title: Dsim female JP rep3

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

description: Ochanomizu University, Japan

data_processing:
100-bp paired-end sequencing reads were mapped to the Drosophila simulans genome (FlyBase r1.3) with TopHat 2.0.6 (Trapnell et al. 2009).  We allowed JPo mismatches in read mapping to the reference genome.
The normalized expression levels of genes were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKMs) by Cufflinks 2.0.0 with bias correction (“--multi-read-correct” and “--frag-bias-correct”) (Trapnell, et al. 2010).
Genome_build: FlyBase D. simulans r1.3
Supplementary_files_format_and_content: genes.fpkm_tracking: FPKM Tracking format, outputed from the Cufflinks suite. FPKM tracking files use a generic format to output estimated expression values.

organism: Drosophila simulans

source_name: Adult antenna

growth_protocol: k-s05; #14021-025.194 flies were raised in standard cornmeal yeast extract media at 25°C. Egg laying was performed on plates with standard vinegar medium and yeast. Embryos were collected in 0.03% Triton-X100, 0.4% NaCl 16-18 hr after egg laying.

extract_protocol:
About 300-700 pairs of fly antennae of each sex from each species were collected for total RNA isolation.  The antennae resected each day were preserved in ~ 50-100 ul Trizol (Life Technology) and stored at -80 °C before further processing.  Right before the RNA isolation, we spun down antennae preserved in Trizol at the max speed for 3 min at 4 °C and put each sample into one MagNA Lyser Green Beads tube (Roche).
The RNA isolation protocol we developed combined steps from conventional Trizol extraction and RNeasy Micro Elute Kit (QIAGEN, Inc.) with some modifications to obtain high yield and quality of total RNA.  Fly antennae were disrupted with MagNA Lyser (Roche) at 7000 rpm for 15 seconds each time and repeated for 4-5 times until the tissue was almost invisible.  After 15 sec, we cooled down the lysate on ice for 10 sec to prevent RNA degradation.  Tissue lysate was transferred to a new RNase free Eppendorf tube.  We used about 400 ul Trizol to rinse the beads of each sample and combine this 400 ul Trizol with the tissue lysate for the RNA isolation.  Based on the suggestion of the Trizol standard protocol, 200 microliters of chloroform per microliter of tissue lysate were added to the lysate and mixed well by shaking vigorously for 15 sec and set 2-3 min at room temperature.  The aqueous phase was separated by centrifuging the lysate at the maximum speed at 4 °C for 15 min and carefully transferred to a new Eppendorf tube after centrifuging. We added 1 volume of 5 µl Carrier RNA (QIAGEN, Inc.) and one microliter of 70% EtOH to the aqueous phase and mixed well by inverting the tubes carefully.  To obtain greater amount of RNA, we kept the samples at -80 °C for overnight to aid in RNA precipitation.  RNA isolation followed manufacturer’s protocol of the RNeasy Micro Elute Kit with increased volumes (700 ul) of RPE buffer and 80% ethanol to wash RNA.  Genomic DNA was removed by applying on-column DNase I treatment at room temperature for 15 min.
For paired-end mRNA-seq library preparation, we used Illumina TrueSeq kits.  A total of 10 µg total RNA was used for mRNA enrichment by oligo-dT beads followed by cation-catalyzed fragmentation for 4 minutes at 94˚C.  The mRNA fragments were then converted into double stranded cDNA by random priming followed by end repair.  The fragmented cDNAs from each sex of each species were then ligated to the barcoded paired-end adaptors and subjected to 15 cycles of PCR amplification and purified by Ampure beads (Beckman Agencourt). The absolute concentrations of the libraries were determined by Qubit fluorometry (Invitrogen) and BioAnalyzer High Sensitivity DNA Kit (Agilent).  We combined barcoded cDNA from 6 samples and loaded them in 3 sequencing lanes of flow cell, and paired-end 2*100nt sequencing was conducted on Illumina HiSeq2000.

value: antenna

tag: developmental stage

value: Adult

value: female

tag: age

value: within 1hr of eclosion


title: 35S-RTL2/dcl234-3

status: Public on Oct 01 2015

type: SRA

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

country: France

institute: INRA

library_source: transcriptomic

data_processing:
Removed adaptor “AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATG” using fastx_clipper
Mapped with bowtie, kept unique matches with no mismatch (-v 0 -a --best --strata -S -m 1)
Retrieve the sequence
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited: sequence, count

molecule: total RNA

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: standard long-day conditions (16h of light and 8 h of dark at 20°C)

extract_protocol:
Frozen tissue was homogenized in a buffer containing 0.1 M NaCl, 2% sodium dodecyl sulphate (SDS), 50 mM Tris–HCl (pH 9.0), 10 mM ethylenediaminetetraacetic acid (pH 8.0) and 20 mM β-mercaptoethanol, and RNAs were extracted two times with phenol and recovered by ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: Col

tag: genotype

value: RTL2 with 35S promoter and dcl2 dcl3 dcl4 triple mutant

tag: tissue

value: flower


title: sub013

city: Austin

first: Russell

last: Poldrack

state: TX

address: 100 East 24th Street, R9975

country: USA

institute: University of Texas at Austin

data_processing:
Illumina RTA version 1.17 used for base calling, and Casava version 1.8 used for extraction from BCL to fastq format
Paired-end reads aligned to hg19 reference assembly using bowtie 2.2.2 via tophat 2.0.11: tophat --rg-id Paired --rg-library RNAseq --rg-platform ILLUMINA  --mate-inner-dist 100  --b2-very-sensitive -p 15 -r 250
Per-gene read counts were obtained using htseq-count [HTSeq package, version 0.5.4p5]
Read counts were  normalized for library size using the estimateSizeFactors function [DeSeq package, version 1.14.0], and genes were then filtered for a mean read count across sessions of at least 4 and no more than 10,000,
Variance-stabilized read counts were obtained using the varianceStabilizingTransformation in DeSeq (version 1.14.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including gene names and variance-stabilized per-gene read counts

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were harvested by Ficoll gradient from whole blood, and immediately placed in lysis solution to eliminate nuclease activity for RNA isolation. RNA was extracted using the Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing according to "Next-Generation Sequencing RNA-Seq Library Construction", Podnar et. al. Curr Protoc Mol Bio 106:4.21, 2014.

tag: collectiondate

tag: rin


title: 35S-RTL2/dcl234-2


title: Dsim female JP rep2

description: Ochanomizu University, Japan

tag: gender


title: Yawa-H-CG-1-b

city: Urrbrae

first: Jason

middle: A

last: Able

state: SA

address: GN10b, Waite Main Buiding, Waite Road

department: School of Agriculture, Food and Wine

country: Australia

institute: University of Adelaide

data_processing: Novel miRNA: Raw data were processed by trimming 3' adapter sequences. The non-redundant (NR) set of 3' adapter trimmed reads of 19-26 bp in length were filtered to remove low quality reads. Clean sRNA-seq data was used to identify candidate pre-miRNA hairpins from the International Wheat Genome Sequencing Consortium’s (IWGSC) Chromosomal Survey Sequences (CSS). For each NR 3' adapter trimmed read, all perfect alignment locations in the IWGSC CSS were identified. Using a subset of reads and CSS contigs involved in those perfect alignments, we also identified all imperfect alignments (two-five mismatches). The candidate pre-miRNA hairpins were defined using all pairwise combinations of perfect to imperfect alignments of a given read within a CSS contig. Additional constraints were applied such that the perfect and imperfect alignments were in opposite orientations and separated by 54-1000 bp. A NR set of these regions ±20 bp, were processed by RNAFold and then miRcheck to ascertain if they could form hairpin structures and have characteristics associated with the miRNA biogenesis pathway in plants with a read coverage profile. All candidate miRNA hairpin sequences were classified into one of eight categories (A-H, where A has a read coverage profile matching our expectations for a true miRNA) using three Boolean metrics based on their read coverage profile. Putative miRNA hairpins were further characterised by identifying if their sequence contained any perfect matches to the 35,828 mature miRNAs from miRBase v21 to determine novel miRNA hairpins. Please see Methods, Liu et al.(2015) for details.

organism: Triticum turgidum subsp. durum

source_name: Yawa,developing head,control treatment,season 1

growth_protocol: Please see Methods, Liu et al.(2015)

extract_protocol:
Total RNA was isolated using the TriPure reagent. Small RNA was excised and purified  from TBE urea polyacrylamide gel.
Small RNA libraries were constructed using NEB Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, UK) following the manufacturer’s instructions.

treatment_protocol: Please see Methods, Liu et al.(2015)

tag: variety name

value: Yawa

tag: water deficit stress tolerance

value: Tolerant

tag: treatment group

value: Control Group (CG)

value: Developing head (H)

tag: growing season

value: Season 1

tag: plant id number


title: Yawa-H-CG-1-a


title: Dsim female JP rep1

description: Ochanomizu University, Japan


title: Dsim male JP rep3

description: Ochanomizu University, Japan

value: male


title: 35S-RTL2/dcl234-1


title: Yawa-FL-WG-2-c

source_name: Yawa,flag leaf,water deficit stress treatment,season 2

value: Water deficit stress treatment group (WG)

value: Flag leaf (FL)

value: Season 2


title: 35S-RTL2-3

value: RTL2 with 35S promoter


title: Dsim male JP rep2

description: Ochanomizu University, Japan

value: antenna


title: Yawa-FL-WG-2-b


title: Yawa-H-WG-1-a

source_name: Yawa,developing head,water deficit stress treatment,season 1


title: 35S-RTL2-2


title: Dsim male JP rep1

description: Ochanomizu University, Japan

value: Adult


title: Yawa-FL-WG-1-c

source_name: Yawa,flag leaf,water deficit stress treatment,season 1


title: Yawa-FL-WG-2-a


title: rtl2-3

value: rtl2 mutant


title: Yawa-FL-WG-1-a


title: 35S-RTL2-1


title: Yawa-FL-CG-2-c

source_name: Yawa,flag leaf,control treatment,season 2


title: Yawa-H-CG-2-a

source_name: Yawa,developing head,control treatment,season 2


title: Yawa-FL-WG-1-b


title: rtl2-1


title: Yawa-FL-CG-2-a


title: COL-2

value: wt


title: COL-1

value: Col


title: Yawa-FL-CG-1-c

source_name: Yawa,flag leaf,control treatment,season 1


title: EGA Bellaroi-H-WG-2-c

source_name: EGA Bellaroi,developing head,water deficit stress treatment,season 2

