title: Thymus_input

city: Charlottesville

first: Chongzhi

last: Zang

institute: University of Virginia

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with -m 1 and default parameters
Uniquely aligned reads were filtered using SICER v1.1 to keep up to 2 copies at each genomic location
Wiggle files for histone modifications were generated using NPS with default parameters
Wiggle files for progenitor cells' H3K4me2 and transcription factors were generated using MACS v1.4
Genome_build: mm9

source_name: Thymocytes

growth_protocol: Single-cell suspensions of mouse fetal livers collected on gestational day 14 were prepared by passage through 40 μm filters and 18- to 23-gauge needles. Mature erythrocytes were lysed in Ammonium Chloride Potassium (ACK) buffer and cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Individual lineages were isolated by depleting other lineages using TER119, GR1, CD41, and CD11b (B-D Pharmingen) monoclonal antibodies (mAb) and immunomagnetic Dynabeads (Invitrogen) or by positive selection using GR1 or TER119 mAb for flow cytometry. MK isolations included additional passage over triple (4%, 3%, 1.5%) gradients of bovine serum albumin, with collection of the supernatant (IMM cells) or pellet (MAT cells). Cell isolations were monitored by viewing May-Grünwald-Giemsa stains of cytocentrifuged preparations with an Olympus BX41 microscope and by flow cytometry using the above-listed mAb. Chromatin marks were pulled down with H3K4me2 or H3K27ac antibodies after MNase digestion or crosslinking + sonication of the cells. Transcription factors were pulled down with the respective antibodies after crosslinking + sonication of the cells
At least 20 ng of precipitated or input DNA from pools of at least 3 replicates was processed for deep sequencing using different library preparation kits for IMM or MAT cells (TruSeq, Illumina) and progenitors (TruPLEX-FD, Rubicon Genetics), following the manufacturers’ instructions. ChIP-seq libraries were sequenced using Illumina HiSeq2000 and tags were mapped to mouse genome build mm9.

treatment_protocol: To expand erythroid cells, granulocytes, and MKs, cultures were supplemented, respectively, with Stem Cell Factor (SCF, R&D Systems, 0.02 mg/10 mL) and erythropoietin (EPO, R&D Systems, 0.02 mg/10 mL); SCF and granulocyte-colony stimulating factor (G-CSF, R&D Systems, 0.05 mg/10 mL); or thrombopoietin (TPO, 1/100 dilution of producer cell supernatant [Villeval, 1997 #2788]). To enrich hematopoietic progenitors, short-term cultures were supplanted with SCF and interleukin-3 (R&D Systems, 0.05 mg/10 mL). Progenitors were harvested after 1 day of culture, IMM lineages after 2 days, and MAT cells after 4 (erythroid, granulocyte) or 5 days (MKs).

value: 4 weeks

value: thymus

value: Thymocytes

tag: genome/variation

value: wild-type

tag: antibody

value: input chromatin


title: Gran4D_input

status: Public on Jul 28 2014

type: SRA

state: VA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Mature granulocytes

tag: strain

tag: age

tag: tissue

value: liver

tag: cell type

value: Mature granulocytes


title: RBC2D_input

source_name: Immature Erythroid

value: Immature Erythroid


title: Gran2D_input

source_name: Immature granulocytes

value: Immature granulocytes


title: RBC5D_input

source_name: Mature Erytrhoid

value: Mature Erytrhoid


title: ribosome footprinting B6J;n-Tr20N/N rep1

city: Farmington

first: Jeffrey

last: Chuang

state: CT

address: 263 Farmington Avenue

department: Computational Biology

institute: The Jackson Laboratory for Genomic Medicine

library_source: transcriptomic

data_processing:
library strategy: ribosome footprinting
fastx_clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -n -v -i $fastqfile -o temp_clipped.fastq
fastx_trimmer -Q33 -f 2 -l 100 -i temp_clipped.fastq -o temp_trimmed.fastq
Mouse ribosomal RNA sets were obtained by searching Genbank for known rRNAs and then filtering these out using the command: bowtie -p 16 rRNA temp_trimmed.fastq -l 23 --un temp_noRRNA.fastq > /dev/null.
Reads with unique mapping to the mm10 genome were computed using tophat and Illumina igenome annotations: tophat -p 16 -a 8 -m 0 -i 70 -I 500000 -g 1 --no-novel-juncs --library-type fr-firststrand –GTF /IlluminaGTF/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf /IlluminaGTF/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex/genome/ temp_noRRNA.fastq. Manual inspection of coding loci with high read counts also revealed an additional rRNA overlapping a coding region, which was removed from consideration in further data analysis (LSU-rRNA_Hsa, on mm10 chr6).
Genome_build: mm10
Supplementary_files_format_and_content: bam files

molecule: total RNA

source_name: ribosome footprinting B6J;n-Tr20N/N

extract_protocol:
Tissue homogenization was performed with a mixer mill (Retsch MM400) in 1.0 ml of 20 mM Tris-Cl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% (v/v) Triton X-100, 25 U/ml Turbo DNase I, 100 mg/ml cycloheximide, and 2 mg/ml harringtonine. RNase I-treated lysates were ultracentrifuged through a sucrose cushion to obtain the ribosome pellet from which RNA was extracted. 26 nt to 34-nt RNA fragments were purified by electrophoresis on 15% polyacrylamide TBE-urea gel.
Linker addition and cDNA generation and circularization were then performed. Subtraction of rRNA with a pool of oligos was performed as indicated in the protocol. The resulting DNAs were amplified with different indexing primers to distinguish each sample as indicated in the protocol. The libraries were analyzed by sequencing on an Illumina HiSeq 2000 platform.

treatment_protocol: Cerebella were immediately frozen in liquid nitrogen upon dissection and three cerebella were pooled from mice of each genotype for library generation.

tag: background strain

tag: genotype/variation

value: Cerebellum


title: MK5D_input

source_name: Mature Megakaryocytes

value: Mature Megakaryocytes


title: Thymus_H3K4me2

growth_protocol: Thymocytes were isolated from the thymus of 4 week old mice. Cells were immediately subjected to H3K4me2 ChIP-seq.

value: H3K4me2, antibody vendor, cat#, lot #:Millipore, 07-030, DAM1724042


title: HSC_input

source_name: HSC

value: HSC


title: Gran2D_DNase


title: Total_PolII_TRIMKD_rep2

city: RTP

first: David

last: Fargo

state: NC

department: HHS

institute: National Institute of Environmental Health Sciences

data_processing:
Basecalls performed using standard Illumina pipeline
Reads with mean Phred quality <20 were filtered
Reads were aligned to mm9 assembly using bowtie 0.12.8 employing parameters -v2 -m1
Duplicates reads were removed using Picard tools 1.74
Reads were extended to mean fragment length (150 nt), replicates were merged, and read coverage tracks were generated using bedtools 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, read coverage

source_name: Embryonic Stem Cells

growth_protocol: ES cells were cultured in M10 medium as described in the manuscript

extract_protocol:
ES cells were crosslinked with formaldehyde and lysed. Chromatin was sonicated, and ChIP was performed as described in the manuscript.
Libraries were constructed using the SPRI-TE Nucleic Acid Extractor (Beckman Coulter, Indianapolis, IN) with a size selection of 200-400bp

treatment_protocol: ES cells were transfected with siRNAs at 50 nM concentration with lipofectamine 2000

tag: chip antibody

value: Total PolII, (sc-899, Santa Cruz Biotechnology)

tag: treatment

value: Trim28 siRNA


title: Gran4D_H3K4me2


title: Gran2D_H3K4me2


title: Input_TRIMKD_rep2


title: Input_TRIMKD_rep1


title: RBC2D_H3K27ac

value: H3K427ac, antibody vendor, cat #, lot #:Abcam, ab4729, 509313


title: RBC5D_H3K4me2

value: H3K4me2, antibody vendor, cat#, lot #:Millipore, 07-030, DAM1570816


title: RBC2D_NFE2

value: NF-E2 TB16+TB17, home made


title: MK2D_NFE2

source_name: Immature Megakaryocytes

value: Immature Megakaryocytes


title: MK5D_NFE2

value: wild-type


title: RBC2D_H3K4me2


title: BY-RNA_-Glu15_Total_Replicate1

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

description:
Total RNA
-Glucose15m

data_processing:
Reads were trimmed of their polyA tail and then aligned to the S. cerevisiae genome using Bowtie-0.12.8.
Reads were aligned to a library of RNA genes
Remaining reads were aligned to the S. cerevisiae genome R64-1-1
Genome_build: http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz
Supplementary_files_format_and_content: Each line in the tab deliminated txt file has the following columns:  Systematic Name:Name:Descript:Start: End :Length: RNA-Glu:RNA+Glu(log2)-BY4741-mRNA Fold Change:Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-BY4741-Ribosome Occupancy Fold Change: RNA-Glu/RNA+Glu(log2)-EY0690-mRNA Fold Change: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-EY0690-Ribosome Occupancy Fold Change: Ribo+Glu_InitiationRegion-BY4741: Ribo+Glu_DownstreamRegion-BY4741: Ribo-Glu_InitiationRegion-BY4741: Ribo-Glu_DownstreamRegion-BY4741: RNA+Glu_InitiationRegion-BY4741_TotalRNA: RNA+Glu_DownstreamRegion-BY4741_TotalRNA: RNA-Glu_InitiationRegion-BY4741_TotalRNA: RNA-Glu_DownstreamRegion-BY4741_TotalRNA: Ribo+Glu_InitiationRegion-EY0690: Ribo+Glu_DownstreamRegion-EY0690: Ribo-Glu_InitiationRegion-EY0690: Ribo-Glu_DownstreamRegion-EY0690: RNA+Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA: RNA+Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA: RNA-Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA: RNA-Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA: Ribo+Glu_RPKM-BY4741: Ribo-Glu_RPKM-BY4741: RNA+Glu_RPKM-BY4741: RNA-Glu_RPKM-BY4741: Ribo+Glu_RPKM-EY0690: Ribo-Glu_RPKM-EY0690: RNA+Glu_RPKM-EY0690: RNA-Glu_RPKM-EY0690

organism: Saccharomyces cerevisiae

source_name: yeast BY4741

growth_protocol: Yeast strain BY4741 was grown at 30C in synthetic complete + glucose media to OD600 =0.3-0.4. Then 15min into SC -glucose media as indicated.

extract_protocol:
Footprints: cells were rapidly harvested, flash-frozen in polysome lysis buffer, and pulverized in a mixer mill, extracts were digested with 100 U Rnase I for 30 min, monosomes were purified by sucrose density gradient or by sucrose cushion, RNA was extracted from the monosome fraction by hot acid phenol; total RNA was prepared from flash-frozen cells by the hot acid phenol protocol, polyA RNA was purified by oligo-dT DynaBeads, or RiboZero selected RNA or Total RNA, and fragmented at 95 C under mild alkali conditions
Libraries were prepared by polyA tailing 28mers followed by reverese transcription with either OTi225 or OTi9pA, see Methods in Zid et al, in submission

treatment_protocol: All samples were treated for 1 min with cycloheximide 100ug/ml

tag: strategy

value: RNA-seq


title: MK2D_H3K4me2

value: liver


title: MK5D_H3K4me2


title: MEP_H3K4me2

source_name: MEP

value: MEP


title: MK2D_input

value: input chromatin


title: HSC_H3K4me2


title: CMP_H3K4me2

source_name: CMP

value: CMP


title: BY-RNA_-Glu15_polyA_Replicate2

description:
PolyA selected RNA
-Glucose15m

data_processing:
Reads were trimmed of their polyA tail and then aligned to the S. cerevisiae genome using Bowtie-0.12.8.
Reads were aligned to a library of RNA genes
Remaining reads were aligned to the S. cerevisiae genome R64-1-1
Genome_build: http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz
Supplementary_files_format_and_content: Each line in the tab deliminated txt file has the following columns: Systematic Name: Name: Descript: Start:  End: Length: RNA-Glu/RNA+Glu(log2)-BY4741-mRNA Fold Change Replicate 1: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 1: RNA-Glu/RNA+Glu(log2)-EY0690-mRNA Fold Change Replicate 1: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-BY4741-mRNA Fold Change Replicate 1: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-BY4741-mRNA Fold Change Replicate 2: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 2: RNA(pA)-Glu/RNA(pA)+Glu(log2)-EY0690-mRNA Fold Change Replicate 1: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-EY0690-mRNA Fold Change Replicate 2: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 2:  Ribo+Glu_RPKM-BY4741 - Replicate 1: Ribo-Glu_RPKM-BY4741 - Replicate 1: RNA+Glu_RPKM-BY4741 TotalRNA - Replicate 1: RNA-Glu_RPKM-BY4741 TotalRNA - Replicate 1: Ribo+Glu_RPKM-EY0690 - Replicate 1: Ribo-Glu_RPKM-EY0690 - Replicate 1: RNA+Glu_RPKM-EY0690 TotalRNA - Replicate 1: RNA-Glu_RPKM-EY0690 TotalRNA - Replicate 1: RNA+Glu_RPKM-BY4741 polyA_RNA - Replicate 1: RNA-Glu_RPKM-BY4741 polyA_RNA - Replicate 1: Ribo+Glu_RPKM-BY4741 - Replicate 2: Ribo-Glu_RPKM-BY4741 - Replicate 2: RNA+Glu_RPKM-BY4741 polyA_RNA - Replicate 2: RNA-Glu_RPKM-BY4741 polyA_RNA - Replicate 2: RNA+Glu_RPKM-EY0690 polyA_RNA - Replicate 1: RNA-Glu_RPKM-EY0690 polyA_RNA - Replicate 1: Ribo+Glu_RPKM-EY0690 - Replicate 2: Ribo-Glu_RPKM-EY0690 - Replicate 2: RNA+Glu_RPKM-EY0690 polyA_RNA - Replicate 2: RNA-Glu_RPKM-EY0690 polyA_RNA - Replicate 2:  Ribo+Glu_InitiationRegion-BY4741 Replicate 1: Ribo+Glu_DownstreamRegion-BY4741 Replicate 1: Ribo-Glu_InitiationRegion-BY4741 Replicate 1: Ribo-Glu_DownstreamRegion-BY4741 Replicate 1: RNA+Glu_InitiationRegion-BY4741_TotalRNA Replicate 1: RNA+Glu_DownstreamRegion-BY4741_TotalRNA Replicate 1: RNA-Glu_InitiationRegion-BY4741_TotalRNA Replicate 1: RNA-Glu_DownstreamRegion-BY4741_TotalRNA Replicate 1: Ribo+Glu_InitiationRegion-EY0690 Replicate 1: Ribo+Glu_DownstreamRegion-EY0690 Replicate 1: Ribo-Glu_InitiationRegion-EY0690 Replicate 1: Ribo-Glu_DownstreamRegion-EY0690 Replicate 1: RNA+Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA+Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA-Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA-Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA+Glu_InitiationRegion-BY4741_polyA_RNA Replicate 1: RNA+Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 1: RNA-Glu_InitiationRegion-BY4741_polyA_RNA Replicate 1: RNA-Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 1: Ribo+Glu_InitiationRegion-BY4741 Replicate 2: Ribo+Glu_DownstreamRegion-BY4741 Replicate 2: Ribo-Glu_InitiationRegion-BY4741 Replicate 2: Ribo-Glu_DownstreamRegion-BY4741 Replicate 2: RNA+Glu_InitiationRegion-BY4741_polyA_RNA Replicate 2: RNA+Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 2: RNA-Glu_InitiationRegion-BY4741_polyA_RNA Replicate 2: RNA-Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 2: RNA+Glu_InitiationRegion-EY0690_polyA_RNA Replicate 1: RNA+Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 1: RNA-Glu_InitiationRegion-EY0690_polyA_RNA Replicate 1: RNA-Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 1: Ribo+Glu_InitiationRegion-EY0690 Replicate 2: Ribo+Glu_DownstreamRegion-EY0690 Replicate 2: Ribo-Glu_InitiationRegion-EY0690 Replicate 2: Ribo-Glu_DownstreamRegion-EY0690 Replicate 2: RNA+Glu_InitiationRegion-EY0690_polyA_RNA Replicate 2: RNA+Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 2: RNA-Glu_InitiationRegion-EY0690_polyA_RNA Replicate 2: RNA-Glu_DownstreamRegion-EY0690_polyA_RNA Replicate

growth_protocol: Yeast strains BY4741 and EY0690 (w303) was grown at 30C in synthetic complete + glucose media to OD600 =0.3-0.4. Then 15min into SC -glucose media as indicated.


title: BY-RNA_logphase_polyA_Replicate2

description:
PolyA selected RNA
+Glucose

value: +Glucose


title: GMP_H3K4me2

source_name: GMP

value: GMP


title: BY-Ribo_-Glu15_Replicate2

description:
Ribosome protected mRNA
-Glucose15m

value: Ribosome Profiling


title: BY-Ribo_-Glu15_Replicate1

description:
Ribosome protected mRNA
-Glucose15m


title: BY-Ribo_logphase_Replicate2

description:
Ribosome protected mRNA
+Glucose


title: BY-RNA_logphase_polyA_Replicate1

description:
PolyA selected RNA
+Glucose


title: ribosome footprinting B6J;n-Tr20J/J rep1

source_name: ribosome footprinting B6J;n-Tr20J/J

value: Cerebellum


title: BY-RNA_-Glu15_polyA_Replicate1

description:
PolyA selected RNA
-Glucose15m


title: BY-Ribo_logphase_Replicate1

description:
Ribosome protected mRNA
+Glucose


title: DMSO treated 3_RNA

status: Public on Jul 27 2014

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

country: China

institute: SJTU

description: Con3 RNA

data_processing:
The ribosome protected RNA sequencing reads were trimed for special adapter (CTGTAGGCACCATCAA) on the 3'end site and mapped to hg19 genome using PALMapper allowing splicing aligning.
The total RNA sequencing reads were mapped to hg19 genome using STAR allowing splicing aligning.
After count the reads for each gene (only exonic region), RPKM was calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene in each sample.

organism: Homo sapiens

source_name: KOPT-K1 cell line

growth_protocol: RPMI, 20% FBS, PSG

extract_protocol: See Ignolia et al., Nature Protocols 2012 PMID: 22836135

treatment_protocol: DMSO or 25 nM Silvestrol for 45 minutes

tag: cell line

value: KOPT-K1 T-ALL cell line

tag: rna purification

value: Total RNA

tag: agent

value: control


title: Silvestrol (25 nM) treated 3_RNA

description: Sil3 RNA

value: Silvestrol


title: Silvestrol (25 nM) treated 2_RNA

description: Sil2 RNA


title: DMSO treated 2_RNA

description: Con2 RNA


title: DMSO treated 1_RNA

description: Con1 RNA


title: DMSO treated 2_RF

description: Con2 RF

value: Ribosome protected RNA fragments


title: Silvestrol (25 nM) treated 2_RF

description: Sil2 RF


title: Silvestrol (25 nM) treated 1_RF

description: Sil1 RF


title: DMSO treated 1_RF

description: Con1 RF


title: Silvestrol (25 nM) treated 1_RNA

description: Sil1 RNA


title: ovary

city: Poznan

first: Aleksandra

middle: Maria

last: Swiercz

address: Piotrowo 2

department: Institute of Computing Science

country: Poland

institute: Poznan University of Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adapter sequence, and low-quality reads were filtered out with quality lower than 30 for at least 80% of the nucleotides
Redundant reads were removed, only single occurence of each sequence were retained (the number of occurence was noted)
Reads were mapped to Sscrofa genome and to miRNA sequences from miRBase using SOAP aligner allowing 1 mismatch
Genome_build: Sscrofa10
Supplementary_files_format_and_content: pdf file with Tables of sequences which appeared in both gonads: miRNA with predicted targets, piRNA with mapped position to chromosomes, and tRF with  match to tRNA sequences; and several FASTA files with libraries of miRNA and piRNA sequences that appeared in ovary, testis and in both libraries; in the FASTA files the name of the sequence corresponds to the reference number of unique sequence and the number of identical reads

organism: Sus scrofa

source_name: extracted tissue

extract_protocol:
The sRNAs were isolated using the mirVana miRNA isolation kit according to the manufacturer’s instructions (Ambion)
RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Prep Kit  according to the manufacturer’s instructions (Illumina)

tag: breed

value: Line 990 breed

tag: deveopmental stage

value: sexually mature

value: ovary


title: testis

value: testis


title: input DNA, A549 cells

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: input genome for Smad3 ChIP in A549 cells

data_processing:
ChIP-seq reads were aligned to the hg18 genome assembly.
peaks were called using CisGenome version 2 using default parameters.
Genome_build: hg18
Supplementary_files_format_and_content: bed and wig files were generated using CisGenome v2.0.

growth_protocol: A549 cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Life Technologies) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin. H441 cells were maintained in RPMI 1640 (#11875; Life Technologies) supplemented with 10% FBS, 100 U/ml penicillin G, and 100 ug/ml streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). SMAD3, SMAD4, or TTF-1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 1.5 h.

tag: ttf-1 expression

value: negative

tag: histology

value: lung adenocarcinoma


title: input DNA #2, H441 cells

description: input genome for Smad4 ChIP in H441 cells

value: positive


title: Smad4 ChIP-seq, H441/siControl cells

description: cut-off FDR value for peak calling: 10%

value: SMAD4 [R&D, Catalog#:AF2097]


title: input DNA #1, H441 cells

description: input genome for Smad3 and TTF-1 ChIP in H441 cells


title: Smad3 ChIP-seq, A549 cells

description: cut-off FDR value for peak calling: 5%

value: SMAD3 [Abcam, Catalog#:ab4085, Lot#:GR27326-2]


title: TTF-1 ChIP-seq, H441 cells, 0h

description: cut-off FDR value for peak calling: 1%

value: TTF-1 [Thermo Scientific, Catalog#:MS-699-P clone 8G7G3/1]


title: Smad4 ChIP-seq, H441/siTTF-1 cells

description: cut-off FDR value for peak calling: 10%

value: depleted by siRNA


title: Smad3 ChIP-seq, H441/siTTF-1 cells

description: cut-off FDR value for peak calling: 1%. H441_Smad3-only.bed is a subset of H441_Smad3_siTTF-1_hg18.bed which does not overlap with H441_TTF-1_0h_hg18.bed. H441_Smad3_TTF-1.bed is a subset of H441_Smad3_siTTF-1_hg18.bed which overlaps with H441_TTF-1_0h_hg18.bed.


title: Smad3 ChIP-seq, H441/siControl cells

description: cut-off FDR value for peak calling: 1%. H441_STRL.bed is a subset of H441_Smad3_siControl_hg18.bed which does not overlap with H441_Smad3_siTTF-1_hg18.bed.


title: TTF-1 ChIP-seq, H441 cells, 1.5h

description: cut-off FDR value for peak calling: 1%


title: ago5-2_Digital_Gene_Indexing_Rep2

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description: Digital Gene Indexing

data_processing: Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana genome (TAIR9).   Only reads with 100% match were retained.

molecule: polyA RNA

organism: Arabidopsis thaliana

growth_protocol: All plants were grown at 20Â°C in 16 hour day lengths.  Mixed Inflorescence tissue was harvested approximately 6-7 weeks post germination.

extract_protocol: RNA was extracted using Trizol Reagent. PolyA RNA cloned using Illumina Digital Gene Expression- Taq profiling for NlaIII

tag: ecotype

tag: ip antibody

value: Mixed Inflorescence


title: AGO5_IP_sRNAs

description: sRNA-seq from IP

extract_protocol: RNA was extracted using Trizol Reagent. Total RNA was size selected using mirVana kit and cloned using Illumina sRNA kit v.2


title: ago5-2_Digital_Gene_Indexing_Rep1

description: Digital Gene Indexing


title: Col-0_Digital_Gene_Indexing_Rep2

description: Digital Gene Indexing


title: ago5-2_total_sRNAs

description: total sRNA seq

extract_protocol: RNA was extracted using Trizol Reagent. Total RNA was size selected using mirVana kit and cloned using Illumina sRNA kit v.4


title: KrasMD21

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description: Sample 9

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Sequence reads were trimmed to remove traces of adapter sequence
PE1:AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG
PE2:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Reads were first mapped to the mouse transcriptome (UCSC annotation, genome build mm9) and un-aligned reads were then mapped to the mouse genome where possible.
Read mapping was performed with TopHat version 2.0.5 using default options. Abundance estimation and differential analysis were performed using Cufflinks version 2.0.2 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) value per gene for each sample

source_name: KP-KrasA cells_day 21

extract_protocol:
mRNA-sequencing was carried out with total RNA purified with the RNeasy reagent (Qiagen) and DNase-treated with TURBO Dnase (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocol.
Barcodes: TTCAGA:KrasAD0, CATCAC:KrasGD0, TCCGGG:KrasMD0, TTCAGA:KrasAD0, CATCAC:KrasGD0, TCCGGG:KrasMD0,
TGCTGT:KrasAD4, GTAACA:KrasGD4, AAGCTC:KrasMD4, TGCTGT:KrasAD4, GTAACA:KrasGD4, AAGCTC:KrasMD4,
ACGGTG:KrasAD21, GGATCT:KrasGD21, CTTAAA:KrasMD21, ACGGTG:KrasAD21, GGATCT:KrasGD21, CTTAAA:KrasMD21.

tag: strain background

value: Kras Lox-STOP-Lox-G12D;p53flox/flox (KP) mouse lung cancer model into which  a doxycycline-inducible shRNA targeting Kras was introduced

value: primary lung adenocarcinoma cells

tag: timepoint


title: KrasGD21

description: Sample 8

tag: cell type


title: KrasAD21

description: Sample 7


title: KrasGD4

description: Sample 5

source_name: KP-KrasA cells_day 4

value: Day 4 (D4


title: A549 cells infected with Ad-LacZ, TGF-beta treated

description: control vector infected, stimulated with TGF-beta

data_processing:
RNA-seq reads were processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files.
parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G
Genome_build: hg19
Supplementary_files_format_and_content: FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with options -m 200 -u). Expression data of the four samples were summarized into single processed file by Cuffdiff.

growth_protocol: A549 cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Life Technologies) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted by using RNeasy mini column (QIAGEN) with DNaseI treatment. PolyA(+) RNA was selected by Dynabeads mRNA DIRECT Micro Kit (Thermo Scientific).
Libraries were prepared using Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed using Ion PI Chip Kit v2, PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 (Thermo Scientific).

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 24 h without starvation.

value: no

value: TGF-beta


title: A549 cells infected with Ad-TTF-1, TGF-beta treated

description: TTF-1 expressed, stimulated with TGF-beta

value: exogenous expression


title: KrasMD0

description: Sample 3

source_name: KP-KrasA cells_day 0

extract_protocol:
mRNA-sequencing was carried out with total RNA purified with the RNeasy reagent (Qiagen) and DNase-treated with TURBO Dnase.  (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocol. Barcodes: TTCAGA:KrasAD0,CATCAC:KrasGD0,TCCGGG:KrasMD0,TTCAGA:KrasAD0,CATCAC:KrasGD0,TCCGGG:KrasMD0,TGCTGT:KrasAD4,GTAACA:KrasGD4,AAGCTC:KrasMD4,TGCTGT:KrasAD4,GTAACA:KrasGD4,AAGCTC:KrasMD4,ACGGTG:KrasAD21,GGATCT:KrasGD21,CTTAAA:KrasMD21,ACGGTG:KrasAD21,GGATCT:KrasGD21,CTTAAA:KrasMD21.

value: Day 0 (D0)


title: KrasAD4

description: Sample 4

extract_protocol: ACGGTG:KrasAD21, GGATCT:KrasGD21, CTTAAA:KrasMD21, ACGGTG:KrasAD21, GGATCT:KrasGD21, CTTAAA:KrasMD21.^SAMPLE = GSM1357143


title: KrasMD4

description: Sample 6


title: KrasGD0

description: Sample 2


title: KrasAD0

description: Sample 1


title: A549 cells infected with Ad-LacZ, control

description: control vector infected, no stimulation


title: A549 cells infected with Ad-TTF-1, control

description: TTF-1 expressed, no stimulation


title: Col-0_Digital_Gene_Indexing_Rep1

description: Digital Gene Indexing

tag: tissue


title: man_r_9d

status: Public on Jul 26 2014

city: Qingdao

first: Fei

last: Xu

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 9th day after shell breakage.

data_processing: use oyster_v9 genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 5 -g 20 -I 10000 --solexa1.3-quals

organism: Magallana gigas

source_name: right mantle

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 Î¼g total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3â dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200Â±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: developmental stage

value: adult

value: right mantle

tag: exptl group

value: tissue


title: man_l_9d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 9th day after shell breakage.

source_name: left mantle

value: left mantle


title: man_l_17d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 17th day after shell breakage.


title: man_r_21d

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 21th day after shell breakage.


title: man_l_5d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 5th day after shell breakage.


title: man_l_1d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 1th day after shell breakage.


title: man_r_3d

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 3th day after shell breakage.


title: man_l_13d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 13th day after shell breakage.


title: man_l_21d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 21th day after shell breakage.


title: man_r_5d

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 5th day after shell breakage.


title: man_r_13d

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 13th day after shell breakage.


title: parental BC69 total RNA

city: Pasadena

first: Adrien

last: Le Thomas

state: CA - California

address: 231 South Hudson Avenue

department: Biology and Biological Engineering

institute: California Institute of Technology

description: total small RNA

data_processing:
mapping with Bowtie to dm3
Genome_build: dm3
Supplementary_files_format_and_content: txt file containing tab delimited sequence, chromosome, start, stop, annotation and frequency

organism: Drosophila melanogaster

source_name: parental BC69

extract_protocol:
ovaries dissected, for IP samples: immunoprecipitation of Argonaute protein, extraction of small RNA, cloning of library. For total RNA libraries: isolation of total RNA after ovary dissection and cloning of small RNA library
custom made protocol for cloning of piRNAs: isolation of small RNAs on acrylamide Gel or through IP of Argonaute, followed by 3' ligration, 5' ligation, Reverse transcription and final PCR amplification

tag: age

value: 1-2 week old

tag: strain

value: parental BC69

value: ovary

tag: antibody


title: man_r_1d

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 1th day after shell breakage.


title: Col-0_total_sRNAs

description: total sRNA seq

extract_protocol: RNA was extracted using Trizol Reagent. Total RNA was size selected using mirVana kit and cloned using Illumina sRNA kit v.3


title: man_r_17d

description: Sequenced reads were generated from the right mantles of the treated oyster individuals sampled at 17th day after shell breakage.


title: NMD total RNA

description: total small RNA

source_name: NMD total RNA

value: NMD; male P-1152 cross to female P-1152

tag: cross type

value: No maternak deposition (NMD) cross


title: parental P1152 total RNA

description: total small RNA

source_name: parental P1152

value: parental P1152


title: man_l_C

description: Sequenced reads were generated from the left mantles of every oyster in control group.


title: man_r_C

description: Sequenced reads were generated from the right mantles of every oyster in control group.


title: EPI6h

description: Sequenced reads were generated from the metabolism competent larvae of Crassostrea gigas, which were treated with epinephrine solution smapled after culturing 6 hours. Eyed larvae was treated for 20 min with 0.1 mM epinephrine solution, in order to induce the larvae metamorphosis while skipping the crwal and attachment stages. Sample was collected 6 hours post the treatment of epinephrine.

source_name: competent pediveliger for metamorphosis

value: competent pediveliger for metamorphosis

value: developmental stage


title: NMD Ago3-IP

description: small RNA from IP

source_name: NMD Ago3-IP

value: Ago3 Ab

tag: antibody info

value: rabbit polyclonal antisera directed against the N-terminal 14–16 AA (Brennecke et al. 2007)


title: EPI

description: Sequenced reads were generated from the metabolism competent larvae of Crassostrea gigas, which was treated with epinephrine solution, and were sampled immediately. Eyed larvae was treated for 20 min with 0.1 mM epinephrine solution, in order to induce the larvae metamorphosis while skipping the crwal and attachment stages. Sample was collected immidiately after the treatment.


title: Juvenile

description: Sequenced reads were generated from the stage of juvenile at 215 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day to the first one month. Then the culutre was performed in natural sea area.

data_processing: use oyster_v9 genome as reference, sequenced reads were aligned onto the corresponding reference using SOAP2.20 with default parameters except -M 0 -l 17 -v 0 -p 7 -r 2

source_name: Juvenile

growth_protocol: The embryo were cultured in sea water with a volume of 20 cubic meters. The temperature of the sea water is 26 ÂºC and the salinity is 30 ppt  before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day. Juvenile and adult individuals were cultured in natural sea.

extract_protocol: For smRNA-seq, we gel-purified 18-30 nts RNAs from the samples utilized for RNA-seq. Illumina 5â and 3â RNA adapter were sequentially  ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina Genome Analyzer.

treatment_protocol: small RNA is extracted by TRIzol Reagent

value: Juvenile

tag: colony

value: F2 progeny of "G3" family


title: NMD Aub-IP

description: small RNA from IP

source_name: NMD Aub-IP

value: Aub-Ab


title: MD Ago3-IP

description: small RNA from IP

source_name: MD Ago3-IP

value: MD; female P-1152 cross to male BC69

value: maternal deposition (MD) cross


title: man_l_3d

description: Sequenced reads were generated from the left mantles of the treated oyster individuals sampled at 3th day after shell breakage.

value: adult

value: tissue


title: MD Aub-IP

description: small RNA from IP

source_name: MD Aub-IP

value: 1-2 week old


title: AC06_cuff_mut_sRNA

description: 19-29nt small RNA squencing

data_processing:
Illumina CASAVA version 1.7 used for basecalling
Mapped to the Drosophila melanogaster genome dm3
Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non-zero expression
Values were quantile-normalized allowing comparisons of the two sets using custom-built software and algorithms as described (Aravin et al., 2008; Olson et al., 2008; Tam et al., 2008)
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimted text file includes reads and their frequencies.

source_name: cuff[wm25]/cuff[qq37] ovaries

extract_protocol:
ovaries dissected, isolation of RNA with Ribozol Reagent
19-29nt sRNA are cloned as detail described in Le Thomas et al. (2014)

value: 3-10 days old

tag: genotype/variation


title: Umbo

description: Sequenced reads were generated from the stage of umbo larvae at 8.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: Umbo

value: Umbo larvae

value: Umbo


title: NMD Piwi-IP

description: small RNA from IP

source_name: NMD Piwi-IP

value: NMD; male P-1152 cross to female P-1152

value: No maternak deposition (NMD) cross

value: ovary

value: Piwi-Ab


title: female

description: Sequenced reads were generated from the female gonad of an individual of "G3" family in Crassostrea gigas.

source_name: female gonad (adult of one years old from the F1 progeny of family "G3")

value: adult (one year old)

value: F1 progeny of "G3" family

value: female gonad


title: Egg

description: Sequenced reads were generated from the egg stage at 0 h in Crassostrea gigas.

source_name: Eggs from the F1 progeny of "G3" family

value: Egg

value: Eggs from the F1 progeny of "G3" family

value: developmental stage


title: MD Piwi-IP

description: small RNA from IP

source_name: MD Piwi-IP

value: MD; female P-1152 cross to male BC69

value: maternal deposition (MD) cross

value: rabbit polyclonal antisera directed against the N-terminal 14–16 AA (Brennecke et al. 2007)


title: AC53_cuff_het_rRNAdel

description: rRNA depleted total RNA squencing

source_name: mixture of cuff[wm25]/CyO and cuff[qq37]/CyO ovaries

extract_protocol:
ovaries dissected, isolation of RNA with Ribozol Reagent, rRNA depleted with Ribo-Zero™ rRNA Removal Kit (epicentre)
NEBNext Ultra Directional RNA Library Prep Kit – #E7420

value: cuff[wm25]/CyO; cuff[qq37]/CyO


title: shRhino RNA seq

description: rRNA depleted total RNA squencing

data_processing:
Bowtie mapping to ribosomal RNA, then to dm3, 0 mismatches, unique mappers
BAM file conversion
big wig file production
Genome_build: dm3
Supplementary_files_format_and_content: big wig file

source_name: shRhino RNA seq

growth_protocol: shRhino flies were obtained from Bloomington stock center (stocks 34071 and 35171) and driven by Nos-Gal4 (stock 4937).

extract_protocol:
ovaries dissected, isolation of RNA with Trizol Reagent
NEBNext mRNA Library Kit

value: shRhino knockdown

value: 1-2 week old


title: male

description: Sequenced reads were generated from male gonad in Crassostrea gigas. The male gonad is sampled from a individual in the F1 generation of the "G3" family.

source_name: male gonad (adult of one years old from the F1 progeny of family "G3")

value: male gonad

value: tissue


title: Remainder

description: Sequenced reads were generated from the mixture of remainder tissues in Crassostrea gigas after sampling the main part of hemolymph, mantle, gonad, digestive gland, gill, labial palp, and adductor muscle.

source_name: Remainder (adult of two years old)

value: mixture tissues of adult (two years old)

value: wild

value: Remainder


title: Blastula

description: Sequenced reads were generated from the stage of blatula at 4 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Blastula

value: Blastula

value: F2 progeny of "G3" family


title: MD total RNA

description: total small RNA

source_name: MD total RNA

value: ovary


title: AC05_cuff_het_sRNA

description: 19-29nt small RNA squencing

value: 3-10 days old


title: Trochophore

description: Sequenced reads were generated from the stage of trochophore at 11 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: Trochophore

value: Trochophore larvae

value: Trochophore


title: wildtype nuclear run-on RNA seq

description: run-on RNA from ovaries, wildtype

source_name: D. mel ovaries

extract_protocol:
ovaries dissected, nuclei isolated, run-on reaction for 25 min, isolation of RNA with Trizol Reagent
NEBNext Directional Library Kit
total RNA directional library

value: wild type


title: early

description: Sequenced reads were generated from early developmental stages in Crassostrea gigas. The early developmetnal stages including the stage of second polar body ejected at 35 min after insemination, four cells stage at 1.5 h, morula stage at 3.5 h, the stage when embryo can rotate at 5.5 h, early gastrula stage at 7.5 h, early trochophore stage at 9.5 h, trochophore at 11.5 h, trochophore at 13.5 h, early D-shaped larvae at 15.5 h, D-shaped larvae at 17.5 h, and D-shaped larvae at 19.5 h.

source_name: mass of larvae at the early developmental stages

value: mixture from zygote to 19.5 hours old embryo

value: developmental stage


title: late

description: Sequenced reads were generated from late planktonic stages and spat in Crassostrea gigas, including the stage of D-shaped larvae at 21.5 h, D-shaped larvae at 1.75 day, D-shaped larvae at 3.77 day, early umbo larvae at 5.73 day, umbo larvae at 7.75 day, umbo larvae at 9.75 day, umbo larvae at 11.75 day, umbo larvae at 13.75 day, umbo larvae at 15.75 day, eyed larvae at 16.75 day, and spat at 22.15 day.

source_name: mass of larvae at the later developmental stage

value: mixture from 21.5 hours old embryo to 22 day old spat


title: shWhite RNA seq

description: rRNA depleted total RNA squencing

source_name: shWhite RNA seq

value: shWhite knockdown


title: shRhino nuclear run-on RNA seq

description: run-on RNA from ovaries, shRhino

value: Rhino knockdown

value: 1-2 week old


title: Spat

description: Sequenced reads were generated from the stage of spat at 22.15 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: Spat

value: Spat


title: F-gonad

description: Sequenced reads were generated from female gonad in Crassostrea gigas. The individual whose organs are isolated and sampled respectively is a female.The gonad is full of eggs as oyster has millions of eggs in the gland at mature season, while the gland tissue maybe only take up very few part.

source_name: Female gonad (adult of two years old)

value: adult (two years old)

value: Female gonad

value: tissue


title: Pediveliger

description: Sequenced reads were generated from the stage of eyed larvae at 18.03 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ÂºC from the 4.77 day.

source_name: Pediveliger

value: Pediveliger larvae

value: Pediveliger


title: L-palps

description: Sequenced reads were generated from labial palp in Crassostrea gigas, an organ just out of the mouth.

source_name: Labial palps (adult of two years old)

value: wild

value: Labial palps


title: Cutoff PFA ChIPseq  Input

description: The Cutoff-EGFP fly line (Nanos-GAL4/UASp-Cutoff-GFP), Cuff^wm25 and Cuff^qq37 were a generous gift from T. Schupbach.

data_processing:
Bowtie mapping on dm3, 0 mismatches, unique mappers
BAM file conversion
wig file production, RPM normalization
Genome_build: dm3
Supplementary_files_format_and_content: wig file

extract_protocol:
100 flies, per IP condition, were put on yeast for 2 to 3 days before ovary dissections. Ovaries were fixed using Paraformaldehyde (PFA) at a final concentration of 1% and incubated for 10min at RT. Samples were quenched by adding directly glycine (finale concentration 25mM) for 5min at RT, and then washed 3 times in PBS. Ovaries were afterwards slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) prior to sonication. Sonication was done using a Bioruptor from Diagenode on Medium power for 20 cycles (30sec ON, 30sec OFF). Samples were centrifuged, supernatant collected and pre-cleared for 2h at 4C using Dynabeads Protein G (Invitrogen) beads. If RNase treatment was required, half of the sample was incubated with 1µl of RNase A (10mg/ml) during pre-clearing and all samples incubated 2h at RT. Meanwhile, in parallel, antibodies were conjugated to Dynabeads Protein G for 2h at 4C too. 5% of pre-cleared samples were saved for Input fraction and the rest was then transferred to the antibody-conjugated beads and incubated for 2h at 4C. Beads were then washed 5 times at 4C using LiCl IP Buffer (10mM Tris ph7.5; 500mM LiCl; 1% NP-40/Igepal; 1% Sodium Deoxycholate), then rinse in TE and finally resuspended in Proteinase K Buffer (200mM Tris ph7.4; 25mM EDTA; 300mM NaCL; 2% SDS) with 100µg of proteinase K. Samples were incubated 3h at 55C then overnight at 65C. DNA was then extracted following standard phenol-chlorophorm extraction and concentration was measured by Qbit. In case of the Cutoff ChIP-seq, the experiment was also performed using an altered protocol: ovaries were treated with Collagenase (2mg/ml) for 3 minutes at room temperature (RT), wash once in PBS, then fixed using fresh EGS (Thermo Scientific, 21565) solution (1,5mg/ml final in PBS) for 30 min at RT. Paraformaldehyde (PFA) was then added to the solution to a final concentration of 1% and incubated for 10min at RT. Consecutive steps were as previously described.
NEBNext ChIPseq Library Kit

treatment_protocol: For Cufoff ChIPseq only, 2 fixation methods used: either PFA, or EGS+PFA.

value: Cutoff-EGFP

value: 1 week old

value: ovary


title: A-muscle

description: Sequenced reads were generated from adductor muscle in Crassostrea gigas.

source_name: Adductor muscle (adult of two years old)

value: Adductor muscle


title: Cutoff PFA ChIPseq

value: GFP

tag: antibody vendor

value: DSHB

tag: antibody cat.#


title: Gill

description: Sequenced reads were generated from gill in Crassostrea gigas.

source_name: Gill (adult of two years old)

value: Gill


title: D-shape

description: Sequenced reads were generated from the stage of D-shaped larvae at 17 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ÂºC and the salinity of 30 ppt.

source_name: D-shape

value: D-shape veliger larvae

value: F2 progeny of "G3" family

value: D-shape

value: developmental stage


title: AC54_cuff_mut_rRNAdel

description: rRNA depleted total RNA squencing

source_name: cuff[wm25]/cuff[qq37] ovaries

value: 3-10 days old


title: Mantle_inner

description: Sequenced reads were generated from the inner part of mantle in Crassostrea gigas. The inner part of mantle and the inner surface of shell are in close proximity.

source_name: Mantle_inner (adult of two years old)

value: adult (two years old)

value: inner mantle

value: tissue


title: Cutoff EGS ChIPseq  Input


title: D-gland

description: Sequenced reads were generated from digestive gland in Crassostrea gigas, the sample includes all the tissues in visceral mass.

source_name: Digestive gland (adult of two years old)

value: wild

value: Digestive gland


title: Mantle_outer

description: Sequenced reads were generated from outer edge of mantle in Crassostrea gigas. This part of tissue is along the edge of shells and is thought to be rich of sensory elements, as well as responsible for the extension of shell.

source_name: Mantle_outer (adult of two years old)

value: outer mantle


title: Cutoff EGS ChIPseq

value: Cutoff-EGFP

value: 1 week old


title: Rhino ChIPseq

description: The Rhino-BioTAP flies were made by fusing the BioTAP tag (Alekseyenko et al. 2014 )to the C-terminal region of the Rhino gene under the UASp promoter.

value: Rhino-BioTAP

value: ovary

value: pan Mouse IgG dynabeads


title: Rhino ChIPseq Input


title: Af_15min+O2-C4

status: Public on Jul 25 2014

city: Jena

first: Steffen

last: Priebe

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Hans-Knöll-Institute (HKI)

data_processing:
FASTQ files were received from GATC, Konstanz, Germany
Sequenced reads were trimmed for low-quality regions (btrim windowsize 15 average 20)
Mapping of reads using TopHat (v2.0.6; -G GFF from CADRE (Central Aspergillus Data REpository); -maxintronlength 10000)
Read counting using htseq-count (-mode union, -s no, -type CDS)
Calculation of RPKM values using raw counts, sum of totally mapped reads and sum of CDS length using CADRE GFF file
Genome_build: Aspergillus fumigatus CEA10 (CADRE)
Supplementary_files_format_and_content: xls

organism: Aspergillus fumigatus

source_name: hyphae

growth_protocol: To analyze the low oxygen response, the fungus was grown in an O2-controlled fermenter (Biostat B-DCU-5l, Braun,  Melsungen, Germany), essentially as described earlier (Barker et al., 2012).  Briefly, conidia were inoculated in AMM with 1% [w/v] of Glucose as the sole source of carbon at a final concentration of 105 ml-1 in a total culture volume of 4 l at 37°C and a constant stirring rate of 250 rpm. A pO2 electrode (InPro6800/12/320, Mettler-Toledo, Steinbach, Germany) was used to monitor the concentration of dissolved O2.

extract_protocol:
Culture aliquots of 200 ml were taken before and at indicated time points throughout the shift. The mycelium was rapidly separated from the medium by filtration, immediately shock frozen in liquid N2 and stored at -80°C until RNA isolation. A phenol-chloroform based method was used to extract total RNA from mycelia. First, 100-mg-aliquots of the deeply frozen mycelium of A. fumigatus were mechanically disintegrated in the presence of 1 ml of TriSureTM (Bioline GmbH, Luckenwalde, Germany) using the FastPrep®24 instrument (MP Biomedicals, Illkirch, France). Following the addition of chloroform and centrifugation, RNA was precipitated from the aqueous phase and solubilized in ultrapure H2O.RNA was e additionally digested with DNaseI and column purified using the RNeasy spin columns (Qiagen, Hilden, Germany) to remove DNA and phenol contaminations, respectively. Concentration and integrity of the RNA were checked by Nanodrop measurements and agarose gel electrophoresis.
tagged random primed cDNA libraries were prepared from fragmented polyA-RNA using standard illumina protocols

treatment_protocol: Cultures were aerated with a continuous flow of air to maintain O2 saturation at 100% (≈260 µmol l-1) at an initial gas flow rate of 0.65 l min-1. After an initial growth phase of 16-18 h (timepoint 0 min) cultures were rapidly shifted to microaerobic conditions by switching to a preadjusted ratio of N2 and air which lowered the initial O2 concentration down to 5% and samples were taken after 15 and 30 min (timepoint 15 and 30 min, respectively). After 60 min, full aeration restored 100% O2 saturation and a last sample was taken after 15 min (timepoint 75 min).

value: CEA 10

tag: treatment protocol

value: timepoint 75 min, 100 % oxygen saturation

tag: cultivation time (minutes)


title: Af_30min-O2-C3

value: timepoint 30 min, 5 % oxygen saturation


title: Af_30min-O2-A3


title: Af_15min-O2-B2

value: timepoint 15 min, 5 % oxygen saturation


title: Af_15min+O2-B4


title: mrna_ko_b

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Wiggle track construction and read quantitation using custom scripts
Genome_build: mm9 with Ensembl release 67 transcripts
Supplementary_files_format_and_content: .bw files contain bigwig tracks with strand-specific alignments. Qexpr.txt files contain three columns: 1. feature name; 2. feature length; 3. feature read count

source_name: Testis

extract_protocol:
lysis in 1% Triton with homogenization, clarification by centrifugation, Trizol extraction
TruSeq RNA-Seq Prep Kit v2 (fragmentation to 120 - 200 bp, random primed cDNA synthesis, non-strand-specific ligation and PCR)

value: testis

tag: genotype

value: Mael-/-

tag: rip antibody


title: Af_15min+O2-A4

tag: cell type


title: Af_0min+O2-B1

value: timepoint 0 min, 100 % oxygen saturation


title: Af_0min+O2-C1


title: ribo_ko_b

extract_protocol:
lysis in 1% Triton with homogenization, clarification by centrifugation, Rnase I footprinting, sucrose cushion ultracentrifugation, Trizol extraction, size selection 26 - 34 nt
preadenylylated linker ligation, strand-specific reverse transcription, first-strand cDNA circularization, PCR amplification

tag: tissue


title: Af_15min-O2-A2


title: Af_0min+O2-A1


title: Hemolymph

description: Sequenced reads were generated from hemolymph in Crassostrea gigas. The RNA were extracted from the blood.

source_name: Hemolymph (adult of two years old)

tag: developmental stage

value: adult (two years old)

value: Hemolymph


title: ribo_wt_b

value: wild type


title: mrna_wt_b


title: ribo_ko_a


title: mrna_wt_a


title: ribo_wt_a


title: pirna_ko_b

extract_protocol:
lysis in 1% Triton with homogenization, clarification by centrifugation, Trizol extraction, size selection by PAGE for 15 - 50 nt
ScriptMiner Small RNA-Seq Library Preparation Kit (sequential 3' and 5' adapter ligations, strand-specific cDNA synthesis and PCR)


title: pirna_wt_b


title: Af_15min-O2-C2


title: Af_30min-O2-B3


title: pirna_ko_a


title: pirna_wt_a


title: mael_medium

extract_protocol:
RNA immunoprecipitation, Trizol extraction, size selection 50 - 150 nt
ScriptMiner Small RNA-Seq Library Preparation Kit (sequential 3' and 5' adapter ligations, strand-specific cDNA synthesis and PCR)

value: anti-Mael


title: mael_a

extract_protocol:
RNA immunoprecipitation, Trizol extraction
TruSeq RNA-Seq Prep Kit v2 (fragmentation to 120 - 200 bp, random primed cDNA synthesis, non-strand-specific ligation and PCR)


title: mael_b


title: 36SB

city: Toronto

first: Rama

last: Khokha

address: 101 College St

department: Medical Biophysics

country: Canada

institute: Ontario Cancer Institute

data_processing:
each read in the Illumina FASTQ file was processed to remove adapters, searching on both strands using cutadapt v0.3 (code.google.com/p/cutadapt/).
Barcodes were identified at the start of each read, requiring exact matches to each specific 5nt sequence, followed by the 23bp lentiviral (LTR) or 24bp transposon (IR/DR) primer sequence.
Each read was matched to one of the 72 barcodes on this basis and demultiplexed into separate files.
The resulting sequences were mapped to the human genome (build HG17/NCBI35) using BWA v0.5.9
Reads mapping to exactly the same genomic coordinates were collapsed using Picard v1.35 (picard.sourceforge.net/), and those only supported by a single read were removed.
Genome_build: hg17
Supplementary_files_format_and_content: Excel file. The first position of plus strand mappings and the last position of minus strand mappings were selected as coordinates of the transposon or lentiviral insertion junctions. All tumor sample and parental cell line data were combined and filtered for non-redundant mappings of SB or LV insertion junctions across the sample panel

source_name: bone explant mesenchymal cell

growth_protocol: Human primary bone explant cultures were generated from discarded surgical samples of patients undergoing hip and knee replacement surgery. The cleaned bone fragments and outgrowths were maintained in DMEM H21 supplemented with 10% FBS. Cells were expanded over 1-3 passages and cryopreserved.

extract_protocol:
Genomic DNA was extracted from tumors after proteinase K digestion (Qiagen) overnight, using phenol-chloroform/ethanol precipitation.
LAM-PCR was used for lentiviral and transposon genomic flank analysis. Nested PCR reactions were performed using primers Illumina-1 and Illumina-2. The PCR products were purified using a ChargeSwitch-Pro PCR Clean-up Kit, and all samples were combined at a 1:1 mass ratio. Internal vector products were further suppressed by implementing a second NarI/BamHI digest on the library, followed by amplification using a small quantity of the digest reaction as a template and the primers Illumina-1 and Illumina-2. The product from reaction was subsequently purified and submitted for next generation sequencing.

treatment_protocol: T5RM-SB/Tet cells were transduced with Lentihop vectors, and then plated either in regular media (Dox-), or media containing 20ng/mL Dox (Dox+), providing 7 days of exposure to Dox, in the case of T5RM-SB/Tet(Dox+) cells). 5x105 cells from each cell population were injected subcutaneously in mice.Tumors yeild were removed and divided into portions to be snap frozen for DNA extraction.

value: Tumor

tag: group

value: Inducible (Dox -)


title: 35LV


title: mrna_ko_a


title: 34SB


title: 33SB


title: 35SB


title: 34LV


title: 29SB


title: 28SB


title: 30LV


title: 32LV


title: 30SB


title: 31SB


title: 33LV


title: 28LV


title: 27LV


title: 27SB


title: 29LV


title: 32SB


title: 26SB


title: mael_small

extract_protocol:
RNA immunoprecipitation, Trizol extraction, 15 - 50 nt
ScriptMiner Small RNA-Seq Library Preparation Kit (sequential 3' and 5' adapter ligations, strand-specific cDNA synthesis and PCR)


title: igg

value: rabbit IgG


title: 25LV


title: 25SB


title: 26LV


title: 24SB


title: 24LV


title: 31LV


title: 36LV


title: 23SB


title: 22SB

value: non-inducible


title: 21LV


title: 21SB


title: 23LV


title: 20LV


title: 22LV


title: 20SB


title: 18LV


title: 16LV


title: 16SB


title: 17SB


title: 19SB


title: 19LV


title: 17LV


title: 14SB


title: 13LV


title: 15LV


title: 12SB


title: 13SB


title: 15SB


title: 14LV


title: 12LV


title: 11SB


title: 11LV


title: 10LV


title: 9SB


title: 8SB


title: 9LV


title: 8LV


title: 7SB


title: 6LV


title: 6SB


title: 5LV


title: 18SB


title: 7LV


title: 3LV

value: cell culture

value: Preinjection


title: 5SB


title: 2SB


title: 3SB


title: 4LV


title: 1LV

value: Base cell culture


title: 2LV


title: 4SB


title: 1SB


title: Pol II ChIP-seq UVB+3H

city: Rotterdam

first: Akos

last: Gyenis

address: Wytemaweg 80

department: Genetics

country: Netherlands

institute: ERASMUS MC

description: UVB treated, Pol II ChIP at 3H

data_processing:
ELAND
2 maximum mismatches
Datasets are normalized by using Bioconductor's DESeq package
Genome_build: UCSC hg19 version
Supplementary_files_format_and_content: BED files

source_name: breast cancer cells

growth_protocol: MCF-7 cells were cultured in DMEM +10% FCS + insulin + antibiotics

extract_protocol:
Standard ChIP protocol
Illumina HiSeq 2000 platform, according to manufacturer's protocol

treatment_protocol: MCF-7 cells were irradiated with 55J/m2 UVB then Pol II ChIP was carried out at different time points

tag: cell line

tag: passages

tag: treatment

value: UVB irradiated

value: RNA Polymerase II ChIP (sc-224x)


title: Pol II ChIP-seq UVB+5H

description: UVB treated, Pol II ChIP at 5H

tag: antibody


title: Pol II ChIP-seq UVB+1H

description: UVB treated, Pol II ChIP at 1H


title: Pol II ChIP-seq UVB+6H

description: UVB treated, Pol II ChIP at 6H


title: Pol II ChIP-seq UVB+2H

description: UVB treated, Pol II ChIP at 2H


title: Pol II ChIP-seq UVB+4H

description: UVB treated, Pol II ChIP at 4H


title: 10SB


title: control rep2

status: Public on Jul 24 2014

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

country: Israel

institute: University of Haifa

data_processing:
Base-calling using RTA VN:1.8.70.0 (rep1 and rep2) or RTA VN:1.13.48.0 (rep3 and rep4), followed by illumina2bam 0.3 for creating unaligned bam files (only rep3 and 4).
Alignment using Bowtie2 v2.0.0 and Tophat v1.4.1
Exon based expression analysis: Analysis of differences in the expression of exon fragments was performed in R using the DEXseq package as described previously (Anders et al., 2012). Differential expression was considered statistically significant if p<0.01. The results of this analysis are included in the processed data files.
Analysis of differential splice junction usage: the number of reads spanning exon-exon junctions in the different conditions were normalized to the total number of mapped reads and for each exon-exon junction (with at least 20 mapped reads in all control conditions) normalized read numbers in control and spk-1(RNAi) were compared using PERL. Differential splice junction usage was considered statistically significant if p<0.01.  The results of this analysis are included in the processed data files.
Genome_build: WS220/ce10
Supplementary_files_format_and_content: DEXseqresultstable.txt: expression estimates and p values of all exons
Supplementary_files_format_and_content: splicejunctionreads.txt: numbers of reads spanning all exon-exon junctions in control and spk-1(RNAi)
Supplementary_files_format_and_content: DEXseqresults_p01.txt: expression estimates and p values of differentially expressed exons
Supplementary_files_format_and_content: splicejunctionanalysis.txt: numbers of reads spanning differentially used exon-exon junctions in control and spk-1(RNAi)

organism: Caenorhabditis elegans

source_name: whole adult worms

growth_protocol: Worms were grown on NGM plates at 20ºC following standard protocols.

extract_protocol:
At least 100 adult worms per condition were collected in 0.1 M NaCl and mRNA was isolated using the Trizol reagent (Life technologies) according to the manufacturer’s protocol. Sample preparation was performed essentially as described previously (Mortazavi et al., 2008). First-strand cDNA synthesis was performed using SuperScript VILO cDNA synthesis kit (Invitrogen) according to the manufacturer’s protocol using 50 ng/µl random hexamers as primers. To preserve strand information, dUTP was used instead of dTTP for second strand synthesis.
Libraries were prepared using standard Illumina protocols.

treatment_protocol: L4 worms were transferred to E.coli containing either the empty feeding RNAi vector (L4440, control) or expressing spk-1 dsRNA. RNAi by feeding was performed for 24h at 25ºC.

tag: strain

tag: Stage

value: adult

value: whole worm


title: spk-1(RNAi) rep1


title: control rep1


title: Male#2 Brain

city: Boston

first: Muhammad

middle: B

last: Ekram

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Library strategy: Targeted Repeat Element Bisulfite Sequencing (HT-TREBS)
Basecalls and initial quality filtering were performed by the Ion Torrent Server (v3.4.1).
Reads in the fastq files were filtered to remove any sequence less than 40bp in length.  This removed any short and redundant seqeunce that may not have enough lengths of the non-repeat unique sequence and the IAPLTR sequence.  The filtered reads were mapped to a curated reference genome using the aligner Bowtie 2 with the following configurations: --local, --sensitive-local, -M 2.  This curated genome is made up of bisulfite-converted top (Original Top: OT) and the bottom (Original Bottom: OB) strands of the IAPLTR sequences (along with the 350-bp flanking sequences) and the complementary sequences to those sequences (Complementary to Original Top: CTOT; Complementary to Original Bottom: CTOB).  The original IAPLTR and their flanking sequences were obtained from the mm9 version of the mouse genome.
The mapped reads were then filtered using custom Python scripts to extract only the sequences that had been mapped to the IAPLTR regions and also had at least 10 bases of the flanking unique sequences to ensure the reads were generated from a specific IAPLTR locus.
The filtered reads from each sample were separately analyzed using the BiQ Analyzer HT tool to derive the CpG methylation status of each IAPLTR locus and also other relevant information regarding the quality of the reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated using custom script.  Values in the data value column (fourth column) represent the methylation fraction of the cytosine that has been refered to by the coordinates.

source_name: Male#2 Brain

growth_protocol: Tissues from wild-type, postnatal day 7 C57BL/6N littermates were were harvested.

extract_protocol:
Tissues were harvested and lysed using tail lysis buffer containing Proteinase K.  Genomic DNA was isolated and purified using the phenol–chloroform extraction method (Sigma-Aldrich, Cat# P2069).
Briefly, 1µg of the isolated genomic DNA was sonicated to fragments with their average size being 700 bp in length (Bioruptor NGS, Diagenode).  Since the average lengths of IAPLTR are 300-350 bp in length and the desired sequences need to contain non-repeat flanking sequences, the optimum size of the fragments are empirically determined to be around 700 bp in length.  The fragmented DNA was immediately end-repaired using the NEB Next End Repair Module (New England BioLabs), and then ligated to custom-made duplex Ion Torrent ‘A’ adaptors using T4 DNA ligase (New England BioLabs).  In these adaptors, all the Cs have been methylated (Integrated DNA Technologies).  The adaptor-ligated DNA fragments were size-selected to remove any fragment smaller than 300 bp in length using the Agencourt AMPure XP beads (Beckman Coulter).  The size and quantity of the selected fragments were analyzed using the Agilent 2100 Bioanalyzer.  The adaptor-ligated DNA library was modified using the bisulfite conversion reaction according to the manufacturer’s protocol (EZ DNA methylation kit, Zymo Research).  The bisulfite-converted ‘A’ adaptor-ligated library was used as a template for a round of PCR (Maxime PCR Premix Kit, Intron Biotech).  In this PCR, the forward primer (CCATCTCATCCCTGCGTGTCTCCGACTCAG) was designed to bind to the 5’-end of the ‘A’ adaptor region whereas the reverse primer was designed to bind to the 24-bp conserved region among the consensus sequences of the IAPLTR subtypes (IAPLTR1, IAPLTR1a, IAPLTR2, IAPLTR2a, and IAPLTR2b).  The 5’-end of the reverse primer also had the sequence of the regular Ion Torrent ‘P1’ adaptor (CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT^CTCCCTAATTAACTACAACCCATC).  The break in the reverse primer sequence indicates the joining point of the P1 adaptor sequence and the IAPLTR-specific sequence.  The amplification cycle number of PCR was individually determined for each of the twelve samples so that the minimum possible cycles were used to generate just enough amount of the PCR product for sequencing.  The PCR product was size-selected for a range of 250-300 bp in length using agarose gel electrophoresis.  The size-selected PCR product was verified for its length and quantity using the Agilent 2100 Bioanalyzer.  Finally, each of the twelve PCR products was individually sequenced in the Ion Personal Genome Machine (PGM) Sequencer using Ion 318 Chips (Ion Torrent, Life Technologies).

tag: gender

value: Male

tag: genotype/variation

value: wild-type

tag: age

value: Postnatal day 7

value: Whole brain


title: Male#2 Kidney

source_name: Male#2 Kidney

value: Whole kidney


title: Male#2 Liver

source_name: Male#2 Liver

value: Whole liver


title: Male#1 Kidney

source_name: Male#1 Kidney


title: Male#1 Liver

source_name: Male#1 Liver


title: Male#1 Brain

source_name: Male#1 Brain


title: Female#2 Liver

source_name: Female#2 Liver

value: Female


title: Female#2 Brain

source_name: Female#2 Brain


title: Female#1 Liver

source_name: Female#1 Liver


title: Female#1 Kidney

source_name: Female#1 Kidney


title: Pol II ChIP-seq control

description: Control dataset

value: Non-treated


title: MYB prom donor B

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

institute: The Weatherall Institute of Molecular Medicine

data_processing:
Basecalls performed using CASAVA version 1.6 (Bustard)
Alignment performed using Bowtie against hg18 reference genome
Only unique mapping reads were used for the ChIP-seq downstream analysis
Genome_build: hg18
Supplementary_files_format_and_content: BigWig

source_name: human erythroid progenitor (HEP)

growth_protocol: Erythroid cells were cultured using a 2-phase liquid system. Mononuclear cells were isolated from peripheral blood by centrifugation on a gradient of Ficoll-Hypaque and cultured for 7 days in phase I medium which consists of serum-free StemSpan (Stem Cell Technologies) supplemented with 1 µg/mL cyclosporin A, 25 ng/mL interleukin-3, 50 ng/mL human stem cell factor (Sigma), and 0.01% bovine serum albumin. Cells were incubated at 37°C, 5% CO2. After 7 days, nonadherent cells were collected and reseeded at a concentration of 2.5 x 105 cells/mL in phase II medium (StemSpan supplemented with 10-7 M dexamethasone σ, 50 ng/mL stem cell factor, and 2 U/mL human recombinant erythropoietin [EPO; Sigma]). The cultures were diluted once or twice to maintain the cell concentration lower than 1 x 106 cells/mL in phase II. Cell samples were collected from phase II cultures on days 0, 2, 3, 4, 5, 6, and 7 and evaluated for number and viability.

extract_protocol:
Cells were harvested at day 7-8 of culture and crosslinked using formaldehyde (1% final volume for ChIP-Seq, 2% final volume for 3C-Seq) and nuclei were isolated. For ChIP-Seq, nuclei were sonicated and protein-DNA complexes isolated using antibodies. For 3C-Seq, nuclei were digested and ligated under dilute conditions with primary and secondary restriction enzymes.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols. 3C-seq library preparation was described in detail in Stadhouders et al. Nature Protocols (2013).

value: human erythroid progenitor (HEP)

value: MYB promoter


title: -84kb enhancer donor A

value: -84kb enhancer


title: spk-1(RNAi) rep2


title: Rabbit IgG HEP

description: ChIP-Seq

tag: antibodies

value: Rabbit IgG


title: MYB prom donor A


title: LDB1 HEP

description: ChIP-Seq


title: Goat IgG HEP

description: ChIP-Seq

value: Goat IgG


title: CTCF HEP

description: ChIP-Seq

value: CTCF


title: Usp3-KO rep2_NaiveB

city: Amsterdam

first: Elisabetta

last: Citterio

address: Plesmanlaan 121

department: Molecular Genetics

institute: Netherlands Cancer Insitute (NKI-AVL)

data_processing:
Sequence reads were mapped to mm9 using tophat version 2.0.3 with parameters --library-type fr-unstranded, --no-coverage-search -M --transcriptome-index, Ensembl GTF version 66
Readcounts were obtained by counting the number of reads per gene using HTSeq-count.
Differential expression was performed using the R package DEGseq. Upon differential expression analysis all values were added with 1. Genes that had no expression in both samples were removed.
Genome_build: mm9
Supplementary_files_format_and_content: The tab-delimited text files contain gene expressions for all samples and the results (including fold change and p-value) of a differential expression analysis for selected samples.

source_name: Naive B cells

extract_protocol:
LSKs (FACS sorted from freshly isolated bone marrow mononuclear cells), naive splenic B cells (freshly FACS sorted) or FACS sorted LPS-activated B cells were used. Cells from individual animals (4 per genotype/ per experiment) were pooled, and total RNA was harvested using Trizol reagent. RNAseq was performed on an Illumina Hiseq2000 machine. Naive splenic B cells were obtained by CD43 depletion using biotynilated anti-CD43 (Clone S7, BD Biosciences), and the Imag system (BD Biosciences). Naive B cells were directly FACS sorted with fluorochrome-conjugated antibody specific for CD19, or cultured in vitro for four days in IMDM+8%FBS and 50 microgram/ml E.coli LPS (Sigma) to obtain activated B cells, followed by sorting. Two independent experiments were performed. Cell sorting was performed by FACSAria (BD Biosciences).
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocols.

value: Spleen

value: 8 weeks


title: Usp3-KO rep1_NaiveB


title: Usp3-KO rep2_LSK

source_name: LSK

value: Bone marrow


title: WT rep1_NaiveB

value: wild type


title: WT rep1_LPSactivatedB

source_name: LPS activated B cells


title: WT rep2_NaiveB


title: Usp3-KO rep1_LPSactivatedB


title: Usp3-KO rep1_LSK


title: WT rep2_LSK


title: Female#2 Kidney

source_name: Female#2 Kidney

value: wild-type


title: Sen1-FRB With Rapamycin (Rep 1 and 2)

city: Baltimore

first: Jeff

last: Corden

state: MD

address: 725 N Wolfe Street

department: Molecular Bio and Gen

institute: JHU

data_processing:
Trimmed: 3' Adaptor using R/BioConductor Package.
Filtered: Reads greater than 13 nucleotides. Script available upon request.
Condensed: Identical sequences into 1 unique read. Script available upon request.
Aligned: All reads to a genome only consisting of the tRNA genes of the yeast SacCer3 (R64) genome using Bowtie 1.0.
Aligned: All reads that did not align to the tRNA yeast genome to the SacCer3 (R64) genome using Bowtie 1.0.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Wig files

source_name: Yeast, Sen1-FRB, with rapamycin

extract_protocol:
PAR-CLIP
Adaptation of NEB-Next Small RNA Library Prep Set for Illumina (Multiplex version).

tag: strain/background

tag: crosslinking device

value: Hamamatsu LC-L5 LED UV Lamp

tag: maximum time of rapamycin exposure

value: 45 mins


title: Rpb2-HTB Control With Rapamycin (Rep 1 and 2)

source_name: Yeast, Rpb2-HTB, with rapamycin


title: Ysh1-FRB With Rapamycin

source_name: Yeast, Ysh1-FRB, with rapamycin


title: -84kb enhancer donor C

tag: cell type


title: control rep4

source_name: whole adult worms

value: adult

tag: tissue

value: whole worm


title: spk-1(RNAi) rep3


title: Nrd1-FRB With Rapamycin (Rep 1 and 2)

source_name: Yeast, Nrd1-FRB, with rapamycin


title: control rep3


title: Nrd1-FRB Without Rapamycin (Rep 1 and 2)

source_name: Yeast, Nrd1-FRB, without rapamycin

value: 0 mins


title: 7_66_LN CD4_IFNRa_D28

status: Public on Jul 23 2014

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
s_2_1_4_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt

data_processing:
RNA-Seq data were aligned to a provisional assembly of Indian Macaca mulatta  (MuSuRCA rhesus assembly v.4) using STAR version 2.3.0e. {Dobin 2012}; parameters were set using the annotation as a splice junction reference, un-annotated non-canonical splice junction mappings and non-unique mappings were removed from downstream analysis.
Transcripts were annotated using the provisional UNMC annotation v4.12 Norgren Accession pending. Transcript assembly, abundance estimates, and differential expression analysis was performed using Cufflinks v2.1.1 and Cuffdiff 2{Trapnell 2013}.
Group 1 was comprised of 166 samples and contained the samples from PBMCs from the saline+SIV, IFN-1ant+SIV, and pegylated IFN_2a-treated+SIV animals, and from samples for the analysis of PBMCS, LN CD4+ T cells and rectal biopsies of uninfected, IFNa treated animals; the average number of mapped reads was 12,188,890 (range: 3,237,374-87,371,564).
Group 2 was comprised of the LN CD4 T cells from the three SIV-infected groups consisting of 37 samples, the average mapped read count for this group was 4,898,448 (range: 1,173,455-19,310,483).
Genome_build: MuSuRCA rhesus assembly v.4
Supplementary_files_format_and_content: Tab delimited text with rows of transcript ID's and columns of sample ID's and sample FPKMs

organism: Macaca mulatta

source_name: lymph node CD4 T cells

extract_protocol:
Total RNA was extracted from samples using RNAzol RT and was enriched for polyadenylated transcripts by hybridization with oligo-dT(25) magnetic beads.
Enriched polyadenylated RNA was fragmented randomly with heat and divalent cations, and reverse-transcribed from random hexamer primers.  Second strand synthesis was then performed using RNAse-H and DNA Polymerase I.  Double-stranded cDNA was end repaired and A-tailed, and then ligated to a hairpin-loop sequencing adaptor (New England Biolabs).  Libraries were then enriched and barcoded by PCR, validated on a Bioanalyzer, and quantified by qPCR.  Individually libraries were then pooled and quantified again before cluster generation and sequencing.

tag: animal id

tag: treatment group

value: IFNRa

tag: day post infection


title: ZE06_LN CD4_IFNRa_D28

description:
s_2_1_5_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_58_LN CD4_IFNRa_D28

description:
s_2_1_3_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_50_LN CD4_IFNRa_D28

description:
s_2_1_1_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_52_LN CD4_IFNRa_D28

description:
s_2_1_2_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: ZE80_LN CD4_IFNRa_D28

description:
s_2_1_6_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 30687_LN CD4_PEG-IFNa2a_D28

description:
s_2_1_14_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: spk-1(RNAi) rep4


title: OF1_LN CD4_Placebo_D28

description:
s_2_1_11_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt

value: Placebo


title: BB85_LN CD4_Placebo_D28

description:
s_2_1_10_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 32960_LN CD4_PEG-IFNa2a_D28

description:
s_2_1_15_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: OF9_LN CD4_Placebo_D28

description:
s_2_1_27_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: WT rep1_LSK

tag: genotype


title: 34766_LN CD4_PEG-IFNa2a_D28

description:
s_2_1_18_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_70_LN CD4_Placebo_D28

description:
s_2_1_9_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 6D7_LN CD4_Placebo_D28

description:
s_1_1_23_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 34774_LN CD4_PEG-IFNa2a_D28

description:
s_2_1_19_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: T4226_LN CD4_Placebo_D28

description:
s_2_1_12_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_68_LN CD4_Placebo_D28

description:
s_2_1_8_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: ZE89_LN CD4_Placebo_D28

description:
s_2_1_7_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_52_LN CD4_IFNRa_D0

description:
s_1_1_2_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_66_LN CD4_IFNRa_D0

description:
s_1_1_4_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 5F0_LN CD4_Placebo_D28

description:
s_2_1_21_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: ZE80_LN CD4_IFNRa_D0

description:
s_1_1_6_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: ZE06_LN CD4_IFNRa_D0

description:
s_1_1_5_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 32960_LN CD4_PEG-IFNa2a_D0

description:
s_1_1_15_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_58_LN CD4_IFNRa_D0

description:
s_1_1_3_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_50_LN CD4_IFNRa_D0

description:
s_1_1_1_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 34774_LN CD4_PEG-IFNa2a_D0

description:
s_1_1_19_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 6D7_LN CD4_Placebo_D-14

description:
s_1_1_22_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 34766_LN CD4_PEG-IFNa2a_D0

description:
s_1_1_18_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 33880_LN CD4_PEG-IFNa2a_D0

description:
s_1_1_16_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: BB85_LN CD4_Placebo_D0

description:
s_1_1_10_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_70_LN CD4_Placebo_D0

description:
s_1_1_9_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_52_PBMC_IFNRa_D84

description:
s_2_1_2_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: PBMC


title: ZE80_PBMC_IFNRa_D84

description:
s_2_1_6_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_66_PBMC_IFNRa_D84

description:
s_2_1_4_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34766_PBMC_PEG-IFNa2a_D84

description:
s_2_1_18_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30297_PBMC_PEG-IFNa2a_D84

description:
s_2_1_13_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30687_PBMC_PEG-IFNa2a_D84

description:
s_2_1_14_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE89_LN CD4_Placebo_D0

description:
s_1_1_7_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_50_PBMC_IFNRa_D84

description:
s_2_1_1_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 33880_PBMC_PEG-IFNa2a_D84

description:
s_2_1_16_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 6D7_PBMC_Placebo_D84

description:
s_1_1_21_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_PBMC_Placebo_D84

description:
s_2_1_12_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34774_PBMC_PEG-IFNa2a_D84

description:
s_2_1_19_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF9_PBMC_Placebo_D84

description:
s_2_1_23_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF9_LN CD4_Placebo_D-14

description:
s_2_1_25_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 7_70_PBMC_Placebo_D84

description:
s_2_1_9_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF1_PBMC_Placebo_D84

description:
s_2_1_11_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: BB85_PBMC_Placebo_D84

description:
s_2_1_10_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_68_PBMC_Placebo_D84

description:
s_2_1_8_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 5F0_LN CD4_Placebo_D-14

description:
s_2_1_20_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 30687_PBMC_PEG-IFNa2a_D28

description:
s_6_1_14_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_52_PBMC_IFNRa_D28

description:
s_6_1_2_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_LN CD4_Placebo_D0

description:
s_1_1_12_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: ZE80_PBMC_IFNRa_D28

description:
s_6_1_6_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE06_PBMC_IFNRa_D28

description:
s_6_1_5_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_50_PBMC_IFNRa_D28

description:
s_6_1_1_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 32960_PBMC_PEG-IFNa2a_D84

description:
s_2_1_15_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30297_PBMC_PEG-IFNa2a_D28

description:
s_6_1_13_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 5F0_PBMC_Placebo_D84

description:
s_1_1_27_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34766_PBMC_PEG-IFNa2a_D28

description:
s_6_1_18_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 33880_PBMC_PEG-IFNa2a_D28

description:
s_6_1_16_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_68_PBMC_Placebo_D28

description:
s_6_1_8_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE89_PBMC_Placebo_D28

description:
s_6_1_7_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF1_LN CD4_Placebo_D0

description:
s_1_1_11_130430_SN622_0218_AC192CACXX
processed data file: Acute_LN-CD4_FPKM_exprs.txt


title: 6D7_PBMC_Placebo_D28

description:
s_5_1_23_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 5F0_PBMC_Placebo_D28

description:
s_6_1_21_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF1_PBMC_Placebo_D28

description:
s_6_1_11_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_70_PBMC_Placebo_D28

description:
s_6_1_9_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 32960_PBMC_PEG-IFNa2a_D28

description:
s_6_1_15_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34774_PBMC_PEG-IFNa2a_D28

description:
s_6_1_19_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: BB85_PBMC_Placebo_D28

description:
s_6_1_10_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_58_PBMC_IFNRa_D28

description:
s_6_1_3_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_PBMC_Placebo_D28

description:
s_6_1_12_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D24

description:
s_6_1_6_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

value: Uninf


title: 7_52_PBMC_IFNRa_D21

description:
s_1_1_2_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF9_PBMC_Placebo_D28

description:
s_6_1_27_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_PBMC_Uninf_D24

description:
s_6_1_5_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D24

description:
s_6_1_4_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_66_PBMC_IFNRa_D21

description:
s_1_1_4_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_58_PBMC_IFNRa_D21

description:
s_1_1_3_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_50_PBMC_IFNRa_D21

description:
s_1_1_1_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE80_PBMC_IFNRa_D21

description:
s_1_1_6_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE06_PBMC_IFNRa_D21

description:
s_1_1_5_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30297_PBMC_PEG-IFNa2a_D21

description:
s_1_1_13_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30687_PBMC_PEG-IFNa2a_D21

description:
s_1_1_14_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34774_PBMC_PEG-IFNa2a_D21

description:
s_1_1_19_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 32960_PBMC_PEG-IFNa2a_D21

description:
s_1_1_15_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 33880_PBMC_PEG-IFNa2a_D21

description:
s_1_1_16_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF1_PBMC_Placebo_D21

description:
s_1_1_11_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_68_PBMC_Placebo_D21

description:
s_1_1_8_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_PBMC_Placebo_D21

description:
s_1_1_12_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_Rectum_Uninf_D21

description:
s_6_1_23_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: Rectum


title: OF9_PBMC_Placebo_D21

description:
s_2_1_22_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 6D7_PBMC_Placebo_D21

description:
s_1_1_20_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 5F0_PBMC_Placebo_D21

description:
s_1_1_25_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_LN CD4_Uninf_D21

description:
s_6_1_13_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34766_PBMC_PEG-IFNa2a_D21

description:
s_1_1_18_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_70_PBMC_Placebo_D21

description:
s_1_1_9_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE89_PBMC_Placebo_D21

description:
s_1_1_7_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_Rectum_Uninf_D21

description:
s_6_1_25_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D21

description:
s_6_1_1_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_PBMC_Uninf_D17

description:
s_5_1_25_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D17

description:
s_5_1_27_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_PBMC_Uninf_D21

description:
s_6_1_2_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_LN CD4_Uninf_D21

description:
s_6_1_15_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D21

description:
s_6_1_3_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D17

description:
s_5_1_23_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_LN CD4_Uninf_D21

description:
s_6_1_14_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D14

description:
s_5_1_20_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D14

description:
s_5_1_22_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_52_PBMC_IFNRa_D10

description:
s_5_1_2_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_PBMC_Uninf_D14

description:
s_5_1_21_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_50_PBMC_IFNRa_D10

description:
s_5_1_1_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_66_PBMC_IFNRa_D10

description:
s_5_1_4_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: BB85_PBMC_Placebo_D21

description:
s_1_1_10_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE06_PBMC_IFNRa_D10

description:
s_5_1_5_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_58_PBMC_IFNRa_D10

description:
s_5_1_3_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE80_PBMC_IFNRa_D10

description:
s_5_1_6_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_Rectum_Uninf_D21

description:
s_6_1_27_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34774_PBMC_PEG-IFNa2a_D10

description:
s_5_1_19_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 32960_PBMC_PEG-IFNa2a_D10

description:
s_5_1_15_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30687_PBMC_PEG-IFNa2a_D10

description:
s_5_1_14_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF1_PBMC_Placebo_D10

description:
s_5_1_11_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE89_PBMC_Placebo_D10

description:
s_5_1_7_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 33880_PBMC_PEG-IFNa2a_D10

description:
s_5_1_16_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30297_PBMC_PEG-IFNa2a_D10

description:
s_5_1_13_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_PBMC_Placebo_D10

description:
s_5_1_12_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34766_PBMC_PEG-IFNa2a_D10

description:
s_5_1_18_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_70_PBMC_Placebo_D10

description:
s_5_1_9_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_68_PBMC_Placebo_D10

description:
s_5_1_8_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: BB85_PBMC_Placebo_D10

description:
s_5_1_10_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 6D7_PBMC_Placebo_D10

description:
s_5_1_22_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE80_PBMC_IFNRa_D7

description:
s_2_1_12_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_50_PBMC_IFNRa_D7

description:
s_4_1_5_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D10

description:
s_5_1_16_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_PBMC_Uninf_D10

description:
s_5_1_18_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D10

description:
s_5_1_19_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_52_PBMC_IFNRa_D7

description:
s_5_1_6_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_66_PBMC_IFNRa_D7

description:
s_4_1_4_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30297_PBMC_PEG-IFNa2a_D7

description:
s_2_1_20_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34774_PBMC_PEG-IFNa2a_D7

description:
s_2_1_27_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE06_PBMC_IFNRa_D7

description:
s_3_1_7_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 32960_PBMC_PEG-IFNa2a_D7

description:
s_2_1_22_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt