title: mRNA_seq_Pontin_KO_OHT4D

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

description:
mRNA-sequencing
Normalized_counts_1.txt

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
For both sequencing data, we first removed adapter sequences (TrueSeq universal and index adapters) and then trimmed the ends of the adapter-free reads for which PHRED scores were lower than 20 using the cutadapter software (Martin, 2011).  Remaining reads were then aligned to the mouse reference genome (NCBIM 37) using TopHat aligner (Trapnell et al., 2009) for mRNA-sequencing and using Bowtie2 (Langmead and Salzberg, 2012) for ChIP-sequencing. For the mRNA-sequencing data, considering the variations in individual genomes and presence of multiple gene copies, we used two mismatches in a read and allowed the reads to be aligned in up to 10 different locations, which are default options in the TopHat aligner.  After the alignment, we counted the number of reads mapped to gene features (GTF file of NCBIM 37) using HTSeq (Van Verk et al., 2013).  To reduce the technical variations across the samples, we normalized the read counts using the TMM method (Robinson and Oshlack, 2010) that uses RNA compositions and library sizes between the samples provided by edgeR package (Robinson et al., 2010) in R.  For the ChIP-sequencing data, among the aligned reads, only the reads uniquely aligned and with MAPQ scores larger than 5 were used for further analysis.
Genome_build: ENSEMBL NCBIM37
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample (mRNA-sequencing)
Supplementary_files_format_and_content: BED files including the aligned reads to reference genome (ChIP-sequencing)

source_name: Pontin KO ES cells

extract_protocol: For mRNA-sequencing, we obtained total RNAs from each sample and then poly(A) mRNA isolation from total RNA (5 µg) and fragmentation were performed using the Illumina Truseq RNA Sample Prep Kit Ver. 2 with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.  Reverse transcription of RNA fragments was performed using Superscript II reverse transcriptase (Life Technologies). For ChIP-sequencing, extracts containing DNA fragments with an average size of 400bp were immmunoprecipitated by using antibodies against GFP (control) or Pontin

value: Pontinf/f; CreER ES cells

tag: time after treatment

value: 4 days post-treatment with OHT

value: OHT


title: mRNA_seq_Oct4_KO_Tc2D

status: Public on Apr 08 2015

type: SRA

country: South Korea

description:
mRNA-sequencing
Normalized_counts_1.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: Oct4 KO ES cells

tag: cell type

value: ZHBTc4 ES cells

value: 2 days post-treatment with Tc

tag: treatment

value: Tc


title: mRNA_seq_Pontin_KO_OHT3D

description:
mRNA-sequencing
Normalized_counts_1.txt

value: 3 days post-treatment with OHT


title: mRNA_seq_WT

description:
mRNA-sequencing
Normalized_counts_1.txt

source_name: WT ES cells


title: mRNA_seq_shRNA_linc1253 rep2

description:
mRNA-sequencing
Normalized_counts_2.txt

source_name: linc1253 KD ES cells

value: 4 days post infection

value: pLKO shlinc1253 lentivirus


title: mRNA_seq_shRNA_control rep2

description:
mRNA-sequencing
Normalized_counts_2.txt

value: pLKO control lentivirus


title: mRNA_seq_shRNA_control rep1

description:
mRNA-sequencing
Normalized_counts_2.txt


title: tj-GAL4>TN-Drosha

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS

description: Manual anion-exchange chromatography (HiTrapQ column) purification

data_processing:
Sequenced reads were stripped of the adapter in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides).
After subtracting reads matching abundant cellular species rRNAs, tRNAs and snRNAs identified by mapping on dataset retrieved from modEncode (http://www.modencode.org/ (Celniker et al. 2009), the remainders, composed of siRNAs, piRNAs and miRNAs were called bonafide reads.
Genome_build: Drosophila melanogaster, release 5
Supplementary_files_format_and_content: Simple tabulated format where column 1 represents bonafide read sequences and column 2 the corresponding read counts

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila ovaries

growth_protocol: Flies were grown at 20 degrees C exept in the last 5 days (25°C)

extract_protocol:
Small RNAs (18-30nt) were isolated by manual anion exchange chromatography procedure
Extracted small RNAs were cloned by Fasteris SA (Switzerland) after being selected on acrylamide gel between 18 and 30 nucleotides

tag: genotype

tag: tissue

value: ovary


title: IP-tj-GAL4>WT-Drosha

description:
Drosha-IP RNA
RNA Trizol extraction

data_processing:
Sequenced reads were stripped of the adapter in the 3' end  and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides).
Mapped reads were further mapped on a data base made from miRNA retrieved from miRBase (http://www.mirbase.org/)
Genome_build: Drosophila melanogaster (release 5)
Supplementary_files_format_and_content: Simple tabulated format where column 1 represents genome localisation, column 2 the miRNA name and column 3 the corresponding read counts

growth_protocol: Flies were grown at 20 degrees °C exept in the last 5 days (25°C)

extract_protocol:
Aliquot of precleared ovary lysates were saved as input.
A double FLAG-HA (anti-FLAG antibody (Sigma A2220); anti-HA antibody (Santa-Cruz SC805)) a immunoprecipitation was parformed on precleared lysates and RNAs from both inputs and IPs were Trizol extracted and rRNA depleted.
RNAs were fragmented (zinc treatment Illumina protocol), reverse transcribed by random hexamer primers, 260 to 280 bp fragments (ie, insert of 160-240nt) were purified from acrylamide gels by Fasteris SA (Switzerland).

value: tj-Gal4/+; WT-Drosha/+

tag: antibody

value: anti-FLAG antibody (Sigma A2220) ; anti-HA antibody (Santa-Cruz SC805)


title: IP-tj-GAL4>TN-Drosha

description:
Drosha-IP RNA
RNA Trizol extraction

value: tj-Gal4/+; TN-Drosha/+


title: IP-tj-GAL4>Ø

description:
Drosha-IP RNA
RNA Trizol extraction


title: Input-tj-GAL4>TN-Drosha

description:
Total RNA
RNA Trizol extraction

value: none (input)


title: Input-tj-GAL4>WT-Drosha

description:
Total RNA
RNA Trizol extraction


title: Control vector infected DN2 cells #1

city: Los Angeles

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

country: USA

institute: University of California, Los Angeles

description: Empty vector control - 1

data_processing:
Sequence reads from each sample were trimmed to remove the adapter sequences and the resulting 50 bp reads were mapped to the NCBI37/mm9 mouse genome assembly
Alignment was done using Tophat (v.2.0.6). command: tophat --no-novel-juncs --library-type fr-unstranded -G Mus_musculus.NCBIM37.66.gtf
Abundance measurements were done using Cufflinks (v.2.1.1). cufflinks (fpkm) command: cuffdiff --dispersion-method blind --library-type fr-unstranded --no-effective-length-correction --library-norm-method quartile -u -b mm9.fa --emit-count-tables Mus_musculus.NCBIM37.66.gtf
Genome_build: UCSC mm9, NCBI37
Supplementary_files_format_and_content: Tab-delimited files with fpkm values generated from Cufflinks

source_name: fetal liver progenitor derived DN2 cells

growth_protocol: Fetal liver progenitors from e14.5 mouse embryos were cultured on OP9-DL1 stromal cells with IL-7 and Flt3L (5 ng/ml each) for 4 days to obtain early DN stage cells.

extract_protocol:
Sorted cells were lysed in the TRIzol reagent (Invitrogen) and total RNA was extracted as per the manufacturer’s protocol. polyA+ mRNA was isolated using the Dynabeads mRNA purification kit (Invitrogen) and used to generate RNAseq libraries using the NEBNeXT Ultra RNA library preparation kit (E7530) reagents (New England Biolabs) following standard procedures.
polyA+ mRNA was isolated by two rounds of selection with Dynabeads (Invitrogen), fragmented to an average size of 200 bp by Mg2+ mediated hydrolysis and used to synthesize cDNA by random priming. The cDNA was end-repaired, the blunt ends were phosphorylated and Illumina adapters were ligated to the fragments. ~300 bp cDNA fragments were then purified by gel electrophoresis and SPRI (Agencourt AMPure XP catalog #A63880) beads were used to remove shorter fragments (<100 bp). The cDNA was then PCR amplified for 15 cycles and the resulting DNA fragments were purified once again with SPRI beads and sequenced on the Illumina HiSeq 2000 sequencer following the manufacturer's protocol.

treatment_protocol: Fetal liver derived DN cells were harvested from OP9-DL1 co-cultures and infected with retroviruses carrying the indicated constructs. Cells were returned to fresh OP9-DL1 monolayers after 4 hours of infection and GFP+ c-Kit+ CD44+ CD25+ DN2 cells were sorted after ~ 18 hours of culture.