value: EGA Bellaroi

value: Sensitive


title: Yawa-FL-CG-1-b

value: Yawa


title: Yawa-FL-CG-1-a

value: Tolerant


title: COL-3

value: flower


title: EGA Bellaroi-H-WG-1-c

source_name: EGA Bellaroi,developing head,water deficit stress treatment,season 1

value: Developing head (H)


title: EGA Bellaroi-H-WG-1-b

value: Season 1


title: EGA Bellaroi-H-WG-2-b


title: EGA Bellaroi-H-WG-1-a


title: Acar_Hemiphallus_Input_DNA

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

library_source: genomic

data_processing:
Basecalls were performed CASAVA version 1.8.2.
Illumina reads were aligned to the mouse genome (mm9) or green anole genome (anoCar2) with Bowtie version 1.1.0 with the options "--best --sam -t -l 28 -n 3 -m 1".
ChIP-Seq data quality and fragment size was assessed from aligned reads for each sample using phantompeaktools (https://code.google.com/p/phantompeakqualtools/).
Regions of H3K27ac enrichment were determined using macs2 (version 2.0.10.20130501) with the options “--bdg --SPMR --nomodel --qvalue=0.05”. Extension size was determined for each sample based on the cross-correlation profile of the aligned reads.
BigWig files of H3k27ac signal visualized as fold enrichment compared to background were generated from treatment and control bedGraph files using macs2 bdgcmp with the options " --tdepth=1 --cdepth=1 --method=FE". BedGraph files were converted to BigWig using BEDtools slopBed command and the bedClip and bedGraphToBigWig from UCSC Kent Utilities as implemented in the bdg2bw script by Tao Liu (https://gist.github.com/taoliu/2469050).
Genome_build: mm9 (Mus musculus); anoCar2 (Anolis carolinensis)
Supplementary_files_format_and_content: BigWig files were generated from treatment and control signal files created by macs2 and represent the fold enrichment of the ChIP sample versus the input DNA control. Bed files were created from the first 6 columns of the narrowPeak format files created by macs2 and represent regions with significant H3K27ac enrichment compared to background signal from input DNA controls with a qvalue cutoff of 0.05.

molecule: genomic DNA

organism: Anolis carolinensis

source_name: embryonic hemiphallus

growth_protocol: Normal gestation

extract_protocol:
After cross-linking in 1% formaldehyde in PBS for 30 minutes, tissues were rinsed and treated with trypsin for 5 minutes to generate a single cell suspension. Samples were then pre-disrupted with a Branson 450 Sonifier, and then sheared with a Bioruptor (Diagenode) to generate a chromatin size range of 200–600 bp. PureProteome Protein G Magnetic Beads (Millipore) were pre-incubated with H3k27ac antibody before incubating overnight with 100-200 μg of sheared chromatin. After washing, immune complexes were eluted from the beads, and protein-DNA crosslinks were reversed by incubating at 65˚C overnight. After treatment with RNase followed by proteinase K, samples were purified with the QIAquick PCR Purification Kit (Qiagen).
ChIP and input chromatin control libraries were produced using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England BioLabs) as directed by the manufacturer with Illumina-compatible adapters. Libraries were sequenced with 50 bp single-end runs on an Illumina HiSeq 2000 at the HudsonAlpha Institute for Biotechnology.

value: embryonic hemiphallus

value: wild type

tag: chip antibody


title: EGA Bellaroi-H-CG-2-c

source_name: EGA Bellaroi,developing head,control treatment,season 2

value: Control Group (CG)


title: EGA Bellaroi-H-CG-2-a

value: Season 2


title: rtl2-2


title: Acar_Hindlimb_H3K27ac

source_name: embryonic hindlimb

value: embryonic hindlimb


title: Acar_Forelimb_Input_DNA

source_name: embryonic forelimb

value: embryonic forelimb


title: Acar_Forelimb_H3K27ac


title: Acar_Hindlimb_Input_DNA


title: Acar_Hemiphallus_H3K27ac


title: EGA Bellaroi-H-CG-2-b


title: Yawa-FL-CG-2-b

value: Flag leaf (FL)


title: EGA Bellaroi-H-CG-1-c

source_name: EGA Bellaroi,developing head,control treatment,season 1


title: EGA Bellaroi-H-CG-1-a


title: EGA Bellaroi-FL-WG-2-c

source_name: EGA Bellaroi,flag leaf,water deficit stress treatment,season 2

value: Water deficit stress treatment group (WG)


title: EGA Bellaroi-FL-WG-2-b


title: EGA Bellaroi-FL-WG-1-c

source_name: EGA Bellaroi,flag leaf,water deficit stress treatment,season 1


title: EGA Bellaroi-FL-WG-1-b


title: EGA Bellaroi-FL-WG-1-a


title: EGA Bellaroi-H-WG-2-a


title: EGA Bellaroi-FL-CG-2-c

source_name: EGA Bellaroi,flag leaf,control treatment,season 2


title: EGA Bellaroi-FL-CG-2-a


title: EGA Bellaroi-FL-CG-1-b

source_name: EGA Bellaroi,flag leaf,control treatment,season 1


title: EGA Bellaroi-FL-CG-1-a


title: Tamaroi-H-WG-2-b

source_name: Tamaroi,developing head,water deficit stress treatment,season 2

value: Tamaroi


title: Tamaroi-H-WG-2-c


title: Tamaroi-H-WG-1-c

source_name: Tamaroi,developing head,water deficit stress treatment,season 1

value: No. 9


title: EGA Bellaroi-H-CG-1-b

value: EGA Bellaroi


title: Tamaroi-H-CG-2-c

source_name: Tamaroi,developing head,control treatment,season 2

value: No. 6


title: Tamaroi-H-WG-2-a


title: Tamaroi-H-WG-1-a

value: No. 7


title: Tamaroi-H-CG-2-b

value: Tolerant

value: No. 5


title: Tamaroi-H-CG-2-a

value: Developing head (H)

value: No. 4


title: Tamaroi-H-WG-1-b

value: Season 1

value: No. 8


title: Tamaroi-H-CG-1-c

source_name: Tamaroi,developing head,control treatment,season 1

value: Control Group (CG)

value: No. 3


title: Tamaroi-FL-WG-2-a

source_name: Tamaroi,flag leaf,water deficit stress treatment,season 2

value: Season 2


title: Tamaroi-H-CG-1-a

value: No. 1


title: Tamaroi-FL-WG-2-c

value: Flag leaf (FL)


title: EGA Bellaroi-FL-WG-2-a

value: Sensitive

value: Water deficit stress treatment group (WG)


title: Tamaroi-FL-WG-1-a

source_name: Tamaroi,flag leaf,water deficit stress treatment,season 1

value: Tamaroi


title: Tamaroi-FL-WG-2-b


title: Tamaroi-H-CG-1-b

value: No. 2


title: Tamaroi-FL-WG-1-c

value: No. 9


title: Tamaroi-FL-CG-2-c

source_name: Tamaroi,flag leaf,control treatment,season 2

value: No. 6


title: EGA Bellaroi-FL-CG-1-c

value: EGA Bellaroi


title: EGA Bellaroi-FL-CG-2-b


title: Tamaroi-FL-CG-2-a

value: Tolerant


title: Tamaroi-FL-CG-1-b

source_name: Tamaroi,flag leaf,control treatment,season 1


title: Tamaroi-FL-CG-2-b

value: No. 5


title: Dsec female JP rep3

description: Ochanomizu University, Japan

data_processing:
100-bp paired-end sequencing reads were mapped to the Drosophila sechellia genome (FlyBase r1.3) with TopHat 2.0.6 (Trapnell et al. 2009).  We allowed two mismatches in read mapping to the reference genome.
The normalized expression levels of genes were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKMs) by Cufflinks 2.0.0 with bias correction (“--multi-read-correct” and “--frag-bias-correct”) (Trapnell, et al. 2010).
Genome_build: FlyBase D. sechellia r1.3
Supplementary_files_format_and_content: genes.fpkm_tracking: FPKM Tracking format, outputed from the Cufflinks suite. FPKM tracking files use a generic format to output estimated expression values.

organism: Drosophila sechellia

source_name: Adult antenna

growth_protocol: k-s10; #14021-0248.25 flies were raised in standard cornmeal yeast extract media at 25°C. Egg laying was performed on plates with standard vinegar medium and yeast. Embryos were collected in 0.03% Triton-X100, 0.4% NaCl 16-18 hr after egg laying.

value: antenna

value: Adult

value: female

value: within 1hr of eclosion


title: Tamaroi-FL-CG-1-a

value: Control Group (CG)

value: Season 1


title: Dsec male JP rep3

description: Ochanomizu University, Japan

value: male


title: Dsec female JP rep1

description: Ochanomizu University, Japan


title: Dsec female JP rep2

description: Ochanomizu University, Japan


title: MCF7 ER ChIP-seq E2 HOTAIR

city: Atlanta

first: Jindan

last: Yu

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Chromatin IP against ER

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file

source_name: prostate tumor

growth_protocol: Cell lines were maintained in DMEM supplemented with 10% FBS, then starved with hormone-free media (FCS) and treated with EtOH or E2.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions.

treatment_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer.

tag: cell line

tag: transgene

value: HOTAIR

tag: treatment

tag: antibody

value: ER


title: MCF7 ER ChIP-seq E2 CTRL

description: Chromatin IP against ER

value: GFP


title: Dsec female TW rep1

description: Academia Sinica, Taiwan

data_processing:
100-bp paired-end sequencing reads were mapped to the Drosophila sechellia genome (FlyBase r1.3) with TopHat 2.0.6 (Trapnell et al. 2009).  We allowed two mismatches in read mapping to the reference genome.
The normalized expression levels of genes were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKMs) by Cufflinks 2.0.0 with bias correction (“--multi-read-correct” and “--frag-bias-correct”) (Trapnell, et al. 2010).
Genome_build: FlyBase D. sechellia r1.3; dsec_caf1
Supplementary_files_format_and_content: genes.fpkm_tracking: FPKM Tracking format, outputed from the Cufflinks suite. FPKM tracking files use a generic format to output estimated expression values.

growth_protocol: Tuson, #14021-0248-25 flies were raised in standard cornmeal yeast extract media at 25°C. Egg laying was performed on plates with standard vinegar medium and yeast. Embryos were collected in 0.03% Triton-X100, 0.4% NaCl 16-18 hr after egg laying.

tag: developmental stage

tag: age


title: Dsec female TW rep3

description: Academia Sinica, Taiwan

tag: genotype


title: MCF7 ER ChIP-seq HOTAIR

description: Chromatin IP against ER

value: EtOH


title: Dsec male TW rep3

description: Academia Sinica, Taiwan


title: Dsec female TW rep2

description: Academia Sinica, Taiwan


title: C4-2B AR ChIP-seq shHOTAIR R1881

description: Chromatin IP against AR

data_processing:
Reads were aligned to the hg19 reference genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS.

