

city: Kunming

first: Pu

last: Yang

address: Bailongsi

institute: Insect

data_processing:
To obtain clean reads, reads with adaptors, those with more than 10% unknown bases, and low-quality reads were removed before data analysis.
Clean reads were mapped to reference sequences using SOAPaligner/soap262. Mismatches of no more than 2 bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Ericerus pela

source_name: Male Pupae

extract_protocol:
The whole body of individuls were used
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

value: insect whole body

tag: age

value: wild type


title: Male Prepupae

source_name: Male Prepupae


title: WT_Tcell_3 RRBS 4

description:
technical replicate 4 biological replicate of WT T cells derived from primary transplant control 3
MG40760_GCCAAT.SE.newmeth.txt

source_name: Thymic cells

value: Thymic cells

value: Mx1-Cre+; Dnmt3a+/+

tag: strain


title: KO3a_AML_4 RRBS 4

description:
technical replicate 4 biological replicate 4 of AML disease
MG40756_CGATGT.SE.newmeth.txt


title: WT_Tcell_3 RRBS 3

description:
technical replicate 3 biological replicate of WT T cells derived from primary transplant control 3
MG40760_GCCAAT.SE.newmeth.txt


title: WT_Tcell_3 RRBS 2

description:
technical replicate 2 biological replicate of WT T cells derived from primary transplant control 3
MG40760_GCCAAT.SE.newmeth.txt


title: WT_Tcell_3 RRBS 1

description:
technical replicate 1 biological replicate of WT T cells derived from primary transplant control 3
MG40760_GCCAAT.SE.newmeth.txt


title: KO3a_AML_4 RRBS 3

description:
technical replicate 3 biological replicate 4 of AML disease
MG40756_CGATGT.SE.newmeth.txt


title: KO3a_AML_3 RRBS 4

description:
technical replicate 4 biological replicate 3 of AML disease
MG40755_ATCACG.SE.newmeth.txt


title: KO3a_TALL_3 RRBS 3

description:
technical replicate 3 biological replicate 3 of T-ALL disease
MG40761_CAGATC.SE.newmeth.txt


title: KO3a_AML_3 RRBS 1

description:
technical replicate 1 biological replicate 3 of AML disease
MG40755_ATCACG.SE.newmeth.txt


title: KO3a_AML_3 RRBS 2

description:
technical replicate 2 biological replicate 3 of AML disease
MG40755_ATCACG.SE.newmeth.txt


title: KO3a_AML_4 RRBS 1

description:
technical replicate 1 biological replicate 4 of AML disease
MG40756_CGATGT.SE.newmeth.txt


title: KO3a_TALL_3 RRBS 2

description:
technical replicate 2 biological replicate 3 of T-ALL disease
MG40761_CAGATC.SE.newmeth.txt


title: WT_LSK_2 RRBS

description: biological replicate of WT LSK cells derived from primary transplant control 2

data_processing:
Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.74 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 --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, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

value: Bone marrow progenitors


title: WT_Tcell_1 RRBS

description: biological replicate of WT T cells derived from primary transplant control 1


title: WT_Tcell_2 RRBS

description: biological replicate of WT T cells derived from primary transplant control 2


title: WT_LSK_1 RRBS

description: biological replicate of WT LSK cells derived from primary transplant control 1


title: Ker_BS-seq

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

data_processing:
Illumina RTA 1.7.45 and Casava 1.8 were used for base calling
Novoalign Bisulfite module was used for mapping to the mouse assembly mm9
The base calls per reference position on each strand were used to identify methylated cytosines in the context of CpG, CHG and CHH.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include methylation percent for mouse keratinocytes

source_name: Mouse primary keratinocytes

growth_protocol: Primary mouse keratinocytes were cultured for 3 days in SMEM medium (Invitrogen) with 10% chealetd FBS.

extract_protocol:
Primary mouse keratinicytes were cultured for 3 days. DNA was extractes using Qiagen DNA purification kit from the primary cells. .
Methylome libraries were prepared for sequencing using standard Illumina protocols

value: Primary keratinocytes

tag: Sex

value: Female

value: FVB/N


title: KO3a_AML_4 RRBS 2

description:
technical replicate 2 biological replicate 4 of AML disease
MG40756_CGATGT.SE.newmeth.txt


title: KO3a_TALL_1 RRBS

description: biological replicate 1 of T-ALL disease


title: KO3a_AML_3 RRBS 3

description:
technical replicate 3 biological replicate 3 of AML disease
MG40755_ATCACG.SE.newmeth.txt


title: WT_Gr1_2 RRBS

description: biological replicate of WT Gr1 cells derived from primary transplant control 2

