title: mouse AT2 cells #3

data_processing:
Fastq files were align to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

extract_protocol: Whole lung dissociation with dispase, collagenase, and DNAse, followed by single cell suspension and FACS sorting. Cells were sorted directly into trizol and whole cellular RNA was prepared and purified on a column.

value: 8 weeks


title: CSF1R-34_L7.N711

status: Public on Jan 08 2018

type: SRA

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

library_source: transcriptomic

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Tumors from C57BL/6N mice subcutaneously inoculated with MC38 cells

extract_protocol:
Tumors were excised and single cell suspensions obtained by mechanical processing and enzymatical digestion (DNAse 0.01%, Dispase 1mg/ml, Collagenase IV 1mg/ml) 16 hrs after treatment. TAM (CD11b+F4/80hiLy6ClowLy6Gneg), monocytic MDSC (CD11b+F4/80-/lowLy6ChiLy6Gneg) were sorted using flow cytometry.  RNA was extracted from multiple FACS-sorted cells or from whole tumor.
1 ng of amplified cDNA was subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: 4 mice/group were treated with 30 mg/kg IgG1 isotype control antibody clone MOPC-21 (BioXCell), 4 mg/kg anti-CD40 rat IgG2a antibody clone FGK45 (BioXCell), 30mg/kg anti-CSF-1R antibody clone 2G2, 4 mg/kg rat IgG2a control clone 2A3 (BioXCell). For depletion experiments 4mg/kg mouse anti-CD4 antibody clone GK1.5 (Biolegend), 4mg/kg anti-NK1.1 antibody clone PK136 (BioXCell) and 4mg/kg anti-CD8α antibody clone 53-6.7 (BioXCell) were administered when tumor size reached 190mm3 in average. Antibodies were given every second day for four times. In between doses two and three of the depleting antibodies, animals were further treated with vehicle control (0,9% sodium saline), MOPC21, FGK45, 2G2 or combination of FGK45 and 2G2. The anti-CSF-1R antibody or respective IgG1 control antibody were administered weekly until tumors regressed completely or animals reached termination criteria, while the anti-CD40 antibody was only administered once at day 11 simultaneously with the anti-CSF-1R antibody. All antibodies were given intraperitoneally. All procedures were performed in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and European Union directives and guidelines.

tag: cell type

value: Ly6ClowLy6Gneg TAM

tag: treatment


title: CSF1R-45_L6

value: Ly6Cpos MDSC

value: IgG controls


title: CSF1R-32_L6.N703


title: CSF1R-28_L26


title: CSF1R-29_L9


title: mouse AT2 cells #2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

source_name: Lung epithelium

tag: age

tag: gender

value: F

tag: tissue

value: lung

value: epithelium


title: CSF1R-30_L17


title: mouse AT2 cells #1


title: mouse AEP cells #2


title: CSF1R-31_L15


title: mouse AEP cells #1


title: Whole population AT2 cell ATAC seq

library_source: genomic

data_processing:
Fastq files were align to the mm9 reference genome using STAR with the following parameters --alignIntronMax 1 --alignEndsType EndToEnd --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4
Peaks were called using MACS2 using the following parameters  '–nomodel --shift -100 --extsize 200 -g mm'
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

extract_protocol: Whole lung dissociation with dispase, collagenase, and DNAse, followed by single cell suspension and FACS sorting. Crude nuclei were prepared from sorted cells and libraries were generated using Tn5 transposase treatment and PCR.

value: epithelial cells


title: Axin2+ AT2 cell ATAC seq


title: MG_UKJ_24_1055_skin

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina's bcl2fastq v1.8.3/ v1.8.4 or CASAVA v1.7 software used for extraction of FASTQ files
Reads were mapped using Tophat (v2.0.6) to the genome taken the annotation into account:  tophat2 -p 24 -o OUTPUTDIR -g 1 --no-coverage-search --transcriptome-index=/transcriptome_data/transcriptome.GRCm38.69 GRCm38.69
Counting of reads per gene was done using either htseq-count v0.5.3p9 (htseq-count --quiet --stranded=no --idattr=gene_id --mode=union SAMFILE Mmu.gtf > OUTPUTFILE) or featureCounts v1.4.3-p1 (featureCounts -T 8 -a Mmu.gtf -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: Ensembl GRCm38.69
Supplementary_files_format_and_content: Excel file contains raw counts and RPKM values of each sample

extract_protocol:
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using either Illumina’s TruSeq RNA sample prep kit or Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.

tag: strain

value: skin


title: MG_UKJ_24_1056_skin


title: MG_UKJ_30_72_skin


title: MG_UKJ_15_234_skin


title: MG_UKJ_30_73_skin


title: MG_UKJ_15_232_skin


title: MG_UKJ_15_233_skin


title: MG_UKJ_30_70_skin


title: MG_UKJ_24_1057_skin


title: MG_UKJ_30_71_skin


title: MG_UKJ_24_1059_skin


title: MG_UKJ_15_230_skin


title: MG_UKJ_09_336_skin


title: MG_UKJ_15_231_skin


title: MG_UKJ_09_337_skin


title: MG_UKJ_09_335_skin


title: MG_UKJ_02_1156_skin

value: young


title: MG_UKJ_09_334_skin


title: MG_UKJ_02_1153_skin


title: MG_UKJ_02_1155_skin


title: MG_UKJ_02_1152_skin


title: MG_UKJ_30_8_liver

value: liver


title: MG_UKJ_30_9_liver


title: MG_UKJ_30_10_liver


title: MG_UKJ_24_1058_skin


title: MG_UKJ_30_69_skin


title: MG_UKJ_30_7_liver


title: MG_UKJ_30_11_liver


title: MG_UKJ_09_338_skin


title: MG_UKJ_24_255_liver


title: MG_UKJ_15_222_liver


title: MG_UKJ_24_256_liver


title: MG_UKJ_15_220_liver


title: MG_UKJ_15_219_liver


title: MG_UKJ_02_1154_skin


title: MG_UKJ_24_254_liver


title: MG_UKJ_15_221_liver


title: MG_UKJ_09_325_liver


title: MG_UKJ_09_324_liver


title: Dmel_120h_repB reanalysis

city: Göttingen

first: Nico

last: Posnien

address: Justus-von-Liebig-Weg 11

department: Department of Developmental Biology

institute: University of Göttingen

description: Reanalysis of GSM1977847

data_processing:
Bowtie2 with parameters –very-sensitive-local –N 1 was used to map the RNA-seq reads to D. melanogaster reference trancripts (FlyBase r5.5 release, CDS only, longest transcript per gene only).
The number of reads mapping to each transcript were summarized using samtools v0.1.19.
HTSFilter was used with default parameters to discard lowly expressed genes across all samples.
The function PoisMixClusWrapper from the library HTSCluster was applied on the rest of genes with the parameters: gmin=1, gmax=25, lib.type=”DESeq”. Djump model was selected. Genes with predicted MAP < 99% were discarded.
Genome_build: FlyBase r5.5 release, CDS only, longest transcript per gene only
Supplementary_files_format_and_content: Dmel_72h_96h_120h_readcount.txt: 10 column text file; first column is the transcript ID, second column is transcript effective length, columns 3 to 10 contain the number of reads mapped to each transcript at each time point and replicate.
Supplementary_files_format_and_content: Cluster_assignment.txt: two column text file, first column contains the transcript ID and second column the cluster it is assigned to.

organism: Drosophila melanogaster

source_name: eye-antennal imaginal disc

growth_protocol: flies were raised at 25ºC and 12h:12h dark/light cycle in density‐controlled conditions (30 freshly hatched LI larvae per vial).

extract_protocol:
Larvae were dissected and eye-antennal imaginal discs were stored in RNALater at 72/96/120h after egg laying. 40-50 discs were dissected for the 120h samples, 80-90 discs for the 96h samples and 120-130 discs for the 72h samples. Total RNA was isolated using Trizol  and the samples were DNAse I treated in order to remove DNA contamination.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit starting from 500 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™dsDNA System . The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp).
cDNA libraries were amplified and sequenced (50 bp single-end reads) using cBot and HiSeq 2000 (Illumina). Sequence images were transformed to bcl files using the software BaseCaller (Illumina). The bcl files were demultiplexed to fastq files with CASAVA (version 1.8.2).

treatment_protocol: no special treatment, wildtype flies were used for all samples

tag: time point

value: 120h AEL (late 3rd instar)

value: OregonR

tag: Sex

value: female


title: Dmel_96h_repB

value: 96h AEL (mid 3rd instar)


title: Dmel_96h_repC


title: MG_UKJ_09_323_liver


title: MG_UKJ_09_320_liver


title: MG_UKJ_09_322_liver


title: Dmel_120h_repC reanalysis

description: Reanalysis of GSM1977848


title: Dmel_120h_repA reanalysis

description: Reanalysis of GSM1977846


title: Dmel_72h_repA

value: 72h AEL (late 2nd instar)

value: male and female


title: MG_UKJ_02_982_liver


title: Dmel_72h_repB


title: Dmel_72h_repC


title: MG_UKJ_02_802_liver


title: MG_UKJ_02_983_liver


title: MG_UKJ_24_252_liver


title: MG_UKJ_24_253_liver


title: MG_UKJ_15_218_liver


title: Dmel_S2_total-RNA-seq_rep1

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: RiboZero total RNA-seq

data_processing:
Base calls performed by standard Illumina pipeline
Read pairs with mean quality <20 (either mate) filtered using custom scripts
Insert size and standard deviation determined via picard tools 1.86 based on bowtie 0.12.8 alignment of 1,000,000 randomly sampled reads (-m1 -v2 -X10000) to fly transcriptome
4sU RNA-seq: Read pairs aligned using tophat v2.0.4 (-g10 --bowtie1 --mate-inner-dist [see below] --mate-std-dev [see below] --library-type fr-firststrand --min-intron-length 25 --max-intron-length 250000)
Total RNA-seq: Read pairs aligned using tophat v2.0.4 (-g10 --bowtie1 --mate-inner-dist [see below] --mate-std-dev [see below] --library-type fr-unstranded --min-intron-length 25 --max-intron-length 250000)
Coverage tracks generated using genomeCoverageBed (-bg -split, bedtools v2.16.2)
Genome_build: dm3
Supplementary_files_format_and_content: bigWig, read coverage

growth_protocol: Drosophila S2 cells from the DGRC were grown in M3 media supplemented with bactopeptone, yeast extract and 10% FBS. For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.

extract_protocol:
For metabolically labeled samples, equal amounts of total RNA (equivalent number of cells) were extracted with Trizol and treated with DNAseI amplification grade (Invitrogen) following manufacturer's guidelines. To enable capture of labeled RNAs these were biotinylated and pulled down with streptavidin beads. 4-thiouridine labeled RNA was eluted with DTT, ethanol precipitated and resuspended in RNAse-free H2O. For total RNA-seq samples, total RNA was extracted with Trizol ethanol precipitated and resuspended in RNAse-free H2O.
All libraries were constructed using the TruSeq Stranded Total RNA, with Ribozero Gold  using random hexamers for cDNA synthesis, and ERCC spikes were added to the metabolically labeled samples were based on cell equivalents.
nascent RNA-seq, total RNA-seq

treatment_protocol: For each timepoint three independent biological replicates were generated where RNA was metabolic labeled for 5, 10 and 20 minutes using 500 μM 4-thiouridine. For total RNA-seq, two biological replicates were generated without 4-thiouridine labeling.