tag: strain

value: In-vitro differentiated DN2 cells

tag: retroviral transduction

value: Retroviral vector backbone without insert


title: tj-GAL4>WT-Drosha


title: tj-GAL4>TN-Drosha*

description: Anion-exchange chromatography (HiTrapQ column) purification with AKTA apparatus

growth_protocol: Flies were grown at 22 degrees C

extract_protocol:
Small RNAs (18-30nt) were isolated by anion exchange chromatography using AKTA FPLC purifier system
Extracted small RNAs were cloned by Fasteris SA (Switzerland) after being selected on acrylamide gel between 18 and 30 nucleotides


title: tj-GAL4>WT-Drosha*


title: FAIRE_seq_Macrophage-oxLDL_277

city: Oxford

first: Christopher

last: O'Callaghan

state: Oxfordshire

address: Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
processed data file: fseq_foam_cells.bed
processed data file: FAIRE_diffreps_FDR2.5.txt
processed data file: dynamic_FAIRE_hotspots.bed

library_source: genomic

data_processing:
Base calls were generated using a standard Illumina HiSeq pipeline using Bustard 1.9.3
Reads were mapped to the UCSC genome browser hg19 reference genome (with a canonical haplotype) using STAMPY v1.021 with default parameters.
Mapped reads were filtered in SAMTOOLS based on a minimum MAPQ score of 15.
For subsequent data analysis paired end files were converted to single end by retaining one read of each proper pair and all improperly paired reads and reads from ENCODE blacklisted sites were removed.
Peak calling was performed using FSEQ on pooled replicates (V1.84, default parameters, peaks merged if within 140bp (fragment size) and removed if < 50bp or >5kb in width. The top 100k peaks were retained) and dynamic FAIRE-seq sites were identified on pooled biological replicates using Diffreps V1.55 (200bp windows, 20bp step, G-test, FDR < 2.5%)
Genome_build: UCSC hg19 (Canonical haplotype)
Supplementary_files_format_and_content: FSEQ files are in BED format and comprise peaks that identify open chromatin sites [column headers are: Chromosome, start, end, peak_signal, peak_width]. Diffreps output is in tab delimited text file output and comprises 13,516 dynamic chromatin sites. Dynamic FAIRE hotspots are in BED format and comprise hotspots of dynamic chromatin identified by Diffreps with p value < 0.05

molecule: genomic DNA

organism: Homo sapiens

source_name: Macrophage-oxLDL

growth_protocol: CD14 positive monocytes were isolated by positive selection from 50ml of peripheral blood from healthy volunteers. Monocytes were cultured for 7 days with 50ng/ml macrophage colony stimulating factor to generate macrophages.

extract_protocol:
FAIRE enriched genomic DNA was extracted using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).
Libraries were generated from gel-purified ~200bp DNA fragments (actual fragment size median 151bp +-39 median absolute deviation (MAD) for samples numbered 279, 280, 277, 278 and 141+-32 MAD for samples 205, 207). After adapter ligation and PCR-based amplification, samples were sequenced on the Illumina HiSeq platform to generated paired end 50bp reads (Illumina, San Diego, CA). Samples were multiplexed across 2 lanes.

treatment_protocol: After 7 days of culture cells were treated for 48 hours with either oxLDL (50mcg/ml, Copper oxidized, endotoxin-free) or control buffer which lacked oxLDL

tag: gender

value: male

value: Macrophage


title: ChIP_seq_Pontin

description: ChIP-sequencing


title: FOXA2KD_2

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

institute: Harvard Medical School

data_processing:
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012).  Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), human body map lincRNA annotations (Cabili et al., 2011)and the recently identified lncRNAs in human pancreatic islet and β cells (Moran et al., 2012).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: differentiated FOXA2-knockdown endoderm cells

growth_protocol: Human ESC line H9 was used to differentiate into definitive endoderm cells and pancreatic progenitors as previously described (Jiang et al., 2011). The following antibodies (all were purchased from BD) were used to label different cell populations: PE-conjugated mouse anti-human SSEA4 and APC-conjugated mouse anti-human CD184 for undifferentiated human ESCs (SSEA4+/CD184-); APC-conjugated mouse anti-human CD184 IgG and PE-conjugated mouse anti-human CD117 for definitive endoderm (CD184+/CD117+); PE-conjugated mouse anti-human CD24 and FITC-conjugated rat anti-human CD49f for pancreatic progenitors (CD24high/CD49flow).

extract_protocol:
Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).
The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illumina’s construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp).

treatment_protocol: Primary human islet were obtained from Integrated Islet Distribution Program (IIDP, study number BS208) and processed according to a previous report with minor modification (Dorrell et al., 2008; Dorrell et al., 2011). The following antibodies were used to label desired cell populations: HPi2 (mouse IgG1), and HPa1 (mouse IgM) as primary antibodies (kindly provided by Dr. Streeter), Alexa647-conjugated donkey anti-mouse IgG and Alexa488-conjugated donkey anti-mouse IgM as secondary antibodies. Beta cells were recognized as HPi+/HPa-, and HPi+/HPa+ for alpha cells as described (Dorrell et al., 2011).

tag: genotype/variation


title: DEANR1KD_2

source_name: differentiated DEANR1-knockdown endoderm cells


title: DEANR1KD_1


title: WT_1

source_name: differentiated endoderm cells

value: WT


title: WT_2


title: tj-GAL4>Ø


title: Input-tj-GAL4>Ø

description:
Total RNA
RNA Trizol extraction


title: ChIP_seq_GFP

description: ChIP-sequencing

value: ZHBTc4 ES cells


title: mRNA_seq_shRNA_linc1253 rep1

description:
mRNA-sequencing
Normalized_counts_2.txt


title: C/EBP beta_Macrophage-oxLDL_208

description:
processed data file: macs2_foam_cells_peaks.txt
processed data file: diffreps_cebpb.txt
paired-end fastqs median absolute deviation: 57

data_processing:
We used off-line base caller 1.8.4
Aligned to hs37d5 using Stampy
Filtered on MAPQ score 4 using Samtools to remove non-uniquely mapped reads
Duplicates removed using Picard 'removeduplicates' tool
One read of each proper pair and all 'improperly' paired reads taken to effectively convert to a single end file – using samtools
Bam files converted to bed files using BamToBed in the Bedtools suite.
Peaks called using MACS2 with default settings using pooled biological replicates for control or oxLDL treated cells. Dynamic sites were identified using diffreps version 1.55.4 with parameters – window size 200, step size 20, FDR 2.5%, Chi sqared test on pooled biological replicates, sites with less than a total of 50 normalized reads in macrophages and foam cells were excluded.
Genome_build: hs37d5
Supplementary_files_format_and_content: [MACS2_foam_cell_peaks.txt and MACS2_control_cell_peaks.txt] MACS2 output on pooled biological replicates for control cells or oxLDL treated cells.
Supplementary_files_format_and_content: [diffreps_cebpb.txt] Diffreps output

growth_protocol: CD14+ monocytes were isolated by positive selection from healthy, consenting adults and differentiated into macrophages over 7 days by culture with 50ng/ml macrophage colony stimulating factor.

extract_protocol:
ChIP was performed using the Invitrogen Magnify ChIP kit according to the manufacturers instructions.
The libraries were prepped using the Apollo ChIP32 No Upper Cut, min lower  cut protocol (non-GUI user maintenance protocol).  We then did a further  size selection (from an E-gel) which removed the >600bp contribution.

treatment_protocol: After 7 days cells were treated either with oxLDL 50mcg/ml or control buffer for 48 hours.

value: oxLDL (50mcg/ml)

tag: chip antibody

value: C/EBP beta antibody (Santa Cruz, catalog# sc-150, lot# co513)


title: FOXA2KD_1


title: C/EBP beta_Macrophage-control_204

description:
processed data file: macs2_macrophages_cells_peaks.txt
processed data file: diffreps_cebpb.txt
paired-end fastqs median absolute deviation: 57

source_name: Macrophage-control

value: Control


title: C/EBP beta_Macrophage-oxLDL_206


title: C/EBP beta_Macrophage-oxLDL_205


title: C/EBP beta_Macrophage-control_203


title: C/EBP beta_Macrophage-control_202


title: C/EBP beta_Macrophage-control_201


title: wt; mock; 6h; Rep_3

status: Public on Apr 07 2015

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Biology of Ageing

data_processing:
TopHat 2.0.9
Cufflinks 2.1.1
Genome_build: GRCm38.78
Supplementary_files_format_and_content: cuffdiff output

source_name: wt

extract_protocol:
RNA isolation was done using TRIzol reagent (Invitrogen, 15596-026) in agreement with manufacturer instructions.
TruSeq® Stranded Total RNA LT kit (with Ribo-Zero™ Human/Mouse/Rat).

treatment_protocol: 20µM Etoposide

value: mock/DMSO

tag: time point

tag: replicate

value: wt


title: wt; mock; 1h; Rep_3


title: DRB

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

description: Drug treatment to inhibit RNA transcription by preventing phosporylation of PTEFb

data_processing:
Basecalls performed using CASAVA version 1.4
Alignemnt to the human genome using TopHat v 2.0.1
Conversion of the aligned reads into bigwig coverages using R and BioConductor
Genome_build: Ensembl hg19 v69
Supplementary_files_format_and_content: BigWig files

source_name: HeLa cells

growth_protocol: Cells grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Total RNA from cells treated with DRB, with siRNAs targeting hnRNP A1 and A2 or not-treated (control) was purified using the RNAeasy mini kit (Qiagen). A total of 10 µg of RNA was used to generate an TruSeq library using the manufacturer’s protocol (Illumina).
Illumina TrueSeq  mRNA Library prep kit

treatment_protocol: For A1-A2-RNAi: 40 nM of total siRNAs using Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Totla treatment time 72 hours. For DRB treatment: 100 µm of DRB for 24 hours.

value: Chemical treatment

tag: compound


title: NS

description: Non-targeting siRNA treatment

value: RNAi knock down

value: siRNAs targeting no expressed gene in the human genome


title: A1-A2-RNAi

description: RNAi knock down targeting the hnRNP A1 and A2

value: siRNAs targeting the hnRNP A1 and A2 mRNA


title: wt; Eto; 6h; Rep_3

value: Etoposide (20µM)


title: C/EBP beta_Macrophage-oxLDL_207


title: Abca4L541P;A1038V/L541P;A1038V RPE 2

city: Cleveland

first: Ning

last: Zhang

state: OH

address: 10900 Euclid Ave.

department: Pharmacology

institute: Case Western Reserve University

data_processing:
Sequencing reads generated from the Illumina platform were trimmed for quality and adapter sequences. Reads were then aligned to the University of California, Santa Cruz (UCSC) mouse genome assembly and transcript notation (mm9).
Reads were mapped with tophat software, which implements the bowtie2 algorithm for sequence alignment and analyzes the mapped reads to identify splice junctions between exons.
The tophat alignments were then analyzed with cufflinks. The RNASeq analysis package recorded the fragments per kilobase of exon per million fragments mapped (FPKM) values.
FPKM values were then used to identify differentially expressed genes by using a significance cutoff for the adjusted p-value (q-value) of <0.05 as a statistically significant differential expression.
Genome_build: mm9

source_name: RPE/choroid

extract_protocol:
Mouse retinas and RPE/choroids were carefully dissected out and immediately placed in RNALater stabilization reagent (Qiagen, Germantown, MD) between 3:00 and 5:00 PM. Retinas and RPE/choroids were immediately homogenized and passed through a QIAShredder column (Qiagen) to amply the homogenization step. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on-column DNase treatment (Qiagen) as per the manufacturer's directions.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded total RNA kit with Ribo-zero Gold by following the protocol provided. Samples were pooled, denatured, and diluted according to Illumina's best practices and loaded onto the HiSeq 2500 instrument using a Rapid Run Paired-end flow cell with a run type of 100 bp paired-end

tag: stain

value: mixed (129SV and C57BL/6)

tag: age

value: post natal day 30


title: WT RPE 3

value: wild type


title: wt; Eto; 1h; Rep_3


title: wt; mock; 6h; Rep_1


title: WT RPE 2


title: wt; mock; 6h; Rep_2


title: wt; Eto; 6h; Rep_2


title: WT RPE 1


title: Abca4L541P;A1038V/L541P;A1038V RPE 3


title: Abca4-/- RPE 2


title: Abca4-/- RPE 1


title: wt; Eto; 1h; Rep_2


title: wt; mock; 1h; Rep_2


title: Abca4L541P;A1038V/L541P;A1038V RPE 1


title: Abca4-/- RPE 3


title: WT retina 2

source_name: Retina


title: wt; mock; 1h; Rep_1


title: WT retina 1


title: WT retina 3


title: Mk2/2 KO; Eto; 1h; Rep_3

source_name: Mk2/3 KO

value: Mk2/2 KO


title: wt; Eto; 6h; Rep_1


title: Mk2/2 KO; mock; 6h; Rep_3


title: Mk2/2 KO; Eto; 6h; Rep_3


title: Abca4L541P;A1038V/L541P;A1038V retina 3


title: Abca4L541P;A1038V/L541P;A1038V retina 1


title: Abca4-/- retina 2


title: Mk2/2 KO; Eto; 1h; Rep_2


title: Mk2/2 KO; mock; 1h; Rep_3


title: Abca4L541P;A1038V/L541P;A1038V retina 2


title: Mk2/2 KO; Eto; 6h; Rep_2


title: Mk2/2 KO; mock; 1h; Rep_2


title: Mk2/2 KO; mock; 1h; Rep_1


title: Mk2/2 KO; Eto; 1h; Rep_1


title: wt; Eto; 1h; Rep_1


title: Mk2/2 KO; mock; 6h; Rep_1


title: Abca4-/- retina 1


title: Mk2/2 KO; Eto; 6h; Rep_1


title: MDBK BFV-Riems Chronic

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

description:
Illumina Index Number: 22
Total small RNA

data_processing:
Initial reads were quality filtered with cassava 1.8.2.
For the 50-bp single-end reads, adapter sequences were clipped, and reads of ≥15 nt were quality filtered using FASTX-toolkit v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Read mates of ≥15 nt from the 50-bp paired-end sequencing were clipped and quality filtered using Trimmomatic v0.30.
Bowtie v.0.12.7 was used to sequentially filter and assign reads to adapter sequences, the viral genome (accession no. JX307862.1), miRbase v.20 bovine miRNA hairpins, and Ensembl annotations of the UMD3.1 bovine noncoding RNAs and genome. While one mismatch was allowed for alignments to the viral and bovine RNA libraries, two mismatches were allowed when aligning to bovine genomic DNA.
Genome_build: JX307862.1
Supplementary_files_format_and_content: Based off of BED format.  Columns are:  Chromosome, start coordinate, end coordinate, reads per million library reads, sense.  Paired-end data is the same except the order is chromosome, start coordinate, lane information, read mate, sense

organism: Bos taurus

source_name: Infected MDBK cell culture

growth_protocol: Madin-Darby bovine kidney (MDBK) cells were maintained in Dulbecco's modified Eagle's medium (DMEM; Sigma) supplemented with 10% fetal horse serum (Sigma).

extract_protocol:
Total RNA was isolated from BFV-infected MDBK cells by use of TRIzol. The RNA fraction containing ~15- to 40-nt RNAs was isolated by polyacrylamide gel electrophoresis on 15% Tris-borate-EDTA (TBE)–urea gels (Bio-Rad), electroeluted from the excised gel slice by use of Gel Eluter (Hoefer) and then desalted using Bio-Spin 6 columns (Bio-Rad).  RNA species of ≤200 nt were isolated from chronically BFV-infected MDBK cells by using a mirVana miRNA isolation kit (Ambion). To prepare the RNA for deep sequencing, the size-fractionated total RNA sample was first treated with calf intestinal phosphatase (CIP; New England BioLabs) in NEB buffer 3 at 37°C for 1 h and then precipitated using ethanol and sodium acetate. This treatment was designed to remove any 5′ triphosphates from the RNA. The RNA was then rephosphorylated with T4 polynucleotide kinase (T4 PNK; New England BioLabs) at 37°C for 1 h. RNAs of >25 nt were collected using Centri-Spin 40 columns (Princeton Separations).
Samples were processed using a TruSeq small RNA sample preparation kit (Illumina). Adapter-ligated small RNAs were reverse transcribed using SuperScript III (Life Technologies), amplified using GoTaq green PCR master mix (Promega) with the TruSeq 3′ indices, and sequenced on an Illumina HiSeq 2000 instrument.

treatment_protocol: The BFV Riems isolate was initially propagated by cocultivation of infected and uninfected calf trachea cells. Subsequently, BFV was adapted to grow by cocultivation with Madin-Darby bovine kidney (MDBK) cells. MDBK-derived BFV was subsequently serially passaged by cocultivation of BFV-infected and noninfected MDBK cells, and corresponding samples are designated chronically BFV-infected cells. In parallel, BFV, which is normally highly cell associated, was adapted to cell-free transmission by using MDBK cells in serial passages using cell-free culture supernatant rather than cell cocultivation. After 10 cell-free serial passages, BFV titers were ~1000 infectious particles/mL, and this stock was used to infect 1,000,000 MDBK cells (acute infection) at a multiplicity of infection of ~0.01.

tag: cell line

value: MBDK

tag: length of infection

value: Chronically-infected


title: MDBK BFV-Riems 3dpi (acute)

description:
Illumina Index Number: 13
Total small RNA

value: 72 hours


title: E13.5 pancreas WT-3

city: Copenhagen

first: Laurence

middle: Anne

last: Lemaire

address: Blegdamsvej, 3b building6 floor4

department: DanStem

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina pipeline Casava 1.82 was used for base calling.
Reads were mapped to the mm9 mouse genome with bowtie v0.12.7 (480M reads mapped in total) and the number of reads per kilobase per million (RPKM) was calculated (Langmead et al., 2009).
The data were then filtered to eliminate genes which had a RPKM below 0.01.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text file containing Ensembl gene accession numbers and RPKMs for each replicate.

source_name: E13.5 dorsal pancreas, WT

extract_protocol:
Dorsal pancreata were snap-frozen and kept at -80 degrees. RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, 74034).
TruSeq RNA libraries were synthesized from 500ng of RNA using TruSeq RNA Sample Preparation Kit v2 from Illumina (RS-122-2001).

tag: strain/background

value: mixed (C57BL/6, ICR)

value: WT

tag: developmental stage

value: dorsal pancreas


title: E13.5 pancreas Bicc1 KO-2

source_name: E13.5 dorsal pancreas, Bicaudal C1 KO

value: Bicaudal C1 knockout


title: E13.5 pancreas Bicc1 KO-3


title: SA1 wild type embrionary brain rep 1_RNA-seq

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Isolation of poly A+ RNA from total RNA

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (GRCm37/mm9) with TopHat-2.0.0 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used were Mus musculus GRCm37.v65 from Ensembl
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: Cufflinks FPKM tracking files were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

source_name: SA1 wild type embrionary brain

extract_protocol:
RNA samples (two independent replicates for condition, with material from four animals in each case) from different tissues were extracted using the guanidine thyocianate buffer, followed by acid phenol chloroform and treated with DNaseI.
2 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 6.9 to 7.6 (average 7.1) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: E17.5 embryo

value: whole brain


title: E13.5 pancreas WT-2


title: SA1 wild type embrionary brain rep 2_RNA-seq

description: Isolation of poly A+ RNA from total RNA


title: E13.5 pancreas Bicc1 KO-1


title: Pancreas rep 2_RNA-seq

description: Isolation of poly A+ RNA from total RNA

source_name: Pancreas

value: 8-10 week old

value: pancreas


title: Pancreas rep 1_RNA-seq

description: Isolation of poly A+ RNA from total RNA


title: Mk2/2 KO; mock; 6h; Rep_2

tag: treatment

value: mock/DMSO


title: SA1 knock out embrionary brain rep 2_RNA-seq

description: Isolation of poly A+ RNA from total RNA

source_name: SA1 knock out embrionary brain

value: SA1 knock out

tag: tissue


title: Abca4-/- retina 3

value: mixed (129SV and C57BL/6)

tag: genotype


title: E13.5 pancreas WT-1


title: SA1 knock out embrionary brain rep 1_RNA-seq

description: Isolation of poly A+ RNA from total RNA

tag: strain


title: TRACK 43-50 kidney 2

city: New York

first: Leiping

last: Fu

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

data_processing:
Reads were aligned to the genome using the Burrows-Wheeler Aligner in Goby web software (goby_1.9.8.3 (20120216154520)), using default parameters.
Differential Expression Analysis were done with Differential Expression Analysis with Goby in Goby web software (goby_1.9.8.3 (20120216154520)), using default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Goby Web software.
Genome_build: NCBI37.55/MM9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: kidney cortex

growth_protocol: Animals were kept at standard conditions in Research Animal Resource Center of WCMC

extract_protocol:
Thin outer slice of kidney cortex was immediately removed from the animals. mRNA was extracted from the kidney cortex slice using mini-RNAeasy columns (Qiagen, Valencia, CA).
illumina TruSeq RNA Sample Preparation kit

treatment_protocol: No treatment

value: kidney cortex

value: male

value: TRACK/gamma-HIF1alphaM3 TG-


title: TRACK 43-75 kidney 1

value: TRACK/gamma-HIF1alphaM3 TG+


title: TRACK 43-50 kidney 1


title: Adult brain rep 1_RNA-seq

description: Isolation of poly A+ RNA from total RNA

source_name: Adult brain

value: wild type

value: cortex


title: TRACK 43-49 kidney 2


title: TRACK 43-49 kidney 1


title: Adult brain rep 2_RNA-seq

description: Isolation of poly A+ RNA from total RNA


title: TRACK 43-29 kidney 2


title: TRACK 43-75 kidney 2


title: TRACK 43-76 kidney 1


title: Fib-4D

city: Dalian

first: Lan

last: Kang

address: 9 West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description: Derived from all-iPS mice with oct4, sox2, klf4 and c-myc inserted in genome and could be induced expression by doxcycline

data_processing:
RNA sequencing reads were aligned to the mouse reference genome mm9 from UCSC using TopHat with a tolerance of 3 mismatches.Only unique mapped reads were used for further analysis.
Cufflinks was used to measure the relative abundance of each transcript using Ensemble Transcript ID. Expression of each transcript was quantified as the number of reads divided by the transcript length (in kb) and the total number of mapped reads (in millions), and defined as fragments per kilobase of exon per million fragments mapped (FPKM). We converted the Ensembl Transcript ID to Gene ID using annotation information downloaded from Ensemble database via BioMart (www.ensembl.org/biomart/martview) .
Genome_build: mm9
Supplementary_files_format_and_content: Normalized expression profiling data was presented as a matrix with 36818 rows (genes) and 18 columns (samples).

source_name: Fibroblast

extract_protocol:
For fibroblasts: RNA was harvested using Trizol reagent.For hematopoietic cells: each of the sample, 25 individual cells were manually picked and transferred into lysis buffer by a mouth pipette, then directly reverse transcribed the released mRNA by a polyT primer, after that, polyA was added to the 3’ end of the first cDNA strand by terminal deoxynucleotidyl transferase, and the second strand cDNA was synthesized by another polyT primer, which was followed by 20+9 cycles of PCR to amplify cDNAs.
For fibroblasts: RNA libraries were prepared for sequencing using standard Illumina protocols. Basically the mRNA was first purified and fragmented. First and second strand cDNAs were synthesized and end repaired, then 3’ end of the cDNA was adenylated and cDNAs were ligated to adaptors. After purification, the adaptor ligated cDNAs were enriched by primers that annealed to the adaptors. The library were validated on an Agilent Technologies 2100 Bioanalyzer.For hematopoietic cells: RNA-seq library was prepared following protocol of NEBNext Singleplex (#E7350) Oligos for Illumina. The cDNAs were fragmented to 200-400 bp by ultrasonication, the fragmented cDNAs were then end repaired, and cleaned up using AMPure XP® Beads (Beckman Coulter , Inc.). dA-tail were added to the end repaired cDNA, and NEBNext Adaptor was then ligated to the dA-tailed cDNA. The adaptor ligated cDNAs were PCR enriched with Universal PCR primer and Index primer, and the enriched cDNAs were then purified by AMPure XP® Beads. The library was quality checked on a Bioanalyzer ® (Agilent Technologies, Inc.).

tag: in vitro culture

value: 4 days

tag: doxcycline treatment

value: Yes

tag: cell type

value: Fibroblast


title: Fib_0

value: 0 days

value: No


title: Fib_2D

value: 2 days


title: TRACK 43-29 kidney 1

tag: gender


title: MP_4N

source_name: Myeloid progenitor cell

value: Myeloid progenitor cell


title: TRACK 43-26 kidney 1


title: ST-HSC_4D

source_name: Short term hematopoietic stem cell

value: Short term hematopoietic stem cell


title: LT-HSC_4N

source_name: Long term hematopoietic stem cell

value: Long term hematopoietic stem cell


title: MP_2D


title: ST-HSC_4N


title: ST-HSC_2D


title: LT-HSC_4D


title: TRACK 43-76 kidney 2


title: Female3_2a_non-obese_ngt_0h

city: Gothenburg

first: Leif

last: Väremo

address: Kemivägen 10

department: Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
Basecalling, demultiplexing and conversion using CASAVA v1.8.2.
The reads were trimmed from adapter sequences and aligned to the human genome (Ensembl GRCh37.73, DNA primary assembly) using STAR 2.3.1u and the Homo_sapiens.GRCh37.73.gtf-file. The following additional flags were used: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outStd SAM --outFilterType BySJout
Samtools 0.1.18 was used for indexing and sorting
FPKM-values for each sample were calculated using Cufflinks 2.1.1
Gene counts were calculated using HTSeq-count 0.5.4p3
Genome_build: Ensembl GRCh37.73
Supplementary_files_format_and_content: The count files contain the gene counts for each sample, as output by HTSeq-count. The FPKM-values of all samples are collected into the single file FPKM-values.xlsx.

source_name: vastus lateralis muscle_female

growth_protocol: Muscle precursor cells (satellite cells) were isolated from human skeletal muscle biopsies obtained from the vastus lateralis muscle using a biopsy needle with suction (Bergström, 1975) as described in detail previously (Broholm et al., 2012). Isolated satellite cells were cultured in growth media 1 (HAM/F10 supplied with 20% Fetal Bovine Serum and 1% penicillin/streptomycin) and plated in 6-well plates. Upon 70-80% confluence, the media was changed to differentiation media 1 (DMEM 4.5 g/L glucose supplied with 10% FBS and 1% penicillin/streptomycin) for two-three days, until the myoblasts were completely confluent and had lined up. Hereafter, media was changed to differentiation media 2 (DMEM 4.5 g/L glucose supplied with 2% horse serum and 1% penicillin/streptomycin) thereby initiating fusion into myotubes. Cultures were fully differentiated by day 5 as determined by visual confirmation of myotube formation (>3 nuclei per myotube in ~70% of the cells). Two hours before harvesting of RNA the media was changed to DMEM 1.0 g/L glucose without any supplements.

extract_protocol:
Total RNA was extracted using Trizol® (Life Sciences) according to the manufactures’ instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA kit

tag: sample id

tag: cell id

tag: disease

value: ngt

tag: weight

value: non-obese

value: female

tag: time after insulin, h

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: TRACK 43-26 kidney 2

tag: tissue

value: kidney cortex

tag: strain

tag: gender

value: male

tag: genotype


title: Female2_13a_non-obese_ngt_0h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: time after insulin, h

tag: age


title: ST-HSC_2N

tag: in vitro culture

tag: doxcycline treatment

tag: cell type


title: MP_2N


title: MP_4D


title: LT-HSC_2D


title: LT-HSC_2N


title: Male1_34a_non-obese_ngt_0h

source_name: vastus lateralis muscle_male

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: MP_0

tag: strain


title: Male2_32a_non-obese_ngt_0h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: ST-HSC_0

tag: in vitro culture

tag: doxcycline treatment

tag: cell type


title: LT-HSC_0


title: L7_FC819_Lane7_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_TuMV_IP

status: Public on Apr 06 2015

city: Lincoln

first: Hernan

last: Garcia-Ruiz

state: NE

address: 4240 Fair Street

department: Plant Pathology

institute: University of Nebraska-Lincoln

description:
3' index CAGATG
Abundance of siRNAs mapping to Arabidopsis Lib-7-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib7_TuMV.gff3

data_processing:
Sequencing reads from small RNA libraries were computationally processed to remove 3' adaptor sequences, and sequences were consolidated to generate read counts per unique small RNA.
Unique small RNAs were aligned to the Arabidopsis thaliana and Turnip mosaic virus genomes using Bowtie v0.12.8 with settings allowing for perfect matches only (bowtie -f -v 0 -a -S -p 10).
Genome_build: Arabidopsis thaliana: GCA_000001735.1
Genome_build: Turnip mosaic virus: NC_002509.2

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: Arabidopsis plants were grown in a growth chamber with 16-hr light/8-hr dark cycle at 22C.

extract_protocol:
Rosette leaves, cauline leaves or inflorescence tissue (1g) were collected from immunoprecipitation. Total RNA was extracted from input and immunoprecipitation fractions. Small RNAs were size fractionated from input samples.
Total RNA was extracted from input fraction and small RNAs separated by size fractionation. Small RNAs in input and HA-AGO or HC-Pro immunoprecipitation fractions were converted to DNA Amplicons by 5' (GUUCAGAGUUCUACAGUCCGACGAUC) or  3’ (CTGTAGGCACCATCAAT) adaptor ligation followed by RT-PCR. DNA Amplicons were sequenced using the Illumina HiSeq2000 platform. Duplicate libraries were made per treatment. For each library, hits to TuMV, to TuMV-HIS and to Arabidopsis thaliana were included in separate files. Sequencing libraries were multyplexed using indexed 3' PCR primers.

treatment_protocol: At 27 days of age, plants were inoculated with enriched TuMV, TuMV-AS9, TuMV-HIS or TuMV-HIS-AS9 virion preparations or with buffer (mock).

tag: plant genotype

value: HA-AGO2-DAD (ago2-1)

tag: days post inoculation (dpi)

value: 10 dpi

tag: fraction

value: HA IP from input 99

tag: ip antibody

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)

tag: virus

value: TuMV


title: Female1_23a_non-obese_ngt_0h

tag: weight

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: Reactivating  vascular cambium

city: Beijing

first: Lin

last: Jinxing

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany

data_processing: Raw sequence reads were produced by the Solexa Genome Analyzer II and processed into clean, full-length reads by the BGI small RNA pipeline. During this procedure, all low-quality reads were removed, including 3' adapter reads and 5' adapter contaminants. The remaining high-quality sequences were trimmed of their adapter sequences and sequences < 18 nt were discarded. All high-quality sequences, including those with only a single unique read, were considered to be significant and further analyzed. Unique small RNA sequences were mapped to Chinese fir mRNA transcriptome database (GenBank: SRA053525) by SOAP according to its default settings (http://www.soap.genomics.org.cn).

organism: Cunninghamia lanceolata

source_name: cambial meristem

growth_protocol: Chinese fir trees (approximately 16 years old, 15 m tall, and 12 cm in diameter) growing under natural conditions in the Forestry Station of Fuzhou, China (25.44°N, 119.36°E).

extract_protocol:
Total RNAs of dormant, reactivating, and active cambial meristem, respectively were isolated using the Concert Plant RNA Reagent. 16-30 nt sRNAs were purified and two adaptors were sequentially ligated to the 5' and 3' ends of purified sRNAs.
To separate the small RNA (16-30 nt) from total RNA:
1) Mix total RNA with 2X loading Buffer of equal volume and then incubate it at 65C for 5 minutes to break the second structure within RNA.
2) After pre-running of the 15% TBU PAGE for 15 minutes, load the samples, 10bp DNA ladder and 14-30nt RNA ladder into the gel separately. Run the gel at 180V for 1 hour.
3) Cut out the band of gel corresponding to the 16-30nt in the marker lane.
Adapter sequences:
5' RNA Adapter: 5' GUUCAGAGUUCUACAGUCCGACGAUC
3' RNA Adapter: 5' P-UCGUAUGCCGUCUUCUGCUUGUidT
The ligation products were further purified and then RT-PCR amplified. The amplification products were purified and utilized for sequencing on an Illumina 2G Genome Analyzer at the Beijing Genomics Institute, Shenzhen.

treatment_protocol: Using cryosectioning to isolate cambial meristem

tag: Stage

value: reactivating

tag: tissue

value: cambial meristem


title: Active  vascular cambium

value: active


title: L6_FC819_Lane6_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
3' index TACGTT
Abundance of siRNAs mapping to Arabidopsis Lib-6-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib6_TuMV.gff3

tag: plant genotype

tag: days post inoculation (dpi)

tag: fraction

value: HA IP from input 98

value: Mock


title: Dormant vascular cambium

value: dormant


title: L2_FC819_Lane6_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
3' index GATCAC
Abundance of siRNAs mapping to Arabidopsis Lib-2-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib2_TuMV.gff3

value: Input 98

tag: ip antibody

tag: virus


title: Male3_35a_non-obese_ngt_0h

tag: sample id

tag: cell id

tag: disease

value: ngt

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: L103_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-103-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib103_TuMVAS9.gff3

data_processing:
Sequencing reads from small RNA libraries were computationally processed to remove 3' adaptor sequences, and sequences were consolidated to generate read counts per unique small RNA.
Unique small RNAs were aligned to the Arabidopsis thaliana and Turnip mosaic virus genomes using Bowtie v0.12.8 with settings allowing for perfect matches only (bowtie -f -v 0 -a -S -p 10).
Genome_build: Arabidopsis thaliana: GCA_000001735.1
Genome_build: Turnip mosaic virus: NC_002509.2
Processed_data_files_format_and_content: *Arabidopsis.gff3 files report abundance of siRNAs mapping to Arabidopsis
Processed_data_files_format_and_content: *TuMV.gff3 files report abundance of siRNAs mapping to TuMV

source_name: Noninoculated cauline leaves

value: HA-AGO10-DAH (ago2-1)

value: 15 dpi

value: HA IP from Input 99


title: L5_FC819_Lane6_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
3' index CAGATG
Abundance of siRNAs mapping to Arabidopsis Lib-5-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib5_TuMV.gff3

value: HA IP from input 97


title: L4_FC819_Lane7_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_TuMV_Input

description:
3' index GATCAC
Abundance of siRNAs mapping to Arabidopsis Lib-4-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib4_TuMV.gff3

value: HA-AGO2-DAD (ago2-1)

value: Input 100


title: L1_FC819_Lane6_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
3' index CGATGT
Abundance of siRNAs mapping to Arabidopsis Lib-1-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib1_TuMV.gff3

value: 10 dpi

value: Input 97


title: L96_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-96-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib96_TuMVHIS.gff3

value: HIS IP from Input 92

value: Anti-HIS 27E8 (Cell Signaling Technology Catalog#236)

value: TuMV-HIS


title: L104_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-104-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib104_TuMVAS9.gff3

value: HA IP from Input 100

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: L102_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_Mock_IP

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-102-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib102_TuMVAS9.gff3

value: HA IP from Input 98

value: Mock


title: L95_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-95-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib95_TuMVHIS.gff3

value: HIS IP from Input 91


title: L94_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS_Input

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-94-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib94_TuMVHIS.gff3

value: Input 92


title: L99_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-99-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib99_TuMVAS9.gff3

value: HA-AGO10-DAH (ago2-1)

value: Input 99


title: L98_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-98-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib98_TuMVAS9.gff3

value: 15 dpi

value: Input 98


title: L101_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_Mock_IP

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-101-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib101_TuMVAS9.gff3

value: HA IP from Input 97


title: L100_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-100-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib100_TuMVAS9.gff3

value: Input 100


title: L91_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS-AS9_IP

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-91-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib91_TuMV-HIS-AS9.gff3

value: HIS IP from Input 89


title: L90_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS-AS9_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-90-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib90_TuMV-HIS-AS9.gff3

value: Input 90


title: L8_FC819_Lane7_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_TuMV_IP

description:
3' index TACGTT
Abundance of siRNAs mapping to Arabidopsis Lib-8-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib8_TuMV.gff3

value: HA-AGO2-DAD (ago2-1)

value: 10 dpi

value: HA IP from input 100

value: TuMV


title: L89_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS-AS9_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-89-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib89_TuMV-HIS-AS9.gff3

value: Input 89


title: L92_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS-AS9_IP

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-92-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib92_TuMV-HIS-AS9.gff3

value: HIS IP from Input 90

value: Anti-HIS 27E8 (Cell Signaling Technology Catalog#236)


title: L88_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-88-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib88_TuMVAS9.gff3

value: HA-AGO1-DAH (ago2-1)

value: HA IP from Input 84

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: L87_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-87-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib87_TuMVAS9.gff3

value: HA IP from Input 83


title: L3_FC819_Lane7_ED50_Inflorescence_HA-AGO2-DAD(ago2-1)_TuMV_Input

description:
3' index CGATGT
Abundance of siRNAs mapping to Arabidopsis Lib-3-Arabidopsis.gff3
Abundance of siRNAs mapping to TuMv Lib3_TuMV.gff3

value: Input 99


title: L86_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_Mock_IP

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-86-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib86_TuMVAS9.gff3

value: 15 dpi

value: HA IP from Input 82

value: Mock


title: L85_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_Mock_IP

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-85-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib85_TuMVAS9.gff3

value: HA IP from Input 81


title: L83_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-83-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib83_TuMVAS9.gff3

