title: ΔsigBDE_standard_biol.rep3

source_name: cells from mutant ΔsigBDE, standard growth conditions, biological replicate 3

tag: genotype/variation


title: s_15 high feed conversion ratio

status: Public on Nov 12 2018

type: SRA

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

library_source: transcriptomic

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (Sscrofa11.1) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: raw.genes.pituitary.csv.gz: raw gene counts
Supplementary_files_format_and_content: res.genes.pituitary.csv.gz: DESeq2 results for differential expressed gene analysis

molecule: total RNA

organism: Sus scrofa

source_name: pituitary

extract_protocol:
The total RNA was isolated using by TriReagent (Ambion, Life Technologies). The fat samples were collected immediately after slaughter and stored in tubes with RNAlater (Ambion). The fat samples were homogenized with the use of zirconium oxide beads (diameter 0.5 mm) in BulletBlender homogenizer (Next Advance Inc., USA).The concentration and quality of RNA were estimated on TapeStation 2200 (Agilent Technologies, Warsaw, Poland) using RNA Screen Tape (Agilent Technologies). The RNA samples with RIN (RNA integrity number) above 8.0 were used to further analyses.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

tag: tissue

value: pituitary

tag: group

value: high feed conversion ratio

tag: age

value: 3 months

tag: strain

value: Pulawska breed

tag: gender

value: female


title: 2 H1975 control 2

type: RNA

city: Heidelberg

first: Michael

last: Meister

state: Select One

address: Roentgenstr. 1

department: STF

country: Germany

institute: Thoraxklinik-Heidelberg

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at 45 °C on GeneChip Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific, Carlsbad (USA)) in a Gene Chip Hybridization Oven 640 (Thermo Fisher Scientific, Carlsbad (USA)). Washing and staining of the GeneChips was done by utilizing the GeneChip Fluidics Station 450 (Thermo Fisher Scientific, Carlsbad (USA)).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Thermo Fisher Scientific, Carlsbad (USA)).

data_processing:
The raw data generated by the microarray analysis was normalized with the software Expression Console (Thermo Fisher Scientific, Carlsbad (USA)) (RMA algorithm). For further evaluation the software Transcriptome Analysis Console (Thermo Fisher Scientific, Carlsbad (USA)) was used.
3' Expression Arrays - RMA

label: biotin

organism: Homo sapiens

source_name: H1975 control 2

label_protocol: Biotinylated cRNA was prepared from 5µM with a GeneChip 3' IVT PLUS Reagent Kit  (Thermo Fisher Scientific, Carlsbad (USA)) according to manufaturer's protocol.

growth_protocol: NSCLC cell lines were seeded into a 12-well-plate at 1.6 x 10^5 cells per well.

extract_protocol: Cells were washed, detached and frozen prior to RNA extraction with a RNeasy Mini Kit (Qiagen, Hilden (Germany)) according to manufacturer's instructions.

treatment_protocol: The next day after seeding the cells, they were serum-starved for about 16 h. H1975 cells (lung adenocarcinoma cell line, ATCC, Manassas (USA)) were then incubated with PMA and the corresponding control at 37 °C and 5 % CO2 for 24 h. 2106T (lung squamous cell carcinoma cell line, [Gottschling et al., Lung Cancer 2012]) cells were treated with LPA, PMA, EGF and HB-EGF under the same conditions, respectively. Three independent experiments were performed (named with 1, 2 and 3).

value: lung

tag: cell line

tag: cell type

value: human non-small cell lung cancer cells

tag: histology

value: adenocarcinoma

tag: treatment

value: control


title: Double expressor

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

country: Italy

institute: Scuola Superiore Sant'Anna

description: Gene expression data from 7-day old seedlings expressing AD-HIFCOOD and GBD-pVHL

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: RMA algorithm using RobinA (PMID:22684630)

organism: Arabidopsis thaliana

label_protocol: Affymetrix standard labeling protocol

growth_protocol: seeds were surface sterilized using ethanol 10% and commercial bleach 10%, rinsed several times with sterile water, sowed in 1/2 strength agarized MS medium supplemented wth 1% sucrose and germinated for 7 days before sampling.

extract_protocol: Total RNA was extracted using the Spectrum RNA isolation Kit (Sigma-Aldrich)

treatment_protocol: no treament

tag: developmental stage

value: seedling

tag: ecotype

tag: genotype

value: double transgenic


title: s_14 high feed conversion ratio


title: ΔsigCDE_standard_biol.rep3 [re-analysis]

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing: The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using  protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.

organism: Synechocystis sp. PCC 6803

source_name: cells from mutant ΔsigCDE, standard growth conditions, biological replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).

treatment_protocol: Cells were grown in standard growth conditions (A730=1, 40 mL). Thre were no treatment for the cells.

value: glucose tolerant


title: s_13 high feed conversion ratio


title: s_12 high feed conversion ratio


title: 19 2106T control 1

source_name: 2106T control 1

value: squamous cell carcinoma


title: MA9LC_C1BWT_RNArep2

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

country: USA

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

data_processing:
RNAseq: The sequenced reads were aligned to the mouse genome (UCSC mm9) with STAR aligner using gene annotations from Ensembl 72, and intronic reads were discarded
RNAseq: Sequencing result was normalized to ERCC spike in and differential gene expression performed with EdgeR (Empirical analysis of digital gene expression data in R) version 3.08 (Robinson et al., 2010). Adjusted p values were computed using the Benjamini-Hochburg method. Protein coding genes, long non-coding RNA and pseudogenes with adjusted p values less than 0.01 were used for the downstream analysis with DAVID.
ChIPseq: Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm).
ChIPseq: For histone marks, ChIP-seq in MLL-AF9 cells peak detection was performed with MACS (model-based analysis of ChIP-Seq) version 1.4.2 using default parameters (Zhang et al., 2008). The average coverage (calculated using rpm tracks described above) across the entire region is shown in the boxplots where p values were calculated with the Wilcoxon signed-rank test. Heatmaps depict log2 fold change of coverage profiles in a 4 kb window around the merged peak center in 25 bp binned averages and sorted by total coverage in this window. Heatmaps and metagene plots of the genes with changed H3K27ac read coverage around the TSS (±3kb) after Chaf1b knockout were plotted with ngs.plot 2.47 and ranked by read intensity. The CHAF1B read coverage at these sites was plotted with the same order.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: anno.txt: Locations of ChIP-seq peaks, as called by MACS, with extra column describing the genomic context of the peak.
Supplementary_files_format_and_content: EdgeR.txt: Normalized counts from EdgeR along with statistics on the degree to which a given gene or accessible region varies between sample sets.

organism: Mus musculus

source_name: MLL-AF9 Leukemic Cells

growth_protocol: MLL-AF9 murine leukemic cells were grown in RPMI-1640 supplemented with 10% FBS, 100 ng/mL SCF, 50 ng/mL IL6, 20 ng/mL IL3. MOLM13/U937/JURKAT cells were grown in RPMI-1640 supplemented with 10% FBS

extract_protocol:
RNA was extracted from MLL-AF9 murine leukemic cells lysed in TRI, and collected on Direct-Zol miniprep columns with on-column DNAse digestion.
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 ¬µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: To induce deletion, MLL-AF9 murine leukemic cells were treated with 10-7M B-estradiol daily for two days (48 hours)

value: wild type


title: MA9LC_C1BWT_RNArep1


title: Untreated RNA without TimeLapse chemistry rep2

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description: Negative control experiment for K562 TimeLapse-seq with neither s6G treatment nor chemical treatment.

data_processing:
[Filtering duplicate reads] Reads were filtered for unique sequences using FastUniq
[Removing adaptors] Reads were trimmed using cutadapt (--minimum-length=20)
[Alignment] Reads were aligned to the GRCh38 genome using HISAT2 aligned with default parameters and --mp 4,2 .
[Sorting and filtering] Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
[Filtering] Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
[Mutation counting ] G-to-A and T-to-C mutations were identified at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
[Filtering SNPs from mutations] SNP sites were filtered from our data in two ways: 1, bcftools was used to identify G-to-A or T-to-C SNP sites in control samples, and these sites were excluded from the respective analysis; 2, sites exhibiting high G-to-A or T-to-C mutation rates in untreated controls were excluded from analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: [Track generation] STAR was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph) in bedgraph format, and tracks were normalized using DESeq2 (estimateSizeFactors).

source_name: immortalized K562s

growth_protocol: K562 cells were cultured in RPMI + 10% FBS (Gibco) with penicillin and streptomycin to 80% confluency in duplicate 6-well plate wells.

extract_protocol:
Metabolically labeled and control cells were collected by centrifugation (3 min, 1000 g, 4C) and lysed in TRIzol (Life Technologies) and RNA was extracted according to Duffy E. E. and Simon M. D. 2016. Extracted RNA was treated with Turbo DNase (Invitrogen) for 1h at 37C, extracted with phenol/chloroform and precipitated as before. Total RNA was treated with TimeLapse chemistry according to Schofield et al. 2018.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input V2 Mammalian (Takara Bio USA, cat. 635005). For targeted sequencing 3 amplicons of ACTB were reverse transcribed and libraries were prepared according to Sexton et al. 2017.

treatment_protocol: Cells were treated with 6-thioguanine (100 µM for genome wide TimeLapse-seq, 500 µM for targeted TimeLapse-seq), or 4-thiourudine (100 µM) or water for 1h.

tag: rt-primer set

value: random hexamers

tag: metabolic label

value: No treatment

value: untreated


title: Untreated RNA without TimeLapse chemistry rep1


title: ΔsigBDE_standard_biol.rep1

source_name: cells from mutant ΔsigBDE, standard growth conditions, biological replicate 1


title: ΔsigBDE_standard_biol.rep2

source_name: cells from mutant ΔsigBDE, standard growth conditions, biological replicate 2


title: 1 H1975 control 1

source_name: H1975 control 1


title: MA9LC_C1BOE_RNArep3


title: s_11 high feed conversion ratio

value: pituitary


title: MA9LC_C1BWT_RNArep3


title: MA9LC_C1BOE_RNArep2


title: s_10 high feed conversion ratio

value: high feed conversion ratio


title: s6G RNA without TimeLapse chemistry rep1

description: Negative control experiment for K562 TimeLapse-seq with s6G treatment but no chemical treatment.


title: MA9LC_C1BOE_RNArep1


title: ΔsigBCE_standard_biol.rep1

source_name: cells from mutant ΔsigBCE, standard growth conditions, biological replicate 1


title: s_9 high feed conversion ratio

value: 3 months


title: ΔsigBCE_standard_biol.rep2

source_name: cells from mutant ΔsigBCE, standard growth conditions, biological replicate 2


title: Untreated RNA with TimeLapse chemistry rep2

description: Negative control experiment for K562 TimeLapse-seq with no s6G treatment but chemical treatment.

value: TimeLapse chemistry


title: Untreated RNA with TimeLapse chemistry rep1


title: ΔsigBCE_standard_biol.rep3

source_name: cells from mutant ΔsigBCE, standard growth conditions, biological replicate 3


title: MA9LC_MIGR1_RNArep2


title: s6G RNA without TimeLapse chemistry rep2


title: s_8 low feed conversion ratio

value: low feed conversion ratio

value: Pulawska breed

value: female


title: MA9LC_MIGR1_RNArep1


title: s4U RNA with TimeLapse chemistry rep2

description: K562 s6G TimeLapse-seq with s4U treatment and chemical treatment


title: s_7 low feed conversion ratio


title: ΔsigBCDE_standard_biol.rep2 [re-analysis]

source_name: cells from mutant ΔsigBCDE, standard growth conditions, biological replicate 2


title: ΔsigBCDE_standard_biol.rep3 [re-analysis]

source_name: cells from mutant ΔsigBCDE, standard growth conditions, biological replicate 3


title: s4U RNA with TimeLapse chemistry rep1


title: s6G RNA with TimeLapse chemistry rep2

description: K562 s6G TimeLapse-seq with s6G treatment and chemical treatment


title: PBS9_S6

city: Coleraine

first: Nigel

middle: G

last: Ternan

state: Co. Londonderry

address: Cromore Road

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Ulster

description: biological replicate 3 of 3 grown in BHIS medium

data_processing:
sequencing reads were mapped onto the annotated C. difficile strain 630 reference genome (http://www.ncbi.nlm.nih.gov/nuccore/115249003)) with appropriate alignment software.  The aligned files were then processed for tag counts per location mapped or normalised tag counts (RPKMs) and differential gene expression analysis.
The DeepSeq (University of Nottingham) Filtering Pipeline for Read Mapping was used to filter reads with low sequencing score, in addition to reads aligned to adaptor sequences.  Reads from the sequencer were QC checked using FASTQC, then trimmed and filtered for low quality bases and adaptor sequences, and QC–checked once more.  Reads that passed this filter were mapped onto the reference genome in the context of known gene exon coordinates using the bwa mapping tool (http://bio-bwa.sourceforge.net/).
Read alignments were recorded in a BAM formatted alignment file (named *.bam), and companion BAM index file (named *.bam.bai).  Read alignments, both primary and unique, were then filtered further according to their mapping quality score (MAPQ).  For gene expression, MAPQ20 uniquely aligned reads were used to generate counts per gene using 'htseq-count', which determines the number of uniquely aligned reads per gene (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html.).  These counts were used as the input for the DESeq program (Anders and Huber, 2010a,b). DESeq models the distribution of the counts data in each sample and then compares the distributions to determine differentially expressed genes, with significantly differentially expressed genes having an adjusted p value <0.05. The program implements a single analytical approach and when RNA-seq samples with biological replicates are available, as is the case here, DESeq analyses the variance between them in order to better model the expression values of individual genes within the group of replicates.
Genome_build: GenBank: AM180355.1
Supplementary_files_format_and_content: tab-delimited text files include base mean values and fold change values  for each gene for which p<0.05

organism: Clostridioides difficile 630

source_name: bacterial cells

growth_protocol: Clostridium difficile 630 (ATCC no. BAA-1382D-5) was grown under anaerobic conditions in a Don Whitley MACS MG500 anaerobic cabinet (Don Whitley Scientific Ltd, Yorkshire, UK) using a single gas mix (BOC, UK) of 80% N2, 10% CO2 and 10% H2, at 37 °C.  Standard growth media consisted of 100 ml of 1X brain heart infusion broth supplemented with 5g L-1 yeast extract and 1g L-1  L-cysteine (BHIS).

extract_protocol:
Cells were harvested by centrifugation at 9,000 x g for 5 min at 4°C. Total RNA was extracted from aliquots of ~4.0 E8 cells using the Qiagen RNAprotect® Bacteria Reagent Handbook Protocol 4: "Enzymatic Lysis and Proteinase K Digestion of Bacteria" with modifications.  A mechanical lysis step was incorporated – cells in TE buffer with proteinase K and lysozyme were added to a Lysing Matrix A tube (MP Biomedicals) and treated in a Fastprep FP120 machine (MP Biomedicals) at speed 5.5 for 30s.  The Qiagen protocol was then followed and both on-column and in-solution DNAse digestions, with a final on-column cleanup were used to purify the RNA. RNA samples were confirmed free of contaminating genomic DNA by PCR with gyrA, rpsJ, and adk primers and stored at -70°C until required. For all six RNA samples (3 Faecal water, 3 BHIS control), an RNA integrity number of >9.6 was obtained, with A260/280 values of > 2.0, and 23S:16S rRNA ratios of ≥ 1.4.
A 1µg amount of Total RNA was used for rRNA depletion using Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Illumina, MRZGP126). Illumina stranded whole transcriptome sequencing libraries were prepared using NEBNext Ultra Directional RNA library prep kit for Illumina (NEB, E7420S).  The standard protocol for use with Ribosome Depleted RNA was followed except, after second strand systhesis the samples were precitiated with 1ul (20ng/ µL) glycogen and 1/10th vol. 3M sodium acetate; pellets were washed once with 80% ethanol, followed by 70% ethanol and after air-drying, the pellet was resuspended in 58 µL of water.  The standard protocol for use with Ribosome Depleted RNA was resumed for the remaining steps, except libraries were size selected using Agencourt AMPure XP beads at a 1.5x ratio to retain the smaller sized fraction (~150bp).  NEB Next Multiplex Oligos for Illumina kit (Primer set 1) (NEB, E7335S) was used to generate barcoded multiplex libraries.  Library QC was performed using bioanalyser HS kit (Agilent biotechnologies, 5067-4626).  Libraries were quantified using qPCR (Kapa Biosystems, KK4824). Libraries were pooled at desired concentrations, denatured and loaded for sequencing according to the manufacturer’s instructions.  Sequencing was performed over 3 runs on the Illumina MiSeq sequencing platform to generate 2 x 75bp reads.

treatment_protocol: Faecal water (FW) was prepared in PBS by standard methods (Gill et al., 2010) from 2 healthy volunteers, filter sterilized through a 0.2micron filter and stored at -80°C in 50ml aliquots until required.  For media containing faecal water (i.e. BHIS-FW), 2-fold concentrated BHIS (50mL) was prepared and a 50mL aliquot of FW added to this aseptically post autoclaving.  Control media was prepared from 2–fold concentrated BHI-S and an equal volume of sterile PBS.  Three starter cultures of C. difficile 630 were set up in 20 mL of BHIS-FW broth in glass universal bottles and each inoculated with a single colony of freshly grown C. difficile 630 from a BHIS agar plate.  Starter cultures were incubated overnight and used to inoculate fresh media, in triplicate, at 5% (v/v).  Growth was recorded hourly as attenuance at 650 nm (D650) (Jain et al., 2011) against uninoculated BHIS and BHIS-FW references

value: grown in BHIS supplemented with PBS

tag: time

value: harvested T=6h


title: s_6 low feed conversion ratio


title: s_5 low feed conversion ratio


title: FW9_S5

description: biological replicate 3 of 3 grown in faecal water medium

value: grown in BHIS supplemented with Faecal water


title: ΔsigBCDE_standard_biol.rep1 [re-analysis]

source_name: cells from mutant ΔsigBCDE, standard growth conditions, biological replicate 1


title: ΔsigBCD_standard_biol.rep3

source_name: cells from mutant ΔsigBCD, standard growth conditions, biological replicate 3


title: s6G RNA with TimeLapse chemistry rep1


title: s_4 low feed conversion ratio

source_name: pituitary


title: s_3 low feed conversion ratio


title: ΔsigBCD_standard_biol.rep1

source_name: cells from mutant ΔsigBCD, standard growth conditions, biological replicate 1


title: PBS7_S2

description: biological replicate 1 of 3 grown in BHIS medium


title: FW8_S3

description: biological replicate 2 of 3 grown in faecal water medium


title: s_2 low feed conversion ratio


title: FW7_S1

description: biological replicate 1 of 3 grown in faecal water medium


title: CS_standard_biol.rep3 [re-analysis control]

source_name: cells from control strain, standard growth conditions, biological replicate 3

value: control strain


title: CS_standard_biol.rep4 [re-analysis control]

source_name: cells from control strain, standard growth conditions, biological replicate 4


title: Myod1 reprogrammed MEFs, biological replicate 1, technical replicate 1

status: Public on Nov 11 2018

city: Dallas

first: Gary

last: Hon

address: 5323 Harry Hines Blvd.

department: Department of Obstetrics and Gynecology

institute: UT Southwestern

description: This record represents two infected MEFs samples mixed together before sequencing library prep. One MEF sample was pooled infected with two retroviral vectors (one vector is Myod1, the other is empty vector), the other MEF sample was infected with an empty vector. These two infected MEF samples were mixed together.

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 2.1.0).
Reads were processed to generate expression (UMI count) matrices using Cell Ranger pipeline (version 2.1.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.
For 10X Genomics, the first 1-16 bp are cell barcode and 17-26 bp are UMI in read 1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrix representing gene expression values (comma-separated) generated as described above. Each column represents a single cell, each row represents a single gene.

molecule: polyA RNA

source_name: Reprogrammed MEFs with Myod1, day 7

growth_protocol: MEFs were maintained in high glucose DMEM supplemented with 10% FBS and 1X penicillin/streptomycin and incubated at 37˚C in 5% CO2.

extract_protocol:
Single cell suspension was washed with 1X PBS (0.04% BSA) before 10x Genomics procedure. The concentration of single cell suspension was adjusted to about 500 to 1000 cells/µL and was loaded on the 10x Genomics’ Chromium™ system (10x Genomics, Pleasanton, CA) with the aim of 6000 to 10000 cells per channel (Chromium™ Single Cell 3' Library & Gel Bead Kit v2, catalog number 120237).
Single cell RNA sequencing libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).

treatment_protocol: MEFs were pooled infected with two retroviral vectors (Myod1 and empty vector) to induce expression of Myod1. Another MEF sample was infected with empty retroviral vector. Both infected MEFs were incubated 7 days and mixed together before library prep. The cells were washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.

value: ICR

tag: internal sample id

value: reprogrammed MEF

tag: infection

value: mixed sample (non-demultiplexed)


title: 10X_Uninfected MEFs, biological replicate 1, technical replicate 1

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 2.1.0).
Reads were processed to generate expression (UMI count) matrices using Cell Ranger pipeline (version 2.1.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.
For 10X Genomics, the first 1-16 bp are cell barcode and 17-26 bp are UMI in read 1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.

source_name: Uninfected MEFs

treatment_protocol: The cells were incubated 7 days and subsequently washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.

value: MEF

tag: background strain


title: 10X_3_Reprogrammed MEFs, biological replicate 1, technical replicate 1

source_name: Reprogrammed MEFs with 3 factors, day 7

treatment_protocol:
MEFs were infected with retroviral vectors to induce expression of specific transcription factors. The cells were incubated 7 days and subsequently washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.
Factors included for reprogramming:
Atf3,Gata6,Hand2


title: 10X_2_Reprogrammed MEFs, biological replicate 1, technical replicate 1

source_name: Reprogrammed MEFs with 10 factors, day 14

treatment_protocol:
MEFs were infected with retroviral vectors to induce expression of specific transcription factors. The cells were incubated 14 days and subsequently washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.
The factors used for reprogramming include:
Atf3,Bnc1,Gata6,Hand2,Tbx18
Tcf21,Myrf,Sox6,Tbx20,Wt1


title: PBS8_S4

description: biological replicate 2 of 3 grown in BHIS medium


title: CS_standard_biol.rep2 [re-analysis control]

source_name: cells from control strain, standard growth conditions, biological replicate 2

tag: genotype/variation


title: 10X_Reprogrammed MEFs, biological replicate 1, technical replicate 1

source_name: Reprogrammed MEFs with 10 factors, day 7

treatment_protocol:
MEFs were infected with retroviral vectors to induce expression of specific transcription factors. The cells were incubated 7 days and subsequently washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.
The 10 pooled factors include:
Atf3,Bnc1,Gata6,Hand2,Tbx18
Tcf21,Myrf,Sox6,Tbx20,Wt1


title: 10X_P0 whole heart, biological replicate 1, technical replicate 2

source_name: P0 whole heart

growth_protocol: Primary cardiac cells were harvested from neonatal mouse hearts. Mice were housed in a standard facility 12hr light/dark cycle, 70-75˚F, and ~50% humidity.

treatment_protocol: Primary cardiac cells were prepared by dissecting and mincing neonatal mouse hearts. The tissue was then incubated in trypsin for a total of 30 minutes in a shaking water bath at 37˚C. Supernatant was strained and transferred to a flask containing cold growth media every 5 minutes--6 fractions total. Cells were spun at 500x G for 5 minutes at 4˚C and resuspended in cold growth media.

tag: tissue

value: whole heart


title: CS_standard_biol.rep1 [re-analysis control]

source_name: cells from control strain, standard growth conditions, biological replicate 1


title: Uninfected MEFs, biological replicate 1, technical replicate 7

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using bcl2fastq (version 2.17.1.14).
After demultiplexing, reads (read 1) with more than one low quality bases (Phred quality score less 10) in barcode or UMI regions were discarded. PolyA tails (read 2) longer than 6 bases were trimmed before mapping.
For Drop-seq, read 1 contains barcode (basepairs 1-12) and UMI (basepairs 13-20).
Reads were aligned to mouse mm10 genome assembly using STAR (version 2.5.3a) with default parameters. Secondary and repetitive alignments were removed. Only unique alignments were kept for downstream analyses.
Cell barcodes within one edit distance were collapsed together. UMI-based PCR duplicate removal was performed using the directional method of UMI-tools with default parameters (version 0.5.3). An inflection point of cumulative number of reads of cells in each library was calculated to determine the number of cells in each experiment. Gene expression matrices were generated using featureCounts (version 1.5.3). The gene annotation used is based on Ensembl release 84 (GENCODE Gene Set M9).
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.

extract_protocol:
Single cell suspension was washed with 1X PBS (0.01% BSA) before Drop-Seq procedure. Drop-seq was performed as described previously (Macosko et al., 2015) with small modifications. Briefly, droplets were generated using microfluidic devices, which encapsulated single cells and barcoded beads (ChemGenes Corporation, Wilmington, MA, catalog number Macosko201110). Beads were collected after the breakage of individual droplets using perfluorooctanol (Sigma-Aldrich, St. Louis, MO, catalog number 370533). RNA hybridized on the barcoded beads was reverse transcribed using Maxima H minus reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, catalog number EP0751) and cDNA was amplified with 13 cycles (KAPA HotStart ReadyMix, Kapa Biosystems, Wilmington, MA, catalog number KK2602).
In-house Tn5 transposase was used to insert sequencing adapters and fragmentate cDNA. Illumina Nextera adapters i5 and i7 were used to amplify the fragmented cDNA with 12 cycles (KAPA HiFi PCR Kits, catalog number KK2102). Agarose gel size selection was performed to recover fragments with length of 400 to 600 bp.


title: Uninfected MEFs, biological replicate 1, technical replicate 6


title: 10X_P0 whole heart, biological replicate 1, technical replicate 1


title: Uninfected MEFs, biological replicate 1, technical replicate 2


title: Uninfected MEFs, biological replicate 1, technical replicate 3


title: Uninfected MEFs, biological replicate 1, technical replicate 1


title: s_1 low feed conversion ratio

tag: group

tag: age

tag: strain


title: old-RSV-d5-#55

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

description:
lung RNA
common reference
FTR files: Cy3 #1, Cy5 #2

hyb_protocol: Samples were hybridized to NimbleGen 12x135 k Mus musculus microarrays, containing probes for 44,170 genes with 3 spots per target probe. Each microarray corresponded to labeled RNA from one individual mouse.

scan_protocol: Slides were scanned in an ozone-free room with a Agilent G2565CA microarray scanner. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen) resulting in a table containing individual probe signal intensities for both dyes.

data_processing: Data for gene-coding probes were normalized in R by using a four step approach consisting of: (1) natural log-transformation, (2) quantile normalization of all scans, (3) correcting the sample spot signal for its corresponding reference spot signal and (4) averaging data from replicate probe spots. This resulted in normalized data for 44170 probes, which was used for further statistical analysis in R and Microsoft Excel.

source_name: Lung

label_protocol: Per sample, 500 ng of RNA was amplified and labeled using the Agilent QuickAmp kit. Samples were labeled with Cy3 and the common reference (made by pooling equimolar amounts of antisense RNA from individual samples) was labeled with Cy5.

growth_protocol: We used adult (6-8 weeks) and old (62-72 weeks) C57BL/6JRccHsd mice. Mice were kept in a 12-hour light/dark cycle under SPF and temperature-controlled conditions, and were fed ad libitum.

extract_protocol: RNA was extracted from homogenized lung tissue using the Qiagen RNeasy kit. RNA concentrations were measured using a NanoDrop spectrophotometer and RNA quality was measured using a Agilent Bioanalyzer.

treatment_protocol: Mice were inoculated intranasally with 50 µl containing an infectious dose of 10^6 TCID50 RSV type A2 or mock as control, under anesthesia by isoflurane. At day 2 and 5 after inoculation, mice were anesthetized with Ketamine/Xylazine, bled and sacrificed to collect lungs. Lungs were perfused with PBS to eliminate blood cells prior to collection of the tissue, immersed in RNAlater RNA stabilization agent (Ambion) and subsequently stored at -80ᵒC until further processing.

value: old

value: RSV

tag: day

tag: animal number

tag: sample type

value: common reference


title: ΔsigBCD_standard_biol.rep2

source_name: cells from mutant ΔsigBCD, standard growth conditions, biological replicate 2

value: glucose tolerant


title: old-mock-d0-#44

value: mock


title: Reprogrammed MEFs, biological replicate 1, technical replicate 36

source_name: Reprogrammed MEFs with 48 factors, day 7

treatment_protocol:
Each sample is reprogramed with the same pool of 48 factors:
Cdkn1a,Hey2,Mir1a-1,Pou6f1
E330017L17Rik,Isl1,Mir208a,Rarg
Foxn4,Jazf1,Mir499,Rxra
Gata4,Lbh,Msc,Shox2
Gata5,Mef2a,Msx1,Smad4
Gata6,Mef2b,Msx2,Smarcd3
Hand1,Mef2c,Myocd,Tbx18
Hand2,Mef2d,Myod1,Tbx2
Hdac1,Meis1,Nkx2-5,Tbx3
Hdac2,Mesp1,Notch1,Tbx5
Hdac4,Mir133a-1,Nr2f2,Tcf3
Hey1,Mir145a,Pou2f1,Xiap
MEFs were infected with retroviral vectors to induce expression of specific transcription factors. The cells were incubated 7 days and subsequently washed with DPBS and trypsinized into a single cell suspension. Cells were spun at 500X G for 5 minutes at 4˚C and resuspended in cold growth media.

tag: cell type


title: MA9LC_C1BKO_H3K27ac

library_source: genomic

molecule: genomic DNA

source_name: MLL-AF9 Leukemic Cells

tag: cell line

value: knock out

tag: chip antibody

value: Cell Signaling:8173


title: Uninfected MEFs, biological replicate 1, technical replicate 4


title: Uninfected MEFs, biological replicate 1, technical replicate 5


title: Reprogrammed MEFs, biological replicate 1, technical replicate 33


title: Reprogrammed MEFs, biological replicate 1, technical replicate 32


title: Reprogrammed MEFs, biological replicate 1, technical replicate 34


title: Reprogrammed MEFs, biological replicate 1, technical replicate 29


title: Reprogrammed MEFs, biological replicate 1, technical replicate 30


title: Reprogrammed MEFs, biological replicate 1, technical replicate 31


title: Reprogrammed MEFs, biological replicate 1, technical replicate 26


title: Reprogrammed MEFs, biological replicate 1, technical replicate 27


title: Reprogrammed MEFs, biological replicate 1, technical replicate 28


title: Reprogrammed MEFs, biological replicate 1, technical replicate 24


title: Reprogrammed MEFs, biological replicate 1, technical replicate 25


title: Reprogrammed MEFs, biological replicate 1, technical replicate 23


title: Reprogrammed MEFs, biological replicate 1, technical replicate 37


title: Reprogrammed MEFs, biological replicate 1, technical replicate 35


title: Reprogrammed MEFs, biological replicate 1, technical replicate 22


title: Reprogrammed MEFs, biological replicate 1, technical replicate 20


title: Reprogrammed MEFs, biological replicate 1, technical replicate 21


title: Reprogrammed MEFs, biological replicate 1, technical replicate 17


title: Reprogrammed MEFs, biological replicate 1, technical replicate 13


title: Reprogrammed MEFs, biological replicate 1, technical replicate 16


title: Reprogrammed MEFs, biological replicate 1, technical replicate 18


title: Reprogrammed MEFs, biological replicate 1, technical replicate 12


title: Reprogrammed MEFs, biological replicate 1, technical replicate 14


title: Reprogrammed MEFs, biological replicate 1, technical replicate 19


title: Reprogrammed MEFs, biological replicate 1, technical replicate 10


title: Reprogrammed MEFs, biological replicate 1, technical replicate 9


title: Reprogrammed MEFs, biological replicate 1, technical replicate 11


title: Reprogrammed MEFs, biological replicate 1, technical replicate 8


title: Reprogrammed MEFs, biological replicate 1, technical replicate 5


title: Reprogrammed MEFs, biological replicate 1, technical replicate 4


title: Reprogrammed MEFs, biological replicate 1, technical replicate 7


title: Reprogrammed MEFs, biological replicate 1, technical replicate 6


title: Reprogrammed MEFs, biological replicate 1, technical replicate 3


title: Reprogrammed MEFs, biological replicate 1, technical replicate 2


title: Reprogrammed MEFs, biological replicate 1, technical replicate 15


title: P0 remainder (except RA), biological replicate 1, technical replicate 5

source_name: P0 remainder (except RA)

value: remainder (except RA)

tag: developemental stage


title: Reprogrammed MEFs, biological replicate 1, technical replicate 1


title: P0 remainder (except RA), biological replicate 1, technical replicate 3


title: P0 remainder (except RA), biological replicate 1, technical replicate 2


title: P0 remainder (except RA), biological replicate 1, technical replicate 6


title: P0 remainder (except RA), biological replicate 1, technical replicate 1


title: P0 right atrium (RA), biological replicate 3, technical replicate 16

source_name: P0 right atrium (RA)

value: right atrium (RA)


title: P0 remainder (except LA RA), biological replicate 1, technical replicate 1

source_name: P0 remainder (except LA RA)

value: remainder (except LA RA)


title: P0 right atrium (RA), biological replicate 3, technical replicate 15


title: P0 right atrium (RA), biological replicate 3, technical replicate 13


title: P0 right atrium (RA), biological replicate 3, technical replicate 9


title: P0 right atrium (RA), biological replicate 3, technical replicate 11


title: P0 right atrium (RA), biological replicate 3, technical replicate 10


title: P0 right atrium (RA), biological replicate 3, technical replicate 12


title: P0 right atrium (RA), biological replicate 3, technical replicate 14


title: P0 right atrium (RA), biological replicate 1, technical replicate 6


title: P0 right atrium (RA), biological replicate 3, technical replicate 8


title: P0 right atrium (RA), biological replicate 1, technical replicate 5


title: P0 right atrium (RA), biological replicate 1, technical replicate 3


title: P0 right atrium (RA), biological replicate 1, technical replicate 2


title: P0 right atrium (RA), biological replicate 1, technical replicate 4


title: P0 right atrium (RA), biological replicate 3, technical replicate 7


title: P0 right atrium (RA), biological replicate 3, technical replicate 6


title: P0 right atrium (RA), biological replicate 2, technical replicate 8


title: P0 right atrium (RA), biological replicate 3, technical replicate 5


title: P0 right atrium (RA), biological replicate 3, technical replicate 2


title: P0 remainder (except RA), biological replicate 1, technical replicate 4


title: P0 right atrium (RA), biological replicate 3, technical replicate 4


title: P0 right atrium (RA), biological replicate 3, technical replicate 3


title: P0 right atrium (RA), biological replicate 3, technical replicate 1


title: P0 right atrium (RA), biological replicate 2, technical replicate 7


title: P0 right atrium (RA), biological replicate 2, technical replicate 5


title: P0 right atrium (RA), biological replicate 2, technical replicate 4


title: P0 right atrium (RA), biological replicate 2, technical replicate 6


title: ABL 72h Vehicle Replicate 1

city: Houston

first: Sean

last: McGuire

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: [DB-SMcG-MPC2.geneQuantification.txt] includes raw FPKM values for each Sample

source_name: ABL Prostate Cancer Cells

growth_protocol: Cells were routinely cultured in RPMI1640 media supplemented with 10% Charcoal-stripped (hormone-depleted) serum.

extract_protocol:
Total RNA was extracted using a TRIzol based kit (Zymo) and Poly-A RNA was purified from total RNA using Dynabeads Oligo dT25 (Invitrogen).
The RNA-Seq library was generated using KAPA strand RNA-Seq library prep kit (KR-0934) and sequenced on a Hiseq2500 sequencer.

treatment_protocol: 72 hour treatments, in biological triplicate, in 10cm dishes as indicated above.

value: Metastatic Human Prostate Cancer cells

tag: hormone dependence

value: castrate resistant

tag: culture condition

value: 10% charcoal stripped-serum, RPMI

tag: treatment

value: control


title: ABL 72h 100µM UK5099 Replicate 3


title: ABL 72h Vehicle Replicate 2


title: P0 right atrium (RA), biological replicate 2, technical replicate 3

tag: internal sample id


title: ABL 72h Vehicle Replicate 3


title: P0 right atrium (RA), biological replicate 2, technical replicate 2

tag: background strain


title: P0 right atrium (RA), biological replicate 2, technical replicate 1


title: ABL 72h 100µM UK5099 Replicate 2


title: P0 right atrium (RA), biological replicate 1, technical replicate 1


title: P0 left atrium (LA), biological replicate 1, technical replicate 5

source_name: P0 left atrium (LA)

value: left atrium (LA)


title: ABL 72h 100µM UK5099 Replicate 1


title: BK03_Epi1

city: New York

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: RNAseq

data_processing:
50-bp sequences were aligned to mm10 using STAR and Gencode release M9 and counts generated from STAR output --quantMode GeneCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited, gene counts

source_name: Skin

growth_protocol: Samples 1-8: Adult P60 (Refer to Yang et al eLife 2015 4:e10870 for detailed description)

extract_protocol:
Total RNA extracted via Trizol/Zymo RNA extraction kit
Illumina TruSeq RNA Sample Preparation
Single Read Clustering and 51 Cycles Sequencing (per lane)

treatment_protocol: Samples 9-13: Adult P60 wound biopsy (Refer to Keyes et al Cell 2016 167:1323-1338.e14 for detailed description

tag: Sex

value: female

tag: cell types

value: adult skin epidermal stem cells

tag: sort markers

value: Lineage Neg, IntA6Hi, CD34-Sca1+


title: BK05_WdEpi

description: RNAseq

value: adult skin epidermal stem cells after wounding

value: Lineage Neg, IntA6Hi


title: BK02_Bu2

description: RNAseq

value: adult skin hair follicle stem cells

value: Lineage Neg, IntA6Hi, CD34+Sca1-


title: BK04_Epi2

description: RNAseq


title: BK01_Bu1

description: RNAseq


title: DS08_TbrEpi

description: RNAseq


title: P0 left atrium (LA), biological replicate 1, technical replicate 2

tag: tissue


title: P0 whole heart, biological replicate 1, technical replicate 7

value: whole heart


title: P0 whole heart, biological replicate 1, technical replicate 6


title: DS07_TbrBu

description: RNAseq

tag: strain


title: DS06_TmTbrLo

description: RNAseq

value: grafted tumor

value: GFP+, IntA6Lo (TbrKO tumor cells GFP+)


title: P0 left atrium (LA), biological replicate 1, technical replicate 4


title: P0 whole heart, biological replicate 1, technical replicate 4


title: P0 whole heart, biological replicate 1, technical replicate 5


title: DS03_TmRasTbrHi

description: RNAseq

value: GFP+, IntA6Hi (HRas TbrKO tumor cells GFP+)


title: DS05_TmTbrHi

description: RNAseq

value: GFP+, IntA6Hi (TbrKO tumor cells GFP+)


title: P0 left atrium (LA), biological replicate 1, technical replicate 3


title: P0 whole heart, biological replicate 1, technical replicate 3


title: DS01_TmRasHi

description: RNAseq

value: GFP+, IntA6Hi (HRas tumor cells GFP+)


title: DS02_TmRasLo

description: RNAseq

value: GFP+, IntA6Lo (HRas tumor cells GFP+)


title: GBG

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

country: China

institute: Yangzhou University

data_processing:
Two small RNA (sRNA) libraries, one each from normal and mutant leaves, were constructed and sequenced by the Novogene Biotechnology Corporation (Beijing, China) using an Illumina HiseqTM 2500 sequencing platform. Raw data of fastq format were firstly processed through custom perl and python scripts.
Sequenced reads (raw data) were trimmed by removing low quality and contaminated reads. The clean reads were mapped to the reference sequences by Bowtie. Small RNA tags without mismatch were analyzed their expression and distribution on the reference. Then, perfectly matched sRNA sequence were used to query against RepeatMasker, the Rfam database, or species-specific databases, and then the sRNAs originating from repeat sequences, protein-coding genes, rRNAs, tRNAs, snRNAs and snoRNAs were excluded. The remaining unique sRNAs were aligned against miRBase 20.0 to seek for known miRNAs (without mismatch). Finally, the remaining unannotated sequences were used to predict novel miRNAs by miREvo and mirdeep2 softwares, through exploring the secondary structure, the Dicer cleavage site and the minimum free energy.
RNA fragments with a poly (A) tail were isolated from the total RNA of mixed samples. A series of steps, including ligation of 5′RNA adaptors, digestion, ligation of double-stranded DNA adaptor, purification, and amplification were conducted and sequencing was done on an Illumina HiSeq 2000. The raw sequencing reads were processed by Illumina’s Pipeline v1.5 to obtain clean reads, which were then used to identify potentially cleaved targets.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/100209, Guan et al. 2016).
Supplementary_files_format_and_content: Text file includes miRNA.readcount (miRNA_name, readcount in GbG, readcount in GbY) and miRNA.targets (gene ID, miRNA, Hit1_id, annotation）

organism: Ginkgo biloba

source_name: normal green leaves

growth_protocol: Healthy leaves, including normal green leaves and yellow-green striped leaves, were collected from a healthy adult G. biloba tree growing under natural conditions at Yangzhou University, Jiangsu, China (32°39'N, 119°43'E)

extract_protocol:
The normal green leaves and the mutant yellow-green striped leaves were collected separately from May to July in 2015 and 2016. Total RNAs of cambium were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf


title: P0 whole heart, biological replicate 1, technical replicate 1


title: P0 whole heart, biological replicate 1, technical replicate 2


title: P0 left atrium (LA), biological replicate 1, technical replicate 1


title: RBR1_ChIP_rep1

status: Public on Nov 10 2018

city: Hamburg

first: Arp

last: Schnittger

address: Ohnhorststr. 18

institute: Biozentrum Klein Flottbek, University of Hamburg

data_processing:
Quality control by FASTQC (version 0.11.5)
Reads were mapped onto the TAIR10 Arabidopsis thaliana genome assembly using Bowtie (version 0.3) run in the sensitive mode, allowing one mismatch and randomly choosing one map position in case of multiple matching
MACS (version 1.4.2 20120305) was used for peak detection including INPUT DNA as control and using the following parameters: Effective genome size = 120000000 bp, tag size = 50 bp, bandwidth = 150 bp, P-value cutoff for peak detection = 1e-05, MFOLD range = 10,30.
Genome_build: TAIR10
Supplementary_files_format_and_content: MACS peak files

source_name: MM2d cell culture

growth_protocol: MMd2 cell culture were grown as described in Menges, M. and Murray, J. A.H. (2002), Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity. The Plant Journal, 30: 203–212.

extract_protocol:
ChIP was performed on cell culture material ground in liquid nitrogen. The protocol includes a double fixation step (1h Disuccinimidyl glutarate (DSG) fixation followed by 5'  formaldehyde fixation)  and a reduced SDS concentration (0.1%) in the nuclear lysis buffer leading to better IP-results.
Libraries were constructed with the MicroPlex Library Preparation kit (Diagenode). Quality of libraries was validated using 2100 Bioanalyzer (Agilent). Multiplexed libraries were sequenced using a HiSeq 2000 system (Illumina) with single-end 50-bp reads.

value: MM2d cell culture

tag: days after subculture

value: 3 d

tag: ecotype

value: Landsberg erecta

tag: antibody

tag: antibody vendor

value: provided by Willhelm Gruissem (ETH, Zurich, Switzerland) and affinity-purified by Hirofumi Harashima in our lab.


title: RBR1_ChIP_rep2


title: DS04_TmRasTbrLo

description: RNAseq

value: female

value: GFP+, IntA6Lo (HRas TbrKO tumor cells GFP+)


title: U937_Input-seq

city: changsha

first: wenzhe

last: yan

address: renmin middle road number 139

institute: the second xiangya hospital

data_processing:
Basecalling performed using CASAVA
ChIP-seq reads were aligned to the hg18 genome
Data were filtered with low quality reads and polluted reads
Genome_build: hg18

growth_protocol: Cells were resuspended in RPMI 1640 (Hyclone, Logan, UT) supplemented with 10% heat-inacti- vated FBS, L-glutamine (2mmol/L), penicillin (100 U/mL), and streptomycin (100 mg/mg) at 106 cells/mL

extract_protocol:
Lysates were digested by micrococcal nuclease and DNA complexes were isolated with antibody
A ChIP-seq library was prepared from approximately 20 ng of ChIP-DNA and an input sample from a mixture of 3 ChIP operations. The concentration and integrity of the DNA sample was checked by gel electrophoresis. The selected libraries for a fragment size of 100 bp to 500 bp were amplified using PCR. ChIP-seq libraries were run on a HiSeq next-generation sequencer (Illumina, San Diego, CA, USA). After abandonment of polluted reads, low-quality reads, and reads with N > 5%, sequenced-50 base short single reads were mapped to the human genome, and the peaks were identified by Model-based Analysis of ChIP-Seq S14 software.

tag: cell line

value: HL-60 cell

tag: cell type

value: human leukemia cells

value: none (input)


title: Col-NAA

city: Qingdao

first: feng

last: zhang

state: Shandong

address: 72 Binhai Road

institute: shandong university

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).

source_name: seedlings

growth_protocol: The seedlings grew on 1/2 MS in dark  for 8 days, the root of the seedlings were extracted for RNA sequencing.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: Roots

tag: genotype

value: wild type


title: U937_fusion-seq

tag: chip antibody

value: anti-flag purchased from CST (#14793)


title: HD20C_CD44

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Single-end read alignment to human genome build GRCh38 with Subread (version 1.5.1), parameters: "-t 0 -I 5 -m 3 -M 3 -T 1"
Paired-end read alignment to human genome build GRCh38 with Subread (version 1.5.1), parameters: "-t 0 -I 5 -m 3 -M 3 -T 1 -S fr"
Single-end read feature counting with featureCounts (version 1.5.1) with grouping exons into genes, parameters: "-g gene -F GTF -Q 0 -s 0 -t exon"
Paired-end read feature counting with featureCounts (version 1.5.1) with grouping exons into genes, parameters: "-g gene -F GTF -Q 0 -s 0 -t exon -B -p"
Genome_build: GRCh38

source_name: Astrocyte Progenitor Cell

extract_protocol: Human emryonic stem cell lines (hESC) were obtained from Genea Biocell (http://geneabiocells.com/services/shelf-products/human-embryonic-stem-cells/). The hESCs were then differentiated into Glial Progenitor Cells (GPCs) and Astrocyte Progenitor Cells (APCs) by previously described methods. The differentiated GPC and APC populations were further purified by FACS targeting CD140a and CD44 cell surface markers, respectively. The FACS-purified cell populations were used in mRNA isolation and sequencing.

value: Brain

tag: facs marker

tag: subject

value: Huntington's Patient

tag: subject gender

value: Female

tag: source

value: hESC

value: APC


title: CTR02D_CD44

value: Control

value: Male


title: CTR02B_CD44


title: CTR02A_CD44


title: GBY

source_name: mutant yellow leaves

value: leaf


title: arf7-MOCK

value: arf7 T-DNA mutant


title: HD18C_CD44


title: arf7-NAA


title: Col-MOCK


title: 19209_1

first: Reem

last: Elorbany

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

description:
Supplementary_Data_Table_S1.xlsx
raw_counts.txt

data_processing:
All RNA-seq samles were aligned to the human genome (GRCh37) using Subread.
We counted reads and estimated gene level expression with reads per kilobase million (RPKM) using the "edgeR" R package.
We filtered to genes that were protein-coding, autosomal, and had at least 10 samples such that RPKM >= .1 and raw read counts >= 6. This yielded 16,319 genes for downstream analysis.
RPKM distribution in each sample was quantile normalized and each gene was standardized across cell samples (with mean 0 and standard deviation 1).
Genome_build: GRCh37
Supplementary_files_format_and_content: Supplementary_Data_Table_S1.xlsx contains metadata information on the 297 samples. Most variables describe the collection and processing steps. Sheet A contains the information for each sample and Sheet B contains descriptions of each category.
Supplementary_files_format_and_content: raw_counts.txt contains the gene expression counts for the 16,319 genes after filtering lowly expression genes for all 297 samples. Each row is a gene labeled with its Ensembl gene ID. Each column is a sample. Each sample is labeled by cell line and differentiation day ("CellLine_Day").

growth_protocol: Feeder-free iPSC cultures were maintained on Matrigel Growth Factor Reduced Matrix with Essential 8 Medium and Penicillin/Streptomycin.

extract_protocol:
We extracted RNA using the Qiagen miRNeasy Kit.
We prepared sequencing libraries using the Illumina TruSeq Kit

treatment_protocol: To begin cardiomyocyte differentiation, E8 media was replaced with "heart media"--RPMI with B27 supplement minus insulin, 2mM GlutaMAX, and 100mg/ml Penicllin/Streptomycin--along with 1:100 Matrigel hESC-qualifed Matrix and 12uM of CHIR99021 trihydrochloride on Day 0. On Day 1, this media was removed and fresh "heart media" was added. On Day 3, new "heart media" was added along with 2uM of Wnt-C59. On Days 5, 7, 10, 12, and 14, old media was removed and replaced with fresh "heart media."

tag: individual

tag: time

value: differentiation day 1


title: 19209_8

value: differentiation day 8


title: 19209_9

value: differentiation day 9


title: 19209_3

value: differentiation day 3


title: 19209_6

value: differentiation day 6


title: 19209_5

value: differentiation day 5


title: 19209_4

value: differentiation day 4


title: 19209_15

value: differentiation day 15


title: 19209_11

value: differentiation day 11


title: CD14+ monocytes isolated from active ASD patient, clinical sample1

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with Factor Analysis for Robust Microarray Summarization (FARMS), using the statistical language R (R-3.1.0) and Bioconductor 2.14.

source_name: CD14+ monocytes isolated from the blood of active ASD patient

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

extract_protocol: Total RNA was isolated using Isogen reagent (Nippon gene, Tokyo, Japan), then purified with an RNeasy micro kit (Qiagen, Venlo, Netherland).

treatment_protocol: The CD14+ monocytes were isolated from from HC (n=3), inactive-ASD (n=3) and active-ASD patients (n=3) by magnetic-activated cell sorting (MACS, Miltenyi Biotec, Bergisch Gladbach, Germany).

tag: disease state

value: active ASD

tag: tissue

value: blood

value: CD14+ monocytes

tag: gender

tag: age

value: 42 years old


title: 19209_14

value: differentiation day 14


title: CD14+ monocytes isolated from active ASD patient, clinical sample3

value: Male

value: 61 years old


title: CD14+ monocytes isolated from healthy volunteer, clinical sample3

source_name: CD14+ monocytes isolated from the blood of healthy volunteer

value: healthy

value: 60 years old


title: 19209_12

value: differentiation day 12


title: CD14+ monocytes isolated from inactive ASD patient, clinical sample2

source_name: CD14+ monocytes isolated from the blood of inactive ASD patient

value: inactive ASD

value: Female

value: 43 years old


title: CD14+ monocytes isolated from inactive ASD patient, clinical sample3


title: CD14+ monocytes isolated from healthy volunteer, clinical sample2

value: 48 years old


title: CD14+ monocytes isolated from inactive ASD patient, clinical sample1


title: 19209_7

value: differentiation day 7


title: 19209_0

source_name: iPSCs

value: differentiation day 0

value: iPSCs


title: 19193_9

value: differentiation day 9


title: 19193_5

value: differentiation day 5


title: 19193_7


title: 19193_6

value: differentiation day 6


title: 19193_3

value: differentiation day 3


title: 19193_2

value: differentiation day 2


title: 19209_10

value: differentiation day 10


title: CD14+ monocytes isolated from active ASD patient, clinical sample2

value: active ASD

value: blood

value: CD14+ monocytes


title: 19193_8

value: differentiation day 8


title: 19193_1

value: differentiation day 1


title: 19193_15

value: differentiation day 15


title: 19193_11

value: differentiation day 11


title: 19193_10


title: CD14+ monocytes isolated from healthy volunteer, clinical sample1

value: healthy

value: Female

value: 45 years old


title: 19193_0

value: differentiation day 0

value: iPSCs


title: 19190_8


title: 19190_9

value: differentiation day 9


title: 19190_5

value: differentiation day 5


title: 19190_2


title: 19190_4

value: differentiation day 4


title: 19190_3

value: differentiation day 3


title: 19190_7

value: differentiation day 7


title: 19190_6

value: differentiation day 6


title: 19190_1


title: 19190_12

value: differentiation day 12


title: 19190_10

value: differentiation day 10


title: 19190_0


title: 19190_13

value: differentiation day 13


title: 19190_11


title: 19190_15


title: 19159_9


title: 19190_14

value: differentiation day 14


title: 19193_12


title: 19193_14


title: 19193_13


title: 19159_6


title: 19159_7


title: 19159_2

value: differentiation day 2


title: 19159_4


title: 19159_1

value: differentiation day 1


title: 19159_8

value: differentiation day 8


title: 19159_13


title: 19159_3


title: 19159_10


title: 19159_0


title: 19159_5


title: 19127_8


title: 19159_15

value: differentiation day 15


title: 19159_14


title: 19127_7


title: 19127_2


title: 19159_12


title: 19159_11

value: differentiation day 11


title: 19127_13


title: 19127_6


title: 19127_5


title: 19127_15


title: 19127_1


title: 19127_4


title: 19127_14


title: 19127_0

value: differentiation day 0


title: 19127_9


title: 19127_12


title: 19127_10


title: 19127_11


title: 19108_6


title: 19108_8


title: 19108_9


title: 19108_7


title: 19108_5


title: 19108_3


title: 19108_2


title: 19127_3


title: 19108_11


title: 19108_15


title: 19108_12


title: 19108_1


title: 19108_14


title: 19108_13


title: 19108_10


title: 19108_0

value: iPSCs


title: 19093_9

value: differentiation day 9


title: 19093_8


title: 19093_6


title: 19093_7


title: 19093_5

value: differentiation day 5


title: 19093_4

value: differentiation day 4


title: 19093_2


title: 19093_15


title: 19093_3

value: differentiation day 3


title: 19093_1


title: 19093_14


title: 19093_12


title: 19093_13


title: 19093_11


title: 19093_10


title: 19093_0


title: 18912_9


title: 18912_7

value: differentiation day 7


title: 18912_5


title: 18912_4


title: 18912_3


title: 18912_2


title: 18912_1


title: 18912_15


title: 18912_14


title: 18912_13


title: 18912_12


title: 18912_10


title: 18912_0


title: 18907_8


title: 18907_9


title: 18907_7


title: 18912_8


title: 18907_5


title: 18907_6

value: differentiation day 6


title: 18907_4


title: 18907_3


title: 18907_15


title: 18907_12

value: differentiation day 12


title: 18907_13


title: 18907_14


title: 18907_1


title: 18912_6


title: 18870_9


title: 18907_10

value: differentiation day 10


title: 18907_11


title: 18907_0


title: 18870_5


title: 18870_6


title: 18870_8


title: 18870_7


title: 18912_11


title: 18870_1


title: 18870_15


title: 18870_2


title: 18870_3


title: 18870_14


title: 18870_13

value: differentiation day 13


title: 18870_12


title: 18870_10


title: 18870_11


title: 18858_9


title: 18870_0


title: 18858_5


title: 18858_8


title: 18858_6


title: 18858_7


title: 18858_4


title: 18858_3


title: 18907_2


title: 18858_2


title: 18858_1


title: 18858_15


title: 18858_13


title: 18858_11


title: A4 [RNA-seq]

first: Harry

last: MacKay

address: 1100 Bates Ave

description:
Nuclear RNA
Genetic background is based in Agrptm1(cre)Lowl mice with or without floxed Dnmt3a alleles from Jackson Labs. Mice are backcrossed onto a C57BL/6 background.
processed data file: hm_deseq.csv

data_processing:
Fastq reads were quality trimmed using TrimGalore (v0.4.4) with a minimum quality score of 20 and a minimum read length of 50. Read quality was analyzed using fastqc (v0.11.5).
WGBS: After trimming, the reads were aligned to the mouse genome (mm10) using Bismark (v0.18.1) set to paired-end mode and using all other default settings. Read groups corresponding to each individual sample were added to these BAM alignments using Picard (v2.10.10) ‘AddOrReplaceReadGroups’ BAM files were query-name sorted using Picard ‘SortSam’, and then deduplicated using Picard ‘MarkDuplicates’.
RNA-Seq: Quality-trimmed reads were aligned to the mouse genome (mm10) using Hisat2 (v2.1.0). Mapped reads were annotated and counted using featureCounts (v1.5.3) along with the gencode comprehensive gene annotation (gencode vM15 gff3 file). Differential expression testing was performed using DESeq2 (v1.16.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.bam.sorted.bismark.cov: Tab-delimited text files.
Supplementary_files_format_and_content: hm_dmrs_annotated.csv: Comma-separated text file includes annotated DMRs from DSS.
Supplementary_files_format_and_content: hm_deseq.csv: Comma-separated text file includes normalized counts from DESeq2.

source_name: Microdissected ARH

extract_protocol:
Arcuate nuclei (ARH) were microdissected from coronal sections. Nuclei were isolated by ultracentrifugation, stained with Anti-NeuN (Millipore ABN78, 1:2000) and purified by FACS. DNA extracted by QIAGEN AllPrep Micro kit, RNA by RNA-STAT60.
WGBS: Tagmentation-based whole-genome bisulfite library preparation was performed on genomic DNA extracted from ARH NeuN+ nuclei as previously described (Wang et al., 2013). Briefly, adaptors were pre-annealed and transposomes were assembled according to the protocol described in (Wang et al., 2013). Next, 10-30 ng of mouse genomic DNA was tagmented by adding the assembled transposome and incubating at 55C for 8 min. Following purification using SPRI beads, oligonucleotide replacement and gap repair were performed using Ampligase and T4 DNA Polymerase. The product was purified using SRPI beads and followed by bisulfite treatment using the EZ DNA Methylation Gold kit (Zymo Research). Subsequently, libraries were generated by PCR amplification using KAPA 2G robust hotstart ready mix. After purification using SPRI beads, libraries were diluted and loaded onto Illumina Hiseq2500 Sequencer for 100 bp paired-end sequencing.
RNA-Seq: Libraries for RNA sequencing were prepared using the SMART-Seq v4 Ultra Low Input kit (Takara Clontech) according to the manufacturer’s instructions. Briefly, purified RNA was incubated with lysis buffer for 5 minutes. First strand cDNA synthesis was performed using the included 3-SMART-seq CDS primer II and V4 oligonucleotide. cDNA was amplified using PCR Primer II A, and subsequently purified using Ampure XP beads (Beckman). Illumina libraries were prepared using Nextera XT DNA library preparation kit (Illumina), and sequenced on the Illumina Hiseq 2500 platform generating 100 bp paired-end reads.

tag: genotype/variation

value: AgRP-Cre; Dnmt3a+/+

value: Neuron

tag: mouse identifier


title: A2 [RNA-seq]


title: B1 [RNA-seq]

value: AgRP-Cre; Dnmt3aF/F


title: A3 [RNA-seq]


title: B3 [RNA-seq]


title: B5 [WGBS]

description:
WGBS
Genetic background is based in Agrptm1(cre)Lowl mice with or without floxed Dnmt3a alleles from Jackson Labs. Mice are backcrossed onto a C57BL/6 background.
processed data file: hm_dmrs_annotated.csv


title: B2 [RNA-seq]


title: A5 [RNA-seq]


title: B3 [WGBS]


title: B2 [WGBS]


title: A1 [WGBS]


title: 18855_9


title: 18858_14

value: differentiation day 14


title: A5 [WGBS]


title: B4 [WGBS]


title: 18855_6


title: 18855_7


title: 18855_5


title: A4 [WGBS]


title: 18855_8

value: differentiation day 8


title: 18858_0


title: 18855_4


title: A2 [WGBS]


title: 18858_12


title: 18855_3


title: 18858_10


title: 18855_1

value: differentiation day 1


title: ivdcon-2

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
Raw RNA-seq data were processed by a computational pipeline after sequencing. Data were aligned to mouse genome (UCSC mm9) using TopHat v2.0.4 with default options. The aligned reads were assembled using Cufflinks v2.2.1. Differentially expressed genes were chosen on the basis of the criteria of fold change > 2 and P < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. The first column is gene name, the second is RPKM value.

source_name: in vitro model of decidualization

growth_protocol: Natural pregnancy decidualization model (NPD) was established using CD-1 mice by co-caging adult females with fertile males. The day of the vaginal plug was designated as day 1 of pregnancy. On day 8 of pregnancy, uterine fragments from implantation sites (decidualized) and inter-implantation sites (control) were collected separately. Embryonic tissues at implantation sites were removed under a stereomicroscope. In addition to NPD, an artificial decidualization model (AD) was also established. In this model, female mice were mated with vasectomized males to induce pseudo-pregnancy. Unilaterally intrauterine injection of 10 μl sesame oil was performed to mimic the stimulation of the embryo on day 4 of pseudo-pregnancy. Uterine samples were collected on day 8 of pseudo-pregnancy. The unstimulated uterine horn served as control. For in vitro model of decidualization (IVD), mouse uterus was split longitudinally on day 4 of pseudo-pregnancy. Luminal epithelial cells were removed by digestion in HBSS containing 1% trypsin (AMRESCO Inc., Solon, OH) and 6 mg/ml dispase (Roche Diagnostics GmbH, Mannheim, Germany). The remaining tissues were incubated with 0.15 mg/ml collagenase I (Invitrogen, Carlsbad, CA). The supernatants were filtrated through 70 mm wire gauze, and centrifuged to collect the stromal cells. The cell pellets were washed twice with HBSS, and resuspended in complete DMEM/F-12 medium (Sigma-Aldrich) with 10% charcoal-treated fetal bovine serum (cFBS, Invitrogen). Cells were seeded onto 24-well culture plates at a concentration of 2 × 105 cells/well. After an initial 30-min culture, cells were further cultured in fresh medium with 2% cFBS. To induce decidualization, cells were treated with 10 nM estradiol-17β and 1 μM progesterone. Culture medium was changed every other day. Cells were harvested on day 4 of IVD.

extract_protocol: Total RNA was extracted with the TRIzol reagent (Invitrogen). The purity and integrity of RNA was respectively evaluated by using the ND-1000 Nanodrop and the Agilent 2200 TapeStation. The RNA quality control parameters were: A260/A280 ratio > 1.8, A260/A230 ratio > 2.0 and RIN (RNA integrity number) value > 7.0. The TruSeq RNA sample preparation kit (Illumina) was used to generate RNA-seq libraries. High-throughput sequencing was conducted on the Illumina HiSeq 2500 system.

value: uterine stromal cells

tag: group

value: ivdcon

tag: strain


title: ivdcon-3


title: 18855_15

value: differentiation day 15

tag: cell type


title: ivd-2

value: ivd


title: ivdcon-1


title: 18855_14


title: A3 [WGBS]


title: ivd-1


title: 18855_11

value: differentiation day 11


title: 18855_10


title: 18520_9

value: differentiation day 9


title: 18855_0

value: differentiation day 0

value: iPSCs


title: adcon-3

source_name: Uterine tissues on day 8 of artificial decidualization

value: uterus

value: adcon


title: 18520_8


title: adcon-2


title: adcon-1


title: ad-2

value: ad


title: 18520_6

value: differentiation day 6


title: npdcon-2

source_name: Uterine tissues on day 8 of natural pregancy

value: npdcon


title: npdcon-3


title: 18855_12

value: differentiation day 12


title: ad-1


title: 18520_7

value: differentiation day 7


title: npdcon-1


title: ivd-3


title: npd-2

value: npd


title: 18520_4

value: differentiation day 4


title: 18520_1

value: differentiation day 1


title: npd-1


title: 18520_15


title: npd-3


title: ad-3


title: 18855_13

value: differentiation day 13


title: 18520_3

value: differentiation day 3


title: 18520_14

value: differentiation day 14


title: 18520_5

value: differentiation day 5


title: FF3_CRE_AF

city: Rehovot

first: Amir

last: Bahat

address: Herzel 234 st

department: Biological regulation

country: Israel

institute: Weizmann institute of science

data_processing:
Fastq files were generated by the usage bcl2fastq-v2.16.0.10 (basecalling)
Sequenced reads were mapped to the Mus Musculus genome version GRCm38 using TopHat (v2.0.10).
Counting reads on genes annotated in ensembl release 82, was done with HTSeq-count (version 0.6.1p1)
Normalization of read counts and differential analysis were computed using Deseq2 (version 1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: Counts.xls - Excel file includes the raw counts, genereted by HTSeq-count and normalized counts (DESeq2 Normalization).
Supplementary_files_format_and_content: DiffExpr -  Excel file includes log2FC and padj (generated by DESeq2) for each pairwise comparisons.

source_name: Epiblast tissue_CRE_AF

extract_protocol:
Total RNA was extracted from the indicated cell cultures using PerfectPure RNA cultured cell kit (cat # 2302340, 5 Prime). To avoid DNA contaminations all samples were treated with DNase (5 Prime). RNA integrity was evaluated on Bioanalyzer (Agilent 2100 Bioanalyzer), requiring a minimal RNA integrity number (RIN) of 8.5. Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit v2 (Cat # RS-122-2001). Sequencing was carried out on Illumina HiSeq2500 according to the manufacturer’s instructions, using 10 pM template per sample for cluster generation, and sequencing kit V2 (Illumina).
TruSeq RNA sample preparation Kit v2 protocol (Illumina)

tag: strain background

tag: developmental stage

value: MTCH2 KO

value: Epiblast tissue

value: post-implantation epiblast-like cells (EpiLCs)


title: FF2_CRE_AF


title: FF3_AF

source_name: Epiblast tissue_AF

value: wild type


title: 18520_12


title: 18520_10

value: differentiation day 10


title: FF2_AF


title: 18520_0

value: differentiation day 0

value: iPSCs


title: FF1_AF


title: FF1_CRE_AF


title: 18517_9

value: differentiation day 9


title: 18517_8

value: differentiation day 8


title: FF2_CRE_2iL

source_name: Epiblast tissue_CRE_2iL

value: mouse embryonic stem cells (ESCs)


title: 18517_7

value: differentiation day 7


title: FF3_2iL

source_name: Epiblast tissue_2iL


title: FF1_CRE_2iL


title: FF3_CRE_2iL


title: 18517_4

value: differentiation day 4


title: FF1_2iL


title: 18517_5


title: FF2_2iL


title: 18517_3


title: 18517_2

value: differentiation day 2


title: 18517_1

value: differentiation day 1


title: 18517_6

value: differentiation day 6


title: 18520_13

value: differentiation day 13


title: H3K27me3_ChIPRx_GSK343_rep2

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

description: processed data file: GSK343_H3K27me3.ext200_RRPM.bw

data_processing:
The sequences were separately aligned to either human genome(hg19) or the D. melanogaster melanogaster genome(dm3) using Bowtie 2 with the options --sensitive --score-min L,-1.5,-0.3. PCR duplicate are removed for further analysis.
PCR duplicate are removed using samtools rmdup for further analysis.
For quantitative comparisons of H3K27me3 ChIPed reads between the samples, the exogenous genome derived normalization factor (α-x) for each experiment was derived according to the protocol of Orlando et al. As follows: 1 over the number of reads mapping to drosophila (dm3) per million. Then, the uniquely aligned readings for homo sapiens (hg19) were standardized using the normalization factor, α-x, for quantitative comparisons between samples.
For quantitative comparisons of MeCP2 ChIPed reads between the samples, the normalization factor (α) for each experiment was derived as follow: 1 over the number of reads mapping to homo sapiens (hg19) per million. Then, the uniquely aligned readings for homo sapiens (hg19) were standardized using the normalization factor, α, for quantitative comparisons between samples.
Genome_build: hg19
Supplementary_files_format_and_content: The bigwig files were generated from exogenous reference normalized alignment read using the deepTools package

source_name: Neuroblastoma

growth_protocol: SH-SY5Y (Korean Cell Line Bank, 22266) were maintained in DMEM/F12 (Gibco, 11320033) supplemented with 10% fetal bovine serum (Welgene, S001-01) and Penicillin/Streptomycin (Lonza, 17-602E) at 5% CO2 in 37°C. Drosophila S2 cells (ATCC, CRL-1963) were cultured in Schneider’s Drosophila Medium (Gibco, 21720024) supplemented with 10% fetal bovine serum (Welgene, S001-01) in 25°C.

extract_protocol:
The SH-SY5Y cells were washed with 10ml of PBS and cross-linked with 1% formaldehyde for 5minutes.   The crosslinking reactions were quenched with 10x Glycine stop solution. The cross-linked SH-SY5Y cells were lysed in lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% IGEPAL CA-630, pH 8.0) using a dounce homogenizer (Kimble-Kontes. 885300-0002) to aid in nuclei release. The released nuclei was pelleted by centrifugation (10min, 5000rpm at 4°C). As a reference exogenous genome, Drosophila S2 cells were cross linked with 1% formaldehyde for 5 minutes and were quenched with 10x Glycine stop solution. The Drosophila S2 cells were then washed 3 times with ice cold PBS. For each ChIP-Rx experiment, SH-SY5Y cells and drosophila S2 cells ratio of 3:1, 12 million crosslinked SH-SY5Y nuclei and 4 million crosslinked S2 cells were combined and sonicated for 15 minutes with 30 second intervals to shear genomic DNA using Bioruptor XL (Diagenode). Each sheared genomic DNA preparation was split into two equal portions and incubated with either H3K27me3 (Diagenode, pAb-069-050), or MeCP2 (Diagenode, pAb-052-050). A magnetic bar was used to pull down antibody corresponding protein-genomic DNA complex. Genomic DNA in the complex was reverse cross-linked by DNase-free Proteinase K and purified.
H3K27me3 ChIPed or input DNA were used to prepare the ChIP-Seq library as described (NEXTflex ChIP-Seq kit, Bio Scientific, NOVA 5143-01 and NEXTflex ChIP-Seq Barcodes-6, NOVA 514120) followed by high throughput sequencing.

treatment_protocol: SH-SY5Y cells (density of 0.5~0.6 x 10^6 cells/ml) were treated with either DMSO or 5 uM GSK343 (an inhibitor of H3K27me3-specific HMTase) for 72hours.

tag: cell line

value: neuroblastoma cell line

tag: spike-in reference

value: Drosophila melanogaster

value: 3 to1

tag: treatment

value: 5 uM GSK343 (an inhibitor of H3K27me3-specific HMTase) for 72hrs

tag: chip antibody

value: H3K27me3(Diagenode, pAb-069-050)


title: H3K27me3_ChIPRx_GSK343_rep1


title: 18520_11

tag: individual

value: differentiation day 11


title: H3K27me3_ChIPRx_DMSO_rep2

description: processed data file: DMSO_H3K27me3.ext200_RRPM.bw

value: DMSO for 72hrs


title: H3K27me3_ChIPRx_DMSO_rep1


title: 18517_13

tag: time


title: Input_ChIPRx_DMSO_rep2

description: processed data file: DMSO_Input.ext200_RPM.bw


title: Input_ChIPRx_GSK343_rep1

description: processed data file: GSK343_Input.ext200_RPM.bw


title: 18517_12

value: differentiation day 12


title: 18517_10

value: differentiation day 10


title: 18517_15

value: differentiation day 15


title: 18517_14

value: differentiation day 14


title: 18517_0

value: differentiation day 0

value: iPSCs


title: Input_ChIPRx_GSK343_rep2


title: 18517_11


title: Input_ChIPRx_DMSO_rep1


title: 18511_9

value: differentiation day 9


title: 18511_8

value: differentiation day 8


title: 18511_7

value: differentiation day 7


title: 18511_5

value: differentiation day 5


title: 18511_6

value: differentiation day 6


title: 18511_4

value: differentiation day 4


title: 18511_14


title: 18511_2

value: differentiation day 2


title: 18511_3

value: differentiation day 3


title: 18511_15


title: 18511_13

value: differentiation day 13


title: 18511_10


title: 18508_9


title: 18511_1

value: differentiation day 1


title: 18511_11

value: differentiation day 11


title: 18511_12

value: differentiation day 12


title: WT ES cells

description: No additional information

data_processing: CEL files were quantified with robust multi-array average (RMA), using the statistical language R (R-3.2.1) and Bioconductor 3.1.

source_name: embryonic stem cells from WT mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: ES cells were maintained in Dulbecco’s modified Eagle’s medium, containing 10% knockout SR (Invitrogen), 1% fetal calf serum, and leukemia-inhibiting factor (103 U/ml).

extract_protocol: Total RNA was isolated and purified using RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: To delete the conditional allele of G9a, ES cells were cultured in the presence of 800 nM 4-hydroxy tamoxyfen (4OHT) for 48hrs. After the removal of 4OHT, cells were futerther cultured for 48hrs, and then applied into RNA purification.

value: murine embryonic stem cells

value: TT2 line (derived F1 embryo from C57BL/6 female and CBA male)


title: 18508_8


title: 18508_7


title: 18508_1


title: 18508_3


title: 18508_4


title: 18508_15

value: differentiation day 15


title: 18508_13


title: 18508_6


title: 18508_11


title: 18508_10

value: differentiation day 10


title: 18508_0

value: differentiation day 0

value: iPSCs


title: 18505_9

value: differentiation day 9


title: G9a-KO ES cells

description: No additional information

source_name: G9-deficient ES cell line

value: TT2 line lacking exons 26 and 27 of G9a allele by conditional targeting


title: 18505_6


title: 18505_3


title: 18505_5

value: differentiation day 5


title: 18505_8

value: differentiation day 8


title: 18511_0


title: 18505_7

value: differentiation day 7


title: 18505_4

value: differentiation day 4


title: 18505_2

value: differentiation day 2


title: 18505_1


title: 18508_5


title: 18505_15


title: 18508_2


title: 18505_12


title: 18505_13

value: differentiation day 13


title: 18505_14

value: differentiation day 14


title: 18505_0


title: 18499_7


title: 18505_10


title: 18499_6

value: differentiation day 6


title: 18499_9


title: 18499_8


title: 18508_12

value: differentiation day 12


title: 18508_14


title: 18499_3

value: differentiation day 3


title: 18499_1

value: differentiation day 1


title: 18499_2


title: 18499_4


title: 18499_13


title: 18499_15

value: differentiation day 15


title: 18499_11

value: differentiation day 11


title: 18499_10

value: differentiation day 10


title: 18499_0

value: differentiation day 0

value: iPSCs


title: 18489_7


title: 18505_11


title: 18489_9

value: differentiation day 9


title: 18489_8


title: 18499_5

value: differentiation day 5


title: 18489_6


title: 18489_3


title: ADAR2_KO repl 2

city: Vienna

first: Cornelia

last: Vesely

address: Schwarzspanierstrasse 17

department: Anatomy

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences using cutadapt, and mapped to mm9 whole genome using bowtie with default parameters.
Differential expression of genes was calculated using DESeq (Anders, S. and W. Huber, Differential expression analysis for sequence count data. Genome Biology, 2010)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including DESeq output with log2fold changes.

source_name: heart

extract_protocol:
RNA was extracted from mouse hearts (Adarb1-/-, Gria R/R and  Adarb1+/+, Gria R/R siblings) using TriFast (Peqlab, Erlangen, Germany)
Generation of libraries for small RNA next generation sequencing was done as described previously (Genome Research, Vesely et al. 2012)

tag: mose age

value: postnatal day 6

tag: genotype

value: Adarb1-/-, Gria2R/R


title: wildtype repl 3

value: wild type


title: ADAR2_KO repl 1


title: ADAR2_KO repl 3


title: 18489_2

city: Chicago

value: differentiation day 2


title: 18499_14


title: wildtype repl 1


title: 18489_15


title: 18499_12


title: 18489_13

value: differentiation day 13


title: Histone_H1_ChIP_OE_rep1

data_processing:
The Histone H1, H3K27me3, and H3K9ac ChIP-seq reads were aligned to the mm9 reference genome using Bowtie 2 with the options --sensitive --score-min L,-1.5,-0.3.
PCR duplicate are removed using samtools rmdup for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bigwig files were generated using the deepTools package

extract_protocol:
Cross-linking was done by incubating MOE cells with 1% formaldehyde for 5 minutes. After washing off the formaldehyde, MOE cells were lysed briefly in SDS containing buffer followed by sonication for 15 minutes with 30 second intervals to shear genomic DNA using Bioruptor UCD200 (Diagenode). The sheared DNA was evaluated by electrophoresis for their size ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was split into two equal portions and incubated with either MeCP2 (Diagenode, pAb-052-050) or Histone H1 (Santa Cruz, sc-34464) or H3K27me3 (Diagenode, pAb-069-050), H3K9ac (Diagenode, pAb-177-050) or Rabbit IgG (Millipore, 12-370) for the negative control. A magnetic bar was used to pull down antibody corresponding protein-genomic DNA complex. Genomic DNA in the complex was reverse cross-linked by DNase-free Proteinase K and purified.
Histone H1, H3K27me3, and H3K9ac ChIPed or input DNA were used to prepare the ChIP-Seq library as described (NEXTflex ChIP-Seq kit, Bio Scientific, NOVA 5143-01 and NEXTflex ChIP-Seq Barcodes-6, NOVA 514120) followed by high throughput sequencing with Illumina Hi-seq.2000

value: 8 weeks

tag: tissue

value: Olfactory epithelium

value: Olfactory sensory neuron

value: Histone H1 (Santa Cruz, sc-34464)


title: Histone_H1_ChIP_OE_rep2

tag: age


title: 18489_14

value: differentiation day 14


title: 18489_5


title: 18489_12

value: differentiation day 12


title: 18489_4

value: differentiation day 4


title: KO_iWAT, rep3

city: Tsukuba

first: Yang

last: LIU

state: Ibaraki.

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

institute: Riken

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG

data_processing: The raw (CEL) data were normalized using the RMA method in the R/ Bioconductor package affy, and the comparisons of gene expression were implemented using the linear models for microarray data (Limma) package

source_name: Inguinal white adipose tissue from male mice

label_protocol: Biotinylated cRNA were prepared by using the WT terminal labeling kit (Ambion) according the manufacturer’s manual.

growth_protocol: The ATF KO and wild-type (WT) littermates derived from Atf7 heterozygotes on a C57BL/6 background and maintained in the specific-pathogen-free(SPF), temperature-control mouse facility.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) based on the manufacturer’s protocol.

treatment_protocol: Fresh inguinal white adipose tissues were dissected from 5-week-old male mice

value: ATF7 KO

value: 5-week old


title: KO_iWAT, rep2


title: WT_iWAT, rep1

value: WT


title: WT_iWAT, rep2


title: 18489_11

value: differentiation day 11


title: wildtype repl 2


title: 18489_10

value: differentiation day 10


title: 18489_1

value: differentiation day 1


title: 18489_0

value: differentiation day 0

value: iPSCs


title: Mecp2KO_rep1_neuropathology

description: KO re1

hyb_protocol: 100ng of total RNA was hybridized to neuropathology panel (XT-CSO-MNROP1-12) using manufacturer's protocol

scan_protocol: Hybridized panels were scanned using nCounter Analyzer

data_processing: The gene expression levels of the two biological replicates showed a strong correlation (r = 0.997 of WT, r= 0.997 of Mecp2 KO) and combined for downstream analysis. Using nSolver ver4.0, gene expression values in nCounter Mouse Neuropathology Panel Kit were normalized with positive ERCC spike-in and reference gene, Abl1.

label: Nanostring

label_protocol: manufacturer's protocol

extract_protocol: Olfactory epithelial tissue from two wild-type and two MeCP2 null mice were dissected. Total RNAs were isolated from the olfactory epithelial tissue using TRIZOL reagent (Invitrogen).

tag: genotype/variation


title: WT_rep2_neuropathology

description: WT re2

value: wild type


title: Mecp2KO_rep2_neuropathology

description: KO re2


title: WT_iWAT, rep3


title: WT_rep1_neuropathology

description: WT re1


title: HeLa_RPBS_cDNA

city: Beijing

first: Liu

last: Fenglin

address: Courtyard 1, Beichen West Road

institute: Chinese Academy of Sciences

description: cDNA

data_processing:
Library strategy: PBS-R
Illumina Casava1.7 software used for basecalling.
The reads were mapped to the hg19 human reference genome using the HISAT aligner.
Bowtie2 and RSEM were used to analyze gene expression, and MACS was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: AllSamples_FPKM txt file include FPKM values for each Sample, and RPBS_peaks txt file include peaks information of protein binding sites on RNAs.

source_name: cervical cancer cells

growth_protocol: HeLa cells (from ATCC) were cultured in DMEM (HyClone, SH30243.01) supplemented with 10% FBS (HyClone, SH30084.03) and 100 U ml-1 penicillin-streptomycin (HyClone, SV30010) and maintained in a incubator at 37˚C and 5% CO2.

extract_protocol:
Cells were UV-crosslinked and lysed, and RNA-protein complexes were isolated with magnetic beads.
cDNA libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa


title: HeLa_RNAseq_totalRNA

description: total RNA


title: KFTX

city: Yonago City

first: Takafumi

last: Nakamura

address: 86 Nishi-cho

department: Department of Biomedical Science

institute: Tottori University

description: SAMPLE 1

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method.Trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: KFTX paclitaxel (PTX)-resistant ovarian cancer cells

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA from each cell line was extracted using the NucleoSpinRNA kit according to the manufacturer’s protocol (TAKARA BIO INC).

value: KF

value: ovarian adenocarcinoma cell line

tag: paclitaxel (ptx) phenotype

value: PTX-resistant