tag: cell line

value: S2 cells


title: MG_UKJ_30_60314_3HS_brain

value: brain  (complete hemisphaere)


title: MG_UKJ_02_801_liver


title: MG_UKJ_30_240214_4HS_brain


title: MG_UKJ_30_60314_6HS_brain


title: Dmel_96h_repA


title: MG_UKJ_30_240214_3HS_brain


title: MG_UKJ_30_190214_3HS_brain


title: MG_UKJ_24_240214_3HS_brain


title: MG_UKJ_24_240214_1HS_brain


title: MG_UKJ_24_60314_3HS_brain


title: MG_UKJ_30_200214_1HS_brain


title: MG_UKJ_24_200214_3HS_brain


title: MG_UKJ_30_190214_1HS_brain


title: MG_UKJ_30_200214_3HS_brain


title: Dmel_S2_total-RNA-seq_rep2

description: RiboZero total RNA-seq


title: BM_shREN

city: Cold Spring Harbor

first: Yali

last: XU

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: processed data file: BM_shREN vs RN2_shREN.txt

data_processing:
Single-end 50bp sequencing reads were mapped into mm9 genome using TopHat with default settings
Structural RNAs were masked
Differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads
Genome_build: mm9/hg19
Supplementary_files_format_and_content: txt files generated from Cuffdiff

molecule: polyA RNA

source_name: bone marrow-derived myeloid progenitor cells

growth_protocol: RN2 cells derived from MLL-AF9/NrasG12D AML mouse model were cultured in RPMI with 10%FBS and P/S under 7.5% CO2. Bone marrow-derived myeloid progenitor cells were cultured in 10%FBS with 10 ng/ul SCF, 2 ng/ul IL-3, 2 ng/ul IL-6 and 50 uM beta-ME under 7.5% CO2. Human AML cell line was cultured in RPMI with 10%FBS and P/S under 7.5% CO2.

extract_protocol:
RNA was extracted using TRIzol following manufacture’s protocol. 2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.

treatment_protocol: For RNA-seq in cells transduced with dox-regulated shRNA, cells were treated with dox for 24 hrs prior to RNA extraction.

tag: cell types

value: cells transduced with shRNA in LEP vector

tag: mouse strain

tag: treatment time

value: day 3 post-infection


title: MG_UKJ_24_200214_1HS_brain


title: MG_UKJ_15_60314_6HS_brain


title: PIG_empty_1_RN2

description: processed data file: TAF4-HFD VS empty_RN2.txt

source_name: murine MLL-AF9/NrasG12D AML cell line(RN2)

value: cells transduced with cDNA/empty in PIG vector


title: MG_UKJ_24_190214_3HS_brain


title: MG_UKJ_24_190214_1HS_brain


title: shREN_dox_24hr_RN2_repeat1

description: processed data file: shMYB VS shREN_RN2.txt

value: cells transduced with dox-regulated shRNA and treated with dox for 24 hrs

value: 24 hrs post dox treatment


title: shMYB.2572_dox_24hr_RN2


title: shREN_dox_24hr_RN2_repeat2


title: PIG_TAF4-HFD_RN2


title: PIG_empty_2_RN2


title: shTADA1.1580_RN2

description: processed data file: shTADA1 vs shREN_RN2.txt


title: shTADA1.1226_RN2


title: shMLL-AF9.1039_RN2

description: processed data file: shMLL-AF9 VS shREN_RN2.txt


title: shTAF2.1635_RN2

description: processed data file: shTAF2 VS shREN_RN2.txt


title: shMLL-AF9.643_RN2


title: MG_UKJ_15_200214_3HS_brain


title: MG_UKJ_15_240214_1HS_brain


title: MG_UKJ_15_200214_1HS_brain


title: shMYB.2652_dox_24hr_RN2


title: shREN_RN2_repeat2

description: processed data file: shTAF12 VS shREN_RN2.txt


title: shREN_RN2_repeat1


title: shTAF4.3818_RN2

description: processed data file: shTAF4 VS shREN_RN2.txt


title: FLAG-TAF12-ChIP_shMYB.2652

data_processing:
50bp single end sequencing reads were mapped to mm9 genome using Bowtie with 2 mismatches allowed
PCR duplicates were removed from sequencing reads using SAMTools.
MACS 1.4.2 was used to call peaks with input genomic DNA as control with other default parameters: 1e-05 Pvalue cutoff for peak detection, 10-30 within MFOLD range
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files converted from wiggle file generated from MACS peaks calling

source_name: murine MLL-AF9/NrasG12D AML

growth_protocol: RN2 cells derived from MLL-AF9/NrasG12D AML mouse model were cultured in RPMI with 10%FBS and P/S.

extract_protocol:
After cross-link, cells were incubated with cell lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40) and then resuspended and sonicated in nuclei lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1%SDS) for 15mins, followed by ChIP
Library was constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture’s protocol. Briefly, ChIP DNA was end repaired, followed by A tailing and size selection (250-500 bp) by gel electrophoresis. 15 PCR cycles were used for final library amplification and the library was analyzed on Bioanalyzer using high sensitivity DNA chip (Agilent) on Bio-analyzer.

treatment_protocol: For FLAG-TAF12 ChIP-seq in dox-regulated shREN and shMYB.2652 cells, cells were treated with doxycycline for 24 hrs. Cell cultures were collected and cross-likned with formaldehyde at room temperature for 15 mins.

value: cells transduced with FLAG-TAF12 cDNA in PIG vector and dox regulated shMYB.2652

tag: chip antibodies

value: F1804, Sigma/Aldrich


title: MG_UKJ_15_240214_3HS_brain


title: shTAF2.4392_RN2


title: PIG_FLAG-TAF4-HFD_RN2


title: MG_UKJ_9_60314_6HS_brain


title: Input_for_FLAG-TAF12_shREN

value: cells transduced with FLAG-TAF12 cDNA in PIG vector and dox regulated shREN


title: MG_UKJ_15_60314_3HS_brain


title: shTAF4.2818_RN2


title: shTAF12.376_RN2


title: shTAF12.364_RN2


title: FLAG-TAF12-ChIP

value: cells transduced with FLAG-TAF12 cDNA in PIG vector


title: MG_UKJ_9_240214_3HS_brain


title: MG_UKJ_15_190214_3HS_brain


title: Sham Operated Carotid Intima Replicate 2

city: Farmington

first: Patrick

middle: A

last: Murphy

state: CT

address: 263 Farmington Ave

department: Center for Vascular Biology

institute: University of Connecticut Health Center

description:
80bp PE + 100bp PE
Pool of 3-5 arterial flushes

data_processing:
reads were mapped with STAR 2.5.1b and options --runThreadN 8 --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM [https://www.ncbi.nlm.nih.gov/pubmed/23104886]
RSEM v.1.2.15 (options --paired-end --calc-ci  -bam -p 8  ) was used to calculate transcript levels [https://www.ncbi.nlm.nih.gov/pubmed/21816040]
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated text file with RSEM output (ENSID, length, effective length, counts, TPM, FPKMs) for each sample, header contains original sequencing run descriptions and data processing details

source_name: Carotid intimal flush

extract_protocol:
Briefly, vessels were isolated and imaged from euthanized mice, flushed with PBS solution and then 150uL Trizol.
RNA isolated byQiagen RNAeasy microcolumns.  Pools of RNA were created and then DNAse-treated in solution, before concentrating on RNAeasy columns with elution in minimal volume.  RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit, and samples were sequenced on Illumina HiSeq 2000 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.
RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit
Samples were sequenced on Illumina HiSeq 2000, 2500 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.

tag: sample type

value: Normal flow

tag: time

tag: genetic background

value: C57BL/6J (Jax)

value: No treatment


title: Input_for_FLAG-TAF12_shMYB


title: MG_UKJ_15_190214_1HS_brain


title: TAF2-ChIP

value: wt cells


title: FLAG-TAF12-ChIP_shREN


title: TAF10-ChIP

value: ab138774, Abcam


title: Input_for_TAF10_TAF2-ChIP


title: MG_UKJ_9_60314_3HS_brain


title: MG_UKJ_9_200214_1HS_brain


title: Contralateral Carotid Intima Replicate 2

value: High flow


title: Sham Operated Carotid Intima Replicate 1


title: Input_for_FLAG-TAF12-ChIP


title: MG_UKJ_9_240214_1HS_brain


title: MG_UKJ_9_200214_3HS_brain


title: Low Flow Carotid Intima Replicate 3

value: Low flow


title: Contralateral Carotid Intima Replicate 3


title: Low Flow Carotid Intima Replicate 1


title: MG_UKJ_9_190214_1HS_brain

value: brain  (complete hemisphaere)


title: Low Flow Carotid Intima Replicate 2


title: MG_UKJ_2_240214_3HS_brain

value: young


title: PAR-CLIP-Roquin-1-1

first: Joao

middle: C

last: Guimaraes

address: Klingelbergstrasse 50 / 70

department: Biozentrum

institute: University of Basel

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse transcriptome based on RefSeq (RNA-seq and Ribo-seq) using segemehl v0.1.7-411 with parameters --accuracy 90. PAR-CLIP reads were analyzed using CLIPZ (http://www.clipz.unibas.ch)
Transcript counts were calculated based on uniquely mapped reads. For Ribo-seq, only the reads mapping to the CDS were considered.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample (RNA-seq and Ribo-seq), as well as Roquin-bound clusters (PAR-CLIP).

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEF cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 10 mM HEPES, pH 7.4 at 37°C in 10% CO2. T cells were cultured in DMEM medium supplemented with 10%FBS, 1x non-essential amino acids, 10 mM HEPES, pH7.4, 50 µM β-mercaptoethanol at 37°C in 5% CO2.

extract_protocol:
For Ribosome profiling lysates were clarified by centrifugation to remove nuclei and treated with ARTSeq Nuclease for 45min or left untreated. RNA fragments protected by the ribosomes and total RNA from lysates were extracted with acid phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5). Total RNA from T cells were directly extracted from cells using TRIzol. For PAR-CLIP lysates were clarified by centrifugation and Roquin-RNA-complexes were isolated with the 3F12 antibody. After proteinase K digestion RNA fragments were isloated by phenol-chloroform extraction.
Libraries of ribosome protected fragments were peprared according to the ARTSeq Ribosome Profiling Kit for mammalian cells (Illumina). RNA libraries from MEF cells were prepared according to the Encore Complete RNA-Seq DR Multiplex Systems (NuGEN Technologies). RNA libraries from CD4+ T cells were prepared according to the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina). PAR-CLIP libraries were prepared according to the small RNA protocol from Hafner et al., Methods 2012.

treatment_protocol: For doxycycline (1µg/mL) treatment cells were treated for 14 hours. For 4' OH-tamoxifen (0.3µM) treatment cells were treated for 5 days. For mepazine (20µM) treatment cells were treated for 3 hours. For ribosome profiling cells were treated with cycloheximide 100µg/ml for 1 minute.

tag: clip antibody

value: Anti-Roquin-1/2, clone 3F12, hybridoma supernatant, produced in the Helmholtz Zentrum München

value: Mouse Embryonic Fibroblasts


title: PAR-CLIP-Roquin-1-3


title: PAR-CLIP-Roquin-1-2


title: B20-4-RNA-Tcells-noMepa

source_name: CD4+ T cells

value: CD4+ T cells


title: B20-3-RNA-Tcells-noMepa


title: B20-2-RNA-Tcells-noMepa


title: MG_UKJ_2_60314_6HS_brain


title: Contralateral Carotid Intima Replicate 1


title: B19-3-RNA-Tcells+Mepa


title: Sham Operated Carotid Intima Replicate 3


title: MG_UKJ_2_60314_3HS_brain


title: B19-4-RNA-Tcells+Mepa


title: MG_UKJ_2_200214_3HS_brain


title: A20-3-Ribo-Tcells-noMepa

data_processing:
Library strategy: Ribosome profiling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse transcriptome based on RefSeq (RNA-seq and Ribo-seq) using segemehl v0.1.7-411 with parameters --accuracy 90. PAR-CLIP reads were analyzed using CLIPZ (http://www.clipz.unibas.ch)
Transcript counts were calculated based on uniquely mapped reads. For Ribo-seq, only the reads mapping to the CDS were considered.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample (RNA-seq and Ribo-seq), as well as Roquin-bound clusters (PAR-CLIP).


title: B19-1-RNA-Tcells+Mepa


title: B19-2-RNA-Tcells+Mepa


title: B20-1-RNA-Tcells-noMepa


title: MG_UKJ_9_190214_3HS_brain


title: A20-4-Ribo-Tcells-noMepa


title: A20-1-Ribo-Tcells-noMepa


title: A20-2-Ribo-Tcells-noMepa


title: MG_UKJ_2_200214_1HS_brain


title: A19-4-Ribo-Tcells+Mepa


title: MG_UKJ_2_190214_1HS_brain


title: A19-3-Ribo-Tcells+Mepa


title: A19-2-Ribo-Tcells+Mepa


title: MG_UKJ_30_73_blood

source_name: 30m_whole blood

value: whole blood


title: B18-1-RNA-MEF-ICOS-Nfkbiz+Tam


title: B17-2-RNA-MEF-ICOS-Nfkbiz-noTam


title: MG_UKJ_2_240214_1HS_brain


title: A19-1-Ribo-Tcells+Mepa


title: MG_UKJ_30_72_blood


title: MG_UKJ_30_71_blood


title: B16-2-RNA-MEF-ICOS-Nfkbid+Tam


title: MG_UKJ_30_70_blood


title: MG_UKJ_24_1059_blood

source_name: 24m_whole blood


title: B15-2-RNA-MEF-ICOS-Nfkbid-noTam


title: B16-1-RNA-MEF-ICOS-Nfkbid+Tam


title: B15-1-RNA-MEF-ICOS-Nfkbid-noTam


title: B14-2-RNA-MEF-ICOS-FL+Tam


title: MG_UKJ_30_69_blood


title: B14-1-RNA-MEF-ICOS-FL+Tam


title: MG_UKJ_24_1056_blood


title: B13-2-RNA-MEF-ICOS-FL-noTam


title: MG_UKJ_24_1055_blood


title: MG_UKJ_2_190214_3HS_brain


title: MG_UKJ_15_232_blood

source_name: 15m_whole blood


title: MG_UKJ_15_234_blood


title: MG_UKJ_15_231_blood


title: B12-2-RNA-MEF-ICOS-CDS+Tam


title: B17-1-RNA-MEF-ICOS-Nfkbiz-noTam


title: B13-1-RNA-MEF-ICOS-FL-noTam


title: B12-1-RNA-MEF-ICOS-CDS+Tam


title: MG_UKJ_09_338_blood

source_name: 9m_whole blood


title: MG_UKJ_09_337_blood


title: MG_UKJ_15_230_blood


title: DM.Ctrl 5

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using TopHat v2.0.10; reads in genes were counted with htseq-count (HTSeq version 0.6.1p1) ; differential expression analysis was performed with DESeq2 (v 1.10.1)
TPM estimation was performed with RSEM (v1.2.25)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample (standard output RSEM)

organism: Homo sapiens

source_name: dermal blood endothelial cell

extract_protocol:
cDNA syntheses were performed with total RNA (10 ng) using a SMARTer Ultra Low Input RNA Kit(Clontech) according to the manufacturers instructions
Sequencing libraries were constructred using a NEBNext Library Prep Kit, following the manufacturers’ protocol (New England BioLabs)

tag: disease state

value: Healthy control

tag: cell type

value: endothelial cell

value: female


title: DM.Ctrl 4


title: B11-2-RNA-MEF-ICOS-CDS-noTam


title: MG_UKJ_24_1057_blood

tag: age


title: DM.Ctrl 3

tag: gender


title: A18-2-Ribo-MEF-Nfkbiz+Tam

tag: tissue


title: MG_UKJ_09_336_blood

tag: strain


title: A18-1-Ribo-MEF-ICOS-Nfkbiz+Tam


title: A17-2-Ribo-MEF-Nfkbiz-noTam


title: DM.Ctrl 2


title: MG_UKJ_15_233_blood


title: DM.Pat 4

value: Diabetic Patient

value: male


title: DM.Pat 3


title: MG_UKJ_09_335_blood


title: MG_UKJ_02_1156_blood

source_name: 2m_whole blood


title: DM.Pat 1


title: MG_UKJ_02_1155_blood


title: MG_UKJ_02_1154_blood


title: DM.Ctrl 1


title: B11-1-RNA-MEF-ICOS-CDS-noTam


title: A16-2-Ribo-MEF-Nfkbid+Tam


title: A15-2-Ribo-MEF-Nfkbid-noTam


title: MG_UKJ_02_1153_blood


title: MG_UKJ_02_1152_blood


title: A14-2-Ribo-MEF-ICOS-FL+Tam


title: A15-1-Ribo-MEF-ICOS-Nfkbid-noTam


title: A14-1-Ribo-MEF-ICOS-FL+Tam


title: MG_UKJ_09_334_blood


title: A17-1-Ribo-MEF-ICOS-Nfkbiz-noTam


title: A16-1-Ribo-MEF-ICOS-Nfkbid+Tam


title: Dmel_CidM_5m_IP_(20160125_PT_Dm_5min_IP_0720)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: ChIP Drosophila melanogaster CENP-A IP 5 min

data_processing: We looked for short specific alpha satellite sequences in the fastq files using grep.

source_name: S2-DRSC cells;anti-CidM

value: S2-DRSC cells

tag: antibody

value: anti-CidM


title: OreR_GFP_5m_IN_(20160810_PT_DmSc_OR_IN_71216)

description: ChIP Drosophila melanogaster input 5 min

source_name: 0-24 hr;OregonR;embryos

value: 0-24 hr;OregonR;embryos


title: Pbrm1_KO_IFNg_rep2

city: Beijing

first: Deng

last: Pan

address: Tsinghua University Medical Science Building

department: School of Basic Medical Sciences

country: China

institute: Tsinghua University

data_processing:
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5).
Raw gene counts were generated from STAR output
Differential gene expression was analyzed by DESeq2 (version 3.5)
Genome_build: Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: STAR_Gene_Counts.csv: Comma-separated text file includes raw gene counts for each sample.

source_name: B16F10 cells

growth_protocol: DMEM media with 10% FBS

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, # 74134) following the manufacturer’s protocol.
Standard mRNA library preparation kit (RS-122-2101, Illumina) was used for library preparation.

treatment_protocol: Cells were either untreated or treated with 10ng/ml of recombinant mouse IFNgamma for 24 hours

value: B16F10 cells

tag: ifng treatment

value: Treated

tag: genotype

value: Pbrm1 KO


title: A13-2-Ribo-MEF-ICOS-FL-noTam


title: Pbrm1_KO_IFNg_rep3

tag: cell line


title: Pbrm1_KO_IFNg_rep1


title: A13-1-Ribo-MEF-ICOS-FL-noTam


title: Dmel_CidM_15m_IP_(20150818_PT_Dm_15m_IP_0720)

description: ChIP Drosophila melanogaster CENP-A IP 15 min


title: A12-2-Ribo-MEF-ICOS-CDS+Tam


title: DM.Pat 2


title: Dmel_CidM_5m_IN_(20160125_PT_Dm_5min_In_0720)

source_name: S2-DRSC cells


title: OreR_GFP_5m_IP_(20160810_PT_DmSc_OR_IP_71216)

source_name: 0-24 hr;OregonR;embryos;anti-GFP

value: anti-GFP


title: A12-1-Ribo-MEF-ICOS-CDS+Tam


title: Brd7_KO_IFNg_rep2

value: Brd7 KO


title: Dmel_CidM_15m_IN_(20150818_PT_Dm_15m_IN_0720)

description: ChIP Drosophila melanogaster input 15 min


title: Brd7_KO_IFNg_rep3


title: A11-2-Ribo-MEF-ICOS-CDS-noTam


title: Dmel_CidM_15m_IP_long_(20151015_PT_Dm_15m_IP_0720)

description: ChIP Drosophila melanogaster CENP-A IP 15 min 250 bp single end

data_processing: 1. We trimmed the 250bp single-end reads with trim_galore/cutadapt using parameters "-f fastq -e 0.1 -q 20 -o 3 -a AGATCGGAAGAGC". The supplementary fasta file contains the trimmed reads. 2. We clustered the trimmed reads with cdhit. 3. We looked for short specific alpha satellite sequences in the trimmed reads with grep.

extract_protocol:
Drosophila ChIP_protocol.rtf
PMID 25827087


title: A11-1-Ribo-MEF-ICOS-CDS-noTam


title: Arid2_KO_IFNg_rep3

value: Arid2 KO


title: Brd7_KO_IFNg_rep1


title: CidGFP_GFP_5m_IP_(20160810_PT_DmSc_CG_IP_71216)

source_name: 0-24 hr;P[Cid-GFP]8-10;embryos;anti-GFP

value: 0-24 hr;P[Cid-GFP]8-10;embryos


title: Dmel_CidM_15m_IN_long_(20151015_PT_Dm_15m_IN_0720)

description: ChIP Drosophila melanogaster input 15 min 250 bp single end


title: B10-1-RNA-MEF-ICOS-Nfkbiz-noDox

value: Mouse Embryonic Fibroblasts


title: B09-2-RNA-MEF-ICOS-Nfkbiz+Dox


title: B10-2-RNA-MEF-ICOS-Nfkbiz-noDox


title: CidGFP_GFP_5m_IN_(20160810_PT_DmSc_CG_IN_71216)

source_name: 0-24 hr;P[Cid-GFP]8-10;embryos


title: Arid2_KO_IFNg_rep2


title: B09-1-RNA-MEF-ICOS-Nfkbiz+Dox


title: Dmel_CidH_5m_IN_(20170502_PT_DmSc_Cid8_in0418)


title: Control_IFNg_rep2

value: WT


title: Arid2_KO_IFNg_rep1


title: Control_IFNg_rep3


title: Control_IFNg_rep1


title: B08-2-RNA-MEF-ICOS-Cot-noDox


title: Pbrm1_KO_rep2

value: Untreated


title: B07-2-RNA-MEF-ICOS-Cot+Dox


title: B08-1-RNA-MEF-ICOS-Cot-noDox


title: Pbrm1_KO_rep3


title: Pbrm1_KO_rep1


title: Dmel_S2_4sU-RNA-seq_20min_rep2

description:
4-thiouridine labeled RNA from Drosophila S2 cells
library strategy: nascent RNA-seq

data_processing:
Base calls performed by standard Illumina pipeline
Read pairs with mean quality <20 (either mate) filtered using custom scripts
Insert size and standard deviation determined via picard tools 1.86 based on bowtie 0.12.8 alignment of 1,000,000 randomly sampled reads (-m1 -v2 -X10000) to fly transcriptome
4sU RNA-seq: Read pairs aligned using tophat v2.0.4 (-g10 --bowtie1 --mate-inner-dist [see below] --mate-std-dev [see below] --library-type fr-firststrand --min-intron-length 25 --max-intron-length 250000)
Coverage tracks generated using genomeCoverageBed (-bg -split, bedtools v2.16.2)
Genome_build: dm3
Supplementary_files_format_and_content: bigWig, read coverage

source_name: Drosophila S2 cells

extract_protocol:
Total RNA was extracted with Trizol. Equal amounts of total RNA were biotinylated and pulled down with streptavidin beads. 4-thiouridine labeled RNA was eluted with DTT, ethanol precipitated and resuspended in RNAse-free H2O.
TruSeq Stranded Total RNA, with Ribozero Gold and ERCC spikes

treatment_protocol: For each timepoint three independent biological replicates were generated where RNA was metabolic labeled for 5, 10 and 20 minutes using 500 μM 4-thiouridine.

value: S2 cells


title: Dmel_S2_4sU-RNA-seq_20min_rep3


title: B07-1-RNA-MEF-ICOS-Cot+Dox


title: Dmel_CidH_5m_IP_(20170502_PT_DmSc_Cid8_IP0418)

source_name: S2-DRSC cells;anti-CidH

value: anti-CidH


title: WT5_CD25-

description: processed data file: tregs_rnaseq_counts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse transcriptome based on RefSeq (RNA-seq) using segemehl v0.1.7-411 with parameters --accuracy 90.
Transcript counts were calculated based on uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample (RNA-seq).

source_name: WT_CD25-_CD4+ YFP+ T cells

growth_protocol: T cells were cultured in DMEM medium supplemented with 10%FBS, 1x non-essential amino acids, 10 mM HEPES, pH7.4, 50 µM β-mercaptoethanol at 37°C in 5% CO2.

extract_protocol:
T cells were isolated from the spleen and lymph nodes, then sorted for CD4+ YFP+ CD25+ or CD4+ YFP+ CD25- and finally lysed in TRIzol.
RNA libraries from the sorted CD25+ or CD25- Treg (CD4+ YFP+) cells were prepared according to the Encore Complete RNA-Seq DR Multiplex Systems (NuGEN Technologies).

treatment_protocol: No treament.

tag: genotype/variation

value: CD4+ YFP+ T cells


title: Brd7_KO_rep2


title: B06-2-RNA-MEF-ICOS-Nfkbid-noDox

source_name: Mouse Embryonic Fibroblasts


title: B06-3-RNA-MEF-ICOS-Nfkbid-noDox


title: Brd7_KO_rep1


title: B06-1-RNA-MEF-ICOS-Nfkbid-noDox


title: B05-3-RNA-MEF-ICOS-Nfkbid+Dox


title: Arid2_KO_rep3


title: WT4_CD25-


title: B05-2-RNA-MEF-ICOS-Nfkbid+Dox


title: Dmel_S2_4sU-RNA-seq_10min_rep1


title: Dmel_S2_4sU-RNA-seq_10min_rep2


title: Dmel_S2_4sU-RNA-seq_5min_rep2


title: Dmel_S2_4sU-RNA-seq_20min_rep1


title: Dmel_S2_4sU-RNA-seq_5min_rep1


title: Arid2_KO_rep2


title: Dmel_S2_4sU-RNA-seq_5min_rep3


title: DM.Ctrl 6

value: Healthy control

value: endothelial cell

value: female


title: Dmel_S2_4sU-RNA-seq_10min_rep3


title: Arid2_KO_rep1


title: WT4_CD25+

source_name: WT_CD25+_CD4+ YFP+ T cells


title: Brd7_KO_rep3


title: B04-3-RNA-MEF-ICOS-FL-noDox


title: Control_rep3


title: WT3_CD25-


title: B05-1-RNA-MEF-ICOS-Nfkbid+Dox


title: Control_rep2


title: WT5_CD25+


title: Control_rep1


title: WT3_CD25+


title: WT2_CD25+


title: B04-1-RNA-MEF-ICOS-FL-noDox


title: B03-3-RNA-MEF-ICOS-FL+Dox


title: Morc2bKO_3

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
Sequenced reads were mapped to reference genome either in unique mapping mode.
Mapped reads were subjected to Cufflinks to estimate the expression levels of genes. The expression of each gene was normalized by calculating fragments per kilobase of exon per million fragments mapped (FPKM). The FPKM values of each gene for both wild type and Morc2b-/- group were used to assess the differential expression with Cuffdiff. Genes with the p value greater than the FDR after Benjamini-Hochberg correction for multiple-testing were considered as differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample ...

source_name: testis

growth_protocol: Testes were diseccted from postnatal day 12 males

extract_protocol:
RNA extraction by TRIzol reagents
Equal amounts (1 mg) of total RNA from each sample were used to generate RNA-seq libraries using TruSeq® Stranded mRNA Library Preparation Kit Set A (Cat. No. RS-122-2101, Illumina) according to the manufacturer’s instruction. The concentration of DNA library templates was determined using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). The quality of libraries was evaluated using the Agilent 4200 TapeStation (Agilent Technologies). Eight individual libraries (4 wild type and 4 Morc2b-/-) were pooled in equal amounts for sequencing using the Illumina NextSeq 500/550 High Output v2 kit (Illumina, 75 cycles, FC-404-2005) and the NextSeq 500 system (Illumina).

tag: strain background

value: mixed

value: postnatal day 12 (d12)


title: Morc2bKO_4


title: WT1_CD25-


title: B03-1-RNA-MEF-ICOS-FL+Dox


title: B03-2-RNA-MEF-ICOS-FL+Dox


title: DKO7_CD25-

source_name: Roquin DKO_CD25-_CD4+ YFP+ T cells

value: Foxp3-IRES-YFP-Cre; Rc3h1-2fl/fl


title: WT1_CD25+


title: B02-2-RNA-MEF-ICOS-CDS-noDox


title: Morc2bKO_2


title: B02-3-RNA-MEF-ICOS-CDS-noDox


title: B02-1-RNA-MEF-ICOS-CDS-noDox


title: DKO6_CD25-


title: B04-2-RNA-MEF-ICOS-FL-noDox


title: DKO5_CD25-


title: Morc2bKO_1


title: Morc2bWT_4

value: wild type


title: Morc2bWT_3


title: B01-3-RNA-MEF-ICOS-CDS+Dox


title: Morc2bWT_1


title: DKO6_CD25+

source_name: Roquin DKO_CD25+_CD4+ YFP+ T cells


title: B01-1-RNA-MEF-ICOS-CDS+Dox


title: Low Flow Carotid Intima Rbfox2 EC-KO Replicate 3

description:
150bp PE
Pool of 3-5 arterial flushes

source_name: Carotid intimal flush

value: Low flow

value: C57 background

tag: treatment

value: Rbfox2 EC-KO


title: Morc2bWT_2


title: DKO4_CD25-


title: A10-2-Ribo-MEF-ICOS-Nfkbiz-noDox


title: B01-2-RNA-MEF-ICOS-CDS+Dox


title: DKO5_CD25+


title: Low Flow Carotid Intima Rbfox2 EC-KO Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

tag: sample type


title: A10-1-Ribo-MEF-ICOS-Nfkbiz-noDox


title: Low Flow Carotid Intima Rbfox2 Control Replicate 3

description:
150bp PE
Pool of 3-5 arterial flushes

tag: time

value: Rbfox2 control


title: DKO7_CD25+


title: Low Flow Carotid Intima Rbfox2 Control Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

tag: genetic background


title: DKO4_CD25+


title: WT2_CD25-


title: A09-2-Ribo-MEF-ICOS-Nfkbiz+Dox

tag: clip antibody

value: Mouse Embryonic Fibroblasts


title: DKO3_CD25-


title: DKO2_CD25-


title: Contralateral Carotid Intima + PBS Liposomes Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: High flow

value: C57BL/6J (Jax)

value: PBS liposomes


title: DKO2_CD25+


title: Contralateral Carotid Intima + PBS Liposomes Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes


title: In Vitro Aortic Endothelial Cell TetOn-SV40 Line + 10% Plasma

description:
150bp PE
From collagenase intimal flush, FACs sorted, TetOn-SV40 immortalized (TetOff in experiment)

source_name: Aortic Endothelial Cell Line

extract_protocol:
RNA from co-culture isolated by Trizol treatment of co-culture in dish
RNA isolated byQiagen RNAeasy microcolumns.  Pools of RNA were created and then DNAse-treated in solution, before concentrating on RNAeasy columns with elution in minimal volume.  RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit, and samples were sequenced on Illumina HiSeq 2000 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.
RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit
Samples were sequenced on Illumina HiSeq 2000, 2500 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.

value: Static

value: 48hrs after treatment

value: 10% plasma


title: DKO1_CD25-

value: CD4+ YFP+ T cells


title: DKO1_CD25+


title: A07-1-Ribo-MEF-ICOS-Cot+Dox


title: A08-2-Ribo-MEF-ICOS-Cot-noDox


title: A07-2-Ribo-MEF-ICOS-Cot+Dox


title: Contralateral Carotid Intima + IgG Control Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

value: IgG non-specific antibody control


title: In Vitro Aortic Endothelial Cell TetOn-SV40 Line + Platelets and Macrophages

value: Platlets and macrophages


title: Contralateral Carotid Intima + IgG Control Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes


title: DKO3_CD25+


title: A06-3-Ribo-MEF-ICOS-Nfkbid-noDox


title: In Vitro Aortic Endothelial Cells Rbfox2 Control

description:
150bp PE
From collagenase intimal flush, FACs sorted

source_name: Sorted aortic endothelial cells (Cd31+, Icam2+)

extract_protocol:
RNA from cultured aortic endothelial cells was isolated after one week in culture by sorting 1-2K endothelial cells (by CD31+ and Icam2+) from BD Aria directly into cold Trizol solution.
RNA isolated byQiagen RNAeasy microcolumns.  Pools of RNA were created and then DNAse-treated in solution, before concentrating on RNAeasy columns with elution in minimal volume.  RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit, and samples were sequenced on Illumina HiSeq 2000 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.
RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit
Samples were sequenced on Illumina HiSeq 2000, 2500 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.

value: 7days in culture


title: In Vitro Aortic Endothelial Cells Rbfox2 EC-KO


title: 24-HC_No3_M2-H3K4me3

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with RTA ver1.18.64 and bcl2fastq ver1.8.4 (Illumina)
3' adapter trimming with FastX-toolkit
Depletion of reads aligned to RepeatMasker sequences with bowtie2 v2.1.0
Alignment to mouse genome (mm9) by bowtie v1.0.0
Suppression of PCR duplicates by samtools v0.1.19
Peak calling by macs14 v1.4.2
Read counts in the peaks by bedtools v2.17.0
Genome_build: Mouse mm9
Supplementary_files_format_and_content: bed files contain following columns: 1.chromosome, 2. peak start, 3. peak end, 4. number of reads

source_name: cerebral cortex

extract_protocol:
Sonicated DNAs complexed with histone were isolated with antibodies.
Libraries were prepared by KAPA LTP Library Preparation Kit (KAPA Biosystems) with TruSeq index adaptors, according to manufacture's instruction.

tag: chip antibody

value: anti-FLAG antibody M2 (#F1804, Sigma) and anti-H3K4me3 monoclonal antibody (#301-34811, Wako)

value: cerebral cortex

tag: replicate


title: 21-HC_No3_input


title: A06-1-Ribo-MEF-ICOS-Nfkbid-noDox


title: 23-HC_No3_M2

value: anti-FLAG antibody M2 (#F1804, Sigma)


title: A05-3-Ribo-MEF-ICOS-Nfkbid+Dox


title: A09-1-Ribo-MEF-ICOS-Nfkbiz+Dox


title: 20-HC_No2_M2-H3K4me3


title: Contralateral Carotid Intima Rbfox2 EC-KO Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

value: C57 background


title: A08-1-Ribo-MEF-ICOS-Cot-noDox


title: Contralateral Carotid Intima Rbfox2 EC-KO Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: Rbfox2 EC-KO


title: 18-HC_No2_H3K4me3

value: anti-H3K4me3 monoclonal antibody (#301-34811, Wako)


title: A04-3-Ribo-MEF-ICOS-FL-noDox

value: Mouse Embryonic Fibroblasts


title: A05-2-Ribo-MEF-ICOS-Nfkbid+Dox


title: A05-1-Ribo-MEF-ICOS-Nfkbid+Dox


title: Contralateral Carotid Intima Rbfox2 Control Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: High flow

value: Rbfox2 control


title: Contralateral Carotid Intima Rbfox2 Control Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes


title: 17-HC_No2_input


title: A06-2-Ribo-MEF-ICOS-Nfkbid-noDox


title: 19-HC_No2_M2


title: A04-2-Ribo-MEF-ICOS-FL-noDox


title: In Vitro Aortic Endothelial Cell TetOn-SV40 Line

value: No Treatment


title: 22-HC_No3_H3K4me3


title: 15-HC_No1_M2


title: In Vitro Aortic Endothelial Cell TetOn-SV40 Line + 10% Plasma, Platelets and Macrophages

value: Static

value: 10% plasma, platelets and macrophages


title: 16-HC_No1_M2_H3K4me3


title: Low Flow Carotid Intima Rbfox2 ECKO Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: Low flow


title: Low Flow Carotid Intima Rbfox2 Control Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes


title: A03-3-Ribo-MEF-ICOS-FL+Dox


title: A02-3-Ribo-MEF-ICOS-CDS-noDox


title: A03-2-Ribo-MEF-ICOS-FL+Dox


title: 14-HC_No1_H3K4me3


title: 12-aH_No3_M2-H3K4me3

value: Rosa CAG-H2B-FLAG


title: 13-HC_No1_input


title: A03-1-Ribo-MEF-ICOS-FL+Dox


title: Low Flow Carotid Intima + Anti-GPIba Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

value: C57BL/6J (Jax)

value: GPIba platelet depleting antibody


title: Low Flow Carotid Intima + Anti-Gr1 Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: Gr1 granulocyte depleting antibody


title: A02-2-Ribo-MEF-ICOS-CDS-noDox


title: Low Flow Carotid Intima + Anti-GPIba Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes


title: 11-aH_No3_M2


title: 10-aH_No3_H3K4me3


title: A04-1-Ribo-MEF-ICOS-FL-noDox


title: 09-aH_No3_input


title: A01-3-Ribo-MEF-ICOS-CDS+Dox


title: A01-2-Ribo-MEF-ICOS-CDS+Dox


title: Low Flow Carotid Intima + IgG Control Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: IgG non-specific antibody control


title: Low Flow Carotid Intima + IgG Control Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes


title: 07-aH_No2_M2

value: cerebral cortex


title: Ohr75B

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Illumina Casava v1.8.4 software used for extraction of FASTQ files
Reads were mapped using Tophat (v2.1.0) to the genome taken the annotation into account:   -p 4  -g 1 –no-coverage-search –library-type fr-unstranded
Counting of reads per gene was done using htseq-count (0.6.1p1): htseq-count  --stranded=no -m=union -a 20 -t exon
Genome_build: UCSC mm10, Gencode vM6
Supplementary_files_format_and_content: tab separated file contains read counts per gene and sample

source_name: total RNA extracted from skin (ear)

extract_protocol:
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.

tag: age

value: 29.5 months

value: old

value: skin


title: 06-aH_No2_H3K4me3

value: anti-H3K4me3 monoclonal antibody (#301-34811, Wako)


title: 08-aH_No2_M2-H3K4me3

value: anti-FLAG antibody M2 (#F1804, Sigma) and anti-H3K4me3 monoclonal antibody (#301-34811, Wako)


title: Low Flow Carotid Intima + Clodronate Liposomes Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

value: Clodronate liposomes


title: Low Flow Carotid Intima + Anti-Gr1 Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes


title: 05-aH_No2_input


title: Ohr75A

value: 24.0 months

value: young


title: 03-aH_No1_M2

value: anti-FLAG antibody M2 (#F1804, Sigma)


title: A02-1-Ribo-MEF-ICOS-CDS-noDox

value: Mouse Embryonic Fibroblasts


title: Low Flow Carotid Intima + PBS Liposomes Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: Low flow

value: PBS liposomes


title: 04-aH_No1_M2_H3K4me3

value: Rosa CAG-H2B-FLAG


title: Low Flow Carotid Intima + PBS Liposomes Replicate 2

description:
150bp PE
Pool of 3-5 arterial flushes

value: C57BL/6J (Jax)


title: Ohr50B

value: 30.0 months


title: 01-aH_No1_input


title: Ohr64B

value: 29.8 months


title: Ohr64A

value: 24.2 months


title: Ohr50A

value: 23.8 months


title: Ohr43A


title: Ohr29B

value: 29.0 months

value: old


title: Ohr29A

value: skin


title: Ohr21B

value: 29.5 months


title: Ohr14B

value: 29.4 months


title: Ohr14A

value: 24.4 months


title: Ohr21A

value: young


title: Low Flow Carotid Intima + Clodronate Liposomes Replicate 1

description:
150bp PE
Pool of 3-5 arterial flushes

value: Clodronate liposomes


title: A01-1-Ribo-MEF-ICOS-CDS+Dox

value: Mouse Embryonic Fibroblasts


title: Dsim_CidM_5m_IP_(20151207_PT_Ds_ML82_IP_5min)

description: ChIP Drosophila simulans CENP-A IP 5 min

organism: Drosophila simulans

source_name: ML82-19a cells;anti-CidM

tag: cell type

value: ML82-19a cells

value: anti-CidM


title: Ohr13B

tag: tissue


title: Dsim_CidM_5m_IN2_(20170622_PT_Ds_ML82_5mIn0530)

description: ChIP Drosophila simulans input 5 min

source_name: ML82-19a cells


title: Ohr13A

tag: strain


title: Dsim_CidM_5m_IN_(20151207_PT_Ds_ML82_In_5min)

description: ChIP Drosophila simulans input 5 min


title: Dsim_CidM_5m_IP2_(20170622_PT_Ds_ML82_5mIP0530)

tag: antibody


title: Dsim_CidM_15m_IP_(20151207_PT_Ds_ML82_IP_15min)

description: ChIP Drosophila simulans CENP-A IP 15 min


title: 02-aH_No1_H3K4me3

value: Rosa CAG-H2B-FLAG

value: anti-H3K4me3 monoclonal antibody (#301-34811, Wako)

value: cerebral cortex


title: Dsim_CidM_15m_IN_(20151207_PT_Ds_ML82_In_15min)

description: ChIP Drosophila simulans input 15 min


title: Dsim_CidM_10m_long_(20151015_PT_Ds_ML82_10m_input)

description: ChIP Drosophila simulans chromatin 10 min


title: Ohr43B

value: 30.1 months


title: Control_704 (sncRNA)

status: Public on Jan 07 2018

city: Portici

first: Elena

last: Alexandrova

state: Napoli

address: Viale Stazione, 22

department: Faculty of Medicine and Surgery

country: Italy

institute: University of Salerno

description:
sncRNA
processed data file: all_sncRNA_RPM_normalized.txt

data_processing:
Basecalls was performed using CASAVA version 1.8
iMir was used to identify members of the following sncRNA families: microRNAs, tRNAs or rRNAs, piRNAs RFam and tiRNAs with Minimum Read Count of 3, Minimum Read Length of 17, minReadlengthTrans of 32 and maxReadLength of 32. Reads were normalized using reads per million method (RPM). ToAdaptor sequences and low-quality terminal nucleotide positions within the reads were removed using Trimmomatic software
Sequenced reads for RNA-Seq libraries were aligned to human reference genome with TopHat (v 2.0.10) using the -G (GTF file of Ensembl release 75) option. Further, the aligned reads are used to quantify mRNA expression by using the HTSeq-count (v 0.6.1) with hg19 GTF (Ensembl release 75).The pre-processed reads were mapped to the human genome, using the software Bowtie2.
Genome_build: hg 19
Supplementary_files_format_and_content: all_sncRNA_RPM_normalized.txt file includes RPM normalized sncRNA expression values for each Sample
Supplementary_files_format_and_content: mRNA-Seq_read_count.txt file contains read counts for genes that have read count ≥10

source_name: lung

growth_protocol: BSM cells were established and grown in RPMI 1640 (Lonza, Basel, Switzerland) supplemented with 5% fetal calf serum (FCS), 8 mM L-glutamine, 20 mM hydroxyethyl piperazine ethane sulfonic acid and 1% modified Eagle’s medium vitamin mix (Gibco, Paisley, UK). Neither antibiotics nor antimycotics were added at any time.

extract_protocol:
RNA isolation was performed with mirVana miRNA isolation kit (Ambion, Life Science, Zug, Switzerland). RNA concentration of each sample was evaluated with a ND-1000 spectrophotometer (NanoDrop) and its quality was analysed with the Agilent 2100 Bioanalyzer using Agilent RNA 6000 nano kit (Agilent Technologies, Milano, Italy).
For small RNA profiling, 1 µg of total RNA was used for library preparation according to the Illumina TruSeq small RNA sample preparation protocol. Sized microRNA libraries were gel purified and sequenced on a Illumina HiSeq1500 sequencer. For polyA RNA sequencing, an equimolar RNA pool was prepared from all 14 RNA samples extracted from both asthmatic and normal primary BSM cells. 1 µg of total RNA was used for library preparation according to the Illumina TruSeq stranded mRNA sample preparation protocol. Resulting mRNA library was sequenced on a Illumina NextSeq sequencer.

value: lung

value: bronchial smooth muscle (BSM) cells

tag: disease state

value: control


title: Asthma_667 (sncRNA)

value: asthma


title: Asthma_738 (sncRNA)


title: Asthma_662 (sncRNA)


title: Control_653 (sncRNA)


title: Asthma_695 (sncRNA)


title: Asthma_669 (sncRNA)


title: Pool healthy and asthma (mRNA)

description: processed data file: mRNA-Seq_read_count.txt

value: pool healthy and asthma


title: Control_685 (sncRNA)


title: Asthma_739 (sncRNA)


title: Control_705 (sncRNA)


title: Asthma_670 (sncRNA)


title: Control_706 (sncRNA)


title: Total_Prmt1 KO_Rep3

status: Public on Jan 06 2018

first: Jialiang

last: Huang

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Total  RNA

data_processing:
The fastq files were aligned to mm10 using STAR with default parameters, followed by counting the aligned reads in the genomic transcripts annotations from GenomicFeatures using Rsamtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (cpm) values by edgeR

source_name: osteosarcoma cells

growth_protocol: Derivation of mOS cell lines from p53 and Rb conditional knockout mice were described previously(25,36). Prmt1f/f OS cell lines were derived from tumors and cultured in αMEM supplemented with 10% FBS, L-glutamine, and penicillin-streptomycin.

extract_protocol:
10 million cells were grown to 70-80% confluence in multiple 15 cm2 plates. Cells were washed once with 5ml 100g/ml cyclohexamide/PBS and scraped into 1ml 100μg/ml cyclohexamide/PBS. Next, cells were pelleted for 10min, at 300xg, 4˚C and then resuspended in 300μl polysome lysis buffer (5mM Tris pH 7.4, 2.4 mM MgCl2, 1.5mM KCl, 2μM DTT, 0.5% Triton-X, 0.5% sodium deoxycholate and 1x cOmplete protease inhibitor (Roche)). Lysates were cleared for 2 minutes at 12000xg, 4˚C. 50μl of cleared lysate was retained for total RNA extraction and 250μl of cleared lysate was loaded onto 12ml 10-50% sucrose gradients (prepared in 15mM Tris pH 7.4, 15mM MgCl2, 150mM NaCl) and spun 2h at 40000rpm, 4˚C on an SW40Ti rotor (Beckman Coulter). 0.5ml fractions were collected immediately following centrifugation, using a BioComp Gradient Master instrument. RNAs from cytoplasmic, pooled light (<3 ribosomes) polysome fractions, and pooled heavy (>3 ribosomes) polysome fractions were precipitated using Trizol-LS (Thermo Scientific)
500 ug of RNAs were used to prepare cDNA libraries using the illumina Truseq v2 kit. cDNA libraries. The libraries were quantified and sequencing sequenced using Illumina Nextseq sequencer.

treatment_protocol: Prmt1f/f mOS cells were engineered to stably express CreER (termed Prmt1f/f CreER). Prmt1 f/f CreER cells were treated with vehicle control (ETOH) or Tamoxifen (4OHT) to generate control cells and conditional KO cells, respectively.

value: Mix background

value: osteosarcoma

value: post natal day 299

tag: genotype


title: Total_Prmt1 KO_Rep1

description: Total  RNA


title: Total_Control_Rep3

description: Total  RNA

value: wild type


title: Asthma_638 (sncRNA)


title: Total_Control_Rep2

description: Total  RNA


title: Control_747 (sncRNA)


title: Light_Prmt1 KO_Rep3

description: RNA with light (<3 ribosomes) polysome fractions


title: Light_Prmt1 KO_Rep2


title: Heavy_Prmt1 KO_Rep2

description: RNA with heavy (>3 ribosomes) polysome fractions


title: Light_Prmt1 KO_Rep1


title: Total_Control_Rep1

description: Total  RNA


title: Light_Control_Rep1


title: Light_Control_Rep3


title: Heavy_Prmt1 KO_Rep1


title: Light_Control_Rep2


title: Total_Prmt1 KO_Rep2

description: Total  RNA


title: Heavy_Control_Rep3


title: Heavy_Control_Rep1


title: toll10b 2-4h cic ChIP-nexus rep 1

status: Public on Jan 05 2018

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: Illumina multiplex barcode: CGATGT

data_processing:
Library strategy: ChIP-nexus
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For ChIP-seq samples, reads were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, normalized to reads per million and saved in BigWig format
For ChIP-nexus samples, custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3. Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were separated by strand and reduced to a single base at the 5' end. Genome-wide coverage counts were calculated for each strand separately and normalized to reads per million
Genome_build: UCSC dm6
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

source_name: 2-4h toll10b embryo

growth_protocol: Fly stocks Toll10b (Meso) and gd7 (Ecto) were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males, and Toll10b, e /TM3, Sb, Ser, e females were crossed to Toll10b, e/TM3, Sb, Ser, e males. Offspring of these crosses were used for embryo collections.  Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).

extract_protocol:
ChIP-nexus libraries were constructed following He et al. (2015)
ChIP-seq and ChIP-nexus was performed according to He et al. (2011) and He et al. (2015) with whole cell extract (WCE) derived from 100 mg embryos per ChIP

treatment_protocol: Embryos were dechorionated in 100% bleach for ~1 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.

value: embryo

value: anti-cic rabbit polyclonal, custom (GenScript)


title: gd7 2-4h cic ChIP-nexus rep 1

description: Illumina multiplex barcode: TGACCA

source_name: 2-4h gd7 embryo


title: Heavy_Control_Rep2


title: Heavy_Prmt1 KO_Rep3


title: toll10b 2-4h wce rep 2

description: Illumina multiplex barcode: ACTGAT

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For ChIP-seq samples, reads were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, normalized to reads per million and saved in BigWig format
For ChIP-nexus samples, custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3. Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were separated by strand and reduced to a single base at the 5' end. Genome-wide coverage counts were calculated for each strand separately and normalized to reads per million
Genome_build: UCSC dm6
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

extract_protocol:
ChIP-seq libraries were constructed following He et al. (2011)
ChIP-seq and ChIP-nexus was performed according to He et al. (2011) and He et al. (2015) with whole cell extract (WCE) derived from 100 mg embryos per ChIP

value: no antibody


title: toll10b 2-4h dl ChIP-nexus rep 1

description: Illumina multiplex barcode: ATCACG

value: anti-dl rabbit polyclonal, custom (GenScript)


title: gd7 2-4h wce rep 2

description: Illumina multiplex barcode: GTTTCG


title: toll10b 2-4h cic ChIP-Seq rep 2

description: Illumina multiplex barcode: GTGGCC


title: toll10b 2-4h dl ChIP-Seq rep 2

description: Illumina multiplex barcode: GTGAAA


title: gd7 2-4h cic ChIP-Seq rep 2

description: Illumina multiplex barcode: AGTCAA


title: gd7 2-4h wce rep 1


title: toll10b 2-4h wce rep 1


title: 3T3_2_1h_R1.fastq.gz

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

institute: The Hospital for Sick Children

data_processing:
Basecalling was performed using Illumina Real-Time Analysis v1.18.54 or later, and bcl2fastq2 v2.17 was used to convert to fastq format (by The Center for Applied Genetics (SickKids)).
Library quality was assessed using FastQC v0.11.5.
Reads were trimmed and clipped for Illumina adaptors using Trimmomatic v0.36 with the following options LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Reads were aligned to merged reference genomes: hg38 (human)  + sacCer3 (yeast), hg38 + dm6 (fly) + sacCer3, hg38 + dm6 + ce10 (worm), and mm10 (mouse) + dm6 + sacCer3 obtained using the UCSC Table Browser and kentUtils v302 on 08 Aug 2015. Reads were mapped using STAR version 2.5.2a_modified. STAR was used with default settings, aside from: outFilterMultimapNmax 10, outFilterMismatchNoverLmax 0.05, outFilterScoreMinOverLread 0.75, outFilterMatchNminOverLread 0.85, alignIntronMax 1, and outFilterIntronMotifs RemoveNoncanonical.
Mapped reads were quantified using two different methods. Firstly, an in-house R script using the GenomicFeatures and rtracklayer packages from Bioconductor and the plyr package was used to select the longest transcript for every gene and create gtf files containing exon and intron annotations. Any introns that overlapped with an exon in any other isoform were not included in the gtf. The htseq-count script from the HTSeq 0.6.1p2 was used to count reads mapping to introns and exons. In addition to HTSeq, an in-house intersection method based around the tools provided by BEDTools suite v2.26.0 was used. Briefly, rather than counting the number of reads mapping to a feature, coverage was determined at the nucleotide level and subsequently averaged at the feature level.
Genome_build: hg38, dm6, sacCer3, ce10
Supplementary_files_format_and_content: Comma separated values files containing: gene read counts and coverage determined for reads mapping to exonic and intronic regions for each gene in each sample, half-lives determined using different methods.

organism:
Saccharomyces cerevisiae
Drosophila melanogaster
Mus musculus

source_name: NIH3T3 cells

growth_protocol: Human HEK293 epithelial cells (ATCC CRL1573) were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin solution. Murine NIH3T3 fibroblasts were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Donor Calf Serum (DCS) and 1% penicillin-streptomycin solution.  Both mammalian cell lines were cultured at 37°C in a humidified incubator with 5% CO2. Drosophila melanogaster Schneider 2 (S2) cells were cultured in ExpressFive SFM media (Thermo Fisher Scientific) supplemented with 10% FBS (heat-inactivated) and 20mM L-Glutamine, at 28°C. Saccharomyces cerevisiae USY006 was grown in liquid YPD (20 g/L bacto peptone, 10g/L yeast extract, 950 mL water) at 30°C on a shaker at 200 rpm to mid-exponential phase.

extract_protocol:
Following PBS washes, cell pellets were lysed in either TRI Reagent (Sigma-Aldrich) or Isol-RNA Lysis Reagent Manual (5Prime), according to manufacturer’s instructions. Briefly, 100 µL of 1-bromo-3-chloropropane was added to each sample, and samples were vortexed for 15 seconds and incubated at room temperature for 2 minutes. Sample were centrifuged in a prechilled centrifuge at 4°C at 15500 x g for 15 min. Aqueous phase was transferred to a new tube and 500µL isopropanol and 2µL glycoblue were added.  Samples were vortexed for 10 s and then incubated for 10 min at room temperature. Samples were then centrifuged at 4°C at 15500 x g for 10 min. Supernatant was discarded and pellet was washed with 1 mL of 75% ethanol and centrifuged at 4°C, 9000 x g for 5 min. Ethanol was removed and pellet was resuspended in 20 µL Milli-Q water.   For Saccharomyces cerevisiae 10 ml of the liquid culture was pelleted for 3 min at 1500 x g at 4°C. Supernatant was discarded and pellet was resuspended in 1 ml of ice-cold milli-Q water and pelleted again. The cell pellet was resuspended in 400 µL TES solution (10 mM Tris-Cl pH 7.5, 10mM EDTA, 0.5% SDS). 400 µL Phenol:Chloroform 5:1 was added, and the sample was vortexed vigorously for 10 s. After incubating at 65°C for 60 min with periodic vortexing, the sample was then centrifuged for 5 min at 21000 x g at 4°C. The aqueous phase was transferred to a new tube and reextracted with acid phenol and then again with chloroform. The aqueous phase was transferred, and RNA was precipitated with 40 µL of 3M sodium acetate, pH5.3 and 1 mL of ice-cold 100% ethanol. RNA was pelleted at 21000 x g for 5 min at 4°C. The RNA pellet was washed with ice-cold 70% ethanol and resuspended in 50 µL of milli-Q water.  For Caenorhabditis elegans, sample volumes were brought up to 100 µL with UltraPure water and resuspended in 4X volume of TRI-Reagent. Samples were vortexed for 10 minutes at room temperature. 10% volume of 1-bromo-3-chloropropane was added and samples vortexed for an additional 10 minutes at room temperature. Samples were then centrifuge for 8 minutes at 10,000 x g at 4 degrees and top aqueous layer was transferred to a new tube. RNA was precipitated with 20 µg glycogen and 4X volume of 100% ethanol for at least 1 hour at -20°C.  For transcription inhibition samples, 4 µg sample RNA was combined with 10 % Saccharomyces cerevisiae RNA.   For metabolically labeled samples a 1 mg/mL solution of HPDP-biotin (Thermo Fisher Scientific) in dimethylformamide was incubated at 37°C for 30 minutes. 40-100 µg of RNA was combined with 20% w/w unlabeled yeast RNA (C. elegans N2 RNA for 293_not_enough samples gifted by the Claycomb lab), 20% w/w 4SU-labeled fly RNA and 120 µL of 2.5x citrate buffer (25 mM citrate pH 4.5, 2.5 mM EDTA) in a total volume of 240 µL. 60 µL of HPDP-biotin solution was added, and the solution was incubated at 37°C for 2 hr, covered and shaking at 200 rpm. Equal volume acid phenol was added, and samples were vortexed and separated at 21000 x g for 5 min at 4°C. Aqueous layer was re-extracted with acid phenol and again with chloroform. RNA was precipitated with 18 µL of 5M NaCl, 750 µL of 100% ethanol, and 2 µL glycoblue for a minimum of 60 min at –20°C. RNA was pelleted for 30 min at 21000 x g at 4°C and supernatural discarded. RNA pellet was resuspended in 200 µL 1x wash buffer (10 mM Tris-Cl pH 7.4, 50 mM NaCl, 1 mM EDTA).  50 µL MACS microbeads (Miltenyi Biotec) were incubated with 48 µL of 1x wash buffer and 2 µL yeast tRNA for 20 min at room temperature with rotation. The microcolumns (Miltenyi Biotec) were washed with 100 µL nucleic acid equilibration buffer (Miltenyi Biotec) and then five times with 100 µL 1x wash buffer. Beads were applied to the column in 100 µL aliquots and washed five times with 100 µL 1x wash buffer. Columns were demagnetized, and beads eluted with two 100 µL washes with 1x wash buffer. 200 µL of bead solution was combined with RNA sample and rotated at room temperature for 20 min. Sample was then applied to the remagnetized column in 100 µL aliquots. Columns were washed three times with 400 µL of wash 1 buffer (10mM Tris-Cl pH 7.4, 6M urea, 10mM EDTA) prewarmed to 65°C and then three times with 400 µL wash 2 buffer (10 mM Tris-Cl pH 7.4, 1M NaCl, 10mM EDTA). Selected RNA was eluted with five washes of 1x wash buffer with 0.1M dithiothreitol. RNA was precipitated for at least 1 hr at –20°C with 30 µL 5M NaCl, 1 mL ethanol, and 2 µL glycoblue and then pelleted for 30 min at 21000 x g and 4°C.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit (Illumina) per the manual (Rev. E).

treatment_protocol: For transcription inhibition experiments HEK293 were treated with either 5 µg/mL actinomycin D or 50 µg α-amanitin for 0, 1, 2, 4, 8, 12, and 24 hours. For metabolic labeling experiments cells were treated with 100 µM 4SU and harvested after 1, 2, 4, 8, 12, and 24 hr. HEK293 and S2 cells treated with 100µM 4SU for 24 h were used for the generation of labeled spike-ins. For 293_not_enough samples, HEK293 cells, were transfected for 2 hours with 1 µg/mL pUC19 using Lipofectamine 2000 (Thermo Fisher Scientific) in Opti-MEM (Thermo Fisher Scientific), 3 hours prior to the addition of 4SU. 1 hour prior to the addition of 4SU, media was changed and DMSO was added 1:2500.

tag: cell line

value: NIH3T3 cells

tag: length of treatment

value: 1 hr

tag: 4su selected

value: TRUE

tag: supplementary file


title: 3T3_2_8h_R1.fastq.gz

tag: treatment

value: 8 hr


title: 3T3_2_12h_R1.fastq.gz

value: 12 hr


title: Nontransgenic total input DNA

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

description:
NT-total
NT (nontransgenic rice plant).
Processed data files: chr*.peak.result_addseq.xlsx

data_processing:
Illumina HiSeq 2000 with single-end reads.
Checked the read quality through the average quality score from FASTQ files and nucleotide distribution at each position using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to identify potential sequencing errors and biases.
Reads were mapped using the alignment software BOWTIE (http://bowtie-bio.sourceforge.net/index.shtml).
Reads were analyzed using HOMER (Hypergeometric Optimization of Motif EnRichment, http://homer.salk.edu/homer/).
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: chr*.peak.result_addseq.xlsx: Excel file

organism: Oryza sativa

source_name: leaves, NT, input

growth_protocol: Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.

extract_protocol:
Leaves of NT and PGD1::6xmyc-Roc10 plants were cross-linked with a buffer (0.4 M sucrose, 10 mM Tris-HCl [pH 8], 5 mM β-mercaptoethanol, and 1% formaldehyde) by vacuum infiltration for 15 min. The chromatin was isolated using sucrose cushion and sonicated to shear DNA to size range of 100-300 bp.
The ChIP-Seq library was constructed according to Illumina's instructions with some modifications. The library was purified using an Agencourt AMPure XP system. Purified DNA were used to prepare libraries with Illumina TruSeq ChIP sample preparation protocol.

tag: cultivar/background

value: Ilmi

tag: genotype/variation

value: nontransgenic

value: leaves

value: 2 weeks


title: 3T3_2_24h_R1.fastq.gz

value: 24 hr


title: PGD1:Roc10

description:
46-RNA
PGD1:Roc10 (whole body promoter transgenic plants).
Processed data file: cuffdiff gene_exp.diff.xlsx

data_processing:
Paired-end seq were generated and raw seq reads were trimmed to remove adaptor seq, and those with a quality lower than Q20 were removed using the clc quality trim software (CLCBIO).
Duplicate paired short reads were removed using FastUniq.
All reads were assembled with the clc_ref_assmble 6 (version 4.06) program, using annotated gene and noncoding RNA seq from the rapdb (http://rapdb.dna.affrc.go.jp).
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: cuffdiff gene_exp.diff.xlsx: Excel file includes abundance measurements.

source_name: leaves, PGD1:Roc10

extract_protocol:
Total RNA was extracted from the leaves of 2-week-old Roc10 overexpressors and NT rice seedlings grown under normal growth conditions using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction.
A modified TruSeq method was used to construct a strand-specific RNA-seq library with different index primers. Libraries were sequenced in the Illumina HiSeq 2000 system in the National Instrumentation Center of Environmental Management College of Agriculture and Life Science, Seoul National University (NICEM).


title: Nontransgenic α-myc ChIPseq (negative control)

description:
NT-myc
NT (nontransgenic rice plant).
Processed data files: chr*.peak.result_addseq.xlsx

source_name: leaves, NT, myc ChIP

value: anti-myc (Santa Cruz, sc-789)


title: Nontransgenic control

description:
NT-RNA
NT (nontransgenic rice plant).
Processed data file: cuffdiff gene_exp.diff.xlsx

source_name: leaves, NT


title: 3T3_2_2h_R1.fastq.gz

value: 2 hr


title: Nontransgenic α-PolII ChIPseq

description:
NT-PolII
NT (nontransgenic rice plant).
Processed data files: chr*.peak.result_addseq.xlsx

source_name: leaves, NT, PolII ChIP

value: anti-PolII


title: 3T3_2_SS_R1.fastq.gz

value: FALSE


title: 3T3_2_4h_R1.fastq.gz

value: 4 hr


title: Roc10-myc α-myc ChIPseq

description:
46-myc
Roc10-myc (overexpression transgenic plant).
Processed data files: chr*.peak.result_addseq.xlsx

source_name: leaves, Roc10-myc, myc ChIP


title: 3T3_1_SS_R1.fastq.gz


title: toll10b 2-4h cic ChIP-Seq rep 1

value: embryo

value: anti-cic rabbit polyclonal, custom (GenScript)


title: Roc10-myc α-PolII ChIPseq

description:
46-PolII
Roc10-myc (overexpression transgenic plant).
Processed data files: chr*.peak.result_addseq.xlsx

source_name: leaves, Roc10-myc, PolII ChIP


title: gd7 2-4h cic ChIP-Seq rep 1


title: toll10b 2-4h dl ChIP-Seq rep 1

value: anti-dl rabbit polyclonal, custom (GenScript)


title: 3T3_1_1h_R1.fastq.gz

value: NIH3T3 cells

value: 1 hr


title: 3T3_1_4h_R1.fastq.gz

value: TRUE


title: 3T3_1_2h_R1.fastq.gz


title: Aman_2_24h_R1.fastq.gz

organism:
Saccharomyces cerevisiae
Homo sapiens

source_name: HEK293 cells

value: HEK293 cells

value: ⍺-amanitin


title: 3T3_1_12h_R1.fastq.gz

value: 12 hr


title: 293_not_enough_24h_R1.fastq.gz

organism:
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens


title: Aman_2_12h_R1.fastq.gz


title: 293_not_enough_12h_R1.fastq.gz


title: Aman_2_8h_R1.fastq.gz

value: 8 hr


title: 293_not_enough_8h_R1.fastq.gz


title: 3T3_1_24h_R1.fastq.gz


title: Aman_2_1h_R1.fastq.gz


title: Aman_2_4h_R1.fastq.gz


title: 3T3_1_8h_R1.fastq.gz


title: Aman_2_2h_R1.fastq.gz


title: Aman_1_24h_R1.fastq.gz


title: Aman_1_8h_R1.fastq.gz


title: 293_not_enough_4h_R1.fastq.gz


title: Tg16+PERKi_In_3

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska Institutet

description:
Cytoplasmic RNA
Sample name: P4505_143

data_processing:
RNA-Seq libraries were prepared per the TruSeq Stranded Total RNA protocol (Illumina) following the manufacturer's instructions and 50 bp single-end reads were obtained using a HiSeq2500 system (Illumina). Resulting reads were mapped to the mm10 genome assembly using HISAT and quantified as described using default settings. Genes with at least one read in all samples were retained after which raw read counts were normalized and transformed using the rlog function of the DESeq2 package (version 1.9.23) in R (r-project.org, version 3.2.3).
Genome_build: mm10
Supplementary_files_format_and_content: csv file with read count

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in high glucose Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% defined fetal bovine serum (FBS), 2mM L-glutamine, 100 units/ml penicillin and 100 microgram/ml streptomycin. Cells were seeded in 150mm culture dishes and grown up to 70% confluence (about 1.0x10^7 cells).

extract_protocol:
Cytosolic and polysome-associated RNA was collected from MEF (4 replicates). Briefly, total cytosolic mRNA ("Cytosolic RNA") was extracted and sedimented on a 10%-50% sucrose gradient to separate mRNA according to the number of associated ribosomes. Gradient fractions corresponding to >4 ribosomes ("Polysome-associated RNA") were collected.
TruSeq

treatment_protocol: Cells were treated with Thapsigargin for 0 hour, 1 hour or 16 hours with or without PERK inhibition for the last 4 hours.

value: MEF

value: Cytoplasmic


title: Tg16+PERKi_H_3

description:
Polysome-associated RNA
Sample name: P4505_145

value: Polysome-associated


title: Tg16+PERKi_H_4

description:
Polysome-associated RNA
Sample name: P4505_148


title: Tg16+PERKi_In_2

description:
Cytoplasmic RNA
Sample name: P4505_140


title: 293_abnormal_12h_R1.fastq.gz

organism:
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens


title: Aman_1_4h_R1.fastq.gz


title: Tg16+PERKi_H_1

description:
Polysome-associated RNA
Sample name: P4505_139


title: Tg16+PERKi_In_4

description:
Cytoplasmic RNA
Sample name: P4505_146


title: Tg16+PERKi_H_2

description:
Polysome-associated RNA
Sample name: P4505_142


title: 293_abnormal_SS_R1.fastq.gz

value: 24 hr


title: 293_abnormal_2h_R1.fastq.gz

value: 2 hr


title: Aman_1_2h_R1.fastq.gz

value: FALSE


title: 293_abnormal_4h_R1.fastq.gz

value: 4 hr


title: 293_abnormal_8h_R1.fastq.gz


title: 293_abnormal_24h_R1.fastq.gz


title: Tg16+PERKi_In_1

description:
Cytoplasmic RNA
Sample name: P4505_137


title: Aman_1_1h_R1.fastq.gz


title: ActD_2_24h_R1.fastq.gz

value: Actinomycin D


title: 293_not_enough_2h_R1.fastq.gz


title: Aman_1_12h_R1.fastq.gz


title: Tg16_H_4

description:
Polysome-associated RNA
Sample name: P4505_136


title: 293_abnormal_1h_R1.fastq.gz


title: 293_2_4SU_SS_R1.fastq.gz


title: Tg16_H_3

description:
Polysome-associated RNA
Sample name: P4505_133


title: 293_2_4SU_24h_R1.fastq.gz


title: Tg16_In_3

description:
Cytoplasmic RNA
Sample name: P4505_131


title: 293_2_4SU_12h_R1.fastq.gz


title: ActD_2_12h_R1.fastq.gz


title: ActD_2_8h_R1.fastq.gz


title: Tg16_H_2

description:
Polysome-associated RNA
Sample name: P4505_130


title: ActD_2_4h_R1.fastq.gz


title: ActD_2_2h_R1.fastq.gz


title: Tg16_In_2

description:
Cytoplasmic RNA
Sample name: P4505_128


title: ActD_2_1h_R1.fastq.gz


title: 293_2_4SU_2h_R1.fastq.gz


title: Aman_ActD_2_0h_R1.fastq.gz


title: 293_2_4SU_4h_R1.fastq.gz


title: ActD_1_24h_R1.fastq.gz


title: Tg16_H_1

description:
Polysome-associated RNA
Sample name: P4505_127


title: 293_2_4SU_1h_R1.fastq.gz


title: ActD_1_12h_R1.fastq.gz


title: 293_1_4SU_24h_R1.fastq.gz


title: 293_1_4SU_12h_R1.fastq.gz


title: Tg16_In_4

description:
Cytoplasmic RNA
Sample name: P4505_134


title: 293_1_4SU_SS_R1.fastq.gz


title: ActD_1_4h_R1.fastq.gz


title: ActD_1_8h_R1.fastq.gz


title: Tg1_H_3

description:
Polysome-associated RNA
Sample name: P4505_121


title: Tg1_In_4

description:
Cytoplasmic RNA
Sample name: P4505_122


title: Tg1_H_4

description:
Polysome-associated RNA
Sample name: P4505_124


title: 293_2_4SU_8h_R1.fastq.gz


title: Tg1_In_3

description:
Cytoplasmic RNA
Sample name: P4505_119


title: ActD_1_2h_R1.fastq.gz


title: Tg1_H_2

description:
Polysome-associated RNA
Sample name: P4505_118


title: 293_1_4SU_4h_R1.fastq.gz


title: Tg1_H_1

description:
Polysome-associated RNA
Sample name: P4505_115


title: Tg16_In_1

description:
Cytoplasmic RNA
Sample name: P4505_125


title: Ctrl_In_3

description:
Cytoplasmic RNA
Sample name: P4505_107


title: Ctrl_H_3

description:
Polysome-associated RNA
Sample name: P4505_109


title: 293_1_4SU_8h_R1.fastq.gz


title: ActD_1_1h_R1.fastq.gz


title: 293_1_4SU_2h_R1.fastq.gz


title: 293_1_4SU_1h_R1.fastq.gz


title: Aman_ActD_1_0h_R1.fastq.gz


title: Tg1_In_1

description:
Cytoplasmic RNA
Sample name: P4505_113


title: Ctrl_H_2

description:
Polysome-associated RNA
Sample name: P4505_106


title: Ctrl_In_2

description:
Cytoplasmic RNA
Sample name: P4505_104


title: CoW3_ChIPseq_H3K27ac

status: Public on Jan 04 2018

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

data_processing:
Mapping Illumina: Bowtie (1.1.0), parameters: -l 45 -n 1 --phred64-quals -- best --strata --chunkmbs 512 -m 1 -S. Peak calling: MACS2 (2.1.0), parameters: callpeak -p 1e-5 -g hs -B --nomodel --extsize 400 --llocal 100000
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: .xls peak files were generated by MACS2 on ChIP-seq data.
Supplementary_files_format_and_content: .bed files were generated by extending MACS2 peaks to 2kb regions.
Supplementary_files_format_and_content: .tdf files were generated for viewing in genome browser such as IGV.
Supplementary_files_format_and_content: .txt files containing readcounts were generated using HTSeq-0.5.4 and Ensembl version 71 on RNA-seq data.
Supplementary_files_format_and_content: .txt files containing RPKM were generated by calculating reads per kilobase million based on readcounts files.

source_name: Circle of Willis blood vessel

extract_protocol:
Frozen in liquid nitrogen, Crosslinked, Lysed and Immunoprecipitated.
Illumina TruSeq DNA library protocol.

value: Circle of Willis

tag: sample id

tag: gender

value: Female

tag: Cause of death

value: Unknown

tag: postmortem delay

value: 5:50 hours

value: H3K27ac (Abcam, ab4729)


title: CoW2_ChIPseq_H3K27ac

tag: age

value: Euthanasia (metastasized non-small cell lung carcinoma)

value: 8:25 hours

tag: chip antibody


title: CoW3_ChIPseq_H3K4me1

tag: tissue

value: H3K4me1 (Abcam, ab8895)


title: CoW4_ChIPseq_H3K27ac

value: Male

value: Aortic aneurysm

value: 9:00 hours


title: CoW2_WCE_input


title: Ctrl_H_4

description:
Polysome-associated RNA
Sample name: P4505_112

tag: cell type

value: MEF

value: Polysome-associated


title: CoW1_ChIPseq_H3K27ac

value: Acute renal failure

value: 8:00 hours


title: Ctrl_In_1

description:
Cytoplasmic RNA
Sample name: P4505_101

value: Cytoplasmic


title: CoW1_WCE_input


title: CoW4_ChIPseq_H3K4me1


title: CoW2_ChIPseq_H3K4me1


title: Tg1_In_2

description:
Cytoplasmic RNA
Sample name: P4505_116


title: Ctrl_In_4

description:
Cytoplasmic RNA
Sample name: P4505_110


title: Ctrl_H_1

description:
Polysome-associated RNA
Sample name: P4505_103


title: GBM4_MV_longRNA

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Raw sequence reads were quality controlled using BGI filter pipeline with multiple filtering steps as follows: 1) removing reads with adapters; 2) removing reads in which unknown bases were more than 10%; and 3) removing reads in which more than 50% of bases had low quality (sequencing quality no more than 10). After filtering, the remaining reads were called “clean reads” and used for downstream bioinformatic analysis. Generally, 20M and 10M clean reads were generated per long RNA library and small RNA library, respectively.
For long RNA libraries, clean reads were mapped to Homo sapiens rRNA database using short read alignment software SOAPaligner/SOAP2 to remove the remaining rRNA reads. The reads left were used to perform transcriptome assembling and quantification. First, non-rRNA reads were mapped to human reference genome hg19 using an improved version of TopHat2, which can align reads across splice junction without relying on gene annotation. Then, the reads mapped to genome were assembled using Cufflinks. We performed Reference Annotation Based Transcript (RABT) assembly with the reference gene annotation to compensate incompletely assembled transcripts caused by read coverage gaps in the regions of reference gene. The set of transfrags generated was then compared with the reference transcripts to remove transfrags that were approximately equivalent to the whole or a portion of a reference transcript. After the assembling, we obtained the whole parsimonious set of transcripts. We blasted these transcripts with the NONCODE database using the filter set (identity > 0.9 and coverage > 0.8) to identify the known long non-coding RNA. Then, we aligned the rest of assembled transcripts to the reference annotation utilizing Cuffcompare. We utilized Cuffmerge to merge several assemblies from different samples together, which automatically filtered a number of transfrags that probably were artifacts and produced a single annotation file for downstream gene expression analysis. Two mismatches were allowed as default for annotation, except that only one was allowed for ERCC spike-ins. mRNA and lncRNA expression analyses were performed by cuffdiff and then normalized based on ERCC spike-in controls using cyclic loess robust local regression.
For small RNA libraries, clean reads were first aligned to carrier RNA (Enterobacteria phage MS2) of miRCURY Spike-in kit with bowtie (parameter: -v 2 -l 7). The unmapped reads were aligned against human rRNA sequences with bowtie (parameter: -v 2 -l 7) to remove the remaining rRNA reads. The rest reads were searched against the human miRNA precursors (miRBase V19) with bowtie (parameter: -v 1), and then the mature miRNAs reads and miRNA precursors reads were separated according to the mapping position. The remaining reads were then searched against spike-ins (UniSp2, UniSp4 and UniSp5; parameter: -v 1). And the remaining ones were searched against other non-coding RNA classes including tRNAs (gtRNAdb), piRNAs (RNAdb), snoRNA (snoRNA-LBME-db), scRNAs (Genbank) and others (Rfam database) (parameter: -v 2). After that, the remaining reads were then searched against the hg19 human genome, and we counted the reads mapped to exons, introns, intergenic regions and repeats (parameter: -v 0). The samtools was used to calculate the reads depth of each base position and R package barplot was used to draw the bar plot of the depth of position.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: xlsx format; fmol per ug total RNA

source_name: GBM4 glioblastoma neurosphere

extract_protocol:
Approximate 100 mL conditioned media was used as input for exRNA isolation. Conditioned media was centrifuged at 300 g, 4 °C for 10 min, following by the additional centrifugation at 2,000 g, 4 °C for 15 min, to remove cells and cell debris. Five uL of SUPERase In RNase Inhibitor (Ambion) was added to the supernatants per 10 mL media. The media was then filtered sequentially through the 2 um filter (GE Healthcare, UK), 0.8 um filter (EMD Millipore, MA), and 0.22 um filter (EMD Millipore), with no/minimal pressure applied. The filtrate was split to 15 mL per sample and further filtered through the 0.02 um filter (GE Healthcare) with up to 75 psi pressure applied. To facilitate the 0.02 um filtration, a mechanical syringe pump was designed and manufactured (Fig. S2). Upon filtration, each filter was washed with 1 mL DPBS (Corning), and the corresponding fractions were lysed with 600 uL Lysis Solution of the miRCURY RNA Isolation Kit – Cell & Plant (Exiqon, Denmark). The fractions collected on 0.02 um filters were lysed with 900 uL Lysis Solution. The last flow-through fractions of 0.02 um filters were pooled together (up to 30mL) and concentrated approximately 60 times using 3 kDa Amicon Ultra Centrifugal Filters (EMD Millipore) at 4,000 g, 4 °C, for 60 min. The concentrates were collected and lysed with six volumes of the same Lysis Solution (Exiqon). Total RNA was then isolated from all fractions as recommended by miRCURY protocol, with on-column DNase treatment (Qiagen, Germany). The corresponding 1.2 mL of the source neurospheres were span down at 300 g, 4 °C for 5 min, and total cellular RNA was isolated from them and analyzed in parallel. The same protocol was carried out for RNA isolation from fresh media, with 500 mL media input. For RNA isolation from primary cells cultured in 24-wells plates, the cells were lysed with 350 uL Lysis Solution per well. The concentrations of cellular and extracellular RNA were determined using the NanoDrop 2000 Spectrophotometer and Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific), respectively. The RNA quality was examined using Agilent 2100 Bioanalyzer (Agilent, CA) and the RNA Integrity Number (RIN) estimated.
Two sets of spike-in RNAs were added to the samples prior to library preparation: ERCC RNA Spike-In Control Mixes (Ambion; 0.02 uL per one ug total RNA), and miRCURY Spike-in kit, part 1, with UniSp2’s final concentrations of 1.25 and 5.0 fmol per one ug of total RNA for cellular and extracellular RNA, respectively. Total RNA, either 40~200 ng of exRNA, or 2 ug of cellular RNA, was rRNA-depleted using the Ribo-Zero rRNA Removal Kits (Illumina, CA). One quarter of the rRNA-depleted RNA was fragmented to 100~500 nt using the 5X First-Strand Buffer (Clontech, CA), and utilized for the long RNA library construction by SMARTer Stranded RNA-Seq Kit (Clontech). The remaining 75% of the rRNA-depleted RNA was treated sequentially with Tobacco Acid Pyrophosphatase (TAP; Illumina) and T4 Polynucleotide Kinase (T4PNK; New England Biolabs, MA) to create more uniform 5’- and 3’- ends for various classes of transcripts. The RNA was then used as input for the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), with size selection of 15-65nt inserts for small RNA libraries. The quality of libraries was examined using the Agilent DNA 1000 kit at the Agilent 2100 Bioanalyzer instrument, and cDNA quantified by qRT-PCR with TaqMan Probe (Thermo Fisher Scientific). The libraries were sequenced on HiSeq 2000 (Illumina) with single read 50 cycles by Beijing Genomics Institute (BGI, China).

tag: growth protocol

value: Human low-passage (below 20) GBM cells were cultured as neurospheres in Neurobasal medium (Gibco) supplemented with 3 mM GlutaMAX (Gibco), 1x B-27 supplement (Gibco), 0.5x N-2 (Gibco), 20 ng/mL EGF (R&D systems, MN), and 20 ng/mL FGF (PEPROTECH, NJ) and passaged by NeuroCult Chemical Dissociation Kit (Mouse) (Stemcell Technologies, Canada). Approximate 0.5 million dissociated cells were seeded per 10 cm dish (Corning) in 10 mL fresh media, and 1/3 volume of fresh medium was added every 3 days. Mature neurospheres were usually formed in 7~10 days, and replated.

tag: library type

value: Long RNA library

tag: sample type


title: MGG75_Exo_longRNA

source_name: MGG75 glioblastoma neurosphere

value: Exosome (0,02-0.22um) RNA


title: MGG75_RNP_longRNA

value: RNP (<0.02um) RNA


title: GBM8_Cell_longRNA

source_name: GBM8 glioblastoma neurosphere

value: Cellular RNA


title: GBM8_Exo_longRNA


title: GBM4_RNP_longRNA


title: MGG75_Cell_longRNA


title: GBM4_Exo_longRNA


title: GBM8_RNP_longRNA


title: GBM4_Cell_longRNA


title: GBM8_MV_longRNA


title: 20-3_RNP_longRNA

source_name: 20/3 glioblastoma neurosphere


title: 20-3_Exo_longRNA


title: hAstrocyte_Cell_smallRNA

source_name: human primary astrocyte

value: Primary neurons, astrocytes, and microglia were cultured as described previously [Absalon S. et al., J Neurosci 2013; Tamashiro T.T. et al., J Vis Exp 2012]. Briefly, cortical tissues of E18 and P1 C57BL/6 mice were dissected for primary cultures of neurons and glial cells, respectively. The tissues were dissociated with 0.25 % Trypsin (Gibco) and 0.1 mg/mL DNaseI (Roche) for 15 min at 37 °C. The cells were plated in poly-D-lysine coated T25 flasks or 24-well plates at ∼80,000 cells per cm2, in the seeding medium consisting of DMEM-F12 (Gibco), 10% FBS (Gibco), and 1% Antibiotic-Antimycotic Solution (Corning). For neuronal cultures, the media was exchanged to Neurobasal (Gibco), 2% B-27 (Gibco), 1% Antibiotic-Antimycotic Solution (Corning) and 0.5 mM Glutamax (Gibco) one day after plating. Mature neurons at 21 days in culture have been utilized for the RNAseq. For glial cultures, the flasks were shaken (200 rpm at 37 °C) three times overnight to remove microglia, and astrocytes trypsinized and further cultured in 24-well plates. For microglia cultures, the media was supplemented with the recombinant M-CSF mouse protein (10 ng/mL; Gibco). Floating microglial cells were collected from the conditioned media by gentle spin (300 g, 10 min), and re-plated in 24-well poly-D-lysine coated plates at ∼100,000 cells per cm2. For human primary neuroglial cultures, fetal cortical tissues (gestational age 18 weeks) were provided by Advanced Bioscience Resources, Inc. (Alameda CA), dissociated with papain (12 U/ml; Worthington), and cultured as previously described [Wang Y. et al., Neurobiology of Aging, in press]. Mature neuronal cultures at 30 days in vitro have been utilized for the RNAseq. Human (HBEC) and mouse (MBEC) primary brain microvascular endothelial cells were purchased from Cell Biologics, IL (Catalog# H-6023; Lot# 021514F14 and Catalog# C57-6023; Lot# 070613T2MP, respectively) and cultured accordingly to the manufacturer.

value: Small RNA library


title: 20-3_Cell_longRNA


title: hBEC_Cell_smallRNA

source_name: human primary brain endothelial cells


title: hNeuroglia_Cell_smallRNA

source_name: human primary neuroglia


title: MGG75_RNP_smallRNA


title: GBM8_RNP_smallRNA


title: MGG75_MV_longRNA


title: MGG75_Exo_smallRNA


title: MGG75_MV_smallRNA


title: GBM8_MV_smallRNA


title: GBM8_Exo_smallRNA


title: GBM8_Cell_smallRNA


title: GBM4_RNP_smallRNA


title: 20-3_MV_longRNA