value: Bone marrow granulocytes


title: Hnf4a-/-;Cdx2-/- biological rep2

city: Boston

first: Adrianna

middle: Katrina

last: San Roman

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute and Harvard Medical School

description:
Hnf4a;Cdx2 KO_2
Hnf4aCdx2KO_773

data_processing:
Alignment: Tophat, version 2.0.9, default options.
Normalized and differential expression: Cufflinks, version 2.1.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals. There are two processed data matrices that apply to all of the samples. First is the normalized expression table, prepared using Cuffnorm, which contains the normalized FPKM expression values for all 4 RNA-seq samples. The second is the differential expression table, prepared using Cuffdiff with an FDR of 5%, which contains average normalized FPKM values for Control and Hnf4a;Cdx2_KO samples, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.

source_name: Hnf4a;Cdx2 double-knockout mouse jejunum epithelium

growth_protocol: Epithelium from mouse jejunum 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.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
The TruSeq RNA Sample Preparation Kit (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: All mice were injected with 1mg tamoxifen for 5 consecutive days to activate Cre recombinase and recombine conditional alleles.

tag: strain/background

value: 129xC57/Bl6xSvJ mixed background

tag: genotype/variation

value: Hnf4a;Cdx2 double-knockout

value: adult jejunal epithelium


title: Tc-zen1 Septic3

description: paired-end experiment (R1,R2)

source_name: eggs, Septic

value: eggs

tag: replicate


title: NN-FB-seq

first: Weiwei

last: Zhang

address: No.3888, Chenhua Road, Songjiang District

department: Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences

institute: Shanghai Chenshan Botanical Garden

data_processing:
Raw data from 454 sequencing were pre-processed to remove adaptor-ligated regions, primers and very short sequences by Seqclean (v86_64) and to trim low-quality regions by LUCY program (v2.19).
The cleaned and qualified reads were then assembled de novo in Newbler (v2.5.3) with optimal parameter.
The assembled unique sequences were separately combined and clustered with CD-HIT 4.0.
Supplementary_files_format_and_content: File includes expression RPKM values

organism: Nelumbo nucifera

source_name: A mixed pool from young flower-buds (35-40mm in length) of three lotus accessions including N. nucifera Honghu Honglian, N. nucifera Tangzhaotisi Lian and N. nucifera Qianban Lian

extract_protocol:
Young flower-buds of three N. nucifera accessions collected in the field were immediately frozen in liquid nitrogen and stored at -80℃. Total RNA was extracted using the Invitrogen TRIzol Reagent. Equal quantity of RNA from the flower-bud tissue of three accessions was blended in a mixed pool for maximizing the diversity of transcriptional units. cDNA synthesis from the total RNA was performed using the Clontech SMART system (Clontech Lab, inc. CA, USA).
For 454 sequencing, the cDNA library was prepared according to the manufacturer’s protocol in the Roche GS-FLX Titanium General Library Preparation Kit.

value: Young flower-buds

tag: Stage

value: 35-40mm in length

tag: accessions

value: Honghu Honglian, Tangzhaotisi Lian, Qianban Lian


title: Hnf4a-/-;Cdx2-/- biological rep1

description:
Hnf4a;Cdx2 KO_1
Hnf4aCdx2KO_759

tag: cell type


title: KO3a_TALL_2b RRBS

description: technical replicate 2 of biological replicate 2 of T-ALL disease (Zymo Gold Bisulfite conversion)

value: Leukemic cells


title: KO3a_MDS_1 RRBS

description: biological replicate 1 of MDS disease

value: Bone marrow cells


title: Control biological rep2

description:
Control_2
Control_783

source_name: Control mouse jejunum epithelium

value: Cre- control


title: Control biological rep1

description:
Control_1
Control_755


title: KO3a_MDS_2 RRBS

description: biological replicate 2 of MDS disease


title: KO3a_AML_1 RRBS

description: biological replicate 1 of AML disease


title: KO3a_AML_2 RRBS

description: biological replicate 2 of AML disease


title: KO3a_ETP_1 RRBS

description: biological replicate 1 of ETP disease


title: Epiderm

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

country: Spain

institute: Institute of Evolutionary Biology

description: Includes endosymbionts

data_processing:
Assembly with MIRA3.2 with the options ‘denovo, est, accurate, 454 454_SETTINGS -LR:mxti=1 -ED:acc=1 -DP:ure=1’
The contigs obtained were annotated with the Blast2GO suite
Supplementary_files_format_and_content: The Processed_data.txt shows the presence or absence of transcripts related to non-essential amino acid biosynthesis in the three tissue libraries.

