title: pUPF1_6

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

description: RNA fractions enriched in > 20-nt RNAs

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - CutAdapt_1.15, "-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT --minimum-length 30 --max-n 1 --pair-filter=any"
CLEANING - CutAdapt_1.15, "-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -a CCGAGCCCACGAGAC -A CCGAGCCCACGAGAC -a GACGCTGCCGACGA -A GACGCTGCCGACGA -a AGATGTGTATAAGAGACAG -A AGATGTGTATAAGAGACAG -a TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -A TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -a GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG -A GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG -n 8 --discard-trimmed --minimum-length 30 --max-n 1 --pair-filter=any"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, "-s 1 -t exon -g gene_name"
Genome_build: REFERENCE - hg19 + RefSeq
Supplementary_files_format_and_content: text file includes raw read counts for each sample

source_name: okadaic acid-treated HEK293T cells

growth_protocol: HEK293T cells were grown in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum.

extract_protocol:
Cell lysates were prepared using Hypotonic Gentle Lysis Buffer (10 mM Tris (pH 7.4), 10 mM NaCl, 10 mM EDTA, 0.5% w/w Triton X-100) and Halt Protease and Phosphatase Inhibitor Cocktail (Thermo Scientific). RNA was extracted and purified using TRIzol reagent (Thermo Fisher Scientific).
HEK293T cells (6 x 108 in a total of eight 150-mm dishes) were treated with okadaic acid (200 nM) for 3 hr. After IP using anti-p-UPF1 (EMD Millipore) and, in parallel as a negative control, rabbit IgG (rIgG; Sigma), RNA was purified using TRIzol Reagent (Thermo Fisher Scientific), incubated following manufacturer’s instruction first with DNase I (Promega) and, subsequently, with Ribozero Gold rRNA Removal Kit (Illumina). Samples were then incubated with recombinant shrimp alkaline phosphatase (rSAP; New England Biolabs) to remove 5'-phosphates from any physiologically uncapped NMD targets; 3'-ends were ligated using T4 RNA ligase 2 (T4 RNA Ligase 2, truncated KQ; New England Biolabs) to a 33-nucleotide DNA adapter having App appended at its 5'-end and dideoxy-C (ddC; Integrated DNA Technologies) appended at its 3'-end; and 5'-ends were then phosphorylated using T4 polynucleotide kinase (T4 PNK; New England Biolabs) and ligated using T4 RNA ligase (Ambion T4 RNA Ligase; Thermo Fisher Scientific) to a 33-nucleotide RNA adapter having a hydroxyl moiety at both its 5'- and 3'-ends (Integrated DNA Technologies). cDNA was synthesized using SuperScript III reverse transcriptase (Invitrogen) and a DNA primer that is antisense to the 3'-end DNA adapter, and subsequently PCR-amplified (20 cycles) using primers complementary to the extreme ends of each adapter and Q5 High-Fidelity DNA Polymerase (New England Biolabs). Products with inserts of >20 base-pairs were size-selected from 6% polyacrylamide to eliminate those that could not be uniquely aligned to the genome, including products without inserts, PCR-amplified using index PCR primers, and submitted for deep sequencing (Illumina HiSeq2500v4 system).

treatment_protocol: 200 nM okadaic acid (Sigma) for 3 hr.

tag: antibody

value: anti-p-UPF1 (EMD Millipore)


title: Oncopeltus_fasciatus_dsRED_MethylC-seq_fastq_3_of_4

status: Public on Jul 05 2018

type: SRA

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

country: USA

institute: University of Georgia

description:
11 days post-RNAi injection targeting RED (control)
B2-5-dsRED-day-11-deep_S1_L003_R1_001

library_source: genomic

data_processing:
DNA methylation. Reads generated from MethylC-seq were aligned to the O. fasciatus v1.1 genome assembly or B. germanica v1 genome assembly using the latest version of methylpy (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). MethylC-seq analysis was performed as described in Schmtiz et al. (2013; doi:10.1101/gr.152538.112).
Genome_build: O. fasciatus: v1.1 (https://www.hgsc.bcm.edu/arthropods/i5k), B. germanica: v1 (https://www.hgsc.bcm.edu/arthropods/i5k)
Supplementary_files_format_and_content: Tab delimited; please see metadata file for column headers.

molecule: genomic DNA

organism: Oncopeltus fasciatus

source_name: Ovary

growth_protocol: Oncopeltus fasciatus cultures were originally purchased from Carolina Biologicals (Burlington, NC). Mass colonies were maintained in incubators under a 12 h:12 h light/dark cycle at 27°C. Colonies and individual experimental animals were fed organic raw sunflower seeds and provided with ad libitum deionized water. Late instar nymphs were separated from the mass colonies and housed under the same conditions. Nymph colonies were checked daily for newly emerged adults. Adults were separated by sex and kept with food and water for 7–10 days until females reached sexual maturity.

extract_protocol:
Ovaries were removed from each female, flash frozen in liquid nitrogen and stored at -80°C until processing. Total RNA and genomic DNA was extracted from pairs of ovaries (from a single female) using a Qiagen RNAeasy micro kit (Qiagen, Venlo, The Netherlands) per manufacturer’s instructions with Qiagen Qiazol as the lysis buffer. Complementary DNA (cDNA) was synthesized from 500 ng RNA with qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD).
DNA methylation. MethylC-seq libraries were prepared using the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114). Lambda phage DNA was used as a control for the sodium bisulfite non-conversion rate. Gene expression. RNA-seq libraries for RNA extracted from three DNMT1 knocked down and three control individuals were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

treatment_protocol: RNAi. Template for the in vitro transcription of reactions was prepared from a PCR reaction in which T7 phage promoter sequences were added to the gene-specific DNMT1 primers. For our control sequence, we used the red fluorescent protein (RED) sequence used in previous parental RNAi experiments in O. fasciatus. Sense and anti-sense RNA was synthesized in a single reaction using the Ambion MEGAscript kit (ThermoFisher Sci, Waltham, MA). After purification, the double-stranded RNA (dsRNA) concentration was adjusted to 2 μg/μL in injection buffer (5 mM KCl, 0.1 mM NaH2PO4). Females were injected with 5 μL of dsRNA between the abdominal sternites using an insulin syringe. Following injection, females were paired with an un-injected male to stimulate oviposition and fertilize eggs.  Individual females with their mate were housed in petri dishes with sunflower seeds, water and cotton wool as an oviposition site. The parental RNAi protocol has been reported to result in 100% penetrance by the third clutch of eggs and this was also our experience. Eggs were collected between days 4–10 post-injection and assessed for development. Oncopeltus fasciatus embryos change from a creamy white color to orange as they develop, which indicates viability. Thus, color change is a useful tool for assessing healthy development. We examined the number of developing eggs at 5 days post-oviposition, at which point viable eggs are clearly distinguishable from inviable eggs, as well as hatching rate of eggs from females injected with double-stranded DNMT1 (dsDNMT1) and double-stranded RED (dsRED).

tag: tissue

value: Ovary

tag: developmental stage

value: Adult female post-mating

tag: genotype

value: Carolina Biologicals


title: Trichoplax_iChip_input

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

data_processing:
scRNA-seq:
.Read_1 files were mapped into the corresponding species genome assembly (see below) using bowtie2, using default parameters.
.Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651)
iChIP:
.Paired reads files were mapped into the corresponding species genome assembly (see below) using bowtie2, using default parameters.
.Duplicate reads were removed using samtools.
.deepTools bamCoverage was used to generate bigWig coverage files, using a total extension of 220bps from the read start position, and a scaleFactor parameter of 0.1
Genome_build: : https://metazoa.ensembl.org/Amphimedon_queenslandica/Info/Index
Genome_build: : https://research.nhgri.nih.gov/mnemiopsis/download/download.cgi?dl=genome
Genome_build: Trichoplax adhaerens: https://genome.jgi.doe.gov/Triad1/Triad1.home.html

organism: Trichoplax adhaerens

source_name: Adult placozoan

extract_protocol:
MARSseq RNA capture: single-cells were FACS-sorted directedly into a lysis solution in 384-well plates. Plates were forzen at -80C, lysis solution (ddH2O, 0.1%triton, RNAse inhibitors) was evaporated and reverse transcription was performed directly in the wells.
MARSseq library prepartion was performed as described in  Jaitin et al. 2014 (10.1126/science.1247651). Briefly, cDNA from different cells (barcoded in the Reverse Transcripiton step) was pooled and amplified by in vitro-transcription. Amplified RNA was then fragmented, reverse transcribed, and Illumina adaptors were added by PCR (14 cycles).
iChIP experiments were performed starting from 200,000 cells, following the iChIP protocol originally described in Lara-Astiaso et al. 2014 (10.1126/science.1256271). Briefly, cells were cross-linked in FA 1% for 10 min and cross-linked chromatin was sonicated using 45 cycles (30"ON/30"OFF). Then chromatin was immobilized using anti-H3 antibody and barcoded, followed by immunoprecipitation using specific anti-H3K4me2 and anti-H3K4me3 antibodies.

tag: stage/cell type

value: Adult

tag: strain

value: Wild type

tag: chip antibody


title: Oncopeltus_fasciatus_dsRED_MethylC-seq_fastq_2_of_4

description:
11 days post-RNAi injection targeting RED (control)
B2-5-dsRED-day-11-deep_S1_L002_R1_001


title: pUPF1_3

description: RNA fractions enriched in > 20-nt RNAs

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: RNA seq - PEN

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
processed data file: normalized_RNA_seq.csv
Sample name in processed data file: Sample 4

data_processing:
RNA-seq reads of each sample were mapped using the STAR_2.4.0i with default parameters.
Gene expression was called by featureCounts v1.5.0-p1. Normalization between the samples was based on the proportionality of the numbers of the mapped reads, and normalized counts are further log2 transformed with the trimming of minimal counts to 10.
Genome_build: hg19
Supplementary_files_format_and_content: text file with the log2 normalized read count.

source_name: Hepatocarcinoma cell

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq samples, cells were treated with 30μM of PEN, PEN-MUT, PEN-WT, or PEN-FFW for 8hrs

tag: cell type

value: Hepatocarcinoma

tag: treatment

value: SNU398 was treated with 30uM PEN (penetratin) peptides for 8hrs


title: Trichoplax_Adult_scRNAseq


title: SNU398 SALL4 ChIP

data_processing:
The paired-end ChIP-seq reads are mapped by bowtie2 to the human reference genome GRCh38 (hg38).
PCR duplicates are filtered out from the resulting BAM files using samtools rmdup.
Alignments with mapping quality below 20 are also filtered out.
Peak calling is performed by macs2. The options for calling SALL4 peaks are: macs2 callpeak -g hs -B -q 0.05.
For calling histone mark peaks, the options are: macs2 callpeak —broad -g hs —broad-cutoff 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. The ChIP-seq signal will be shrunk to fit the size of its control if the control is smaller in size.

extract_protocol:
Cell were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antbodies
Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing

value: SALL4 (Cell Signaling Technolog, cat# 8459BF, Lot 2)


title: pre-IP_4

description: RNA fractions enriched in > 20-nt RNAs

value: rabbit IgG (rIgG; Sigma)


title: Oncopeltus_fasciatus_dsDNMT1_MethylC-seq_fastq_4_of_4

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2-18-dsDNMT1-day-11-deep_S1_L004_R1_001


title: Blattella_germanica_MethylC-seq_fastq_4_of_4

organism: Blattella germanica

source_name: Whole-body minus gastrointestinal tract

value: Whole-body minus gastrointestinal tract

value: Lab colony


title: Oncopeltus_fasciatus_dsRED_MethylC-seq_fastq_1_of_4

description:
11 days post-RNAi injection targeting RED (control)
B2-5-dsRED-day-11-deep_S1_L001_R1_001


title: LDLS

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

description: Caught from wild

data_processing:
Adapter trimming was done using Universal adaptor sequences by Trimmomatic
The HQ reads so obtained were further processed as per new-tuxedo protocol (Pertea et al., 2016)
Genome_build: FicAlb_1.4
Supplementary_files_format_and_content: gtf file

organism: Emberiza melanocephala

source_name: Testis

extract_protocol:
The tissues were homogenized to powder form in the liquid Nitrogen with the help of mortar and pestle and total RNA extraction was done using Tri reagent (AM7020; Ambion, Austin, TX, USA).
RNA libraries were prepared for sequencing using standard Illumina sequencing protocols

value: Testis

tag: testicular state

value: Late Stimulated


title: Blattella_germanica_MethylC-seq_fastq_3_of_4


title: LDRF

description: Caught from wild

value: Refractory


title: SE

description: Caught from wild

value: Sensitive


title: pUPF1_9

description: RNA fractions enriched in > 20-nt RNAs


title: pre-IP_7

description: RNA fractions enriched in > 20-nt RNAs


title: Amphimedon_Larva_scRNAseq

organism: Amphimedon queenslandica

source_name: Sponge larva

value: Larva


title: Blattella_germanica_MethylC-seq_fastq_2_of_4


title: LDES

description: Caught from wild

value: Early Stimulated


title: pre-IP_1

description: RNA fractions enriched in > 20-nt RNAs


title: Oncopeltus_fasciatus_dsDNMT1_MethylC-seq_fastq_2_of_4

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2-18-dsDNMT1-day-11-deep_S1_L002_R1_001

value: Ovary


title: Amphimedon_Adult_scRNAseq

source_name: Adult sponge


title: Blattella_germanica_MethylC-seq_fastq_1_of_4


title: CP_ZnF7_r3

status: Public on Jul 04 2018

city: Beijing

first: Ma

last: Xin

state: --- Select a state ---

address: 2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China

country: China

institute: China Agricultural University

data_processing:
Raw reads were mapped to the reference genome by TopHat using default parameters.
Cuffdiff was used to calculate the FPKM (fragments per kilobase of exon per million mapped reads) of each gene and to identify the differentially-expressed genes (fold change ≥ 2, P < 0.001) between the CP-PROG1, CP-ZnF5, CP-ZnF7, CP-ZnF8 and control plants.
The functional category analysis of the differentially-expressed genes was performed by the AgriGO and KEGG databases.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0, MSU7

organism: Oryza sativa Japonica Group

source_name: Tiller bases

extract_protocol:
Total RNA was isolated using TRIzol according to the instructions.
P-aired-end libraries were constructed using a TruSeq RNA Sample Preparation Kit v2.

tag: experiment objectives

value: analysis of differentially expressed genes

value: Tiller bases

tag: development stage

value: Tillering stage

value: transgenic plants of ZnF7

tag: phenotype

value: semi-prostrate growth


title: CP_ZnF8_control_r1

value: control plants of ZnF8 transgenic lines

value: erect growth


title: CP_ZnF5_ZnF7_control_r1

value: control plants of ZnF5 and ZnF7 transgenic lines


title: CP_ZnF8_control_r2


title: Oncopeltus_fasciatus_dsDNMT1_MethylC-seq_fastq_1_of_4

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2-18-dsDNMT1-day-11-deep_S1_L001_R1_001

value: Adult female post-mating

value: Carolina Biologicals


title: CP_ZnF8_r1

value: transgenic plants of ZnF8


title: CP_ZnF8_r3


title: CP_ZnF8_r2


title: CP_ZnF5_ZnF7_control_r2


title: CP_ZnF8_control_r3


title: CP_ZnF7_r2


title: CP_ZnF7_r1


title: Oncopeltus_fasciatus_dsDNMT1_MethylC-seq_fastq_3_of_4

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2-18-dsDNMT1-day-11-deep_S1_L003_R1_001


title: CP_ZnF5_r3

value: transgenic plants of ZnF5


title: CP_ZnF5_r1


title: CP_ZnF5_r2


title: CP_PROG1_control_r3

value: control plants of PROG1 transgenic lines


title: CP_PROG1_control_r1


title: CP_PROG1_r3

value: transgenic plants of PROG1

value: prostrate growth


title: CP_PROG1_control_r2


title: CP_PROG1_r2


title: CP_ZnF5_ZnF7_control_r3


title: Tbk1+/-;Tak1ΔM/+ rep2

city: Boston

first: Daichao

last: Xu

state: MA

address: 240 Longwood Ave.

department: Cell Biology

institute: Harvard Medical School

data_processing:
The reads were mapped into mm10 genome by STAR and counted by featurecounts
Genome_build: mm10
Supplementary_files_format_and_content: counts

organism: Mus musculus

source_name: microglia

growth_protocol: Forebrains of 2-d-old mouse pups were digested with 0.01% trypsin and triturated with DMEM containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. Dissociated cells were plated onto poly-d-lysine coated 75 cm2 flasks and changed the medium after 7 days, then the cells were cultured for another 7 days. Following an initial 5 min shake of the culture, microglia were collected and cultured in DMEM+10%FBS.

extract_protocol:
Cells were lysated, total RNA was harvested using Quick-RNA MiniPrep Plus kit (ZYMO)
Each library was prepared using the Smart-seq2 protocol with a tagged oligo (dT) primer to make first strand cDNA from 1 ng total RNA  input. Double-stranded cDNA was generated for library construction with 12 cycles of PCR and 0.3 ng of cDNA was used as input to the NexteraXT kit (Illumina). Libraries were sequenced with a NextSeq (Illumina) to generate 50 base paired end reads. Reads were aligned to the mm10 UCSC mouse transcriptome and expression values were determined using RSEM.

value: brain

tag: age

value: postnatal day 2


title: Tak1ΔM/+ rep3


title: Tbk1+/-;Tak1ΔM/+;Ripk1D138N/+ rep1


title: Tbk1+/-;Tak1ΔM/+ rep3


title: Tbk1+/-;Tak1ΔM/+ rep1


title: Tbk1+/-;Tak1ΔM/+;Ripk1D138N/+ rep3


title: Tbk1+/-;Tak1ΔM/+;Ripk1D138N/+ rep2


title: Tbk1+/-;Ripk1D138N/D138N rep3


title: Tbk1+/-;Ripk1D138N/D138N rep2


title: Tak1ΔM/+ rep2


title: Tbk1+/-;Ripk1D138N/D138N rep1


title: Tak1ΔM/+ rep1


title: Tbk1+/- rep3


title: CP_PROG1_r1

value: analysis of differentially expressed genes


title: Tbk1+/- rep1


title: Tbk1+/- rep2


title: WT rep3

value: WT


title: WT rep1


title: WT rep2


title: healthy volunteer, rep3 [whole genome]

type: RNA

city: Harbin

first: Zhibo

last: Guo

state: Heilongjiang

address: No.23 Street

institute: Harbin Medical University

description:
C3
Gene expression of normal bone marrow mononuclear cells.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent p/n G2565BA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: bone marrow mononuclear cells, healthy

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Freshly drawn bone marrow from EMI, non-EMI AML patients and healthy volunteers were separated, then total RNA was extracted based on standard protocol.

tag: disease state

value: healthy

value: bone marrow mononuclear cells

tag: gender

value: female


title: non-extramedullary infiltration, rep1 [whole genome]

description:
T2.1
Gene expression of AML patients without extramedullary infiltration.

source_name: bone marrow mononuclear cells, AML without EMI

value: AML without EMI

value: male


title: non-extramedullary infiltration, rep4 [whole genome]

description:
T2.4
Gene expression of AML patients without extramedullary infiltration.


title: non-extramedullary infiltration, rep2 [whole genome]

description:
T2.2
Gene expression of AML patients without extramedullary infiltration.


title: healthy volunteer, rep4 [whole genome]

description:
C4
Gene expression of normal bone marrow mononuclear cells.


title: extramedullary infiltration, rep3 [whole genome]

description:
T1.3
Gene expression of AML patients with extramedullary infiltration.

source_name: bone marrow mononuclear cells, AML with EMI

value: AML with EMI


title: non-extramedullary infiltration, rep3 [whole genome]

description:
T2.3
Gene expression of AML patients without extramedullary infiltration.


title: extramedullary infiltration, rep4 [whole genome]

description:
T1.4
Gene expression of AML patients with extramedullary infiltration.


title: extramedullary infiltration, rep2 [whole genome]

description:
T1.2
Gene expression of AML patients with extramedullary infiltration.


title: healthy volunteer, rep2 [whole genome]

description:
C2
Gene expression of normal bone marrow mononuclear cells.


title: healthy volunteer, rep1 [whole genome]

description:
C1
Gene expression of normal bone marrow mononuclear cells.


title: R08_AM_Allo24h

city: Chicago

first: Stephen

middle: Francis

last: Chiu

state: IL

address: 251 E Huron

department: Thoracic Surgery

institute: Northwestern University Feinberg School of Medicine

data_processing:
Reads were demultiplexed using bcl2fastq
Alignment was performed using TopHat2
Mapping was performed using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: murine lung transplant model_24hrs post reperfusion

extract_protocol:
PicoPure (Thermofisher) RNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse genotype

tag: Sex

value: 14 weeks

tag: time point

value: 24 hours post reperfusion

value: lung

value: alveolar macrophage


title: R04_AM_Allo2h

source_name: murine lung transplant model_2hrs post reperfusion

value: 2 hours post reperfusion

tag: tissue


title: N04_AM_Naive

source_name: murine lung transplant model_naive

value: Naïve


title: R01_AM_Allo2h


title: R06_AM_Allo24h


title: R07_AM_Allo24h


title: R03_AM_Allo2h


title: R02_AM_Allo2h


title: N03_AM_Naive


title: R05_AM_Allo24h


title: extramedullary infiltration, rep1 [whole genome]

description:
T1.1
Gene expression of AML patients with extramedullary infiltration.


title: Lenti-LASS2 4

city: Xuzhou

first: ning

last: sheng

state: Jiangsu

address: Shanghai road

institute: JSNU

description: Gene expression data from Lenti-LASS2 cells

hyb_protocol: Array hybridization was performed using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: Slides were scanned by Agilent DNA Microarray Scanner (Part number G2505C).

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: 3AO cells transduced by a Lentivirus carrying the LASS2 gene

label_protocol: RNAs were amplified and labeled using Agilent Quick Amp Labeling kit to obtain Cy3-UTP labeled cRNA.

growth_protocol: Lenti-LASS2 and Lenti-vector cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin mixture. Cells were maintained in a 37 ℃ humidified incubator with 5% CO2 atmosphere.

extract_protocol: Total RNA was exacted using TRIZOL Reagent (Cat#15596-026, Invitrogen, Carlsbad, CA, USA) and purified by RNeasy mini kit and RNase-Free DNase Set (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: We established stable cell lines transduced by a lentivirus carrying the LASS2 gene or vector control, which were designed as Lenti-LASS2 and Lenti-vector, respectively, in the ovarian cancer cell line 3AO.

value: ovarian cancer cell


title: Lenti-vector 3

description: Gene expression data from Lenti-vector cells

source_name: 3AO cells transduced by a Lentivirus carrying vector control


title: N02_AM_Naive


title: N01_AM_Naive


title: Lenti-vector 1


title: Lenti-LASS2 6


title: Trteg_KO_72h_2

first: Xueping

last: Zhu

address: 1 st West Beichen, Chaoyang

institute: Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of  the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were  aligned to the reference genome using TopHat  v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time.(Trapnell, Cole, et al., Nat. Biotechnol 2010)
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each sample

source_name: Noc4L deficient mice

extract_protocol:
Lymphocytes were isolated from the LN and spleen of Foxp3CreNoc4l+/fl (Het) or Foxp3CreNoc4l+/fl (cKO) mice and enriched for CD4+ T cells using magnetic beads. Then, CD4+GFP+CD62Lhigh Tregs were sorted to a typical purity of >90% using CD4, CD25, CD62L and CD4 Abs.  SMART-SeqTM v4 UltraTM Low Input RNA Kit for Illumina was used with 10 pg-10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Treg cells

tag: genotype/variation

value: Foxp3CreNoc4lfl/fl (cKO)


title: Lenti-vector 2


title: B3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in the adenocarcinomic human alveolar basal epithelial cells infected with pMIRNA1—miR-155.

hyb_protocol: 825 ng from each of the Cy5-labeled sample of A549 cells infected with pMIRNA1—miR-155 and C3-labeled samples used for another experiment were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) human (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., doi: 10.18632/oncotarget.23417.

source_name: A549 cells purchased from the American Type Culture Collection (ATCC) infected with pMIRNA1—miR-155 _Replicate 3

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Cell were cultured following the recommendations in the Product Information Sheet (ATCC)

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: A549 cells were infected with with miR155 in pMIRNA1 vectors obtained from System Biosciences.

value: 58 years old

tag: race

value: caucasian

tag: agent


title: ED6.5_defeated_BNST

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

data_processing:
Sequenced reads were trimmed for adaptors and aligned to mouse genome GRCm38/mm10 using STARv 2.5.0c with default settings.
Aligned reads were annotated to gene exons with HTSeq v0.6.11 using GTF release 86 (update 2016-10), using non-stranded union model for vHPC and stranded intersection-nonempty for mPFC and BNST.
Count matrixes for mPFC, BNST, vHPC were TMM and voom normalized with limma and batch adjusted with ComBat.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log(CPM) values, normalization was done separately for each brain region.

source_name: bed nucleus of the stria terminalis

growth_protocol: Mice (Charles River Laboratories, Sulzfeld, Germany) were housed in groups in a temperature and humidity controlled facility on a 12h light/dark cycle for the acclimatization period. All mice had ad libitum access to food and water throughout the experiment (except for the durations of behavioral tests). Animal procedures were approved by the Regional State Administration Agency for Southern Finland (license numbers ESAVI-3801-041003-2011 and ESAVI/2766/04.10.07/2014) and carried out in accordance to directive 2010/63/EU of the European Parliament and of the Council, and the Finnish Act on the Protection of Animals Used for Science or Educational Purposes (497/2013).

extract_protocol:
Brain regions were dissected on a sterile chilled petri dish within 7 minutes and tissue was flash-frozen in liquid N2. Total RNA was extracted with TriReagent (Molecular Research Center, Inc.) and RNA integrity was controlled with Bioanalyzer (Agilent). The rRNA was depleted with either Ribo-Zero Gold rRNA Removal Kit (Illumina; mPFC and vHPC) or custom designed Insert dependent adaptor cleavage (InDA-C) primers (BNST).
Sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), and Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits.

treatment_protocol: Mice were killed by cervical dislocation between 8 am and 11 am to avoid circadian differences in gene expression, and the order was counterbalanced across experimental conditions.

tag: strain

tag: age on dissection

value: 8  weeks

tag: csds phenotype

value: susceptible


title: Trteg_KO_48h_2


title: ED1.7_defeated_BNST

value: resilient


title: Trteg_Het_72h_3

source_name: Nco4L sufficient mice

value: Foxp3CreNoc4l+/fl (Het)


title: ED6.40_control_BNST

value: male

value: control


title: ED4.3_defeated_BNST


title: ED4.1_defeated_BNST


title: ED4.4_defeated_BNST


title: Lenti-LASS2 5

value: female

tag: cell type

tag: cell line


title: No_TX_9_USR16088082L_HGJ5YBBXX

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
alignment: Partek® Flow® software, version 6.0, STAR - 2.3.0e
Quantify to annotation model (Partek E/M): Partek® Flow® software, version 6.0
Partek® Flow® software, version 6.0, Normalization methods Total count Add: 1.0E-4
Partek® Flow® software, version 6.0: differential gene expression (GSA), ANOVA
Genome_build: RefSeq Transcripts 83 - 2017-11-01 mouse whole genome
Supplementary_files_format_and_content: tab-delimited text files include coverage report for each Sample, xlsc files include pre alignment QC and STAR aligner results

source_name: Bone Marrow

growth_protocol: Tibias and femurs were collected from healthy mice and bone marrow cells were harvested, Bone marrow cells were cultured in PermaLife bags (OriGen Biomedical, PL30) with 10 ng/ml rM-CSF (R&D Systems, 416-ML-010) for one week. 50,000 M-CSF-cultured macrophages were washed with medium to remove M-CSF and plated in 96-well polystyrene cell culture plates (Corning, 353072) for 48 hours with or without treatment before use in experiments

extract_protocol:
total RNA was extracted using RNeasy micro Kit
After the RNA QC procedures, mRNA was enriched using oligo(dT) beads and fragmented randomly, then cDNA was synthesized by mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina, San Diego, CA)
Libraries were run on Illumina PE150 (HiSeq) with 250 to 300bp insert cDNA library for 20M raw reads/sample

treatment_protocol: PD-L1 antibody (BioXcell, BE0101) and irrelevant isotype-matched control antibody (BioXcell, BE0090) were used at 100 ug/ml, which represents the reported minimum desired plasma antibody concentration for patients treated with PD-L1 antibody

value: macrophage

tag: origin

value: Primary cells

tag: antibody

tag: genotype

value: Wild-type


title: Trteg_Het_48h_1


title: B4

source_name: A549 cells purchased from the American Type Culture Collection (ATCC) infected with pMIRNA1—miR-155 _Replicate 4

tag: age

value: adenocarcinomic human alveolar basal epithelial cells

value: lung


title: ED3.4_defeated_BNST


title: Trteg_KO_72h_4


title: Trteg_Het_72h_1


title: B2

source_name: A549 cells purchased from the American Type Culture Collection (ATCC) infected with pMIRNA1—miR-155 _Replicate 2


title: ED2.1_defeated_BNST


title: No_TX_8_USR16088081L_HGJ5YBBXX


title: ED1.3_defeated_BNST


title: No_TX_7_USR16088080L_HGJ5YBBXX


title: Iso_6_USR16088079L_HGJ5YBBXX

value: isotype-matched control antibody (BioXcell, BE0090)


title: ED6.39_control_BNST


title: ED6.38_control_BNST


title: ED3.12_control_BNST


title: PDL1_3_USR16088076L_HGJ5YBBXX

value: PD-L1 antibody (BioXcell, BE0101)


title: B1

source_name: A549 cells purchased from the American Type Culture Collection (ATCC) infected with pMIRNA1—miR-155 _Replicate 1


title: ED4.15_control_BNST


title: PDL1_2_USR16088075L_HGJ5YBBXX


title: EC4.4_defeated_BNST


title: EC3.3_defeated_BNST


title: EC4.3_defeated_BNST


title: EC4.8_defeated_BNST


title: Iso_4_USR16088077L_HGJ5YBBXX


title: EC4.10_defeated_BNST


title: GFP2

city: San Francisco

first: James

last: Bayrer

state: CA

address: 550 16th St, 5th Floor, Box 0136

department: Pediatrics

institute: UCSF

data_processing:
illumina Casava1.8 software used for producing FastQ files.
RNA-seq data analyses were performed in the Galaxy platforms (https://usegalaxy.org/)
Raw reads were groomed (Galaxy version 1.1.4) and run quality was checked by FastQC (tool version 0.63)
Removed low quality sequences using FastQ quality trimmer (tool version 1.0.0)
Aligned to the mouse mm10 genome sequence in Galaxy using Tophat v2.0.14 (with default setting)
FPKM calculation was done by Cufflinks (cufflinks v2.2.1) using Tophat bam output and mm10_genes.gtf mouse genomic list from Ensemble. Parameters;  Max Intron length: 300000, Min Isoform Fraction : 0.1, Pre mRNA Fraction: 0.15, Reference annotation: mm10_genes.gtf, Count hits compatible with reference RNAs only: Yes, Perform Bias Correction: No, Use multi-read correct: No, Apply length correction: Cufflinks effective length correction. All cufflinks files were merged by Cuffmerge using Cufflinks assembled transcripts file.
Compare expression in samples were dene by Cuffdiff (Tool version cuffdiff v2.2.1)
Genome_build: Mouse Dec. 2011 (GRCm38/mm10) (mm10)
Supplementary_files_format_and_content: Cufflinks.tabular.txt

source_name: small intestinal organoid culture

growth_protocol: standard intestinal organoid culture

extract_protocol:
Total RNA extracted in Trizol reagent and purified by Direct-zol spin columns (Zymo Research)
Ovation RNA-Seq System V2 (NuGEN) was used to generate the cDNA library for sequencing on an Illumina HiSeq 4000 by using standard protocol.

treatment_protocol: Samples treated with 4OH-Tamoxifen (300 nM) at Day -2. Infected with AAV at Day 0. Harvested at Day 4 for total RNA purification.

value: small intestinal organoid culture

value: Lrh1-/- + AAV-GFP


title: EC3.10_defeated_BNST


title: EC3.6_defeated_BNST


title: EC4.12_defeated_BNST


title: hLRH1_2

value: Lrh1-/- + AAV-hLRH1


title: GFP1


title: EC3.5_defeated_BNST

value: 8  weeks


title: PDL1_1_USR16088074L_HGJ5YBBXX


title: hLRH1_1


title: hLRH1_3


title: IKO3


title: GFP3


title: EC3.2_defeated_BNST


title: EC4.20_control_BNST


title: IKO2


title: IKO1


title: EC4.19_control_BNST


title: EC4.17_control_BNST


title: FF3

value: wild type


title: FF2


title: EC3.15_control_BNST


title: EC3.12_control_BNST


title: FF1


title: D8.14_defeated_mPFC

source_name: medial prefrontal cortex

value: susceptible


title: D4.7_defeated_mPFC


title: D10.9_defeated_mPFC


title: D10.7_defeated_mPFC


title: Iso_5_USR16088078L_HGJ5YBBXX


title: D10.21_defeated_mPFC


title: D5.3_control_mPFC


title: Mitosis IAA rep3

city: Berkeley

first: Sheila

middle: S

last: Teves

state: California

address: 475D Li Ka Shing Center

department: Molecular Cell Biology

institute: UC Berkeley

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced paired mates were mapped on mm10 genome build using Bowtie2 with the following parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 –I 10 –X 2000.
From the length distribution of sequenced reads, we performed in silico size selection for short reads (under 100 bp) and for 180 - 250 bp reads (mono-nucleosome sized fragments).
DeepTools (bamCoverage) was used to generate bigwig files for the corresponding fragment size using the following parameters: -bs 10 -ignoreDuplicates --minFragmentLength 20 --maxFragmentLength 100 ; or -bs 10 -ignoreDuplicates --minFragmentLength 180 --maxFragmentLength 250
The resulting bigwig file was used to generate the genome browser shot in IGV, the TSS plots and heatmaps using Deeptools (computeMatrix and plotHeatmap functions), and the person correlation heatmap analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for reads under 100 bp and 180-250 bp reads generated using Deeptools

source_name: Mitosis IAA, ESCs

extract_protocol: Libraries were processed using Nextera DNA Librarpy Prep Kit

treatment_protocol: Mitosis samples were synchronized by addition of 100ng/uL of Nocodazole for 6 hours, samples were either treated with DMSO or IAA for 4-6 hours/

value: Embryonic stem cells

tag: cell state

value: Mitosis

value: IAA


title: Mitosis DMSO rep3

source_name: Mitosis DMSO, ESCs

value: DMSO


title: Mitosis DMSO rep2


title: Async IAA rep2

source_name: Async IAA, ESCs

value: Async


title: Async DMSO rep3

source_name: Async DMSO, ESCs


title: Mitosis IAA rep2


title: Async IAA rep3


title: M30 30 min release rep 2 TBP-degraded

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped on mm10 genome build using Tophat with the following parameters:--library-type=fr-firststrand --b2-very-sensitive --no-coverage-search and de-duplicated using samtools rmdup function
Sequenced spike in reads were mapped on the ERCC92 build using Tophat with the following parameters:--library-type=fr-firststrand --b2-very-sensitive --no-coverage-search and de-duplicated using samtools rmdup function
DeepTools (bamCoverage) was used to generate bigwig files for all reads or for forward and reverse strands separately, and reads were extended to 200 bp for coverage. The resulting bigwig file was used to generate the genome browser shot in IGV, the TSS plots and heatmaps using Deeptools (computeMatrix and plotHeatmap functions), and the person correlation heatmap analysis.
Intronic transcripts per million (TPM) counts for each gene were calculated using Bioconductor R, which were then inputted for principal component analysis. Scatter plots were generated using R ggplots package.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for forward strand and reverse strand for each replicate, and bigwig files for all reads with replicates combined. The bigwig files for the log ratio of M30 and M60 samples relative to the M samples. The bed file of genes after k-means clustering with k=3. The Intronic TPM counts for each gene and for each replicate sample.

source_name: JM8.N4 mAID-TBP C94

extract_protocol: Libraries were processed using stranded Illumina single end library protocol

treatment_protocol: Mitosis samples were synchronized by addition of 100ng/uL of Nocodazole for 6 hours, and TBP degraded samples were treated with Auxin (IAA) at 500 uM for 4-6 hours

value: JM8.N4 mAID-TBP C94


title: Async DMSO rep2


title: M60 60 min release rep 2 TBP-degraded


title: D10.19_control_mPFC

value: male

value: control


title: Mitosis (M) rep 2 TBP-degraded


title: Asynchronous (A) rep 2 TBP-degraded


title: D5.8_defeated_mPFC


title: D10.12_control_mPFC


title: D10.10_control_mPFC


title: M60 60 min release rep 1 TBP-degraded


title: D10.5_defeated_mPFC


title: D10.20_defeated_mPFC


title: M30 30 min release rep 1 TBP-degraded


title: Mitosis (M) rep 1 TBP-degraded


title: C7.19_defeated_mPFC


title: Async (A) rep 1 TBP-degraded


title: M60 60 min release rep 2 untreated


title: D10.8_control_mPFC


title: C7.15_defeated_mPFC


title: C7.14_defeated_mPFC


title: M30 30 min release rep 2 untreated


title: C5.7_defeated_mPFC

value: resilient


title: Asynchronous (A) rep 2 untreated


title: M60 60 min release rep 1 untreated


title: D10.22_control_mPFC


title: M30 30 min release rep 1 untreated


title: Mitosis (M) rep 2 untreated


title: C5.4_defeated_mPFC


title: C5.19_defeated_mPFC


title: Mitosis (M) rep 1 untreated


title: C2.14_defeated_mPFC


title: C7.21_defeated_mPFC


title: C1.8_defeated_mPFC


title: Async (A) rep 1 untreated


title: C2.6_defeated_mPFC


title: Pol II 60R replicate 2

city: Boulder

first: Jennifer

last: Kugel

state: Colorado

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

data_processing:
Read quality was assessed using FastQC.
reads were mapped to the mm10 genome using Bowtie (version 1.0.0) in the -v alignment mode, allowing one mismatch per read and reporting only reads with unique alignments.
Analysis of mapped reads was performed using the suite of tools available in HOMER, including making tag directories, generating bedGraph files, tag counting across RefSeq genes, and generating histograms and heatmaps of Pol II occupancy flanking regions of interest.
Bedtools2.19.1 was also used to count reads in intergenic regions downstream of genes.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files generated using the default makeUCSCfile command in HOMER.

source_name: embryonic fibroblast

growth_protocol: Cells were grown in  5% CO2 at 37ºC in DMEM containing 10% FBS, 100 U/ml penicillin, and 100 mg/ml streptomycin.  Cells were subcultured multiple times a week to keep the cell confluency below 75%

extract_protocol:
Sheared chromatin was prepared by sonicating nuclei, Pol II-DNA complexes were immunoprecipitated.
Libraries were made using the Ovation Ultralow System V2 from NuGEN. Libraries were sequenced on an Illumina HiSEQ 4000

treatment_protocol: Cells were grown to ~70% confluency and then cell flasks were placed in a waterbath at 45ºC for heat shock, and placed back at 37ºC for the recovery timepoint. Cell were crosslinked with formaldehyde for 10 minutes prior to harvesting chromatin for ChIP assays.

value: NIH 3T3 fibroblast cell line

tag: treatment

value: heat shock followed by recovery

tag: chip antibody

value: D8L4Y, Cell Signalling Technology


title: C7.7_control_mPFC

tag: Sex


title: Pol II HS replicate 1

value: heat shock


title: Pol II HS replicate 2


title: C7.17_defeated_mPFC


title: Pol II NHS replicate 2


title: C2.5_control_mPFC


title: Pol II 60R replicate 1


title: Pol II NHS replicate 1


title: C2.17_control_mPFC


title: C1.7_control_mPFC


title: C1.5_control_mPFC


title: C2.3_control_mPFC


title: C2.20_defeated_mPFC


title: At_silique_H3K27me3

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

institute: CUHK

description:
At_silique
sequencing instrument(s): HiSeq X Ten

data_processing:
Most of the sequencing and base-calling services were provide by CloudHealth Genomics, Ltd. (Shanghai).
For RNA-Seq dataset, raw data was aligned to a home maintained rDNA database using Bowtie2 (version 2.1.0) with default parameters to filter out any rRNA sequence. Retained reads were then mapped to genome reference using TopHat2 (v2.1.1) with parameters: --read-realign-edit-dist 0 --max-intron-length 10000 --max-segment-intron 10000 --prefilter-multihits. FPKM value of each gene was calculated using StringTie (v1.3.1c) with parameters: -e -j 3 -f 0.2 -A. Raw read counts of genes were calculated using HTSeq (version 0.9.1) with parameters: --nonunique all.
For DNase-Seq and ChIP-Seq dataset, raw reads were mapped to the genome reference using Bowtie2 (version 2.1.0) with option: -3 100.  For DNase-Seq and transcription factor ChIP-Seq datasets, peaks were called using MACS (ver 2.1.1.20160309), with the parameters: --nomodel -q 0.01 and -q 0.01, respectively. For H3K27me3 ChIP-Seq dataset, peaks were called using SICER (version 1.1) with the settings: window size 150, gap size 300, FDR 0.01. H3K27me3 candidate peaks were filtered further by their length, fold of enrichment and FDR: 1. peaks shorter than 300 bp was discarded; 2. for peaks shorter than 1kb, fold of enrichment and FDR requirement cutoff were setted as 5 and 1e-50, respectively for apple and tomato datasets,  4 and 1e-50 repectively for banana, grape and pear datasets, 3 and 1e-5  for datasets of other species; 3. for peaks longer than 1kb, fold of enrichment cutoff were setted as 4 for apple and tomato datasets, 3 for banana, grape and pear datasets, 2 for datasets of other species; Alignments with mapping score less than 10 and PCR duplicates were discarded using samtools before peak calling. bedgraph file generated by MACS with --SPMR enabled was converted to bw file using bedGraphToBigWig.
For Bisulfite-Seq dataset, raw data was mapped to genome reference using BSMAP (version 2.90) with the parameters: -A AGATCGGAAGAGC -w 100 -r 0 -q 10. Methylation ratio of each cytosine was calculated using methratio.py with the parameters: -z -r. The result file was compressed using bgzip and index using tabix.
Genome_build: Arabidopsis thaliana: genome release 9 (assembly), TAIR10 (annotation), https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Athaliana
Genome_build: Apple: GDDH13 Version 1.1 (assembly), GDDH13 Version 1.1 (annotation), https://iris.angers.inra.fr/gddh13/
Genome_build: Banana: DH-Pahang v2 (assembly), DH-Pahang v2 (annotation), http://banana-genome.cirad.fr/content/download-dh-pahang
Genome_build: Cucumber: Chinese long v2 (assembly), Chinese long v2 (annotation), ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/
Genome_build: Grape: Genoscope (12X) (assembly), CRIBI V2.1 (annotation), http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Genome_build: Melon: v3.5 (assembly), v3.5 (annotation), https://melonomics.net/files/Genome/Melon_genome_v3.5_Garcia-Mas_et_al_2012/
Genome_build: Papaya: ASGPBv0.4 (assembly), ASGPBv0.4 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Cpapaya
Genome_build: Peach: v1.0 (assembly), v1.0 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ppersica
Genome_build: Pear: Pbr_v1.0 (assembly), NCBI Annotation Release 101 (annotation), https://www.ncbi.nlm.nih.gov/genome/12793
Genome_build: Strawberry: v1.1 (assembly), v1.1 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Fvesca
Genome_build: Watermelon: v1 (assembly), v1 (annotation), ftp://www.icugi.org/pub/genome/watermelon/97103/v1/
Genome_build: Tomato: v2.5 (assembly), ITAG2.4 (annotation), ftp://ftp.solgenomics.net/tomato_genome/assembly/build_2.50/
Genome_build: Rice: Os-Nipponbare-Reference-IRGSP-1.0 (assembly), MSU release 7.0 (annotation), https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Osativa
Supplementary_files_format_and_content: For RNA-Seq dataset, tab delimited abundance file gives FPKM of each gene, tab delimited count file gives read counts of each gene
Supplementary_files_format_and_content: For Dnase-Seq dataset, bw file shows the read density across the entile genome, tab delimited file in narrowPeak format shows peak calling information generated by MACS2
Supplementary_files_format_and_content: For Bisulfite-Seq dataset, bgzip compressed tab delimited file gives all and mC counts of each genomic cytosine across the entile genome. Index file are also provided, so one can fast retrieve the data randomly using tabix.
Supplementary_files_format_and_content: For ChIP-Seq dataset, bw file shows the read density across the entile genome. For transcription factor ChIP-Seq dataset, tab delimited file in narrowPeak format shows peak calling information generated by MACS2. For H3K27me3 ChIP-Seq dataset, tab delimited file shows peak calling information generated by SICER.

organism: Arabidopsis thaliana

source_name: silique

extract_protocol:
conventional TruSeq protocol or more recent Tn5-based ChIP-Seq library construction protocol
histone-DNA complexes were isolated with H3K27me3 antibody (RevMAb and Millipore).

tag: cultivar

value: not collected

tag: tissue

value: silique

tag: developmental stage

value: old


title: At_carpel_H3K27me3

description:
At_carpel
sequencing instrument(s): HiSeq X Ten

source_name: carpel

value: carpel


title: Young_pax7_low quiescent satellite cells 3

city: Paris

first: Shahragim

last: Tajbakhsh

state: Ile de France

address: 25 rue du docteur Roux

department: Stem cell and development

country: France

institute: Institut Pasteur Paris

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analysed using the following R packages : Oligo for reading raw files and RMA normalisation, and Limma for differential gene expression analysis

label: biotin

source_name: facs sorted cells

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted from cells isolated by FACS directly into cell lysis buffer (RLT; Qiagen Rneasy Micro Kit)

value: quiescent skeletal muscle satellite cells


title: Old_Pax7_low quiescent satellite cells 3


title: Young_Pax7_high quiescent satellite cells 3


title: Young_pax7_low quiescent satellite cells 1


title: Old_Pax7_low quiescent satellite cells 2


title: Old_Pax7_low quiescent satellite cells 1


title: Young_pax7_low quiescent satellite cells 2


title: Young_Pax7_high quiescent satellite cells 1


title: Young_Pax7_high quiescent satellite cells 2


title: At_carpel_RNA-seq_1

description:
Carpel_rep1
sequencing instrument(s): HiSeq X Ten

extract_protocol:
Standard non-stranded illumina RNA-Seq libraries protocol
mRNA was extracted from tissue using standard protocol


title: At_cauline_leaf_RNA-seq_1

description:
Cauline_leaf_rep1
sequencing instrument(s): HiSeq X Ten

source_name: leaf

value: cauline leaf


title: Old_Pax7_high quiescent satellite cells 3


title: At_old_silique_RNA-seq_1

description:
Old_silique_rep1
sequencing instrument(s): HiSeq X Ten

source_name: old silique


title: postmortem (Day 4) quiescent satellite cell 3

value: postmortem (Day 4)


title: postmortem (Day 4) quiescent satellite cell 2


title: Old_Pax7_high quiescent satellite cells 2


title: Tau_small_4

city: San Antonio

first: Habil

last: Zare

address: 7703 Floyd Curl Drive

department: Department of Cell Systems & Anatomy

institute: University of Texas Health Science Center in San Antonio

description:
piRNA.txt
Tau-4

data_processing:
Base-calling was done using Real-Time Analysis (RTA) Version 2.7.6
The rRNA reads were removed using SortMeRNA Version 2.1
Illumina adaptors were removed using Trimmomatic v0.36 with these parameters: ILLUMINACLIP:<Trimmomatic-directory>/adapters/TruSeq3-SE.fa:3:30:10 SLIDINGWINDOW:5:20 MINLEN:15"
The sequences that were differentially expressed in tau transgenic Drosophila compared to controls were identified using DESeq2 v1.14.1.
Genomic locations of the differentially expressed transcripts were assigned using Ensembl BioMarts.
Genome_build: The transposon reference FASTA file (FlyBase Release 6.12, dmel r6.12) for RNA-Seq, and piRNABank for small RNA-Seq data.
Supplementary_files_format_and_content: .txt files including the counts, p-values, and other data from the differential expression analysis. All columns are described in the accompanying paper.

organism: Drosophila melanogaster

source_name: head

growth_protocol: Drosophila crosses and aging were performed at 25°C with a 12 h light/dark cycle at 60% relative humidity on a standard diet (Bloomington formulation).

extract_protocol:
RNA was extracted from Drosophila heads using a standard Trizol protocol.
Library preparation and sequencing were performed by the Genome Sequencing Facility at Greehey Children’s Cancer Research Institute at the University of Texas Health San Antonio. For standard RNA-seq, three independent biological replicates were sequenced, each consisting of 500 ng of total RNA from six pooled Drosophila heads (18 heads total). Extracted RNA was used for library preparation according to the KAPA Stranded RNA-seq Kit with RiboErase (HMR) sample preparation guide.  For small RNA-seq, four independent biological replicates were sequenced. 500 ng of total RNA from pooled Drosophila heads was used for library preparation according to the NEBNext small RNA sample preparation guide. Due to the abundance of the 2S rRNA in Drosophila, we included an additional 2S block step using the oligo (5’-TAC AAC CCT CAA CCA TAT GTA GTC CAA GCA/3SpC3/-3’) as described48. 2S rRNA blocking was performed directly after 3' SR adapter ligation. 1 μM of the 2S rRNA block oligo was added directly to each ligation reaction on ice, and reactions were incubated at 90°C for 30 sec, then 65°C for 5 min. After 5 min, 1 μl of SR RT primer was added and we proceeded as described in the NEBNext protocol.

value: tau transgenic

value: head


title: Old_Pax7_high quiescent satellite cells 1


title: postmortem (Day 2) quiescent satellite cell 1

value: postmortem (Day 2)


title: Tau_small_3

description:
piRNA.txt
Tau-3


title: adult (24-26-month) quiescent satellite cell 1

value: 24 - 26 months


title: At_leaf_H3K27me3

description:
At_leaf
sequencing instrument(s): HiSeq X Ten


title: Tau_small_2

description:
piRNA.txt
Tau-2


title: Tau_small_1

description:
piRNA.txt
Tau-1


title: postmortem (Day 4) quiescent satellite cell 1


title: CTRL_small_4

description:
piRNA.txt
Con-4

value: Wild type


title: CTRL_small_3

description:
piRNA.txt
Con-3


title: CTRL_small_2

description:
piRNA.txt
Con-2


title: adult (24-26-month) quiescent satellite cell 2


title: Mitosis IAA rep1

value: Embryonic stem cells

value: Mitosis

tag: agent

value: IAA


title: CTRL_small_1

description:
piRNA.txt
Con-1


title: Mitosis DMSO rep1

value: DMSO


title: Tau_3

description:
TE.txt
Tau-3


title: Async IAA rep1

value: Async


title: Trem2 Covi-Ox only 3

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

description: Trem2(-/-) mice treated with both cuprizone and Covi-Ox for 4 weeks, rep3

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Expression levels were assessed using the Affymetrix Mouse Gene ST 1.0 platform.  Resulting data was processed at the Washington University Genome Center. Robust multi-array average (RMA) normalization was used, genes were prefiltered for expression values of greater than 120.

label_protocol: standard Affymetrix protocol

growth_protocol: Mice were anesthetized with ketamine and xylezine.  Animals were perfused with PBS containing additional glutamine and 1 U/ml of heparin sulfate and brains were removed.  Brains were digested using the MACS Miltenyi Biotec Neural Tissue Dissociation Kit (T) according to manufactures instructions.  Single cell suspensions were resuspended in 30% percoll and spun at 850 RCF for 10 minutes with a slow break.

extract_protocol: Myelin was removed and cells were stained with anti-CD11b APC (clone M1/70), anti-CD45 Brilliant Violet 421 (clone 30-F11), and anti-F4/80 FITC (clone BM8).  Cells were sorted on a BD FACS Aria-II cell sorter.  Cells that were triple positive were considered to be microglia.  Cells were sorted into RLT buffer (QIAGEN) with β-mercaptoethanol.  RNA was extracted using an RNeasy plus micro kit (QIAGEN) according to manufactures instructions.

treatment_protocol: Cuprizone was purchased from Sigma-Aldrich (catalog 14690) and Covi-ox T70 mixed tocopherols was kindly provided by BASF. Envigo Laboratories produce the diets containing either 0.2% cuprizone (TD.01453), 0.1% Covi-ox T70 supplemented with and additional 1100 IU/g of alpha tocopherol (TD.150145), or both 0.2% cuprizone and 0.1% Covi-ox T70 with an additional 1100 IU/g of alpha tocopherol (TD.150144).  Mice were fed the diet ad libitum. Mice fed cuprizone and tocopherols were placed on the Covi-ox T70 with additional tocopherols diet for 2 weeks prior to feeding with Covi-ox T70 and cuprizone together for either 4 additional weeks or 7 weeks followed by 1 week of normal chow diet. Mice fed cuprizone only were maintained on normal chow for 2 weeks and then changed to cuprizone containing feed for 4 weeks or 7 weeks followed by 1 week of normal chow diet.

value: sorted microglia

value: Trem2 knockout


title: Tau_2

description:
TE.txt
Tau-2


title: postmortem (Day 2) quiescent satellite cell 2


title: Trem2 Covi-Ox only 2

description: Trem2(-/-) mice treated with both cuprizone and Covi-Ox for 4 weeks, rep2


title: Async DMSO rep 1


title: Trem2 cuprizone only 3

description: Trem2(-/-) mice treated with cuprizone for 4 weeks, rep3

value: treated with cuprizone for 4 weeks


title: Trem2 neg 1

description: Trem2(-/-) mice, negative control, rep1

source_name: Trem2(-/-) mice, negative control, rep1

value: negative control


title: Trem2 neg 2

description: Trem2(-/-) mice, negative control, rep2

source_name: Trem2(-/-) mice, negative control, rep2


title: Trem2 cuprizone Covi-Ox 2

description: Trem2(-/-) mice treated with Covi-Ox for 4 weeks, rep2

value: treated with Covi-Ox for 4 weeks


title: Trem2 cuprizone only 2

description: Trem2(-/-) mice treated with cuprizone for 4 weeks, rep2


title: Trem2 Covi-Ox only 1

description: Trem2(-/-) mice treated with both cuprizone and Covi-Ox for 4 weeks, rep1


title: CTRL_3

description:
TE.txt
CTRL-3


title: WT Covi-Ox only 3

description: WT mice treated with Covi-Ox for 4 weeks, rep3

value: WT


title: Trem2 cuprizone Covi-Ox 3

description: Trem2(-/-) mice treated with Covi-Ox for 4 weeks, rep3


title: Mutant_LowExpression_Rep4

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

data_processing:
Reads aligned to mm9 using Bowtie2 with unique alignments
HTSeq and CuffDiff2 packages were used for generating count tables
CuffDiff2 and DESeq2 were used for identifying differentials
Genome_build: mm9
Supplementary_files_format_and_content: Raw fragment counts generated using CuffDiff2

source_name: fetal kidney cells

extract_protocol:
RNA from Six2-expressing progenitors isolated by FACS was extracted using TRIzol. 10 ng of total RNA were subjected to cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing. 5ng of cDNA were then used in a NEBNext DNA Library Prep kit (E6040S) to generate sequencing libraries according to the manufacturer’s instructions.
5ng of cDNA was used in a NEBNext DNA Library Prep kit (E6040S) to generate sequencing libraries according to the manufacturer’s instructions.

tag: construct

value: R26R-tdTomato reporter cells

value: fetal kidney cells


title: WT cuprizone Covi-Ox 2

description: WT mice treated with both cuprizone and Covi-Ox for 4 weeks, rep2


title: CTRL_2

description:
TE.txt
CTRL-2

value: head


title: Trem2 cuprizone Covi-Ox 1

description: Trem2(-/-) mice treated with Covi-Ox for 4 weeks, rep1


title: Tau_1

description:
TE.txt
Tau-1

value: tau transgenic


title: Trem2 cuprizone only 1

description: Trem2(-/-) mice treated with cuprizone for 4 weeks, rep1


title: Mutant_LowExpression_Rep2


title: WT cuprizone Covi-Ox 1

description: WT mice treated with both cuprizone and Covi-Ox for 4 weeks, rep1


title: WT Covi-Ox only 1

description: WT mice treated with Covi-Ox for 4 weeks, rep1


title: Mutant_LowExpression_Rep1


title: D5.8_defeated_vHPC

source_name: ventral hippocampus

tag: strain

tag: age on dissection

value: 8  weeks

value: male

value: susceptible


title: D5.6_defeated_vHPC

tag: csds phenotype


title: WT cuprizone only 3

description: WT mice treated with cuprizone for 4 weeks, rep3


title: D4.7_defeated_vHPC


title: D5.4_defeated_vHPC


title: WT cuprizone only 2

description: WT mice treated with cuprizone for 4 weeks, rep2


title: WT Covi-Ox only 2

description: WT mice treated with Covi-Ox for 4 weeks, rep2


title: CTRL_1

description:
TE.txt
CTRL-1

value: Wild type


title: WT cuprizone Covi-Ox 3

description: WT mice treated with both cuprizone and Covi-Ox for 4 weeks, rep3


title: D4.3_defeated_vHPC


title: Mutant_HighExpression_Rep2

tag: cell type


title: WT neg 2

description: WT mice, negative control, rep2

source_name: WT mice, negative control, rep2


title: WT neg 1

description: WT mice, negative control, rep1

source_name: WT mice, negative control, rep1


title: Mutant_LowExpression_Rep3


title: D5.3_control_vHPC

value: control


title: Mutant_HighExpression_Rep1


title: AN1358_Rep1

city: Ribeirão Preto

first: Liliane

middle: Fraga Costa

last: Ribeiro

state: São Paulo

address: 3900, Bandeirantes avenue

country: Brazil

institute: University of São Paulo

description: There are two SRR for this sample. Each file represents a technical replicate.

data_processing:
Sequenced reads were trimmed for adaptor sequence,RNA-Seq output data  was checked for base quality and aligned to the reference genome of Aspergillus nidulans  (www.aspgd.org/) using bowtie2 and the read counts were normalized using HT-Seq.  Differential expression analysis was done using DESeq software (Anders and Huber, 2010)
Genome_build: Aspergillus nidulans
Supplementary_files_format_and_content: Tab-delimited text files include Differential expression log2fold values.
1358_1405.a.table.txt.func.txt includes comparison between strain 1358 and 1405.
1405_AN1405.table.sig.txt.func.txt includes comparison between replicates of strain 1405.

organism: Aspergillus nidulans

source_name: PkaA kinase deletion

growth_protocol: Spores were spread on MAGV plates [2% malt extract, 1.5% agar, 2% glucose, 1mL/L Hutner’s solution (FGSC), 1mL/L vitamin solution (FGSC)] and incubated for 2 days at 28⁰C. Harvested cells (1x107 spores) were inoculated into 50mL of rich, low pH media [YGV: 0.5% yeast extract, 2% glucose, 1mL/L Hutner’s solution (FGSC), 1mL/L vitamin solution (FGSC) adjusted to pH 3.3 with 1M HCl] and grown for 12 hours at 250 rpm and 28⁰C. This flask was used to seed 1.2L of YGV media in a 2.8L Fernbach flask at 250 rpm and 28⁰C. After approximately 20 hours (or until late exponential growth phase), mycelia were harvested and immediately frozen with liquid nitrogen and stored at -80⁰C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 ((Illumina, Inc. San Diego, CA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PkaA kinase deletion


title: WT cuprizone only 1

description: WT mice treated with cuprizone for 4 weeks, rep1


title: D5.5_control_vHPC


title: D4.8_control_vHPC


title: Control_HighExpression_Rep2


title: D4.6_control_vHPC


title: D4.4_control_vHPC


title: AN1405_Rep1

source_name: Parental strain

value: parental strain


title: D4.2_control_vHPC


title: AN1358_Rep2


title: Control_HighExpression_Rep1


title: Os_carpel_H3K27me3

description:
Os_carpel
sequencing instrument(s): HiSeq X Ten

organism: Oryza sativa

value: Fengsizhan

value: carpel

value: not collected


title: C2.2_defeated_vHPC


title: C1.19_defeated_vHPC


title: C2.24_defeated_vHPC

value: resilient


title: C2.8_defeated_vHPC


title: Os_leaf.young_H3K27me3

description:
Os_leaf.young
sequencing instrument(s): HiSeq X Ten

source_name: young leaf

value: leaf

value: young stage


title: Control_LowExpression_Rep2

value: R26R-tdTomato reporter cells


title: Control_LowExpression_Rep3

value: fetal kidney cells


title: C2.6_defeated_vHPC


title: Os_leaf.old_H3K27me3

description:
Os_leaf.old
sequencing instrument(s): HiSeq X Ten

source_name: old leaf

value: old stage


title: Control_LowExpression_Rep1


title: Control_LowExpression_Rep4


title: C1.2_defeated_vHPC


title: C1.18_defeated_vHPC


title: C1.12_defeated_vHPC


title: Mitotic IgG

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced paired mates were mapped on mm10 genome build using Bowtie2 with the following parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 –I 10 –X 2000.
From the length distribution of sequenced reads, we performed in silico size selection for short reads (under 120 bp).
DeepTools (bamCoverage) was used to generate bigwig files for the correspinding fragment size using the following parameters: -bs 1 -p 2 --normalizeTo1x 2725537669 --ignoreDuplicates --minFragmentLength 20 --maxFragmentLength 120
The resulting bigwig file was used to generate the genome browser shot in IGV, the TSS plots and heatmaps using Deeptools (computeMatrix and plotHeatmap functions), and the person correlation heatmap analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for reads under 100 bp  generated using Deeptools

extract_protocol: Libraries were processed using standard Illumina paired end library protocol

treatment_protocol: Mitosis samples were synchronized by addition of 100ng/uL of Nocodazole for 6 hours

value: Embryonic stem cells

tag: cell line

value: ChromPure Mouse IgG (Jackson 015-000-003


title: AN1405_Rep2


title: C2.23_control_vHPC

value: 8  weeks

value: male


title: Os_carpel_RNA-seq_2

description:
Carpel2_rep2
sequencing instrument(s): HiSeq X Ten


title: Os_carpel_RNA-seq_1

description:
Carpel2_rep1
sequencing instrument(s): HiSeq X Ten


title: C2.20_defeated_vHPC


title: Asynchronous IgG


title: C2.5_control_vHPC


title: C2.13_control_vHPC


title: Os_leaf_old_RNA-seq_2

description:
Leaf_old_rep2
sequencing instrument(s): HiSeq X Ten

value: old


title: Os_leaf_old_RNA-seq_3

description:
Leaf_old_rep3
sequencing instrument(s): HiSeq X Ten


title: Mitotic TBP ChIP seq rep 2

value: TBP (Abcam #51841)


title: C2.18_defeated_vHPC


title: Os_leaf_old_RNA-seq_1

description:
Leaf_old_rep1
sequencing instrument(s): HiSeq X Ten


title: C1.3_control_vHPC

value: control


title: Os_leaf_young_RNA-seq_3

description:
Leaf_young_rep3
sequencing instrument(s): HiSeq X Ten

value: young


title: Mitotic TBP ChIP seq rep 1


title: Asynchronous TBP ChIP seq rep 1


title: Os_leaf_young_RNA-seq_1

description:
Leaf_young_rep1
sequencing instrument(s): HiSeq X Ten

value: Fengsizhan


title: C1.14_defeated_vHPC


title: C1.7_control_vHPC


title: 17-wildtype

city: Cambridge

first: Murray

last: Tipping

address: 16 Divinity Ave

department: MCB

institute: Harvard University

data_processing:
Basecalling done in Bauer core with Illumina CASAVA 1.8
Sequences were matched to BB2000 reference genome PMID: 24009111 using TopHat2, default arguments
mRNA abundance data were generated using Cufflinks 2.1.1, max-multiread-fraction 0.9, -multi-read-correct
Samples combined using cuffmerge, default arguments
Differential expression data were generated using Cuffdiff 2.1.1, total-hits-norm
Genome_build: PMID: 24009111
Supplementary_files_format_and_content: 1 xlsx file containing complete Cuffdiff output, including differential expression data

organism: Proteus mirabilis

source_name: Wildtype consolidator cells

growth_protocol: Samples were grown on CM55 swarming agar and harvested by scraping into RNA-Protect solution

extract_protocol:
Lysates were prepared from RNA-protect cell suspension using RNEasy minikit. rRNA was digested with terminator 5' phosphate dependent exonuclease according to manufacturer's instructions.
Libraries were constructed using NEBNext Ultra library prep kit.

value: wild type


title: 17-rffg

source_name: ∆rffG colonies

value: rffG mutant


title: Cl_34DPA_H3K27me3

description:
Cl_34DPA
sequencing instrument(s): HiSeq X Ten

organism: Citrullus lanatus

source_name: 34DPA fruit flesh

value: fruit flesh

value: 34 days post anthesis


title: Cl_leaf_H3K27me3

description:
Cl_leaf
sequencing instrument(s): HiSeq X Ten

value: leaf

value: not collected


title: Asynchronous TBP ChIP seq rep 2


title: Os_leaf_young_RNA-seq_2

description:
Leaf_young_rep2
sequencing instrument(s): HiSeq X Ten


title: 15-wildtype


title: Cl_10DPA_H3K27me3

description:
Cl_10DPA
sequencing instrument(s): HiSeq X Ten

source_name: 10DPA fruit flesh

value: 10 days post anthesis


title: Cl_leaf_BS-seq

source_name: leaf

extract_protocol:
Whole-genome bisulfite sequencing was carried out as previously described in Zhong, S. et al., Nat. Biotechnol., 2013. The sonicated genomic DNA was end-repaired, dA-tailed and ligated to a fully methylated Y-shape adapter.
Genomic DNA was extracted from different tissues using the DNeasy Plant Kit (Qiagen)


title: Watermelon_leaf_RNA-seq_2

description:
Leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: Watermelon_leaf_RNA-seq_1

description:
Leaf_rep1
sequencing instrument(s): HiSeq X Ten


title: forelimb 24hpa replicate 2

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

description: Microarray RAW data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod 24 hours post amputation.

hyb_protocol: Affymetrix Gene Chip 3'IVT Reagent Kit was used according to manufacturer's instructions.

scan_protocol: Affymetrix Command Console was used according to manufacturer's instructions

data_processing: RMA was performed in Affymetrix Expression Console.

organism: Ambystoma mexicanum

source_name: 1.0mm distal tip of regenerating axolotl limb amputated at mid zeugopod at 24hpa

label_protocol: Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: Animals were maintained at 17-18C and fed California blackworms once a week.  Rearing water (40% modified Holtfretter's solution) was changed three times per week.

extract_protocol: RNA was extracted using TRIzol Reagent followed by followed by RNeasy mini kit, as detailed in Voss et al. 2015.

treatment_protocol: Animals were anesthetized in 0.001% benzocaine and limbs were amputate mid-stylopod with a sterile razor blade.

value: forelimbs

tag: time (hpa)

tag: amputation site

value: mid zeugopod


title: E10.5 WT-3

city: Houston

first: Jiang

last: Chang

address: 2121 W. Holcombe Blvd.

department: Center for Translational Cancer Research

institute: Texas A&M University Institute of Biosciences and Technology

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.19935

source_name: wild-type mouse embryonic E10.5 heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Mouse embryonic hearts were harvested at E10.5 Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: Wild-type

tag: age

value: embryo heart


title: Cl_10DPA_DNase-seq

extract_protocol: DNase-Seq was performed as described in 1. Grøntved, L. et al., Epigenetics Chromatin 5, 10 (2012). The purified nuclei were suspended in 500 ul of nuclease digestion buffer (30 mM Tris-HCl pH 8.0, 14 mM MgCl2, 0.5% NP-40, 0.2% BSA) containing different concentration of DNase (Cyanase, RiboSolutions). After a short incubation at 37°C for 3 min, the digestion was immediately terminated by adding EDTA and SDS. RNase A was then added to digest the RNA. The DNA was purified by Phenol/Chloroform extraction and ethanol precipitation. The purified total DNA was run on a 2% agarose gel and the small fragments released by the DNase digestion were purified and converted to Illumina TruSeq libraries as described in He, H.H. et al., Nat. Methods, 2014.


title: Cl_34DPA_DNase-seq


title: forelimb 0hpa replicate 1

description: Microarray RAW data from 1.0mm distal tip of heterogeneous tissue from axolotl limb amputated at mid zeugopod immediately post amputation.

source_name: 1.0mm distal tip of regenerating axolotl limb amputated at mid zeugopod at 0hpa


title: VED_10DPA_H3K27me3

description:
VED_10DPA
sequencing instrument(s): HiSeq X Ten

organism: Cucumis melo

source_name: 10DPA fruit

value: Vedrantais

value: fruit flesh and peel


title: Cl_leaf_DNase-seq


title: VED_40DPA_2_H3K27me3

description:
VED_40DPA_2
sequencing instrument(s): HiSeq X Ten

source_name: 40DPA fruit flesh

value: 40 days post anthesis


title: E10.5 WT-1


title: 15-rffg

tag: genotype


title: E10.5 KO-1

source_name: RhoE knocout mouse embryonic E10.5 heart

value: RhoE KO


title: PS_40DPA_2_H3K27me3

description:
PS_40DPA_2
sequencing instrument(s): HiSeq X Ten

source_name: 40DPA fruit

value: Piel de Sapo


title: PS_10DPA_H3K27me3

description:
PS_10DPA
sequencing instrument(s): HiSeq X Ten


title: forelimb 24hpa replicate 3


title: VED_leaf_H3K27me3

description:
VED_leaf
sequencing instrument(s): HiSeq X Ten


title: forelimb 24hpa replicate 1


title: PI_40DPA_3_H3K27me3

description:
PI_40DPA_3
sequencing instrument(s): HiSeq X Ten


title: forelimb 0hpa replicate 3


title: PI_10DPA_H3K27me3

description:
PI_10DPA
sequencing instrument(s): HiSeq X Ten


title: forelimb 0hpa replicate 2


title: PI_leaf_H3K27me3

description:
PI_leaf
sequencing instrument(s): HiSeq X Ten


title: PI_40DPA_BS-seq

description:
PI_40DPA
sequencing instrument(s): HiSeq X Ten

value: PI _40DPA (ripe)


title: PS_40DPA_BS-seq

description:
PS_40DPA
sequencing instrument(s): HiSeq X Ten

value: PS _40DPA (ripe)


title: E10.5 KO-2


title: PS_leaf_BS-seq

description:
PS_leaf
sequencing instrument(s): HiSeq X Ten


title: E10.5 WT-2


title: PS_10DPA_BS-seq

value: PS_10DPA (immature)


title: EIL4_Ripe_ChIP-seq

description:
EIL4_Ripe
sequencing instrument(s): HiSeq X Ten

organism: Solanum lycopersicum

source_name: ripe fruit

extract_protocol:
conventional TruSeq protocol or more recent Tn5-based ChIP-Seq library construction protocol
TF-DNA complexes were isolated with the anti-GFP antibody (Millipore) using transgenic plants expressing their cDNA fused to GFP under the 35S promoter.

value: AC

value: fruit flesh

value: ripe


title: E10.5 KO-3


title: PI_leaf_BS-seq

value: leaf

value: not collected


title: RIN_47DPA_H3K27me3

description:
RIN_47DPA
sequencing instrument(s): HiSeq X Ten

source_name: 47DPA fruit

value: rin

value: 47 days post anthesis


title: NOR_47DPA_3_H3K27me3

description:
NOR_47DPA_3
sequencing instrument(s): HiSeq X Ten

value: nor


title: NOR_47DPA_2_H3K27me3

description:
NOR_47DPA_2
sequencing instrument(s): HiSeq X Ten


title: VED_20DPA_BS-seq

description:
VED_20DPA
sequencing instrument(s): HiSeq X Ten

source_name: 20DPA fruit

value: VED_20DPA (immature)


title: VED_leaf_BS-seq

value: Vedrantais


title: NR_47DPA_H3K27me3

description:
NR_47DPA
sequencing instrument(s): HiSeq X Ten

value: nr


title: VED_40DPA_2_DNase-seq

value: 40 days post anthesis


title: PS_leaf_H3K27me3


title: CNR_47DPA_H3K27me3

description:
CNR_47DPA
sequencing instrument(s): HiSeq X Ten

value: cnr


title: VED_10DPA_DNase-seq

description:
VED_10DPA
sequencing instrument(s): HiSeq X Ten

value: fruit flesh and peel

value: 10 days post anthesis


title: PI_10DPA_BS-seq

value: PI_10DPA (immature)


title: NOR_47DPA_H3K27me3

description:
NOR_47DPA
sequencing instrument(s): HiSeq X Ten


title: AC_mature_H3K27me3

description:
AC_mature
sequencing instrument(s): HiSeq X Ten


title: VED_40DPA_BS-seq

description:
VED_40DPA
sequencing instrument(s): HiSeq X Ten

value: VED_40DPA (ripe)


title: PS_10DPA_DNase-seq

description:
PS_10DPA
sequencing instrument(s): HiSeq X Ten

value: Piel de Sapo


title: AC_17DPA_H3K27me3

description:
AC_17DPA
sequencing instrument(s): HiSeq X Ten

source_name: 17DPA fruit

value: AC

value: fruit flesh

value: 17 days post anthesis


title: AC_leaf_H3K27me3

description:
AC_leaf
sequencing instrument(s): HiSeq X Ten

value: leaf

value: not collected


title: VED_leaf_DNase-seq

description:
VED_leaf
sequencing instrument(s): HiSeq X Ten


title: PS_leaf_DNase-seq


title: AC_52DPA_BS-seq

description:
AC_52DPA
sequencing instrument(s): HiSeq X Ten

source_name: 52DPA fruit flesh

extract_protocol:
Please refer to Zhong, S. et al., Nat. Biotechnol., 2013
Please refer to Zhong, S. et al., Nat. Biotechnol., 2013

value: 52 days post anthesis


title: PS_40DPA_DNase-seq

description:
PS_40DPA
sequencing instrument(s): HiSeq X Ten


title: Par_442

city: New York

first: Kalpana

last: Gopalakrishnan

state: NY

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

description:
Par_442
Gene expression data from normal adult parous rat mammary tissues at postnatal day 181.

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: The data was preprocessed in Expression Console software (Affymetrix) using RMA-sketch workflow and default settings. Batch effects were removed using the ComBat package in R (Leek J. T. et al., 2012). Data submitted here have not been corrected for batch effects. Batch information is provided in the 'characteristics' field.

organism: Rattus norvegicus

source_name: Parous rat mammary tissues, postnatal day 181

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, Affymetrix 2015).

extract_protocol: Mammary tissues were pulverized in liquid nitrogen and total RNA was extracted using the Maxwell 16 LEV simplyRNA Blood kit (Promega, WI) for most of the animals or the Direct-zol RNA MiniPrep kit (Zymo Research, CA) for some of the adult parous and nulliparous rats which were more 'fatty' in nature. RNA extraction information ('Promega' or 'Zymo') is provided in the 'characteristics' field. Total RNA concentration was determined using Nanodrop (Thermo Scientific, MA), and RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, CA).

treatment_protocol: Animals examined in this study are part of controls for a study on effects of environmental chemicals on developing mammary glands. These rats were regularly fed with olive oil, the vehicle for chemical treatment in the parent study, by gastric intubation (oral gavage). Five animals each were sacrificed at six developmental time-points reflective of distinct stages of mammary gland development – pre-pubertal, peri-pubertal, pubertal, lactation, parous and nulliparous. Pre-pubertal animals were sacrificed at postnatal day (PND) 21, peri-pubertal group at PND 42 and pubertal group at PND 63. Animals in the lactation group were sacrificed at the end of lactation at lactating day 28 (PND 146). Parous and nulliparous animals were sacrificed at PND 181. Animals were housed with their dams until weaning at PND 28. 0.5 mL olive oil was administered until PND 63, and 1 mL thereafter until PND 180. Animals were euthanized via carbon dioxide inhalation and necropsy was immediately performed for collection of selected tissues. All animals belonging to the same developmental group were sacrificed on the same day and at random during the estrous cycle. The 5th left and right caudal mammary glands of experimental animals were collected in cryovials on ice and stored at -80C, following which total RNA was extracted.

tag: strain/background

value: Sprague-Dawley

tag: gender

value: Female

tag: stage of development

value: Adult parous

tag: age at sacrifice

value: Postnatal day 181

tag: batch

value: One

tag: rna extraction kit

value: Promega


title: Par_444

description:
Par_444
Gene expression data from normal adult parous rat mammary tissues at postnatal day 181.

tag: tissue

value: 5th left and right caudal mammary glands

value: Three

value: Zymo


title: PI_40DPA_DNase-seq

description:
PI_40DPA
sequencing instrument(s): HiSeq X Ten

tag: cultivar

value: fruit flesh and peel

tag: developmental stage

value: 40 days post anthesis


title: Par_441

description:
Par_441
Gene expression data from normal adult parous rat mammary tissues at postnatal day 181.


title: Par_440

description:
Par_440
Gene expression data from normal adult parous rat mammary tissues at postnatal day 181.


title: Par_446

description:
Par_446
Gene expression data from normal adult parous rat mammary tissues at postnatal day 181.


title: Null_431

description:
Null_431
Gene expression data from normal adult nulliparous rat mammary tissues at postnatal day 181.

source_name: Nulliparous rat mammary tissues age-matched with parous rats, postnatal day 181

value: Adult nulliparous


title: PI_leaf_DNase-seq

description:
PI_leaf
sequencing instrument(s): HiSeq X Ten


title: PI_10DPA_DNase-seq

description:
PI_10DPA
sequencing instrument(s): HiSeq X Ten

value: 10 days post anthesis


title: Null_430

description:
Null_430
Gene expression data from normal adult nulliparous rat mammary tissues at postnatal day 181.


title: AC_leaf_BS-seq

value: AC


title: AC_17DPA_DNase-seq

value: fruit flesh

value: 17 days post anthesis


title: AC_17DPA_BS-seq

source_name: 17DPA fruit flesh


title: Null_429

description:
Null_429
Gene expression data from normal adult nulliparous rat mammary tissues at postnatal day 181.


title: H3_20DPA_RNA-seq_1

description:
H3_fruit_20DPA
sequencing instrument(s): HiSeq X Ten

source_name: 20DPA fruit flesh

value: Harukei 3

value: 20 days post anthesis


title: H3_50DPA_RNA-seq_1

description:
H3_fruit_50DPA
sequencing instrument(s): HiSeq X Ten

source_name: 50DPA fruit flesh

value: 50 days post anthesis


title: AC_47DPA_DNase-seq

description:
AC_47DPA
sequencing instrument(s): HiSeq X Ten

value: fruit flesh,leaf

value: 47 days post anthesis,not collected


title: Lac_2

description:
Lac_2
Gene expression data from normal rat mammary tissues at postnatal day 146.

source_name: Rat mammary tissues at end of lactation, postnatal day 146

value: Sprague-Dawley

value: Female

value: End of lactation

value: Postnatal day 146

value: Two


title: Pub_422

description:
Pub_422
Gene expression data from normal rat mammary tissues at postnatal day 63.

source_name: Rat mammary tissues at pubertal stage, postnatal day 63

value: 5th left and right caudal mammary glands

value: Pubertal

value: Postnatal day 63

value: Promega


title: Null_427

description:
Null_427
Gene expression data from normal adult nulliparous rat mammary tissues at postnatal day 181.

value: Adult nulliparous

value: Postnatal day 181

value: One


title: Pub_423

description:
Pub_423
Gene expression data from normal rat mammary tissues at postnatal day 63.


title: Pub_421

description:
Pub_421
Gene expression data from normal rat mammary tissues at postnatal day 63.


title: Lac_3

description:
Lac_3
Gene expression data from normal rat mammary tissues at postnatal day 146.


title: VED_40DPA_RNA-seq_2

description:
VED_fruit_40DPA_rep2
sequencing instrument(s): HiSeq X Ten

extract_protocol:
Strand specific RNA library protocol described in Zhong, S. et al., Cold Spring Harb. Protoc, 2011. Second stranded.
mRNA was extracted from tissue using standard protocol

value: Vedrantais

value: fruit flesh and peel

value: 40 days post anthesis


title: Pub_420

description:
Pub_420
Gene expression data from normal rat mammary tissues at postnatal day 63.


title: Lac_1

description:
Lac_1
Gene expression data from normal rat mammary tissues at postnatal day 146.


title: VED_40DPA_RNA-seq_1

description:
VED_fruit_40DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: Null_428

description:
Null_428
Gene expression data from normal adult nulliparous rat mammary tissues at postnatal day 181.


title: Peri_414

description:
Peri_414
Gene expression data from normal rat mammary tissues at postnatal day 42.

source_name: Rat mammary tissues at peri-pubertal stage, postnatal day 42

value: Peri-pubertal

value: Postnatal day 42


title: AC_leaf_2_DNase-seq

description:
AC_leaf_2
sequencing instrument(s): HiSeq X Ten

source_name: leaf

value: AC

value: leaf

value: not collected


title: Peri_415

description:
Peri_415
Gene expression data from normal rat mammary tissues at postnatal day 42.

value: Sprague-Dawley

value: Female


title: Pub_419

description:
Pub_419
Gene expression data from normal rat mammary tissues at postnatal day 63.

value: 5th left and right caudal mammary glands


title: AC_leaf_old_RNA-seq_2

description:
AC_leaf_old_rep2
sequencing instrument(s): HiSeq X Ten

source_name: old leaf

value: old


title: Peri_413

description:
Peri_413
Gene expression data from normal rat mammary tissues at postnatal day 42.


title: AC_leaf_old_RNA-seq_1

description:
AC_leaf_old_rep1
sequencing instrument(s): HiSeq X Ten


title: AC_leaf_adult_RNA-seq_2

description:
AC_leaf_mature_rep2
sequencing instrument(s): HiSeq X Ten

source_name: mature leaf

value: adult


title: VED_40DPA_RNA-seq_4

description:
VED_flesh_40DPA_rep2
sequencing instrument(s): HiSeq X Ten

source_name: 40DPA fruit flesh

value: fruit flesh


title: VED_40DPA_RNA-seq_3

description:
VED_flesh_40DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: AC_leaf_adult_RNA-seq_1

description:
AC_leaf_mature_rep1
sequencing instrument(s): HiSeq X Ten


title: VED_fruit_30DPA_RNA-seq_2

description:
VED_fruit_30DPA_rep2
sequencing instrument(s): HiSeq X Ten

source_name: 30DPA fruit flesh

value: 30 days post anthesis


title: Prep_409

description:
Prep_409
Gene expression data from normal rat mammary tissues at postnatal day 21.

source_name: Rat mammary tissues at pre-pubertal stage, postnatal day 21

value: Pre-pubertal

value: Postnatal day 21

value: Two

value: Promega


title: Peri_412

description:
Peri_412
Gene expression data from normal rat mammary tissues at postnatal day 42.

value: One


title: Prep_408

description:
Prep_408
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: Prep_410

description:
Prep_410
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: N2_Sample

city: GuangZhou

first: Ying

last: Wei

address: JuQuanLu 3

institute: Geneseed Biotech Co.,Ltd

description: total circRNA

data_processing:
TMM (trimmed mean of M-values) was used to normalize the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: txt TMM normalized junction read counts

source_name: corresponding para-cancer tissues

growth_protocol: The cells were maintained in high-glucose Dulbecco's modified Eagle's medium (DMEM) (Gibco, Australia) supplemented with 10% fetal bovineserum (Gibco, Australia).

extract_protocol:
Total circRNA was extracted using Trizol reagent (Invitrogen, CA, USA)
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number>7.0.Approximately 10ug of total RNA representing aspecific adipose type was used to deplete ibosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA or circRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

tag: cell type

value: corresponding para-cancer cell

value: colon

value: wild type


title: Prep_407

description:
Prep_407
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: Prep_406

description:
Prep_406
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: Peri_411

description:
Peri_411
Gene expression data from normal rat mammary tissues at postnatal day 42.

value: Peri-pubertal

value: Postnatal day 42


title: AC_leaf_young_RNA-seq_2

description:
AC_leaf_young_rep2
sequencing instrument(s): HiSeq X Ten

source_name: young leaf

value: AC

value: leaf

value: young


title: T2_Sample

description: total circRNA

source_name: colorectal cancer biopsies

value: colorectal cancer cell


title: T1_Sample

description: total circRNA


title: VED_30DPA_RNA-seq_1

description:
VED_fruit_30DPA_rep1
sequencing instrument(s): HiSeq X Ten

value: Vedrantais

value: fruit flesh and peel


title: N1_Sample

description: total circRNA


title: Fv_mature_H3K27me3

description:
Fv_mature
sequencing instrument(s): HiSeq X Ten

organism: Fragaria vesca

source_name: ripe receptacle

extract_protocol:
conventional TruSeq protocol or more recent Tn5-based ChIP-Seq library construction protocol
histone-DNA complexes were isolated with H3K27me3 antibody (RevMAb and Millipore).

value: receptacle without seed

value: ripe


title: VED_20DPA_RNA-seq_1

description:
VED_fruit_20DPA_rep1
sequencing instrument(s): HiSeq X Ten

value: 20 days post anthesis


title: AC_leaf_young_RNA-seq_1

description:
AC_leaf_young_rep1
sequencing instrument(s): HiSeq X Ten

extract_protocol:
Standard non-stranded illumina RNA-Seq libraries protocol
mRNA was extracted from tissue using standard protocol


title: VED_fruit_20DPA_RNA-seq_2

description:
VED_fruit_20DPA_rep2
sequencing instrument(s): HiSeq X Ten


title: Fv_immature_H3K27me3

description:
Fv_immature
sequencing instrument(s): HiSeq X Ten

source_name: immature receptacle

value: immature


title: VED_fruit_10DPA_RNA-seq_2

description:
VED_fruit_10DPA_rep2
sequencing instrument(s): HiSeq X Ten

source_name: 10DPA fruit flesh

value: 10 days post anthesis


title: top3A-2::TOP3A-N-Term rep2

city: Karlsruhe

first: Annika

last: Dorn

address: Fritz-Haber-Weg 4

department: Botanical Institute II

country: Germany

institute: Karlsruhe Institute of Technology

data_processing:
Reads were aligned to the Arabidopsis reference genome (TAIR10) and data processing was performed using the CLC Genomics Workbench 7.5
Genome_build: TAIR 10
Supplementary_files_format_and_content: Excel file including read count for each gene in the different samples and statistical analysis

source_name: 2 week old plantlet

extract_protocol:
Total RNA from two-week-old plantlets was extracted using the RNeasy Plant Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 2 weeks

value: whole plant


title: top3A-2::TOP3A-N-Term rep3


title: Prep_405

description:
Prep_405
Gene expression data from normal rat mammary tissues at postnatal day 21.

value: Sprague-Dawley

value: Female

value: 5th left and right caudal mammary glands

value: Pre-pubertal

value: Postnatal day 21

value: Two

value: Promega


title: Fv_leaf_H3K27me3

description:
Fv_leaf
sequencing instrument(s): HiSeq X Ten

value: leaf

value: not collected


title: TAGL1_Br_ChIP-seq

description:
TAGL1_Br
sequencing instrument(s): Illumina HiSeq 2000

source_name: 42DPA fruit

value: AC

value: fruit flesh

value: 42 days post anthesis


title: VED_10DPA_RNA-seq_1

description:
VED_fruit_10DPA_rep1
sequencing instrument(s): HiSeq X Ten

value: Vedrantais

value: fruit flesh and peel


title: top3A-2::TOP3A-N-Term rep1


title: top3A-2 rep3


title: Prep_402

description:
Prep_402
Gene expression data from normal rat mammary tissues at postnatal day 21.

value: One


title: Prep_404

description:
Prep_404
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: Prep_403

description:
Prep_403
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: VED_leaf_RNA-seq_2

description:
VED_leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: Prep_401

description:
Prep_401
Gene expression data from normal rat mammary tissues at postnatal day 21.


title: Cl_34DPA_BS-seq

description:
Cl_34DPA
sequencing instrument(s): Illumina HiSeq 2000

source_name: 34DPA fruit flesh

value: 34 days post anthesis


title: top3A-2 rep2

value: 2 weeks

value: whole plant


title: Fv_immature_BS-seq

value: receptacle

value: immature


title: VED_leaf_RNA-seq_1

description:
VED_leaf_rep1
sequencing instrument(s): HiSeq X Ten


title: Fv_ripe_BS-seq

description:
Fv_ripe
sequencing instrument(s): HiSeq X Ten

value: ripe


title: RIN_ChIP-seq

description:
RIN ChIP-seq
sequencing instrument(s): Illumina HiSeq 2000


title: Cl_10DPA_BS-seq

description:
Cl_10DPA
sequencing instrument(s): Illumina HiSeq 2000

value: 10 days post anthesis


title: PS_40DPA_ethylene_RNA-seq_1

description:
PS_fruit_40DPA_Eth1.5h
sequencing instrument(s): HiSeq X Ten

value: Piel de Sapo

value: 40 days post anthesis


title: Fv_leaf_BS-seq

value: leaf


title: WT rep3

value: wild type


title: Cs_40DPA_2_H3K27me3

description:
Cs_40DPA_2
sequencing instrument(s): HiSeq X Ten

organism: Cucumis sativus

value: Chinese Long (line9930)


title: top3A-2 rep1


title: PS_fruit_40DPA_RNA-seq_2

description:
PS_fruit_40DPA_rep2
sequencing instrument(s): HiSeq X Ten


title: Fv_ripe_DNase-seq

value: receptacle without seed


title: Cs_10DPA_H3K27me3

description:
Cs_10DPA
sequencing instrument(s): HiSeq X Ten

value: fruit flesh


title: WT rep2


title: Fv_immature_DNase-seq

description:
Fv_immature
sequencing instrument(s): HiSeq X Ten


title: Fv_leaf_DNase-seq

description:
Fv_leaf
sequencing instrument(s): HiSeq X Ten

value: not collected


title: WT rep1


title: PS_40DPA_RNA-seq_1

description:
PS_fruit_40DPA_rep1
sequencing instrument(s): HiSeq X Ten

value: fruit flesh and peel


title: PS_fruit_20DPA_RNA-seq_2

description:
PS_fruit_20DPA_rep2
sequencing instrument(s): HiSeq X Ten

source_name: 20DPA fruit flesh

value: 20 days post anthesis