treatment_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

value: HOTAIR knockdown R1881

value: AR (Millipore; catalog:06-680; lot number:2328016


title: WNV rep1

city: Geelong

first: Prasad

middle: N

last: Paradkar

state: Victoria

address: 5 Portarlington Road

institute: CSIRO-AAHL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Culex quinquefasciatus transcriptome (CpipJ2) tophat 1.4 with parameters --read-mismatches 5 --splice-mismatches 2 --min-anchor-length 5 --min-intron-length 30 --no-novel-juncs --library-type fr-unstranded
Data analysis followed using protocol given in Trapnell et al 2012
Genome_build: CpipJ2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Culex quinquefasciatus

source_name: Cell line

growth_protocol: Hsu cells were maintained in L15 media at 28C

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit; mRNA was prepared using polydT columns
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with West Nile virus (NY99-4132 strain) for 48 hours

value: infected with West Nile Virus


title: MCF7 ER ChIP-seq CTRL

description: Chromatin IP against ER


title: LNCaP Input

description: This sample is identical to GSM1691162.

value: LNCaP GIPZ

value: FBS

value: input


title: Control rep2

value: control


title: WNV rep2


title: Dsec male TW rep1

description: Academia Sinica, Taiwan

value: Adult


title: C4-2B AR ChIP-seq shHOTAIR Ethl

description: Chromatin IP against AR

value: HOTAIR knockdown Ethl


title: C4-2B AR ChIP-seq shCTRL R1881

description: Chromatin IP against AR

value: control knockdown R1881


title: Control rep1


title: C4-2B AR ChIP-seq shCTRL Ethl

description: Chromatin IP against AR

value: control knockdown Ethl


title: LNCaP AR ChIP-seq HOTAIR R1881

description: Chromatin IP against AR

value: LNCaP

value: HOTAIR R1881


title: Dsec male JP rep2

description: Ochanomizu University, Japan

tag: tissue

value: antenna

value: male

value: within 1hr of eclosion


title: Dsec male TW rep2

description: Academia Sinica, Taiwan


title: Tamaroi-FL-WG-1-b

value: Tamaroi

value: Tolerant

value: Water deficit stress treatment group (WG)

value: Flag leaf (FL)

value: Season 1

value: No. 8


title: LNCaP AR ChIP-seq HOTAIR Ethl

description: Chromatin IP against AR

value: HOTAIR Ethl

value: AR (Millipore; catalog:06-680; lot number:2328016


title: LNCaP AR ChIP-seq CTRL R1881

description: Chromatin IP against AR

value: control R1881


title: Allo733

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing: 40 bp of Illumina raw reads from four silique cDNA libraries (C24XAa, LerXAa, ColXAa, Allo733) were mapped to TAIR9 genome and cDNA sequences using BFAST software (http://bfast.sourceforge.net). We used both unique and multiple best mapped reads to calculate RPKM (Reads Per Kilobases in Million mapped reads) value per gene as described in Shi et al. (Nature Communication, 2012) Initially, all unique reads without alternative splice isoforms were used to calculate a preliminary RPKM, followed by weighting the isoform exons with the unique reads using preliminary RPKM. Finally, RPKMs were calculated by combining the unique and weighted-multiple mapped reads. The Allo733 RPKMS are included on the Samples with the C24XAa, LerXAa, and ColXAa RPKMs.

organism: Arabidopsis thaliana x Arabidopsis arenosa

source_name: 4 DAP silique tissue

growth_protocol: Seeds of Arabidopsis thaliana Col-0 (4x, 1757), Ler (4x, 1752), C24 (4x), Arabidopsis arenosa (4x, CS3901), and Allo733 (CS3895, F8) were sterilized in 10% bleach with 0.01% triton for 10 min and rinsed with ddH2O for four times. These seeds were planted on agar plates containing sterilized liquid Murashige and Skoog medium  and cold-treated at 4oC for 2 days before transferring to growth chamber at 22oC under a long-day condition (16/8 hours of the light/dark cycle). After 10 days seedlings were transferred to soil and grown under the same growth condition as above. At 3-4 weeks after germination, crossing was performed via manual emasculation and pollination next day.

extract_protocol:
Total RNAs from 4 DAP siliques tissues were extracted using Plant Reagent (Invitrogen) according to the manufacture’s instructions. RNA quality and quantity were examined by Nanodrop 2000 and agarose gel electrophoresis. Total RNAs (10 ug) from each of three F1 hybrids, their progenitor lines, and Allo733 were used to isolate poly (A) mRNA.
RNA-Seq librarys were prepared using Illumina RNA-Seq 8-sample prep kit (Illumina). mRNAs were fragmented using high temperature, and ~200-bp fragments are recovered and converted into cDNAs. After adaptor ligation to cDNAs, cDNAs were amplified by PCR.

tag: cell type

value: Silique tissue

value: 4 DAP (days after pollination)

tag: ecotype of arabidopsis thaliana

value: Ler

tag: sample type

value: F8 allotetraploid


title: ColXAa

value: Col

value: F1 interspecific hybrid


title: C24XAa


title: sample_15

city: State college

first: Etya

last: Amsalem

state: Pennsylvania

address: Orchard Road  University Park

department: Entomology

institute: Pennsylvania State University

description: Fat body

data_processing:
We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10 using Trimmomatic.
The transcriptome sequencing reads were aligned to the most recent Bombus terrestris genome assembly using Tophat.
The data was normalized using a trimmed mean of M-values (TMM) method.
The DESeq package in R statistical program was used to identify significantly differentially expressed genes.
Genome_build: Bombus terrestris v1.1 (Sadd et al. 2015) ftp://ftp.ncbi.nlm.nih.gov/genomes/Bombus_terrestris/ARCHIVE/BUILD.1.1
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample

molecule: polyA RNA

organism: Bombus terrestris

growth_protocol: Queens were maintained in the laboratory in nest boxes at a constant dark, temperature of 28-30°C and 50% relative humidity, and supplied with unlimited food (50% sucrose and fresh honey-bee collected pollen) during their entire developmental period (except during diapause) until sampling. Diapausing queens were kept in 4 C until sampling

extract_protocol:
Queens sampled were flash frozen with dry ice and were immediately transfer to -80°C until further analyses. Eviscerated abdomens with attached fat bodies from individual bees were dissected under dry ice. Total RNA samples were extracted from the abdominal fat bodies using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA quantity and quality were assayed with a ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington DE) and a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All queens are mated. Mating was done under lab conditions with unrelated males at the age of 5-10 days. CO2 or diapause treatment were done on the day of mating. mated queens were grouped in a sealed cage and treated with pure CO2 until they were anesthetized (for approximately 1 minute). Queens subsequently were kept in a sealed cage for 30 minutes post treatment and were CO2-treated again 24 hours later. The cage was ventilated between treatments. CO2 treated queens were sampled 24 h or one month post treatment, after they laid eggs and established a colony. In order to induce diapause queens were kept in 4 C for 9-10 weeks. diapausing queens were sampled by the end of the diapause period or were exposed to room temp and daylight and were sampled a month later after they laid eggs and established a colony.

tag: gender

value: female

tag: social status

value: queen

value: Eviscerated abdomen with attached fat bodies

value: 5-10 days

tag: strain

value: genetic line_141


title: sample_17

description: Fat body

source_name: Mated

value: genetic line_191


title: LerXAa


title: sample_33

description: Fat body

source_name: Diapause

value: 3 months


title: sample_80

description: Fat body

source_name: Founder post diapause

value: 4 months

value: genetic line_51


title: sample_42

description: Fat body

value: genetic line_296


title: sample_32

description: Fat body

source_name: Founder post CO2

value: 1.5 months


title: WT - 475

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment with Bowtie2 version 2.2.1 using the default parameters against mm10 from mirBase v20
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on April 2014
Normalization using DeSeq2
Genome_build: mm10

organism: Mus musculus

source_name: mESC

growth_protocol: mES cells were cultivated in complete mES medium (FCS+LIF). Before analysis, harvested cells were subjected to SSEA-1 MACS sorting to correct for spontanious differentiation during culture. Two different mES cell clones were used in this study (with each WT and KO condition)

extract_protocol:
Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufactures’ protocol
Illumina TruSeq RNA Sample Preparation Kit v2
200 bp paired-end run was performed on a HiSeq1500

treatment_protocol: Trim71 conditional ("WT") cells were treated with 500 nM 4-OHT for 2 days to induce Trim71 mutation. Cells were further cultivated before cell harvest for at least 7 days.

tag: Sex

value: male

value: embryonic stem cells

tag: day

tag: clone

value: Trimfl/fl


title: WT - 467


title: WT - 471


title: KO - 477

value: Trim-/-


title: KO - 481


title: KO - 473


title: KO - 469


title: WT - 459


title: KO - 461


title: LNCaP AR ChIP-seq CTRL Ethl

description: Chromatin IP against AR

tag: cell line

value: LNCaP

value: control Ethl

value: AR (Millipore; catalog:06-680; lot number:2328016


title: 475 - WT

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on April 2014
Normalization using DeSeq2
Genome_build: mm10

extract_protocol:
Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufactures’ protocol
Illumina TruSeq RNA Sample Preparation Kit v2

treatment_protocol: Trim71 conditional ("WT") cells were treated with 500 nM 4-OHT for 2 days to induce Trim71 mutation. Cells were further cultivated before cell harvest for at least 7 days to minimize indirect effects of the drug treatment.


title: Stress-treated 7B-1 Mutant

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
Adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. Adapter guessing strategy was also used to double check the adapter removal procedure.
Quality checks including size class distributions and complexity analyses were done before genome matching.
Reads were mapped full length, no mis-matches or gaps allowed to the tomato genome using PatMan [Prueffer et al, 2008]
Differentially expressed small RNAs were determined and annotated.
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
Genome_build: GCF_000188115.2
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

organism: Solanum lycopersicum

source_name: seedling

growth_protocol: The 7B-1 mutant and wild type (cv. Rutgers) tomatos were grown under continues blue light (BL) in temperature controlled growth chamber set at 23°C.

extract_protocol:
Total RNA was extracted using RNeasy plant miniRNA extraction kit (Qiagen) from stress-treated 7B-1 and WT seedlings and pooled separately in equimolar ratio
Two small RNA libraries were constructed using the TruSeq Small RNA Sample Preparation Kit from Illumina (Illumina, San Diego, CA, USA). In brief, small RNA fractions of 18–28 nt were isolated from 15% denaturing polyacrylamide gels. The fractionated small RNAs were ligated to 3’ TruSeq adaptors and then converted to DNA by RT-PCR following the kit protocol.