organism: Blattella germanica

source_name: Epidermis, including cuticle layers

growth_protocol: Blattella germanica specimens used for the whole transcriptome analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

extract_protocol:
Total RNA was extracted with the GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
cDNA was synthesized using the Smart cDNA Construction Kit (Clontech)

tag: developmental stage

value: Nymph 6

value: Epidermis, including cuticle layers


title: Ovary

description: Includes endosymbionts

source_name: Ovary

value: Adult

value: female

value: Ovary


title: RNA DSE010 S1

status: Public on Dec 06 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description:
prototrophic reference
Sequencing was performed using Illumina HiSeq 2500 and carried out by Basecelar (Leiden, The Netherlands).  Dataset of 51 bp single reads of at least 1-Gb were generated. The genome sequence of CEN.PK113-7D (Nijkamp JF et al  (2012) De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact 11(36): doi:10.1186/1475-2859-11-36.) was used for all analyses.

data_processing:
At Baseclear FASTQ sequence reads were generated using Illumina Casava pipeline version 1.8.2
Quality assesment was based on data passing the Ilumina Chastity filtering. Subsequently, reads containing adapters and/or PhiX control signal were removed using an in-house (At Baseclear) filtering protocol.
RNA-seq reads were mapped with BWA (version 0.5.9-r16) to S. cerevisiae CEN.PK113-7D whole genome
samtools (version 0.1.7-r510) was used to convert the BWA sam output to sorted bam format
cuffdiff, from the cufflinks packages (version 1.0.3), was used to calculate the differential expression between the CEN.PK113-7D reference strain and the Minimal glycolysis strain IMX372
genome build: ASM26988v1

organism: Saccharomyces cerevisiae

source_name: Aerobic batch fermentor

growth_protocol: Growth experiments were conducted in synthetic medium containing salts, trace elements and vitamins, prepared and sterilized as described previously (Verduyn C, Postma E, Scheffers WA & Vandijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeasts - A continuous culture study on the regulation of respiration and alcoholic fermentation. Yeast 8(7):501-517). Glucose was added to a final concentration of 20.0 g L-1. Aerobic batch cultivations were performed in 2 L laboratory fermenters (Applikon, Schiedam, The Netherlands) with 1 L working volume. SM medium was used and set at pH 5 before autoclaving at 121° C for 20 min. Antifoam Emulsion C (Sigma) was added to a concentration of 0.2 g L-1 from a 20% (v/v) solution autoclaved separately (121° C, 20 min). Prior to inoculation, glucose was added to a final concentration of 20 g L-1 from a sterile (110° C, 90 min) 50% glucose solution and 1 mL of a vitamin solution (Verduyn et al., 1992). The pH was maintained at 5 by the automatic addition of 2 M KOH. Compressed air  for aerobic cultivations, was sparged to the bioreactor at the rate of 500 mL min-1  via an Ion Science Saga digital flow meter (Cambridge, UK). Temperature in the fermenters was kept at 30° C. Complete mixing of the medium was ensured by stirring at 800 rpm. Four independent batch cultivations were performed for each condition and each strain. Pre-cultures were started by inoculating SMG shake-flasks with 1 stock vial of the appropriate strain. After ca. 16 h incubation these cultures were used to inoculate new SMG shake-flasks. The starting OD was tightly controlled as to reach an OD = 1 after 8 hours of incubation. These exponentially growing cultures were washed twice with demineralized water (spinning 5000 rpm, 4 minutes) and resuspended in 100 mL demineralized water, cell suspension that was used to inoculate fermenters with starting OD of 0.1.

extract_protocol:
Biomass samples for RNA extractions were sampled from mid-exponential phase of grown in aerobic batch cultivations in bioreactors with chemically defined medium . Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously ( Hazelwood LA, Walsh MC, Pronk JT, Daran JM. 2010. Involvement of vacuolar sequestration and active transport in tolerance of Saccharomyces cerevisiae to hop iso- -acids. Appl. Environ. Microbiol. 76:318 –328. http://dx.doi.org/10.1128/AEM.01457-09.)
cDNA libraries for the Illumina platform were generated and sequenced at BaseClear BV (Leiden, The Netherlands). cDNA was used as input for library preparation using the Illumina TruSeq DNA library preparation kit (Illumina). Briefly, the DNA was fragmented by nebulization and subjected to end-repair, A-tailing, ligation of adaptors including sample-specific barcodes and size-selection to obtain a library with median insert-size around 200-400 bp. After PCR enrichment, the resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2500 with paired-end protocol

treatment_protocol: Optical density (OD) of diluted cell suspensions (measured OD ranging between 0.1 and 0.3) was measured at 660 nm using a spectrophotometer Libra S11 (Biocrom, Cambridge, UK). Biomass dry weight was determined by filtration as previously described (103). The concentration of extracellular metabolite in culture supernatants was by HPLC analysis using a Aminex HPX-87H ion exchange column operated at 60° C with 5 mM H2SO4 as mobile phase at flow rate of 0.6 mL min-1.

value: MATa MAL2-8c SUC2


title: RNA DSE011 S2


title: WT_Gr1_1 RRBS

description: biological replicate of WT Gr1 cells derived from primary transplant control 1

value: Bone marrow granulocytes

tag: cell surface marker

tag: genotype

value: Mx1-Cre+; Dnmt3a+/+


title: b17_lung_mac2_Exp2

status: Public on Dec 05 2014

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: tophat with deafult parameters
Normalized expression values are produced using ESAT software available at http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: mRNA molecule count values for each Sample

source_name: Lung macrophages

extract_protocol:
10^4-10^5 cells from each macrophage subpopulation were sorted in 100-200 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80°C. Cell lysates were thawed and mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines. Purified messenger RNA was eluted at 70°C with 10 ul of 10 mM Tris-Cl pH 7.5 and stored at -80°C
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

value: Lung

value: Lung macrophages


title: Standard minimal medium, DMSO

city: Berkeley

first: António Pedro

last: Gonçalves

address: 341A Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
Illumina Casava1.8.0 software used for basecalling.
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G --compatible-hits-norm --max-bundle-frags=100000000)
Differential Expression was estimated with Cuffdiff (options: -u -N -b --compatible-hits-norm --max-bundle-frags=100000000)
Genome_build: OR74A version 10 (call 5) from the Broad Institute (n_crassa_or74a__transcripts_plus_mito_jan_2012)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Neurospora crassa

source_name: 6h+1h DMSO

growth_protocol: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium (with the indicated concentrations of calcium) for 6 hours (26ºC, 140 rpm, constant light).

extract_protocol:
Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies).
The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturer’s protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analyzed in a Agilent 2100 Bioanalyzer.

treatment_protocol: Addition of staurosporine (or DMSO) and growth for 1 more hour.

value: Wild type

tag: growth stage

value: 6h+1h conidia culture

tag: growth protocol

value: Standard minimal medium

tag: agent

value: DMSO


title: 20 mM CaCl2 minimal medium, Staurosporine

source_name: 6h+1h 20 μM STS

value: 20 mM CaCl2 minimal medium

value: Staurosporine


title: 20 mM CaCl2 minimal medium, DMSO


title: Standard minimal medium, Staurosporine


title: 0 Ca2+ minimal medium, DMSO

value: 0 Ca2+ minimal medium


title: b02_lung_Exp2

city: Rehovot

tag: tissue


title: a11_SI_Mac4_Exp1_m

source_name: Small intestine macrophages

value: Ileum

value: Small intestine macrophages


title: a13_LI_Mac3_Exp1_m

source_name: Large intestine macrophages

value: Colon

value: Large intestine macrophages


title: Fat_body

description: Includes endosymbionts

source_name: Fat body

value: Adult

value: female

value: Fat body


title: KO3a_TALL_2a RRBS

description: technical replicate 1 of biological replicate 2 of T-ALL disease (Qiagen Epitect Bisulfite conversion)

value: Leukemic cells


title: a10_SI_Mac3_Exp1_m


title: b15_Kupffer2_Exp2

source_name: Kupffer cells

value: Liver

value: Kupffer cells


title: a12_LI_Mac2_Exp1_m


title: b04_Kupffer_Exp2


title: Ex vivo1

first: BERNARDO

last: BELLO ORTI

state: Barcelona

address: Bellaterra

department: Bacteriology

institute: CReSA

data_processing:
For both in vivo and ex vivo experiments, bioinformatic analysis was performed following the count-based differential expression method (Anders et al., 2013), with some modifications.
Genome_build: Haemophilus parasuis str. Nagasaki
Supplementary_files_format_and_content: Tab-delimited text files include counts for each gene.

organism: Glaesserella parasuis str. Nagasaki

source_name: ex vivo incubation

growth_protocol: 24h chocolate agar plate culture at 37ºC

extract_protocol:
Bacteria were recovered by centrifugation and pellets were used for RNA extraction. An additional low speed centrifugation step was added to ex vivo and in vivo samples in order to eliminate mammalian cells. All bacterial samples were processed for RNA extraction as follows. Pellets were resuspended in 2% SDS 16 mM EDTA 10 mM TRIS (pH XX) and incubated for 5 min at 100 ºC. Afterwards, samples were processed by two hot acid phenol-chloroform extractions, followed by two chloroform/ isoamyl alcohol extractions. RNA was then precipitated with 0.6 volumes of isopropanol 0.1 volumes of 5M ammonium acetate and 1μL of glycogen. After centrifugation the pellet was washed with 70% ethanol, dried and resuspended in warmed RNase-free water. To ensure that contaminating bacterial DNA was eliminated from the samples, treatment with RNase-free DNase (Qiagen) was performed. In addition, ribosomal RNA was eliminated with the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies, Madison, WI, USA) following manufacturer’s instructions. PCR reactions using primers specific for H. parasuis 16S rRNA gene were carried out to ensure that no bacterial DNA was left in the sample.
Sequencing library was generated using an Ion Torrent RNA-Seq v2 kit (Life Technologies) and RNA was sequenced using an Ion Torrent PGM instrument (Life Technologies) with an Ion 316 chip (Life technologies) at the Centre for Research in Agricultural Genomics (CRAG, Campus de Bellaterra-UAB, Spain). As control, RNA from the Nagasaki strain grown overnight on chocolate agar plates was purified and sequenced in the same manner.

value: Nagasaki

tag: culture time

value: wild type


title: In vivo

source_name: in vivo incubation

extract_protocol:
Bacteria were recovered by centrifugation and pellets were used for RNA extraction. An additional low speed centrifugation step was added to ex vivo and in vivo samples in order to eliminate mammalian cells. All bacterial samples were processed for RNA extraction as follows. Pellets were resuspended in 2% SDS 16 mM EDTA 10 mM TRIS (pH XX) and incubated for 5 min at 100 ºC. Afterwards, samples were processed by two hot acid phenol-chloroform extractions, followed by two chloroform/ isoamyl alcohol extractions. RNA was then precipitated with 0.6 volumes of isopropanol 0.1 volumes of 5M ammonium acetate and 1μL of glycogen. After centrifugation the pellet was washed with 70% ethanol, dried and resuspended in warmed RNase-free water. To ensure that contaminating bacterial DNA was eliminated from the samples, treatment with RNase-free DNase (Qiagen) was performed. In addition, ribosomal RNA was eliminated with the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies, Madison, WI, USA) following manufacturer’s instructions. PCR reactions using primers specific for H. parasuis 16S rRNA gene were carried out to ensure that no bacterial DNA was left in the sample.
Libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. Sequencing in one paired-end Illumina MiSeq run was performed at Institut de Biotecnologia i Biomedicina (IBB, Campus de Bellaterra-UAB, Spain). As control, RNA from the Nagasaki strain grown overnight on chocolate agar plates was purified and sequenced in the same manner.


title: Plate3

source_name: agar plate culture


title: b08_Spleen_Mac1_Exp2

source_name: Spleen red pulp macrophages

value: Spleen

value: Spleen red pulp macrophages


title: b09_Spleen_Mac2_Exp2


title: a07_peritoneum_Mac2_Exp1_m

source_name: Peritoneal cavity macrophages

value: Peritoneal cavity

value: Peritoneal cavity macrophages


title: 0 Ca2+ minimal medium, Staurosporine

value: Wild type

value: 6h+1h conidia culture

value: 0 Ca2+ minimal medium

value: Staurosporine


title: KO3a_TALL_3 RRBS 1

description:
technical replicate 1 biological replicate 3 of T-ALL disease
MG40761_CAGATC.SE.newmeth.txt

source_name: Leukemic cells


title: Plate1


title: a02_brain_microglia2_Exp1_m

source_name: Brain microglia

value: Brain

value: Brain microglia


title: Y. pseudotuberculosis RNA-seq at 37C

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

description:
Y. pseudotuberculosis RNA-seq at 37C
Sample 7

data_processing:
Base trimming (5nt from 5' and 5nt from 3') with CLC Genomic Workbench 4.5.1
Trimmed reads from polyA and rRNA-depleted samples) were aligned to Yersinia pseudotuberculosis YPIII chromosome with 95% match, trimmed reads from polyA depeleted and non-rRNA depleted samples were aligned to NCBI 16SMicrobial Database with 100% match  with CLC Genomic Workbench 4.5.1
Dublicate reads were removed with CLC Genomic Workbench 4.5.1
SNP calling was done with CLC Genomic Workbench
RPKMO values were calculated with statistical analysis on Gaussian data with Bonferroni correction as paired data with CLC Genomic Workbench
Genome_build: NC_010465 and NC_006153
Supplementary_files_format_and_content: Processed data files are in txt format. Processed data files contain expression values of ORFs of Yersinia pseudotuberculosis YPIII (NC_010465) and its virulence plasmid pYV (NC_006153) during early and late (sample 1 and 2) and for at 26C growth and 37 growth (Sample 6 and 7), processed data files contain number of reads mapped to 16SMicrobial NCBI database (Sample 3, 4 and 5)

organism: Yersinia pseudotuberculosis YPIII

source_name: in vitro 37C growth

growth_protocol: Overnight grown Yersinia pseudotuberculosis YPIII were inoculated to new medium grown two hours at 26C and there after temperature shifted to 37C in a calcium depleted medium for 4 hours

extract_protocol:
Tissues are taken from the animal and kept in RNALater (Ambion) at +4C for overnight. Tissues are homogenized with two step homogenization for tissue and cell homogenization with a bead beater. RNA extracted based on Trizol method.
RNA libraries for sequencing were prepared using TruSeq RNA kits (Illumina, CA, USA) according to the manufacturer's instructions with the following changes. The RNA samples were EtOH precipitated and subsequent protocols (starting from cDNA synthesis in the Illumina provided protocol) automated using an MBS 1200 pipetting station (Nordiag AB, Sweden). All purification steps and gel-cuts were replaced by the magnetic bead clean-up methods described previously (Borgstrom et al., 2011)

treatment_protocol: Mouse were uninfected/infected for 2 days/ infected 42 days with Yersinia pseudotuberculosis YPIII with oral infection low dose (107CFUs)

tag: rrna depleted

value: rRNA-depleted RNA


title: Y. pseudotuberculosis RNA-seq at 26C

description:
Y. pseudotuberculosis RNA-seq at 26C
Sample 6

source_name: in vitro 26C growth

growth_protocol: Yersinia pseudotuberculosis YPIII were grown at 26C for overnight in LB medium


title: Un-infected cecal tissue

description:
Un-infected FVB/N mouse cecal tissue
Sample 5

source_name: Uninfected

growth_protocol: Un-infected mouse cecal tissue

tag: infection phase

value: Un-infected data

tag: polya depletion

value: poly(A) depleted RNA

value: non-rRNA-depleted RNA

tag: host

value: mouse


title: b10_Monocyte1_Exp2

source_name: Monocytes

tag: strain

value: Bone marrow

value: Monocytes


title: b11_Monocyte2_Exp2


title: a01_brain_microglia1_Exp1_m


title: b05_Neutrophil1_Exp2

source_name: Neutrophils

value: Neutrophils


title: b07_Neutrophil3_Exp2


title: MC_h9_Chimera_kupffer2_K27Ac

data_processing:
Basecalls performed using CASAVA version 1.4
alignment using bowtie 0.12 using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Kupffer cells with CD45.1 mark

extract_protocol:
Chromatin was eluted from the beads, then treated with RNase (Roche) for 30 min at 37°c and with Proteinase K (NEB) for 2 hrs at 37°c. Reverse cross-linking was performed at 65°c overnight. DNA was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter) at 2.3x ratio. Sequential steps of end-repair, A-base addition, adapter-ligation and amplification were performed, with DNA purification with SPRI beads after each step. Following the amplification step, DNA concentration was measured, and equivalent amounts of barcoded ChIPed DNA from each sample were pooled together. An additional size-selection step was performed
Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
Nat Protoc. 2013 Mar;8(3):539-54. doi: 10.1038/nprot.2013.023. PMID: 23429716

value: Lung

value: Kupffer cells with CD45.1 mark

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Y. pseudotuberculosis RNA-seq_persistent infection, non-rRNA-depleted

description:
FVB/N cecal tissue at 42 days postinfection
Sample 4

growth_protocol: Taken from mouse cecal tissue infected with Yersinia pseudotuberculosis YPIII at 42 days post infection

value: Persistent infection data


title: MC_h8_Chimera_kupffer2_K4Me2

tag: cell type


title: MC_h6_Chimera_Spleen2_K27Ac

source_name: Spleen red pulp macrophages with CD45.1 mark


title: Y. pseudotuberculosis RNA-seq_early infection, non-rRNA-depleted

description:
FVB/N cecal tissue at 2 days postinfection
Sample 3

source_name: Early infection (non-rRNA-depleted)

growth_protocol: Taken from mouse cecal tissue infected with Yersinia pseudotuberculosis YPIII at 2 days post infection

value: Early infection data


title: MC_h5_Chimera_Spleen2_K4Me2

value: Spleen red pulp macrophages with CD45.1 mark


title: MC_h7_Chimera_kupffer2_K4Me1

tag: chip antibody vendor/cat.#

value: Abcam ab8895 and Millipore 07-436 mixed ratio 1:1


title: MC_h2_Chimera_Perit2_K4Me2

source_name: Peritoneal cavity macrophages with CD45.1 mark


title: MC_h4_Chimera_Spleen2_K4Me1


title: Y. pseudotuberculosis RNA-seq _persistent infection

description:
FVB/N cecal tissue at 42 days postinfection
Sample 2

source_name: Persistent infection


title: MC_h3_Chimera_Perit2_K27Ac

value: Peritoneal cavity macrophages with CD45.1 mark


title: a06_peritoneum_Mac1_Exp1_m

value: Peritoneal cavity

value: Peritoneal cavity macrophages


title: MC_h1_Chimera_Perit2_K4Me1


title: MC_h12_Chimera_Lung2_K27Ac

source_name: Lung macrophages with CD45.1 mark

value: Lung macrophages with CD45.1 mark


title: MC_h10_Chimera_Lung2_K4Me1


title: Extracted RNA from Control Stomach organoids Control_Sto_1

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwaPaired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: data_counts_ORG.txt: Processed data for Organoid1. Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the sample type, SI for intestine and Sto for stomach, Cdx2null for Cdx2 knock out and Cdx2+ for Cdx2 overexpression. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

growth_protocol: Cdx2null, Control SI and Control Sto clonal organoids were generated and expanded in Matrigel from FACS sorted Lgr5-EGFPhi single cells in stomach specific culture medium (ENRWfg). Cdx2+ Stomach (Sto) organoids were generated by infection of the wild type stomach organoids with lentiviral stock expressing Cdx2 and were cultured in stomach medium (ENRWfg). Medium was refreshed every 2 days. Organoids were passaged about once per week by mechanical disruption in split ratios of 1:4.

extract_protocol:
Organoids were freed from Matrigel and resuspended in RTL buffer (Qiagen). RNA was extracted from Cdx2null SI, Control SI, Control Sto and Cdx2+ Sto organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).
10ng of total RNA per sample was processed using the previously described CEL-seq technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: Control

value: Stomach organoids


title: Extracted RNA from Control small intestine organoids Control_SI_2

value: small intestine organoids


title: MC_f12_Chimera_Lung1_K27Ac


title: Extracted RNA from  Cdx2 overexpressing stomach organoids Cdx2+_Sto_1

value: Cdx2 overexpressing

value: stomach organoids


title: MC_f08_Chimera_kupffer1_K4Me2

value: Liver


title: MC_f10_Chimera_Lung1_K4Me1

value: Lung


title: MC_f09_Chimera_kupffer1_K27Ac

value: Kupffer cells with CD45.1 mark


title: MC_f05_Chimera_Spleen1_K4Me2

value: Spleen

value: Abcam


title: MC_f06_Chimera_Spleen1_K27Ac


title: MC_f07_Chimera_kupffer1_K4Me1


title: MC_f04_Chimera_Spleen1_K4Me1


title: Extracted RNA from Control small intestine organoids Control_SI_1


title: Extracted RNA from Cdx2null small intestine organoids Cdx2null_SI_1

value: Cdx2 null


title: MC_f02_Chimera_Perit1_K4Me2


title: Extracted RNA from Cdx2null small intestine organoids Cdx2null_SI_2


title: Extracted RNA from  Cdx2 overexpressing stomach organoids Cdx2+_Sto_4


title: Yersinia pseudotuberculosis RNA-seq_early infection

description:
FVB/N cecal tissue at 2 days postinfection
Sample 1

source_name: Early infection

value: Early infection data

value: poly(A) depleted RNA

value: rRNA-depleted RNA

value: mouse


title: Extracted RNA from Control Stomach organoids Control_Sto_3


title: MC_f14_Chimera_Spleen_WCE

value: Spleen red pulp macrophages with CD45.1 mark

value: none (whole cell extract)


title: MC_f15_Chimera_Kupffer_WCE


title: MC_f13_Chimera_Perit_WCE

value: Peritoneal cavity

value: Peritoneal cavity macrophages with CD45.1 mark


title: MC_f03_Chimera_Perit1_K27Ac


title: MC_f16_Chimera_Lung_WCE

value: Lung macrophages with CD45.1 mark


title: MC_h11_Chimera_Lung2_K4Me2


title: Extracted RNA from Control small intestine organoids Control_SI_3

value: Control

value: small intestine organoids


title: Spleen_K27Ac_rep1

value: Spleen red pulp macrophages


title: MC_f11_Chimera_Lung1_K4Me2

value: Lung


title: Spleen_K4Me1_rep2

value: Abcam ab8895 and Millipore 07-436 mixed ratio 1:1


title: Neutrophils_K4Me2_rep2

value: Bone marrow

value: Neutrophils


title: Extracted RNA from Control small intestine organoids Control_SI_4


title: Neutrophils_K4Me1_rep2


title: Neutrophils_K27Ac_rep2

value: Abcam


title: Spleen_K4Me1_rep1

value: Spleen


title: Extracted RNA from Control Stomach organoids Control_Sto_4

value: Stomach organoids


title: Extracted RNA from Cdx2null small intestine organoids Cdx2null_SI_4

value: Cdx2 null


title: MC_f01_Chimera_Perit1_K4Me1


title: monocyte_K4Me2_rep2

value: Monocytes


title: Neutrophils_K4Me1_rep1


title: monocyte_K4Me1_rep2


title: Neutrophils_K27Ac_rep1


title: Extracted RNA from Cdx2 overexpressing stomach organoids Cdx2+_Sto_2

value: Cdx2 overexpressing

value: stomach organoids


title: Extracted RNA from  Cdx2 overexpressing stomach organoids Cdx2+_Sto_3


title: Extracted RNA from Control Stomach organoids Control_Sto_2


title: peritoneal mac_K27Ac_rep2

value: Peritoneal cavity

value: Peritoneal cavity macrophages


title: peritoneal mac_K4Me2_rep1


title: peritoneal mac_K4Me1_rep2


title: peritoneal mac_K27Ac_rep1


title: peritoneal mac_K4Me2_rep2


title: monocyte_K4Me1_rep1


title: Lung_K27Ac_rep2

source_name: Lung macrophages

value: Lung macrophages


title: Lung_K4Me1_rep2


title: Lung_K4Me1_rep1


title: peritoneal mac_K4Me1_rep1


title: Lung_K4Me2_rep2


title: Lung_K27Ac_rep1


title: SI_K4Me2_rep2

source_name: Small intestine macrophages

value: Small intestine

value: Small intestine macrophages


title: monocyte_K27Ac_rep2


title: LI_K27Ac_rep2

source_name: Large intestine macrophages

value: Large intestine

value: Large intestine macrophages


title: SI_K4Me1_rep2

value: Abcam ab8895 and Millipore 07-436 mixed ratio 1:1


title: SI_K4Me1_rep1


title: SI_K27Ac_rep2


title: monocyte_K27Ac_rep1

value: Bone marrow


title: LI_K4Me2_rep2


title: LI_K4Me1_rep1


title: Kupffer cells_K27Ac_rep2

source_name: Kupffer cells

value: Liver

value: Kupffer cells


title: LI_K4Me1_rep2


title: LI_K27Ac_rep1

value: Abcam


title: Kupffer cells_K27Ac_rep1


title: Kupffer cells_K4Me1_rep2


title: MA_g02_ATAC_Spleen2

data_processing:
HISEQ split using cassava Y60,I10
alignment using bowtie 1.0.0. command (bowtie -a -m 1 --sam --best --strata -v 2 mm9)
makeTagDirectory -tbp
makeUCSCfile  -bigWig -fsize 1e20
Genome_build: mm9

source_name: Spleen red pulp macrophages

extract_protocol:
Cells were sorted into MACS buffer, washed and lysed in 10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% or 0.5% Igepal CA-630. Nuclei were pelleted by centrifugation for 30min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol (some samples used read2 to read molecule barcodes only)

value: Spleen

value: Spleen red pulp macrophages


title: ATAC_Microglia_Rep1

source_name: Brain microglia

value: Brain

value: Brain microglia


title: Microglia_K27Ac_rep2


title: Kupffer cells_K4Me1_rep1


title: MA_i3_ATAC_Kupffer2


title: Microglia_K4Me1_rep1


title: Microglia_K27Ac_rep1


title: MA_i5_ATAC_LI2


title: Microglia_K4Me2_rep2


title: MA_i2_ATAC_Monocyte2

value: Monocytes


title: MA_i4_ATAC_LI1


title: MA_g12_ATAC_Mono1


title: SI_K27Ac_rep1


title: MA_i1_ATAC_Neutrophil2

value: Neutrophils


title: MA_g10_ATAC_Perit2

source_name: Peritoneal cavity macrophages

value: Peritoneal cavity

value: Peritoneal cavity macrophages


title: MA_g09_ATAC_Perit1


title: MA_i7_ATAC_Spleen1


title: MA_g08_ATAC_SI2

value: Small intestine


title: MA_g06_ATAC_Lung2

value: Lung

value: Lung macrophages


title: MA_g05_ATAC_Lung1


title: Microglia_K4Me1_rep2