value: Input 83


title: L84_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-84-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib84_TuMVAS9.gff3

value: Input 84


title: L82_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-82-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib82_TuMVAS9.gff3

value: Input 82


title: L79_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_TuMV_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-79-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib79_TuMV.gff3

source_name: Inoculated rosette leaves

value: HA-AGO10-DDH (Col-0)

value: 7 dpi

value: HA IP from Input 75


title: L80_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_TuMV_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-80-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib80_TuMV.gff3

value: HA IP from Input 76

value: TuMV


title: L81_FC1040_Lane6_ED97_Cauline_HA-AGO1-DAH(ago2-1)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-81-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib81_TuMVAS9.gff3

value: HA-AGO1-DAH (ago2-1)

value: Input 81


title: L97_FC1104_Lane4_ED99_Cauline_HA-AGO10-DAH(ago2-1)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-97-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib97_TuMVAS9.gff3

value: HA-AGO10-DAH (ago2-1)

value: Input 97


title: L78_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_TuMV_Input

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-78-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib78_TuMV.gff3

value: Input 76


title: L77_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_TuMV_Input

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-77-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib77_TuMV.gff3

value: Input 75


title: L93_FC1045_Lane6_ED93_Cauline_ago2_TuMV-HIS_Input

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-93-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib93_TuMVHIS.gff3

value: 10 dpi

value: Input 91

value: TuMV-HIS


title: L76_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-76-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib76_TuMV.gff3

value: HA IP from Input 74

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)

value: Mock


title: L73_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-73-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib73_TuMV.gff3

value: HA-AGO10-DDH (Col-0)

value: Input 73


title: L75_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-75-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib75_TuMV.gff3

value: 7 dpi

value: HA IP from Input 73


title: L74_FC997_Lane6_ED89_Rosette_HA-AGO10-DDH(Col)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-74-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib74_TuMV.gff3

value: Input 74


title: L72_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_TuMV_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-72-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib72_TuMV.gff3

value: HA IP from Input 68

value: TuMV


title: L71_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_TuMV_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-71-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib71_TuMV.gff3

value: HA IP from Input 67


title: L68_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-68-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib68_TuMV.gff3

value: HA IP from Input 66


title: L70_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_TuMV_Input

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-70-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib70_TuMV.gff3

value: Input 68


title: L67_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-67-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib67_TuMV.gff3

value: HA IP from Input 65


title: L61_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_TuMV_Input

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-61-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib61_TuMV.gff3

value: HA-AGO1-DAH (Col-0)

value: Input 59


title: L60_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-60-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib60_TuMV.gff3

value: HA IP from Input 58


title: L62_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_TuMV_Input

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-62-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib62_TuMV.gff3

value: Input 60


title: L63_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_TuMV_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-63-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib63_TuMV.gff3

value: HA IP from Input 59

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: L66_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-66-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib66_TuMV.gff3

value: HA-AGO10-DDH (Col-0)

value: 10 dpi

value: Input 66

value: Mock


title: L64_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_TuMV_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-64-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib64_TuMV.gff3

value: 7 dpi

value: HA IP from Input 60


title: L58_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-58-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib58_TuMV.gff3

value: Input 58


title: L55_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_TuMV_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-55-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib55_TuMV.gff3

value: HA-AGO2-DAD (ago2-1)

value: HA IP from Input 53

value: TuMV


title: L57_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-57-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib57_TuMV.gff3

value: Input 57


title: L59_FC971_Lane7_ED88_Rosette_HA-AGO1-DAH (Col)_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-59-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib59_TuMV.gff3

value: HA-AGO1-DAH (Col-0)

value: HA IP from Input 57


title: L54_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_TuMV_Input

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-54-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib54_TuMV.gff3

value: Input 54


title: L56_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_TuMV_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-56-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib56_TuMV.gff3

value: HA IP from Input 54


title: L53_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_TuMV_Input

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-53-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib53_TuMV.gff3

value: Input 53


title: L52_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-52-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib52_TuMV.gff3

value: HA IP from Input 50

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: L50_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-50-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib50_TuMV.gff3

value: Input 50


title: L49_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-49-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib49_TuMV.gff3

value: Input 49


title: L48_FC954_Lane2_ED79_Cauline_Col_TuMV-HIS_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-48-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib48_TuMV-HIS.gff3

source_name: Noninoculated Cauline leaves

value: 10 dpi

value: HIS IP from Input 46

value: Anti-HIS 27E8 (Cell Signaling Technology Catalog#236)

value: TuMV-HIS


title: L47_FC954_Lane2_ED79_Cauline_Col_TuMV-HIS_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-47-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib47_TuMV-HIS.gff3

value: HIS IP from Input 45


title: L69_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_TuMV_Input

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-69-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib69_TuMV.gff3

value: HA-AGO10-DDH (Col-0)

value: Input 67


title: L46_FC954_Lane2_ED79_Cauline_Col_TuMV-HIS_Input

description:
small RNAs
3' Index: TCAGGC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-46-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib46_TuMV-HIS.gff3

value: Input 46


title: L45_FC954_Lane2_ED79_Cauline_Col_TuMV-HIS_Input

description:
small RNAs
3' Index: GCCAAT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-45-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib45_TuMV-HIS.gff3

value: Input 45


title: L42_FC954_Lane2_ED79_Cauline_Col_Mock_Input

description:
small RNAs
3' Index: TGCTAG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-42-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib42_TuMV-HIS.gff3

value: Input 42

value: Mock


title: L43_FC954_Lane2_ED79_Cauline_Col_Mock_IP

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-43-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib43_TuMV-HIS.gff3

value: HIS IP from Input 41


title: L40_FC954_Lane1_ED79_Inflorescence_Col_TuMV-HIS_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-40-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib40_TuMV-HIS.gff3

value: HIS IP from Input 38


title: L44_FC954_Lane2_ED79_Cauline_Col_Mock_IP

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-44-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib44_TuMV-HIS.gff3

value: HIS IP from Input 42


title: L65_FC990_Lane5_ED89_Inflorescence_HA-AGO10-DDH(Col)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-65-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib65_TuMV.gff3

value: Input 65


title: L37_FC954_Lane1_ED79_Inflorescence_Col_TuMV-HIS_Input

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-37-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib37_TuMV-HIS.gff3

value: Input 37


title: L36_FC954_Lane1_ED79_Inflorescence_Col_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-36-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib36_TuMV-HIS.gff3

value: HIS IP from Input 34


title: L32_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-32-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib32_TuMVAS9.gff3

value: HA-AGO2-DAD (ago2-1)

value: 15 dpi

value: HA IP from Input 30

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: L38_FC954_Lane1_ED79_Inflorescence_Col_TuMV-HIS_Input

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-38-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib38_TuMV-HIS.gff3

value: 10 dpi

value: Input 38

value: TuMV-HIS


title: L35_FC954_Lane1_ED79_Inflorescence_Col_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-35-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib35_TuMV-HIS.gff3

value: HIS IP from Input 33

value: Anti-HIS 27E8 (Cell Signaling Technology Catalog#236)


title: L39_FC954_Lane1_ED79_Inflorescence_Col_TuMV-HIS_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-39-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib39_TuMV-HIS.gff3

value: HIS IP from Input 37


title: L31_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-31-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib31_TuMVAS9.gff3

value: HA IP from Input 29


title: RN2_Trim33 ChIP-Seq_rep1

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

description: ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4 software was used.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were converted from wiggle files generated by MACS 1.4 software.

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep and 55 μM 2-mercaptoethanol.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

treatment_protocol: Cells were treated with DMSO or nothing before crosslinking. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.

tag: strain

tag: cell type

value: B cell leukemia

tag: antibody

value: Trim33 (A301-060A; Bethyl)

tag: genotype

value: MLL-AF9/NrasG12D (AML)


title: L34_FC954_Lane1_ED79_Inflorescence_Col_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-34-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib34_TuMV-HIS.gff3

tag: plant genotype

tag: days post inoculation (dpi)

tag: fraction

value: Input 34

value: Mock


title: L33_FC954_Lane1_ED79_Inflorescence_Col_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-33-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib33_TuMV-HIS.gff3

value: Input 33

tag: ip antibody

tag: virus


title: RN2_Input ChIP-Seq

description: ChIP-Seq


title: L51_FC971_Lane6_ED88_Rosette_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-51-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib51_TuMV.gff3

value: HA-AGO2-DAD (ago2-1)

value: 7 dpi

value: HA IP from Input 49


title: L29_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-29-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib29_TuMVAS9.gff3

value: 15 dpi

value: Input 29


title: L27_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
small RNAs
3' Index: CTTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-27-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib27_TuMVAS9.gff3

value: HA IP from Input 25

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: 38B9_Trim33 ChIP-Seq_rep2

description: ChIP-Seq

source_name: pro B-Cell

value: transformed pro B-Cell


title: 38B9_Trim33 ChIP-Seq_rep1

description: ChIP-Seq


title: T-ALL_Trim33 ChIP-Seq_rep1

description: ChIP-Seq

source_name: TAL transgenic/HEB heterozygous with Notch truncations (provided by I.Aifantis, NYU)

value: T-ALL


title: L28_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
small RNAs
3' Index: TCAGGC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-28-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib28_TuMVAS9.gff3

value: HA IP from Input 26


title: L41_FC954_Lane2_ED79_Cauline_Col_Mock_Input

description:
small RNAs
3' Index: CTTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-41-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib41_TuMV-HIS.gff3

value: 10 dpi

value: Input 41


title: L26_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
small RNAs
3' Index: TGCTAG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-26-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib26_TuMVAS9.gff3

value: Input 26


title: L25_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
small RNAs
3' Index: GCCAAT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-25-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib25_TuMVAS9.gff3

value: Input 25


title: RN2_Trim33 ChIP-Seq_rep2

description: ChIP-Seq

value: B cell leukemia

value: Trim33 (A301-060A; Bethyl)

value: MLL-AF9/NrasG12D (AML)


title: L23_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: ATCACG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-23-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib23_TuMVAS9.gff3

value: HA-AGO2-DAD (ago2-1)

value: HA IP from Input 21


title: L24_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_TuMV-AS9_IP

description:
small RNAs
3' Index: ACTTGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-24-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib24_TuMVAS9.gff3

value: 7 dpi

value: HA IP from Input 22


title: L30_FC939_Lane6_ED78_Cauline_HA-AGO2-DAD(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-30-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib30_TuMVAS9.gff3

value: 15 dpi

value: Input 30


title: L21_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: TTACCA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-21-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib21_TuMVAS9.gff3

value: Input 21


title: T-ALL_Trim33 ChIP-Seq_rep2

description: ChIP-Seq


title: H3K4me3 ChIP-Seq rep1

description: ChIP-Seq

source_name: Bcr-Abl transformed p19Arf null B-ALL

value: H3K4me3 (07-473; Millipore)

value: Bcr-Abl overexpressed, p19Arf -/- (B-ALL)


title: L16_FC837_Lane5_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_TuMV_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-16-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib16_TuMV.gff3

value: HA-AGO1-DAH (Col-0)

value: HA IP from Input 12

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)

value: TuMV


title: T-ALL_Input ChIP-Seq

description: ChIP-Seq

value: T-ALL


title: L22_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_TuMV-AS9_Input

description:
small RNAs
3' Index: ACTGTA
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-22-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib22_TuMVAS9.gff3

value: Input 22


title: Pu1 ChIP-Seq_rep2

description: ChIP-Seq

value: B cell leukemia

value: Pu.1 (SC-352, Santa Cruz)


title: L12_FC837_Lane5_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_TuMV_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-12-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib12_TuMV.gff3

value: 10 dpi

value: Input 12


title: H3K27ac ChIP-Seq rep1

description: ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: Pu1 ChIP-Seq_rep1

description: ChIP-Seq

value: Pu.1 (#2266, Cell Signaling)


title: L20_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-20-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib20_TuMVAS9.gff3

value: HA-AGO2-DAD (ago2-1)

value: 7 dpi

value: HA IP from Input 18

value: Mock


title: H3K4me3 ChIP-Seq rep2

description: ChIP-Seq

value: H3K4me3 (07-473; Millipore)

value: Bcr-Abl overexpressed, p19Arf -/- (B-ALL)


title: L19_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-19-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib19_TuMVAS9.gff3

value: HA IP from Input 17


title: L10_FC837_Lane4_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-10-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib10_TuMV.gff3

value: HA-AGO1-DAH (Col-0)

value: Input 10


title: L17_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-17-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib17_TuMVAS9.gff3

value: Input 17


title: Trim33 ChIP-Seq rep2

description: ChIP-Seq

value: Trim33 (A301-060A; Bethyl)


title: L14_FC837_Lane4_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_Mock_IP

description:
small RNAs
3' Index: TACGTT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-14-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib14_TuMV.gff3

value: HA IP from Input 10

value: Anti-HA 12CA5 (Roche Catalog# 11666606001)


title: L9_FC837_Lane4_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_Mock_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-9-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib9_TuMV.gff3

value: 10 dpi

value: Input 9


title: L15_FC837_Lane5_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_TuMV_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-15-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib15_TuMV.gff3

value: HA IP from Input 11

value: TuMV


title: Trim33 ChIP-Seq rep1

description: ChIP-Seq

value: B cell leukemia


title: B-ALL_Input ChIP-Seq rep2

description: ChIP-Seq


title: H3K27ac ChIP-Seq rep2

description: ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: RNASeq - FAMAp::GFP-FAMA (FGF) - replicate 1

city: Stanford

first: Dominique

middle: C

last: Bergmann

state: CA

address: 371 Serra Mall

department: Biology Department

institute: Stanford University

description:
Microarray-based expression profiles of FACS-sorted mature guard mother cells and young guard cells
FGF_1

data_processing:
Reads were aligned to the TAIR10.18 genome assembly via Bowtie2 using default settings.
All possible pairwise comparisons amongst the stomatal lineage cell types were used for differential expression analysis via DESeq2.
Count data was regularized log transformed into the log2 scale
Genome_build: TAIR10.18
Supplementary_files_format_and_content: Series supplementary text file includes log2 transformed normalized counts for each sample.

source_name: Mature guard mother cells and young guard cells

growth_protocol: Seedlings were grown for 10 days on 1/2 strength Murashige and Skoog (MS) medium under long day (16-hours light, 8-hours dark) conditions at 25C.

extract_protocol:
GFP/YFP-positive protoplasts were identified with a FACS Aria II cell sorter and directly sorted into RNA extraction buffer. Total RNA of sorted protoplasts was extracted with the RNeasy Micro Kit (QIAGEN) including on column DNase treatment according to the manufacturer’s instructions. RNA quality was checked on a Bioanalyzer (Agilent).
cDNA libraries were prepared from ~10 ng of total RNA from each cell sample. Ribosomal RNAs were depleted using an oligo-dT25 magnetic bead (Life Technologies) and the rRNA depleted RNA samples were checked on Bioanalyzer (Agilent). Using Apollo 324 (WaferGen), cDNA was generated using the PrepX SPIA RNA-Seq Kit and libraries were generated using the ILM DNA Library Kit (Wafergen) according to the manufacturer’s protocol.

treatment_protocol: Arial tissue of seedlings was harvested and incubated in protoplasting solution for 2 hours.

tag: marker line

value: FAMAp::GFP-FAMA in Col

tag: tissue

value: FACS-sorted protoplasts from aerial tissue of 10-day old seedlings


title: RNASeq - E1728::GFP (E1728G) - replicate 2

description:
Microarray-based expression profiles of FACS-sorted mature guard cells
E1728G_2

source_name: Mature guard cells

value: Enhancer trap line E1728::GFP in Col


title: RNASeq - FAMAp::GFP-FAMA (FGF) - replicate 2

description:
Microarray-based expression profiles of FACS-sorted mature guard mother cells and young guard cells
FGF_2


title: RNASeq - E1728::GFP (E1728G) - replicate 1

description:
Microarray-based expression profiles of FACS-sorted mature guard cells
E1728G_1


title: B-ALL_Input ChIP-Seq rep1

description: ChIP-Seq

value: Bcr-Abl overexpressed, p19Arf -/- (B-ALL)


title: L18_FC939_Lane5_ED78_Rosette_HA-AGO2-DAD(ago2-1)_Mock_Input

description:
small RNAs
3' Index: GATCAC
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-18-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib18_TuMVAS9.gff3

value: HA-AGO2-DAD (ago2-1)

value: 7 dpi

value: Input 18

value: Mock


title: L13_FC837_Lane4_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_Mock_IP

description:
small RNAs
3' Index: CAGATG
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-13-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib13_TuMV.gff3

value: HA-AGO1-DAH (Col-0)

value: HA IP from Input 9


title: BF_Glut-Rep2

city: Pittsburgh

first: Amit

last: Vikram

state: PA

address: 3700 O'Hara Street

department: Civil and Environmental Engineering

institute: University of Pittsburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequenced were adapter trimmed. The resulting files were then trimmed for low quality scores (q30) and length (<70 nt discarded) on CLC Genomics Workbench 7.5.1
RNAseq analysis in CLC Genomics Workbench v6.5.1 was conducted by merging both R1 (Forward) and R2 (Reverse) reads for each sample and obtaining single output files for 62.5 ppm and 0 ppm glutaraldehdye exposure.
The reads mapping to rRNA were manually removed and RPKM was recalculated. The data was further normalized using scaling based normalization method in CLC Genomics Workbench.
Differentially expressed genes were identified by comparing normalized gene reads between PBS and glutaraldehyde treated biofilm samples using Baggerley’s test on proportions for replicated experiment. FDR was calculated and genes with FDR corrected p ≤ 0.001 were considered significant.
Genome_build: NC_012660

organism: Pseudomonas fluorescens

source_name: 72 h biofilm exposed to 62.5 ppm glutaraldehyde

growth_protocol: The P. fluorescens was maintained on cetrimide agar plates. Overnight broth cultures of P. fluorescens were diluted 100 fold in fresh LB broth and palced in 6 well plates. Biofilms were grown for 72 h.

extract_protocol:
RNA was extracted using TRIZOL according to manufacturer's protocol and processed using ScriptSeq Complete kit for Bacteria. RNA-sequencing was performed on MiSeq.
RNA libraries were prepared using ScriptSeq Complete Kit for Bacteria (Epicenter, Madison, WI).

treatment_protocol: P. fluorescens 72 h old biofilms were exposed to 62.5 ppm or 0 ppm glutaraldehyde for 10 min at room temperature.

value: Wild type

tag: treatment

value: exposed to 62.5 ppm glutaraldehyde for 10 min


title: BF_PBS-Rep1

source_name: 72 h biofilm exposed to 0 ppm glutaraldehyde

value: exposed to 0 ppm glutaraldehyde for 10 min


title: BF_PBS-Rep2


title: Trim33 KD RNA-Seq rep2

description: RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence to map with mouse genome (mm9) using Tophat with default parameters.
Cufflinks software was used to compare gene expression profiles by calculting Reads Per Kilobase of exon per Megabase of library size (RPKM) for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, without filtering.

extract_protocol:
Total RNAs were extracted using Trizol reagent.
These libraries were made following the instructions of illumina Truseq RNA sample prep kit v2.

treatment_protocol: B-ALL cells were infected with Rluc or TRIM33.1272 shRNA-mCherry for 96 hours, and only viable cells were sorted at that time point.

value: Bcr-Abl overexpressed, p19Arf -/-

tag: shRNA


title: BF_Glut-Rep1


title: Control KD RNA-Seq rep1

description: RNA-Seq

value: shRen.713 (Rluc control)


title: L11_FC837_Lane5_ED57_Inflorescence_HA-AGO1-DAH(Col-0)_TuMV_Input

description:
small RNAs
3' Index: CGATGT
processed data file (Abundance of siRNAs mapping to Arabidopsis): Lib-11-Arabidopsis.gff3
processed data file (Abundance of siRNAs mapping to TuMV): Lib11_TuMV.gff3

value: 10 dpi

value: Input 11

value: TuMV


title: RNASeq - SPCHp::SPCH-YFP (SSY) - replicate 3

description:
Microarray-based expression profiles of FACS-sorted meristemios mother cells and young meristemoids
SSY_3

source_name: Meristemios mother cells and young meristemoids

value: SPCHp::SPCH-YFP in Col

value: FACS-sorted protoplasts from aerial tissue of 10-day old seedlings


title: eIF3g library for replicate 3

city: Boston

first: Amy

middle: Si-Ying

last: Lee

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

description: Replicate 3 - eIF3g

data_processing:
Library strategy: PAR-CLIP
Raw illumina reads were collapsed using the fastx_collapser tool, and 3' adapters were removed using Cutadapt
Reads were mapped using Bowtie to the hg19 genome
Read clusters were identified using PARalyzer
Clusters were annotated using bedtools intersect
Genome_build: hg19
Supplementary_files_format_and_content: Reproducible cluster chromosomal locations, annotation, and number of supporting reads and T/C conversions from the union of the three replicates

source_name: Human 293T cells

growth_protocol: 293T cells were grown in DMEM + 10% FBS

extract_protocol:
Cells were lysed in NP40 lysis buffer, and immunoprecipitation was performed using an eIF3b antibody. After a high salt wash, RNAs were digested with RNase T1, radiolabeled with T4 PNK, and protein-RNA complexes were excised after SDS-PAGE gel electrophoresis
cDNA libraries were constructed using a standard small RNA library protocol

treatment_protocol: Cells were treated with 100uM 4-thiouridine for 14h, and crosslinked on ice with 0.15 J cm-2

tag: par-clip antibody

value: anti-eIF3b (Bethyl A301-761A)

tag: cell line


title: RNASeq - SPCHp::SPCH-YFP (SSY) - replicate 1

description:
Microarray-based expression profiles of FACS-sorted meristemios mother cells and young meristemoids
SSY_1


title: RNASeq - MUTEp::nucGFP (MG) - replicate 1

description:
Microarray-based expression profiles of FACS-sorted late meristemoids and young guard mother cells
MG_1

source_name: Late meristemoids and young guard mother cells

value: MUTEp::nucGFP in Col


title: Control KD RNA-Seq rep2

description: RNA-Seq

value: B cell leukemia


title: RNASeq - SPCHp::SPCH-YFP (SSY) - replicate 2

description:
Microarray-based expression profiles of FACS-sorted meristemios mother cells and young meristemoids
SSY_2


title: RNASeq - ML1p::YFP-RCI2A (ML1Y) - replicate 1

description:
Microarray-based expression profiles of FACS-sorted epidermis cells
ML1Y_1

source_name: Epidermis cells

value: ML1p::YFP-RCI2A in Col


title: RNASeq - MUTEp::nucGFP (MG) - replicate 2

description:
Microarray-based expression profiles of FACS-sorted late meristemoids and young guard mother cells
MG_2


title: RNASeq - ML1p::YFP-RCI2A (ML1Y) - replicate 2

description:
Microarray-based expression profiles of FACS-sorted epidermis cells
ML1Y_2


title: eIF3g library for replicate 2

description: Replicate 2 - eIF3g


title: Trim33 KD RNA-Seq rep1

description: RNA-Seq


title: FBXL10 T/T (RNA-Seq)

city: St. Louis

first: John

middle: R.

last: Edwards

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were mapped to the mouse genome (mm9) using TopHat (v1.4.1). Mapped reads were assigned to annotated genes using htseq-count (v 0.5.3p9). Differential expression was assessed via edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file of EdgeR results, including log-fold change and cpm values for each sample.

source_name: ESC

growth_protocol: ES cells were cultured at 37°C under conditions of 5% CO2 on Mitomycin C inactivated mouse embryonic fibroblasts (MEF) in KO Dulbecco modified Eagle medium (KO DMEM) supplemented with 15% fetal bovine serum, 2 mM L-glutamine, MEM non-essential amino acids, 100 IU/mL penicillin, 100 μg/mL streptomycin, 0.12 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF) from the conditioned medium of LIF-secreting cells. Prior to use, MEF feeder cells were depleted by plating and recovery of nonadherent cells after 60 min.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life technologies), treated with DNase I (Roche) and then purified using the RNeasy Mini Kit (Qiagen). RNA integrity number (RIN) was measured using a 2100 Bioanalyzer (Agilent Technologies).
Purified RNA with RIN greater than 8 served for preparation of poly(A)+ RNA Seq libraries using the mRNA-Seq Sample Preparation Kit (Illumina).

value: ES cell

value: Fbxl10 T/T


title: eIF3d library for replicate 2

description: Replicate 2 - eIF3d


title: eIF3d library for replicate 3

description: Replicate 3 - eIF3d


title: eIF3d library for replicate 1

description: Replicate 1 - eIF3d


title: eIF3b library for replicate 3

description: Replicate 3 - eIF3b


title: Eed -/- (RRBS)

data_processing:
RRBS data was limited to the first 29bp of the read and were mapped to the mouse genome (mm9) using BSmap (v 2.74).
RNA-seq reads were mapped to the mouse genome (mm9) using TopHat (v1.4.1). Mapped reads were assigned to annotated genes using htseq-count (v 0.5.3p9). Differential expression was assessed via edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited output from Bsmap with counts for each converted cytosine and the overall fraction (ratio) of methylated counts.

growth_protocol: mES cells are cultured in ESC Serum + LIF under standard conditions.

extract_protocol:
Genomic DNA was extracted by proteinase K and RNase A digestions followed by phenol-chloroform extraction and ethanol precipitation.
RRBS libraries were constructed according to the protocol described by Gu et al. (2011) with the following modifications. Cytosine-methylated and indexed adapters obtained form the TruSeq ChIP Sample Preparation Kit (Illumina) were ligated to MspI digested DNA. Indexed fragments from different samples were pooled together in equimolar amounts prior to size selection and bisulfite conversion. Sodium bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research). In vitro CpG methylated DNA was included to serve as an internal control for complete bisulfite conversion.

value: Eed -/-


title: FBXL10 T/T (RRBS)

extract_protocol:
Genomic DNA was extracted by proteinase K and RNase A digestions followed by phenol-chloroform extraction and ethanol precipitation.
RRBS libraries were constructed according to the protocol described by Gu et al. (2011) with the following modifications. Cytosine-methylated and indexed adapters obtained form the TruSeq ChIP Sample Preparation Kit (Illumina) were ligated to MspI digested DNA. Indexed fragments from different samples were pooled together in equimolar amounts prior to size selection and bisulfite conversion. Sodium bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research). In vitro CpG methylated DNA was included to serve as an internal control for complete bisulfite conversion. The genomic DNA used for the RRBS analysis was extracted from ES cells cultured in serum and harvested at passage 17.


title: Ezh2 -/- (RRBS)


title: Ring1B -/- (RRBS)

value: Ring1B -/-


title: eIF3g library for replicate 1

description: Replicate 1 - eIF3g


title: eIF3a library for replicate 2

description: Replicate 2 - eIF3a


title: WT (RRBS)

value: WT


title: WT (RNA-Seq)


title: eIF3a library for replicate 1

description: Replicate 1 - eIF3a


title: OB1

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

description: Sample 1

data_processing:
Illumina 1.8.2 software used for basecalling.
RNA-seq reads were mapped to hg19_canonical genome assembly and GRCh37/hg19 gtf using TopHat version 2.0.9.
FPKMs were calculated by Cuffdiff 2.1.1, minimum alignment count = 10, false discovery rate = 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file includes FPKM values for each sample.

source_name: osteoblasts

extract_protocol:
RNeasy Midi Kit (QIAGEN, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

value: osteoblasts


title: OB2

description: Sample 2


title: OB3

description: Sample 3