treatment_protocol: Two-week old seedlings grown on MS medium under BL were transferred to mediums supplemented with 10 µM ABA or 140 mM mannitol or 120 mM NaCl and incubated for 0, 2, 4, 8, 12, and 24 h under BL. Cold treatment was carried out by incubating the seedlings at 4°C for 0-24 h under BL.

value: stress-tolerant

tag: genotype/variation

value: 7B-1 Mutant

tag: cultivar

value: Rutgers


title: Wild type control

value: Wild type


title: Dsec male JP rep1

description: Ochanomizu University, Japan

value: antenna

value: Adult

value: within 1hr of eclosion


title: Wild type

data_processing:
Adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. Adapter guessing strategy was also used to double check the adapter removal procedure.
Quality checks including size class distributions and complexity analyses were done before genome matching.
Reads were mapped full length, no mis-matches or gaps allowed to the tomato genome using PatMan [Prueffer et al, 2008]
Differentially expressed small RNAs were determined and annotated.
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
Genome_build: S. Lycopersicum, v 2.4 (SL2.40, http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.2)
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

source_name: anther tissue

growth_protocol: The 7B-1 mutant and wild type (cv. Rutgers) tomatos were grown in a growth chamber set for long day condition (16/8 h light/dark). Flower buds of different sizes, smaller, equal and larger than 4-5 mm were collected from WT and 7B-1 flowers and the stamens were dissected under a microscope.

extract_protocol:
Total RNA was extracted using RNeasy plant miniRNA extraction kit (Qiagen) from 7B-1 and WT anthers of different sizes and pooled separately in equimolar ratio
Two small RNA libraries were constructed using the TruSeq Small RNA Sample Preparation Kit from Illumina (Illumina, San Diego, CA, USA). In brief, small RNA fractions of 18–28 nt were isolated from 15% denaturing polyacrylamide gels. The fractionated small RNAs were ligated to 3’ TruSeq adaptors and then converted to DNA by RT-PCR following the kit protocol.

value: Meiosis

value: anther


title: Mutant

value: 7B-1 mutant


title: 471 - WT

value: male


title: WT - 479

value: embryonic stem cells


title: 467 - WT

value: Trimfl/fl


title: Exp1 C2 iMEFs Ezh2 -/-, replicate 2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

data_processing:
Experiment 1 : Single-end reads were mapped on the Mouse reference genome (mm9) Using the Bowtie software (v0.12.8, Langmead B. Et al. 2012) Allowing one mismatch in the seed (28bp) And reporting one location in case of multiple mapping hits.
Experiment 1 : Peak calling for each sample was done with MACS2 2.0.10 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA as Control.
Experiment 2 : Single-end 100bp reads were mapped on the Mouse reference genome (mm9) Using the Bowtie2 software (v2.1.0, Langmead B. Et al. 2012) Allowing one mismatch in the seed (22bp) And reporting one location in case of multiple mapping hits.
Experiment 2 : PCR duplicates were then removed using samtools
Experiment 2 : Peak calling for each sample was done with CCAT 3.0 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA BAM file as Control.
Genome_build: mm9
Supplementary_files_format_and_content: bed files are the output of peak calling.
Supplementary_files_format_and_content: BigWig files are generated with HOMER (v3.17)

source_name: C2 iMEFs Ezh2 -/-

growth_protocol: Sample 1 to 16 iMEF cells grown in DMEM medium supplemented with 10% FCS, 100 mM non essential amino acids, 1 mM L-Glutamine.

extract_protocol: DNA was extracted by phenol-chloroform and precipitated. Experiment 1 : Sequencing was performed on SOLiD 5500 single reads 75bp. Experiment 2 : Sequencing was performed on Hi-Seq 2500 Illumina single reads 100bp.

treatment_protocol: 4-hydroxytamoxifen was used at a final concentration ranging from 1 nM to 1 μM

value: iMEFs

tag: antibody

value: H3K27me3 ChIP (Active Motif 39155)


title: Exp1 C2 iMEFs Ezh2 -/-, replicate 1


title: 459 - WT


title: 473 - KO

value: Trim-/-


title: Exp1 C2 iMEFs Ezh2 WT/WT, replicate 1

source_name: C2 iMEFs Ezh2 WT/WT


title: Exp1 C2 iMEFs Ezh2 WT/WT, replicate 2


title: sample_83

description: Fat body

value: female

value: queen

value: Eviscerated abdomen with attached fat bodies

value: 4 months

value: genetic line_191


title: 477 - KO


title: WT - 463


title: 469 - KO


title: sample_41

description: Fat body

value: genetic line_141


title: sample_40

description: Fat body

value: genetic line_207


title: sample_36

description: Fat body

value: 3 months


title: sample_37

description: Fat body


title: phlAphlDphlG 12.5 ng/mL phloroglucinol rep 3

city: Corvallis

first: Jeff

state: OR

address: 3098 Cordley Hall

department: Botany and Plant Pathology

institute: Oregon State University

data_processing:
RNAseq reads were pre-processed by trimming six and five nucleotides from the beginning and end.
Reads were aligned to the P. protegens Pf-5 reference genome sequence using CASHX version 2.3.
Those that mapped to 16s and 23s rRNA, PFL_6307 (RNase), and PFL_6294 (tmRNA) were removed in silico.
Differential expression was determined using GENE-Counter v0.4.4
Genome_build: NCBI RefSeq: NC_004129.6
Supplementary_files_format_and_content: tab delimited text file include fold change for pairwise comparisons of samples

organism: Pseudomonas protegens

source_name: bacterial cells

growth_protocol: P. protegens strain Pf-5 was grown at 28C, 200rpm to an OD600 of 2.0-2.2 in Nutrient Broth supplemented with 1% (w/v) glycerol.

extract_protocol:
RNA isolation was performed following the manufacturer’s instructions using an RNeasy Mini kit with in-sample DNase treatment followed by two on-column DNase treatment steps. Enrichment for mRNA was performed by depleting rRNA using the MicrobExpress bacterial mRNA enrichment kit.
RNAseq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2.

treatment_protocol: Phlorogucinol dissolved in methanol was  added to the cultures to a final concentration of 12.5 µg mL-1 for the phlAG mutant and 12.5 ng mL-1 for the phlADG mutant.

value: phlAphlDphlG mutant

tag: treatment

value: 12.5 ng/mL phloroglucinol


title: phlAphlDphlG 12.5 ng/mL phloroglucinol rep 2


title: phlAphlDphlG 12.5 ng/mL phloroglucinol rep 1


title: phlAphlDphlG 0 ng/mL phloroglucinol rep 2

value: 0 ng/mL phloroglucinol


title: sample_35

description: Fat body

tag: age

value: genetic line_296


title: phlAphlDphlG 0 ng/mL phloroglucinol rep 1

tag: genotype


title: phlAphlDphlG 0 ng/mL phloroglucinol rep 3


title: sample_31

description: Fat body

tag: tissue

value: 1.5 months


title: phlAphlG 12.5 ug/mL phloroglucinol rep 3

value: phlAphlG mutant

value: 12.5 ug/mL phloroglucinol


title: Exp1 C2 iMEFs Ezh2 WT/WT

tag: cell type

value: iMEFs


title: sample_30

description: Fat body


title: phlAphlG 0 ng/mL phloroglucinol rep 3


title: sample_22

description: Fat body

value: 5-10 days

value: genetic line_426


title: sample_20

description: Fat body

value: female

value: queen


title: 465 - KO

value: embryonic stem cells

value: male

value: Trim-/-


title: sample_19

description: Fat body

value: Eviscerated abdomen with attached fat bodies

value: genetic line_141


title: phlAphlG 12.5 ug/mL phloroglucinol rep 2


title: phlAphlG 0 ng/mL phloroglucinol rep 2


title: sample_12

description: Fat body

value: genetic line_191


title: phlAphlG 0 ng/mL phloroglucinol rep 1


title: sample_9

description: Fat body

value: genetic line_51


title: sample_8

description: Fat body


title: Pf-5 0 ng/mL phloroglucinol rep 3

value: WT

value: 0 ng/mL phloroglucinol


title: Pf-5 0 ng/mL phloroglucinol rep 2


title: Pf-5 0 ng/mL phloroglucinol rep 1


title: sample_7

description: Fat body

value: genetic line_207


title: sample_4

description: Fat body


title: AP2-G2 ChIP-seq experiment-2 INPUT

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 9.1) with a complete match within 60 bp using in-house scripts. Bedgraph files were ceated from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using  approximately 0.5 × 107 reads (IP). Numbers of INPUT reads used for normalization were 2.3 × 107 in the experiment-1 and 1.5 × 107 in the experiment-2, respectively. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: Mapping data, bedgraph;Peak-calling, text.

organism: Plasmodium berghei ANKA

source_name: AP2-G2 ChIP_input

growth_protocol: Balb/c mice were pre-treated with phenylhydrazine and then infected with P. berghei expressing GFP-fused AP2-G2.

extract_protocol:
Erythrocytes in the fixed culture were removed by lysis in 0.84% NH4Cl, and the remaining ookinetes were subjected to ChIP. ChIP was performed using the ChIP Assay Kit (Millipore, USA) according to the manufacturer’s protocol. Briefly, samples in the lysis buffer were sonicated with a Bioruptor (Tosho Denki, Yokohama, Japan) until chromatin DNA was fragmented to 150 bp for sequencing with a SOLID 5500 system (Life Technologies). Immunoprecipitation (IP) was performed with anti-GFP antibodies, and the harvested DNA fragments were subjected to sequencing. Input DNAs were obtained from the chromatin without IP. Anti-GFP antibodies used for ChIP were purchased from Abcam (Cat. No. ab290, Lot No.GR19413-1).
Single read - SOLiD 5500 (ABI)

treatment_protocol: Sulfadiazine was added to their drinking water (10 mg/L) in order to deplete asexual blood-stage parasites. When the exflagellation of the male gametes reached approximately 300 per 1 μL of blood, the blood was harvested and cultured in an ookinete culture medium for 16 h, and then fixed with 1% paraformaldehyde.

value: ANKA

tag: Stage

value: gametocyte

value: GFP-fused AP2-G2 expressing

tag: host mouse strain

value: Balb/c


title: Gb gel purified RBS-seq

city: Adelaide

first: Alice

middle: Louise

last: Burgess

address: Frome road

department: Genetics and Evolution

description: gel purified RNA

data_processing:
Illumina Casava1.8 software used for base calling.
Sequenced reads were trimmed to remove adaptor sequences, filtered for low-quality reads, then mapped to tRNA reference sequences or in silico bisulfite converted tRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
tRNA abundance measurements from the Arabidopsis thaliana RNA-seq library were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Read counts were normalized to reads per million (RPM)
Genome_build: TAIR10 annotated transfer RNAs and the plantRNA database (http://plantrna.ibmp.cnrs.fr)
Supplementary_files_format_and_content: Excel file with methylation percentages for cytosine residues in tRNAs from A. thaliana, G. biloba, B. rapa, N. occulata, C. taxifolia and T. durum from bisulfite treated RNA, enriched for tRNAs.
Supplementary_files_format_and_content: Excel file with RPM values for tRNAs from Arabidopsis wild type tRNA enriched RNA-seq.
Supplementary_files_format_and_content: Excel file with Arabidopsis tRNA consensus reference sequences.

organism: Ginkgo biloba

source_name: leaf tissue

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) and RNA was gel purified to enrich for tRNAs
RNA libraries were prepared for sequencing using standard Illumina protocols except BS treated RNA was not fragmented.

value: leaf

value: wild type


title: sample_3

description: Fat body

tag: gender

value: female

value: queen

value: 5-10 days

value: genetic line_296


title: Gb gel purified RNA-seq

description: gel purified RNA


title: AP2-G2 ChIP-seq experiment-1 INPUT


title: phlAphlG 12.5 ug/mL phloroglucinol rep 1

value: phlAphlG mutant

value: 12.5 ug/mL phloroglucinol


title: Gb total RNA RBS-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequence, filtered for low-quality reads, then mapped to rRNA reference sequences or in silico bisulfite converted rRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
Arabidopsis TAIR10 rRNA sequences were used for guided reference assemby of rRNAs from other species using RNA-seq libraries and alignments made using CLC genomics workbench 7 (Qiagen)
Genome_build: TAIR10 annotated ribosomal RNAs for Arabidopsis thaliana and species specific rRNA sequences for plants other than Arabidopsis thaliana
Supplementary_files_format_and_content: Excel file with methylation percentages for cytosine residues in rRNAs from A. thaliana, G. biloba, B. rapa, N. occulata, C. taxifolia and T. durum from bisulfite treated total RNA.
Supplementary_files_format_and_content: Excel file with rRNA reference sequences from A. thaliana, G. biloba, B. rapa, N. occulata, C. taxifolia and T. durum.

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) total RNA was used either with or without bisulfite conversion before Illumina library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except BS treated RNA was not fragmented.


title: AP2-G2 ChIP-seq experiment-2 IP

source_name: AP2-G2 ChIP

tag: chip antibody

value: Anti-GFP

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: ASC

city: Kaohsiung

first: Kuang-Den

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

institute: Kaohsiung Chang Gung Memorial Hospital

data_processing:
Illumina Miseq reporter software 2.1 used for basecalling.
The Strand NGS software (version 2.1) was performed using default parameters for pre-alignment and post-alignment quality control analysis.
Differentially expressed genes (DEGs) from resected livers 3 days after intravenous treatments of saline, ASCs-siRNC and ASCs-miR27b compared with naive liver samples were calculated from the raw reads using the DESeq method.
The significance was determined by MannWhitney un-paired test or 2-way ANOVA and a Benjamini and Hochberg false discovery rate (FDR) multiple gene correction was applied.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample

organism: Rattus norvegicus

source_name: PH-ASCs-siRNC

extract_protocol:
Total RNA will be isolated from liver tissues using TRIzol® reagent (Invitrogen). Total RNA (15 μg) for each sample will be used for purifying the poly(A)-containing mRNA molecules, RNA ampliﬁcation, and synthesis of double stranded cDNAs that will be ligated to adapters, following the Illumina (San Diego, California, USA) TruSeq RNA Sample Prep guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: LEWIS

tag: allotype

value: liver


title: Gb total RNA RNA-seq


title: sample_18

description: Fat body

tag: social status

value: Eviscerated abdomen with attached fat bodies

value: genetic line_141


title: 27b


title: Td gel purified RBS-seq

description: gel purified RNA

source_name: flag leaf tissue

value: flag leaf


title: AP2-G2 ChIP-seq experiment-1 IP

value: ANKA

value: gametocyte

value: GFP-fused AP2-G2 expressing


title: Td gel purified RNA-seq

description: gel purified RNA

value: wild type


title: Td total RNA RNA-seq


title: Ct total RNA RNA-seq

organism: Caulerpa taxifolia

source_name: frond tissue

value: frond


title: No total RNA RBS-seq

organism: Nannochloropsis oculata

source_name: cells


title: Ct total RNA RBS-seq


title: No total RNA RNA-seq


title: Br gel purified RBS-seq

description: gel purified RNA

organism: Brassica rapa

value: leaf


title: No gel purified RNA-seq

description: gel purified RNA


title: sample_34

description: Fat body

value: female

value: queen

value: 3 months

value: genetic line_51


title: Br total RNA RBS-seq


title: Saline

source_name: PH-Saline


title: No gel purified RBS-seq

description: gel purified RNA

value: cells


title: Br total RNA RNA-seq


title: NaiveRNA

source_name: Naïve control


title: Ct gel purified RBS-seq

description: gel purified RNA


title: Td total RNA RBS-seq


title: Ct gel purified RNA-seq

description: gel purified RNA


title: 1024644

status: Public on Sep 30 2015

city: Mosgiel

first: Kathryn

last: McRae

address: Puddle Alley

department: Animal Productivity

country: New Zealand

institute: AgResearch

data_processing:
Illumina CASAVA 1.8.0 software used for basecalling.
Trim Galore (v0.3.3) was applied to the RNAseq reads using the default settings for paired end data. Base calls with a Phred score < 20 were removed.
Trimmed reads were mapped to the ovine genome (OARv3.1) using STAR, with the Ensembl (Ensembl 74) Ovis aries transcriptome annotation supplied. Alignments were output only if the ratio of mismatches to mapped length per read pair was less than 0.02. Only uniquely mapped reads were kept for read counts.
The mapped reads were used to estimate raw counts per gene using HTSeq (v0.5.3p3) with the union overlap resolution mode.
The Bioconductor package EdgeR (v 3.0.8) was used with R software (v 3.0.2) to analyse differential expression of read counts. Comparisons were made between HighFEC and LowFEC animals at either 7 or 14 dpi or within phenotype over time between 7 and 14 dpi. Low expression tags were filtered, keeping only genes that achieved at least one count per million (CPM) in at least 5 samples. Trimmed mean of M-values (TMM) normalisation was used to account for differences in RNA composition between samples. Data were analysed using both common and tagwise dispersions. To account for multiple testing, genes were filtered using a Benjamini and Hochberg false discovery rate (FDR)  of ≤0.1 or ≤0.05 for tagwise and common dispersion analyses respectively. All genes identified as differentially expressed (DE) using common dispersion estimates were included in pathway analysis.
Pre-calculated 1-to-1 orthologs were obtained from Human version (74) using Ensembl's Biomart tool. Ingenuity® Systems Pathway Analysis (IPA; Ingenuity Systems, Redwood City, CA, USA; v18841524) was used to identify the top networks, canonical pathways, diseases and functions from DE genes
Genome_build: OARv3.1
Supplementary_files_format_and_content: Tab deliminated text files containing raw counts per gene from HTSeq

organism: Ovis aries

source_name: Abomasal lymph node

extract_protocol:
Abomasal lymph node (ALN) tissue, recovered at slaughter, was immediately cut into pieces approximately 0.5 cm3 and submerged in 10 volumes of RNAlater® (Ambion). This was stored overnight at 4 °C followed by long-term storage at -80 °C. Total RNA was extracted from the ALN tissue using Sigma TRI Reagent® (Sigma Aldrich, UK) according to the manufacturer’s instructions. Small RNAs (<200 nucleotides) and residual genomic DNA were removed with the RNeasy Mini Kit (Qiagen, Germany) and an in-solution DNase digestion (RNase-free DNase set; Qiagen, Germany) according to the manufacturer’s instructions. RNA quality was assessed using an Agilent® RNA 6000 Nano Assay on the 2100 Bioanalyzer, and total RNA was quantified using the NanoDrop® ND-1000 spectrophotometer (Thermo Fisher Scientific, UK).
Illumina TruSeq™ libraries were prepared following the TruSeq™RNA sample preparation v2 guide (Part #15026495 Rev. B) for total RNA with the following modifications: (i) the number of PCR cycles was reduced to 10 to minimise overcycling and (2) to avoid bead contamination the PCR products were purified using a Qiagen MinElute column rather than AMPure XP beads. Libraries were visualised using an Agilent® DNA 1000 assay on the 2100 Bioanalyzer, and quantified using the Qubit® dsDNA BR assay (Invitrogen, UK) according to the manufacturer’s instructions. The indexed cDNA libraries containing the specific Illumina TruSeq adapters were sent to GATC Biotech (Kontanz, Germany), where they were pooled. Each pool was sequenced on two lanes of an Illumina HiSeq2000 with 50 bp paired-end reads.

tag: phenotype

tag: day post infection

value: abomasal lymph node

tag: pathogen

value: Teladorsagia circumcincta larvae (L3)


title: 1024704


title: 1024596


title: 1024649


title: 1024715


title: 1024689


title: 1024659


title: 1024580


title: 1024647


title: 1024572


title: 1024619


title: 1024558


title: 1024551


title: 1024630


title: 1024626


title: 1024613


title: 1024570


title: Mycoplasma pneumoniae (strain 5954)_PER6

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: CRG core facilities

country: Spain

institute: Centre for genomic regulation (CRG)

data_processing:
Gene annotation was transferred from the reference (Mycoplasma Pneumoniae M129) on the indicated assembled strains by using blat / liftover.
Reads were aligned to the corresponding assembled strain with bowtie2 (version 2.2.5) and sorted with samtools (version 1.2)
"Bedtools coverage" (version 2.15.0) was used to calculate the coverage for each gene then used for calculating the logCPKM as indicated in the following formula
logCPKM=log2 ( coverage /( (tot coverage / 1,000,000) * gene size / 1,000)
Genome_build: Mycoplasma pneumoniae strains 6009 (LHQG00000000) and 2882 (LHPQ00000000) and annotations from NC_000912.1
Supplementary_files_format_and_content: tabular files reporting the gene name (column 1), the total gene coverage (column 2), and the logCPKM (column 3). In column 1, ncMPN is the identifier for non coding RNAs found in the transcriptome analysis of M. pneumoniae M129 strain.

organism: Mycoplasmoides pneumoniae

source_name: M. pneumoniae  culture

growth_protocol: M. pneumoniae was grown in 50 mL of modified Hayflick medium supplemented with glucose at 37ºC

extract_protocol:
After growing M. pneumoniae for 6h at 37°C, cells were washed twice with PBS and lysed with 700 µl of Qiazol buffer. Then, samples were lysed with 700 µl of Qiazol buffer. RNA extractions were performed by using the miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer.
Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 µg of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5’ and 3’ ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3’ adapters and subsequently 5’ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3’ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries was performed using 6% Novex® TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 µl of elution buffer. Double-stranded templates were cluster amplified and sequenced on an Illumina HiSeq 2000.

treatment_protocol: No treatment was applied

tag: strain type

tag: country of isolation

value: France

tag: year

tag: isolated from

value: NAP (nasopharyngeal aspirate)


title: 1024566

tag: tissue


title: Br gel purified RNA-seq

description: gel purified RNA

tag: genotype


title: Mycoplasma pneumoniae (strain 5954)_PER8


title: 1024624


title: 1024690


title: Frankia seq-Dglomerata symbiont

city: Davis

first: Alison

middle: M

last: Berry

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California

data_processing:
Basecalls were performed with CASAVA version 1.7
Sequenced were mapped to reference genome of Frankia symbiont of D. glomerata (GenBank: CP002801- CP002803) using Bowtie
SAM format sequence files were filtered for exact repeat reads sorted and converted to BAM files using the samtools package
Gene expression was calculated as the number of mapped reads per kilobase of gene sequence (rpkb) using custom R scripts. Standard database fields in NCBI were used for gene annotation.
Genome_build: ASM17761v2
Supplementary_files_format_and_content: Frankia_datisca_processed.txt, tab delimited file containing: chromosome, start coordinate of locus, stop coordinate of locus, strand, locus_ID, length of locus, seqeuence tags mapping to locus, tags per kpb, next columns are standard annotations

organism: Frankia

source_name: Root nodule tissue

growth_protocol: D.glomerata seedlings were grown in the greenhouse and inoculated with rhizosphere soil from previously-nodulated Ceanothus spp.

extract_protocol:
Total nodule RNA was extracted after grinding tissue in liquid nitrogen, using the Plant RNeasy kit (Qiagen).  Ribosomal RNA was twice subtracted from total RNA with the RiboMinus Plant Kit for RNAseq (Invitrogen).
A cDNA library was constructed according to Illumina protocols.

treatment_protocol: Nodules from 2 batches of 4 plants each were snap-frozen in liquid nitrogen at 4 or 6 weeks after inoculation, and samples pooled by weight.

tag: phylogeny

value: Cluster II

value: nitrogen-fixing root nodule

tag: host

value: Datisca glomerata


title: Tamaroi-FL-CG-1-c

data_processing: Novel miRNA: Raw data were processed by trimming 3' adapter sequences. The non-redundant (NR) set of 3' adapter trimmed reads of 19-26 bp in length were filtered to remove low quality reads. Clean sRNA-seq data was used to identify candidate pre-miRNA hairpins from the International Wheat Genome Sequencing Consortium’s (IWGSC) Chromosomal Survey Sequences (CSS). For each NR 3' adapter trimmed read, all perfect alignment locations in the IWGSC CSS were identified. Using a subset of reads and CSS contigs involved in those perfect alignments, we also identified all imperfect alignments (two-five mismatches). The candidate pre-miRNA hairpins were defined using all pairwise combinations of perfect to imperfect alignments of a given read within a CSS contig. Additional constraints were applied such that the perfect and imperfect alignments were in opposite orientations and separated by 54-1000 bp. A NR set of these regions ±20 bp, were processed by RNAFold and then miRcheck to ascertain if they could form hairpin structures and have characteristics associated with the miRNA biogenesis pathway in plants with a read coverage profile. All candidate miRNA hairpin sequences were classified into one of eight categories (A-H, where A has a read coverage profile matching our expectations for a true miRNA) using three Boolean metrics based on their read coverage profile. Putative miRNA hairpins were further characterised by identifying if their sequence contained any perfect matches to the 35,828 mature miRNAs from miRBase v21 to determine novel miRNA hairpins. Please see Methods, Liu et al.(2015) for details.

organism: Triticum turgidum subsp. durum

source_name: Tamaroi,flag leaf,control treatment,season 1

growth_protocol: Please see Methods, Liu et al.(2015)

extract_protocol:
Total RNA was isolated using the TriPure reagent. Small RNA was excised and purified  from TBE urea polyacrylamide gel.
Small RNA libraries were constructed using NEB Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, UK) following the manufacturer’s instructions.

tag: variety name

value: Tamaroi

tag: water deficit stress tolerance

value: Tolerant

tag: treatment group

value: Control Group (CG)

value: Flag leaf (FL)

tag: growing season

value: Season 1

tag: plant id number

value: No. 3


title: Sample B

data_processing:
Raw reads were processed using RTA 1.18.54 (Illumina)
Trim Galore (v0.3.7) was used to remove Illumina adapters, along with bases with a median Phred scaled quality score below 20.
Trimmed reads were mapped to the ovine reference genome (OARv3.1) using STAR, with the Ensembl Ovis aries transcriptome annotation (release 78) supplied. Only uniquely mapped reads with a maximum of 2 mismatches to the reference genome were retained for further analysis.
The mapped reads were used to estimate raw read counts per gene using HTSeq (v 0.6.1p1) with the union overlap resolution mode.
Genome_build: OARv3.1
Supplementary_files_format_and_content: Tab deliminated text files containing raw counts per gene from HTSeq

source_name: Rumen papillae

extract_protocol:
Rumen papillae, recovered at slaughter, were snap frozen in liquid nitrogen the stored at -80 °C. Total RNA was isolated ~10 mg of tissue using an RNeasy mini kit (Qiagen, Hilden, Germany) and an on-column DNase digestion (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. . RNA quality was assessed using an Agilent® RNA 6000 Nano Assay on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and total RNA was quantified using the NanoDrop® ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA).
Illumina cDNA libraries were prepared following the TruSeq™ Stranded mRNA sample preparation guidelines. Libraries were visualised using an Agilent® DNA High Sensitivity assay on an Agilent 2100 Bioanalyzer, and quantified using the Qubit® dsDNA HS assay (Invitrogen, Life Technologies) according to the manufacturer’s instructions. Qubit concentrations were used to pool the two indexed cDNA libraries containing the specific Illumina TruSeq adapters. The denatured cDNA templates and PhiX control (Illumina, CA, USA) were pooled together and sequenced using an Illumina MiSeq Nano Kit v2 (300 cycles), resulting in 150 bp paired-end reads.

value: rumen papillae


title: USP10 overexpression

city: Ashburn

first: Robert

last: Tjian

state: VA

address: 19700 Helix Dr

institute: HHMI Janelia Research Campus

description: Directional mRNA-seq

data_processing:
Reads Mapping: Bowtie 2
Differential Gene expression analysis: Cuffdiff (library normalization: geometric)
Significance Thresholding: R
Genome_build: mm10
Supplementary_files_format_and_content: Table containing differential gene expression information

source_name: C2C12, differentiation medium for 6 days

growth_protocol: DMEM containing 10% FBS, differentiation medium DMEM containing 2% Horse serum

extract_protocol:
Total RNA was extracted with Rneasy Mini Kit (Qiagen)
Libraries were prepared with ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre)

tag: cell line

value: USP10 cDNA driven by EF1a promoter


title: Sample A


title: Huwe1 knockdown myotubes 1

description: Directional mRNA-seq

source_name: C2C12, differentiation medium for 8 days

value: shRNA sequence:GCACTCTTCATAACTCACTTT


title: Control myotubes

description: Directional mRNA-seq

value: non-targeting RNA


title: Mycoplasma pneumoniae (strain 2882)_FIL8

tag: strain

value: Spain

value: Synovial fluid


title: Mycoplasma pneumoniae (strain 6009)_CRO8

value: France

value: BAL (bronchoalveolar)


title: Mycoplasma pneumoniae (strain 5817)_PAU6


title: Mycoplasma pneumoniae (strain 2882)_FIL6


title: Huwe1 knockdown D0 2

description: Directional mRNA-seq

source_name: C2C12, growth medium

value: shRNA sequence:GAGAAGAGGACAACTAGTA


title: Mycoplasma pneumoniae (strain 6009)_CRO6


title: P300_TA+TNFα

city: Nijmegen

first: Shuang-Yin

last: Wang

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Illumina RTA 1.6.47.1 used for basecalling of GAII data.
Library strategy: ChIP-seq. The reads were aligned to build version hg19 of the human genome using bwa (version 0.6.2) with default parameters. Only unique mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 1.4.2), was used to identify regions of ChIP-seq enrichment over background using parameters -p 1e-9 –nomodel.
Library strategy: ChIA-PET. The first 72bp of each sequenced read carries the complete ChIA-PET ligation product (linker plus genomic DNA) was taken for the further analysis after trimming the ends of each read.  Subsequently, single end sequenced reads were split at the linker ligation junction (linkerA/B-|-linkerA/B) and flipped to make the data compatible (similar to paired end sequencing reads) for the ChIA-PET data analysis pipeline (doi:10.1186/gb-2010-11-2-r22).
Library strategy: 4C-seq. The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (fragment ends). Repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome hg19.
Genome_build: hg19

organism: Homo sapiens

source_name: HeLa B2 cells

growth_protocol: HeLa B2 cells were maintained as described in previous study (doi:10.1101/gr.118042.110). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% charcoal stripped fetal calf serum (FCS) for 72-96 hours before subsequent treatment and/or harvesting.

extract_protocol: Libraries were prepared according to Illumina's instructions.

value: HeLa

tag: treatment protocol

value: 1μM of Triamcinolonacetonide (T6501, Sigma-Aldrich) with 10ng/ml Tumor necrosis factor α (T0157, Sigma-Aldrich) for the last 1 hour.

tag: chip antibody

value: P300 (sc-585x, Santa Cruz biotechnology)


title: Huwe1 knockdown D0 1

description: Directional mRNA-seq

value: shRNA sequence:GGGAACCTGTGATTCGAGA


title: P300_DMSO


title: P300_TNFα

value: 10ng/ml Tumor necrosis factor α (T0157, Sigma-Aldrich) for 1 hour.


title: 3 day-old Ezh2 cKO calvaria (Prrx1-Cre)

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19, mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Mouse calvaria

extract_protocol:
RNA was isolated using the miRNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Ezh2 cKO

tag: passage

value: Primary tissue

tag: Sex

value: Female


title: 3 day-old wild type calvaria

value: wild type


title: D10_RH1

city: Singapore

first: Benson

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

data_processing:
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and rRNA reads were removed by aligning to the mm9 genome assembly using Bowtie 2-2.1.0
Transcript quantification using RSEM
Differentially expressed genes were identified by DESeq2 (Bioconductor-package)
Genome_build: mm9
Supplementary_files_format_and_content: Output from DESeq2. 1. Gene ID 2. baseMean 3. Log2FoldChange 4. lfcSE 5. stat 6. pvalue 7. padj.  Log2FoldChange was calculated by comparing RNaseH1-overexpressing cells to control cells at each time point during differentiation.

source_name: mouse embryonic stem cells

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol:
RNA was isolated with TRIzol reagent, as per the manufacturers instructions.
5 μg of total RNA was depleted of rRNA using a Ribo-Zero Gold kit (Epicentre) and first strand cDNA was made using 200 ng RNA, 3 ug random hexamers, 1 μg Superscript III, and standard dNTPs in the presence of Actinomycin D. First strand cDNA was purified by PCI extraction, ethanol precipitated, and resuspended in water. Second strand cDNA was synthesized with E. coli DNA polymerase, in the presence of E. coli DNA ligase and RNase H (all from NEB), using dNTPs in which dUTP was substituted for dTTP, at 16°C for 2 hrs. After purification on a Clean and Concentrate column (Zymo Research), cDNA was fragmented using Fragmentase (NEB), PCI extracted and precipitated as above. End repair, A-tailing, and barcoded adapter ligation were performed as described (Illumina), and the second strand cDNA was digested with USER enzyme (NEB). Libraries were amplified from the resulting adapter-ligated first-strand cDNA using Phusion (NEB) and 16 cycles of amplification. Libraries were size-selected on 1.5% agarose gels to a size range of ~180-250 bp.

treatment_protocol: For ESC differentiation, 106 ESC cells were suspended in medium lacking LIF and cultured in non-cell culture treated petri dishes for 2 days. Subsequently, cells were transferred to gelatin-coated cell culture dishes in media lacking LIF for the number of days indicated. Cells were fixed or RNA was isolated at the indicated time points.

tag: cell type

value: differentiation

tag: time

value: Day 10

tag: protocol

value: RNaseH1 overexpression


title: Huwe1 knockdown myotubes 2

description: Directional mRNA-seq

tag: genotype

value: shRNA sequence:GCACTGCTCATCAAAGATGTT


title: D10_RH2


title: Huwe1 knockdown D6 2

description: Directional mRNA-seq


title: Mycoplasma pneumoniae (strain 5817)_PAU8

tag: strain type

tag: country of isolation

tag: year

tag: isolated from


title: D4_RH2

value: Day 4


title: Wildtype D6

description: Directional mRNA-seq

value: wildtype


title: Wildtype D0

description: Directional mRNA-seq


title: D10_Control2

value: Control


title: D10_Control1


title: P300_TA

value: 1μM of Triamcinolonacetonide (T6501, Sigma-Aldrich)


title: D4_RH1


title: Huwe1 knockdown D6 1

description: Directional mRNA-seq


title: D4_Control2


title: D2_RH1

value: Day 2


title: D4_Control1


title: D2_RH2


title: D0_Control1

value: control

value: Day 0


title: D0_RH2


title: D2_Control1


title: RIP_Ruvbl1_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and reads were aligned to the mm9 genome assembly using TopHat2 allowing at most one mismatch in every alignment.
Aligned sequences were processed in HOMER by using “analyzeRNA” command to calculate, normalize and present in reads per kilobase per million mapped reads (rpkm) for each reference gene.
Fold-change was caluculated by dividing rpkm from IP with IgG control
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph and RPKM files

extract_protocol:
Cells were lysed using an NE-PER Extraction kit (Thermo Fisher) to isolate cytoplasmic and nuclear fractions. For immunoprecipitation, 1.5 mg of nuclear extracts were treated with DNase I (New England Biolabs) and pre-cleared with Protein A magnetic beads (New England Biolabs) for 3 hours. Cleared nuclear extract was incubated with specific antibodies in IP buffer (50 mM Tris-HCl pH7.4, 250 mM NaCl, 0.1% Triton X-100), plus 1X HALT protease inhibitors (Thermo Fisher) and SUPERaseIn (Life Technologies) overnight at 4°C. The next day, pre-washed Protein A magnetic beads were added to IP samples and incubated for another 4 hours at 4°C. The magnetic beads were sequentially washed with IP buffer twice, high-salt IP buffer (50 mM Tris-HCl pH7.4, 500 mM NaCl, 0.1% Triton X-100, 0.5 % sodium deocycholate) four times, and IP buffer two more times. RNA was eluted from beads and purified by TRIzol (Life Technologies) extraction and precipitated at -80°C for at least 2 hours.
10-50 ng of RIP enriched RNA and Adaptor 1 (5’-CTGAACCGCTCTTCCGATCTNNNNNN-3’) were used for first-strand cDNA synthesis with Superscript III Reverse Transcription Kit (Life Technologies). After first-strand cDNA synthesis, RNA was degraded by sodium hydroxide and cDNA was purified by SILAN beads (Life Technologies). To preserve strand information, Adaptor 2 with the modification of 5’ phosphorylated and 3’ dideoxy-C (5’-p-NNACGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’ddC) was ligated to the 3’ end of first-strand cDNA using T4 RNA ligase 1 (New England Biolabs). The ligated material was purified by SILAN beads and PCR amplified with Illumina primers using 18 cycles of PCR. To remove PCR primers, libraries were purified by AMPure XP beads (Beckman Coulter).

tag: rip antibody

value: Ruvbl1 (10210-2-AP; Proteintech)


title: RIP_p400_rep2


title: D2_Control2


title: D0_RH1


title: D0_Control2


title: RIP_Ruvbl1_rep1


title: DRIP_RNAseq_RNaseH

data_processing:
library strategy: DRIP-RNAseq
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and reads were aligned to the mm9 genome assembly using TopHat2 allowing at most one mismatch in every alignment.
Aligned sequences were processed in HOMER by using “annotatePeaks” command to bin the regions of interest in 20 bp windows and sum the reads within each window
Average enrichment was calculated by normalizing the reads in each window to total reads, dividing by the number of regions of interest and presented in reads per million (rpm).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Genomic DNA was extracted from mouse ESC and was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
The immunoprecipitated material (with and without RNase H treatment) were denatured at 94°C for 1 min and cooled on ice. To reduce DNA background, the samples were treated with DNaseI at 37°C for 30 minutes and RNA was purified using Phenol/Chloroform/Isoamylalcohol extraction. 38 pmol of adaptor 1 (CTGAACCGCTCTTCCGATCTNNNNNN) was combined with 50 ng of S9.6 enriched RNA for first-strand cDNA synthesis with a Superscript III Reverse Transcription Kit (Life Technologies). After first-strand cDNA synthesis, RNA was degraded by sodium hydroxide and cDNA was purified by SILAN beads (Life Technologies). To preserve strand information, Adaptor 2 (5’-p-NNACGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’ddC) was ligated to the 3’ end of first-strand synthesized cDNA. The ligation material was purified by SILAN beads and then PCR amplified with Illumina primers using 18 cycles of PCR. To remove PCR primers, libraries were purified by AMPure XP beads (Beckman Coulter).

treatment_protocol: RNaseH digestion 37degree overnight

tag: cell  type

value: pre-treated RNaseH

tag: rna/dna hybrid enrichment

value: mAb S9.6 was used to enrich for RNA/DNA hybrids


title: RIP_IgG_rep1

value: rabbit IgG (ab37415; GR90135-1; Abcam)


title: DRIP_RNAseq_Control


title: Suz12IP_WT_2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.0.0 allowing at most one mismatch in every alignment.
For multimappers, only one alignment was chosen randomly by the -M 1 parameter setting.
Aligned sequences were processed in HOMER by using “annotatePeaks” command to bin the regions of interest in 20 bp windows and sum the reads within each window.
Average enrichment was calculated by normalizing the reads in each window to total reads, dividing by the number of regions of interest and presented in reads per million (rpm)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Cells from ~80 % confluent 10 cm dishes were crosslinked by adding fixation solution (1% formaldehyde, 0.1M NaCl, 1mM EDTA, 50mM HEPES⋅KOH pH 7.6) for 10 minutes at room temperature. Crosslinking was quenched with 125mM Glycine for 5 minutes. Cells were washed twice with cold PBS containing protease inhibitors (Roche), and pelleted at 1000g for 5 minutes at 4°C. Cell pellets were either flash frozen in liquid nitrogen and stored at -80°C or immediately sonicated. Pellets were resuspended in Lysis buffer 1 (50mM HEPES⋅KOH pH 7.6, 140mM NaCl, 1mM EDTA, 10% (v/v) Glycerol, 0.5% NP-40, 0.25% Triton X-100) including protease inhibitors and incubated for 10 minutes at 4°C. After centrifugation at 1350g for 5 minutes, pellets were resuspended in Lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) containing protease inhibitors and incubated for another 10 minutes at 4°C. Pellets were collected after centrifugation at 1350g for 5 minutes and resuspended in Lysis buffer 2 for sonication. Samples were transferred into 15 ml tubes (Falcon) and sonicated in a Bioruptor set to high for 2 cycles (10 minutes for one cycle with 30 sec on/ 30 sec off). The supernatants were collected after a 13000 rpm spin for 10 minutes at 4°C. 50μl Protein G Magnetic beads (NEB) were washed twice with PBS with 5mg/ml BSA and 10μg of anti-Flag M2 antibody (Sigma) coupled in 500μl PBS with 5mg/ml BSA overnight at 4°C. Immunoprecipitation was performed with antibody-coupled beads and sonicated supernatants in ChIP buffer (20mM Tris-HCl pH8.0, 150mM NaCl, 2mM EDTA, 1% Triton X-100) overnight at 4°C. Magnetic beads were washed twice with ChIP buffer, once with ChIP buffer including 500mM NaCl, 4 times with RIPA buffer (10mM Tris-HCl pH8.0, 0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% Na⋅Deoxycholate), and once with TE buffer (pH 8.0). Chromatin was eluted twice from washed beads by adding elution buffer (20mM Tris-HCl pH8.0, 100mM NaCl, 20mM EDTA, 1% SDS) and incubating for 15 minutes at 65°C. The crosslinking was reversed at 65°C for 6hr and RNase A (Sigma) was added for 1hr at 37°C followed by proteinase K (Ambion) treatment overnight at 50°C. ChIP-enriched DNA was purified using Phenol/Chloroform/Isoamyl alcohol extractions in phase-lock tubes.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with Phusion polymerase using 16 cycles of PCR before size selection of 200-300 bp fragments on a 2% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing (50 bp) was performed on an Illumina HiSeq2000.

treatment_protocol: In one 10 cm2 dish, 1X10^6 cells were treated with 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) or Triptolide (TRI) for 9 or 4 hours respectively. The RNaseH1-overexpressing cells were made by transfection of pCAGGS-RNaseH1-ires-Hygro plasmid into the Tip60-H3F line and selection with Hygromycin B (Roche) for 1 week.

value: WT


title: Suz12IP_WT


title: Suz12IP_RH_2


title: p400IP_DRB

value: DRB treatment


title: p400IP_WT


title: p400IP_TRI

value: TRI treatment


title: IgG

description: IgG is the control IgG that we used for p400 ChIPseq data.

value: Rabbit-IgG (ab37415; GR90135-1; Abcam)

value: IgG control


title: FlagIP_RH

value: Flag-M2 (Sigma, F1804)

value: RNaseH1 overexpression


title: IgG_WT

description: IgG_WT is the control IgG that we used for Suz12 ChIPseq data.


title: FlagIP_DRB


title: RIP_p400_rep1


title: FlagIP_TRI


title: RIP_IgG_rep2


title: TG378_TAC_2_RISC

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: RISC (Ago2-immunoprecipitated RNA)

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
This gtf is supplied as a 'processed data file'.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: mm10 / UCSC
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each mRNA.

source_name: Mouse

extract_protocol:
Hearts were removed and coronal sections from adult hearts (without right ventricle) were flash frozen in liquid nitrogen. Total RNA was harvested using Trizol reagent (Invitrogen), while cleared lysates were prepared from frozen tissue for Ago2 immunoprecipitation and RISC RNA isolation, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
RISC RNA was isolated from immunoprecipitated Ago2 via direct incubation of immunoprecipitates with Trizol reagent (Invitrogen).  Chemical fragmentation and preparation of single-end RNA-Seq libraries proceeded as for polyadenylated RNA.

tag: strain

value: FVB/N

value: transgenic

tag: tissue

value: Heart

tag: age (weeks)

value: M

tag: surgery

value: TAC


title: TG378_TAC_3_RISC

description: RISC (Ago2-immunoprecipitated RNA)

tag: genotype/variation


title: TG378_TAC_5_RISC

description: RISC (Ago2-immunoprecipitated RNA)

tag: Sex


title: TG378_TAC_7_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: TG378_TAC_1_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_TAC_7_RISC

description: RISC (Ago2-immunoprecipitated RNA)

value: non-transgenic


title: ntg_TAC_5_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_TAC_2_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_TAC_6_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_TAC_4_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_TAC_3_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: TG378_TAC_6_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: TG378_TAC_4_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: FlagIP_untag

tag: cell type

tag: chip antibody

value: No tag control


title: Suz12IP_RH

tag: protocol


title: ntg_sham_3_RISC

description: RISC (Ago2-immunoprecipitated RNA)

value: sham


title: TG378_sham_1_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: TG378_sham_2_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: TG378_sham_3_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_sham_2_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_sham_1_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: TG378_TAC_6_mRNA

description: polyadenylated RNA


title: p400IP_RH

tag: genotype


title: TG378_TAC_5_mRNA

description: polyadenylated RNA


title: TG378_TAC_7_mRNA

description: polyadenylated RNA


title: TG378_TAC_4_mRNA

description: polyadenylated RNA


title: FlagIP_WT


title: ntg_TAC_6_mRNA

description: polyadenylated RNA


title: ntg_TAC_5_mRNA

description: polyadenylated RNA


title: TG378_TAC_1_mRNA

description: polyadenylated RNA


title: TG378_TAC_3_mRNA

description: polyadenylated RNA


title: TG378_TAC_2_mRNA

description: polyadenylated RNA


title: ntg_TAC_1_RISC

description: RISC (Ago2-immunoprecipitated RNA)


title: ntg_TAC_1_mRNA

description: polyadenylated RNA


title: ntg_TAC_4_mRNA

description: polyadenylated RNA


title: ntg_TAC_3_mRNA

description: polyadenylated RNA


title: TG378_sham_3_mRNA

description: polyadenylated RNA


title: TG378_sham_1_mRNA

description: polyadenylated RNA


title: ntg_sham_3_mRNA

description: polyadenylated RNA


title: ntg_sham_1_mRNA

description: polyadenylated RNA


title: ntg_TAC_2_mRNA

description: polyadenylated RNA


title: ntg_sham_2_mRNA

description: polyadenylated RNA


title: old_C57BL6_STHSC_population_1

city: Cambridge

first: Monika

middle: Sylwia

last: Kowalczyk

state: MA

address: 415 Main Street

institute: Broad Institute

description:
pop_old_ST_HSC_1_1
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

data_processing:
Paired-end 25bp reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters. TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed.
We filtered out cells in which less than 2500 UCSC genes were detected above a log2(TPM+1) threshold of 2. We excluded transcripts whose log2(TPM+1) was lower than 4 in the aggregated data for each of the 6 populations, retaining 8422 transcripts
Genome_build: mm9
Supplementary_files_format_and_content: GEO_HSC_single_data.xlsx is an Excel sheet that contain the log-transformed expression levels, log2(TMP+1) of 8422 mouse transcripts in 1429 single cells and in six population averages, including young and old LT-HSCs, ST-HSCs and MPPs. The first row contains cell ID (a unique index for each single cell) or "pop" for the population averages. The second row indicates the type of population (age and cell type) that the cell (or population average) belongs to. The first and second columns include gene symbols and UCSC transcript names, respectively. (The processed data file only represents samples that were of sufficient quality to analyze)

source_name: hematopoietic stem and progenitor cells

growth_protocol: cells were profiled immediately

extract_protocol:
for single cells - direct lysis; for populations we used PrepEase (Affymetrix) according to manufacturers protocol.
cDNA from each sample was prepared using the SMARTer cDNA synthesis (Clontech). RNA libraries were prepared for sequencing using Nextera XT (Illumina).

tag: age

value: 2-3 months old

value: short term hematopoietic stem cell


title: old_C57BL6_STHSC_population_2

description:
pop_old_ST_HSC_1_2
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_STHSC_population_3

description:
pop_old_ST_HSC_1_3
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_MPP_population_1

description:
pop_old_MPP_1_1
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

value: multipotent progenitor


title: old_C57BL6_MPP_population_3

description:
pop_old_MPP_1_3
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_MPP_population_2

description:
pop_old_MPP_1_2
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: HB9PO4-ChIP

city: Bethesda

first: Sunita

last: Agarwal

state: MD

address: 10 Center Drive,

department: NIDDK,MDB

institute: NIH

data_processing:
Basecalls performed using Illumina HISeq2000
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2
Data was filtered using pvalue cutoff:0.001, bandwidth:300
MACS (v1.42) was used for peak calling with following setting: Threshhold :  log2(fold change)>or=1 for enrichment, log2(fold change)< or= 1 for depletion. Pvalue_threshhold=0.05
Genome_build: mm9
Supplementary_files_format_and_content: bed and bam files generated from data processed using MACS (v1.42)

source_name: MIN6-4N cells

growth_protocol: MIN6-4N cells were cultured in DMEM low glucose medium supplemented with 15% FBS and, antibiotic and antimycotic, at 37˚C and 5% CO2

extract_protocol:
Millipore ChIP-assay kit
Illumina ChIP-Seq DNA sample preparation kit (catalog #: IP-102-1001) protocol was used

treatment_protocol: MIN6-4N cells were transfected with pcDNA3.1-myc-his-HLXB9 using lipofectamine 2000. Chromatin was prepared 48 hours post-transfection.

value: Mouse Insulinoma cells

tag: antibody

tag: sample type

value: IP


title: Input

value: input


title: ntg_TAC_7_mRNA

description: polyadenylated RNA


title: TG378_sham_2_mRNA

description: polyadenylated RNA


title: old_C57BL6_LTHSC_population_2

description:
pop_old_LT_HSC_1_2
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

value: long term hematopoietic stem cell


title: old_C57BL6_LTHSC_population_1

description:
pop_old_LT_HSC_1_1
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_population_3

description:
pop_old_LT_HSC_1_3
population RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_STHSC_population_4

description:
young_ST_HSC_population_biol2_tech2
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

data_processing:
Paired-end 25bp reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters. TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed.
We filtered out cells in which less than 2500 UCSC genes were detected above a log2(TPM+1) threshold of 2. We excluded genes whose log2(TPM+1) was lower than 4 in the aggregared data for each of the 6 populations, and those UCSC genes that were not associated with a HUGO gene Symbol, leaving 7823 genes for the final dataset.
Genome_build: mm9
Supplementary_files_format_and_content: GEO_HSC_single_data.xlsx is an Excel sheet that contain the log-transformed expression levels, log2(TMP+1) of 8422 mouse transcripts in 1429 single cells and in six population averages, including young and old LT-HSCs, ST-HSCs and MPPs. The first row contains cell ID (a unique index for each single cell) or "pop" for the population averages. The second row indicates the type of population (age and cell type) that the cell (or population average) belongs to. The first and second columns include gene symbols and UCSC transcript names, respectively. (The processed data file only represents samples that were of sufficient quality to analyze)


title: young_C57BL6_STHSC_population_6

description:
young_ST_HSC_population_biol2_tech3
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_STHSC_population_1

description:
young_ST_HSC_population_biol1_tech1
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_STHSC_population_3

description:
young_ST_HSC_population_biol1_tech2
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_9

description:
young_MPP_population_biol2_tech5
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_8

description:
young_MPP_population_biol2_tech4
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_STHSC_population_5

description:
young_ST_HSC_population_biol1_tech3
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_4

description:
young_MPP_population_biol2_tech2
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_5

description:
young_MPP_population_biol1_tech3
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_6

description:
young_MPP_population_biol2_tech3
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_7

description:
young_MPP_population_biol1_tech4
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_MPP_population_1

description:
young_MPP_population_biol1_tech1
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_population_4

description:
young_LT_HSC_population_biol2_tech2
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_population_3

description:
young_LT_HSC_population_biol1_tech2
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_population_2

description:
young_LT_HSC_population_biol2_tech1
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_STHSC_population_2

description:
young_ST_HSC_population_biol2_tech1
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_MPP_192

description:
old_MPP_192
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

value: 22 months old


title: young_C57BL6_LTHSC_population_1

description:
young_LT_HSC_population_biol1_tech1
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_MPP_191

description:
old_MPP_191
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_MPP_190

description:
old_MPP_190
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_MPP_188

description:
old_MPP_188
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx