title: NPC.CL31.Aux

status: Public on Dec 08 2019

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

institute: Ecole Normale Superieure

data_processing:
All data were mapped to the mouse genome mm10, using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142)
Data were processed with HiC-Pro 3 (v2.11.0) in allele specific mode. Only pairs with both   reads having MAPQ>30 were kept. Matrices were made using cooler cload (v 0.8.5) at 1kb resolution, using HiGlass for visualisation and snapshots.
Genome_build: mm10
Supplementary_files_format_and_content: HiC matrix (cool file)

growth_protocol: Spen-degron mESCs were differentiated in NPCs and subcloned as in (Giorgetti et al., 2016). NPCs were grown in N2B27 medium supplemented with EGF and FGF (10ng/ml each), on 0.1% gelatin-coated 6-well plates.

extract_protocol:
Hi-C was performed as previously described (Belaghzal et al., 2017), except that ligated DNA size selection was omitted, and dA-tailing was performed prior to biotin pull-down. Briefly, each Hi-C experiment was performed on 10 million cells (NPCs) per sample. Cells were digested with DpnII at 37°C overnight. DNA ends were filled with biotin-14-dATP at 23°C for 4 hours. DNA was then ligated with T4 DNA ligase at 16°C overnight. Binding proteins were removed by treating ligated DNA with proteinase K at 65°C overnight. Purified proximally ligated molecules were fragmented to obtain an average fragment size of 200 bp. After DNA end repair, dA-tailing and biotin enrichment, DNA molecules were ligated to Illumina TruSeq sequencing adapters at room temperature for 2h.
Final library PCR productions were carried out following the Illumina TruSeq Nano DNA Sample Prep Kit manual.

treatment_protocol: Cells were treated with auxin (500uM) for 0h, 48h.

value: BL/6J x CAST-EiJ


title: NPC.CL30.UT

type: SRA

department: Biology

country: France

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: treatment

value: UT

tag: strain


title: NPC.CL30.Aux


title: Control, rep 4

status: Public on Dec 09 2019

type: RNA

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: gene expression data from myelinating cultures 18 DIV untreated

hyb_protocol: Hybridized, washed and stained using GeneTitan hybridization, wash and stain kit for WT Array Plates and GeneTitan Operating Software, and scanned by means of an Affymetrix GeneTitan scanner

scan_protocol: GeneTitan scanner

data_processing: Partek Genomics Suite (version 6.6), probeset level data were normalised using GCRMA normalisation and summarised to transcript cluster level using One-Step Tukey's Biweight method.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: myelinating cultures, 19 DIV

label_protocol: Labelled with biotin using Ambion WT Expression Kit following the Affymetrix GeneChip WT Terminal Labeling kit

growth_protocol: Neurospheres were generated from striata of P1 Sprague-Dawley rats by resuspending enzymatically dissociated cells in 20ml neurosphere media [DMEM/F12 (1:1, DMEM containing 4,500 mg/L glucose), supplemented with 0.105 % NaHCO3, 2 mM glutamine, 5,000 IU/ml penicillin, 5µg/ml streptomycin, 5.0mM HEPES, 0.0001% bovine serum albumin, (all from Invitrogen), 25 µg/ml insulin, 100 µg/ml apotransferrin, 60M putrescine, 20nM progesterone, and 30nM sodium selenite (all from Sigma)] and plating them into a 75 cm3 tissue culture flask. The culture was supplemented with 20ng/ml mouse submaxillary gland epidermal growth factor (R&D Systems) and maintained at 37ºC in a humidified atmosphere of 7% CO2/93% air. Every 2-3 days, 5 ml NSM and 4 µl EGF were added to the flask. Neurosphere-derived astrocytes (NsAs) were obtained by triturating neurospheres and plating them onto Poly-L lysine (PLL, 13g/ml, Sigma) -coated coverslips (13 mm diameter, VWR International, Leicestershire, UK) in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine (Sigma) until they formed confluent monolayer.      Myelinating spinal cord cultures were derived from E15.5 Sprague-Dawley (SD) embryos. Spinal cords were dissected out, cleared of meninges, minced with a scalpel blade and enzymatically dissociated with 2.5% trypsin (Invitrogen) and 1.33% collagenase (ICN Pharmaceuticals, UK). Enzymatic activity was stopped by adding 1 ml of a solution containing 0.52 mg/ml soybean trypsin inhibitor, 3.0 mg/ml bovine serum albumin, and 0.04 mg/ml DNase (Sigma). The tissue was then triturated, centrifuged and resuspended in plating medium (PM, 50% DMEM, 25% horse serum, 25% HBSS) and 150,000 cells per 100 µl plated on cover slips coated with a confluent monolayer of NsAs. Coverslips were placed in 35-mm Petri dishes (3 per dish) and left in the incubator to attach for 2 hours, after which 300 µl of PM and 500 µl of differentiation medium (DM) [DMEM (4,500 mg/ml glucose), 10 ng/ml biotin, 0.5% hormone mixture (1 mg/ml apotransferrin, 20 mM Putrescine, 4 μM progesterone, and 6 μM selenium; formulation based on Bottenstein and Sato, 197940), 50 nM hydrocortisone, and 0.1 μg/ml insulin (all reagents from Sigma) ] were added. Cultures were fed every 2 days by removing 500 µl of media and replacing it with fresh DM media, after 12 days insulin was removed from the DM used to feed the cultures.  The effect of FGF2 variants on these in vitro myelinating cultures was investigated by adding them to the culture media from day 18 (i.e. when myelination has just begun)for 24 hoursin vitro.

extract_protocol: RNA was extracted using the Qiagen Rneasy Micro kit according to manufacturer's instructions

treatment_protocol: The in vitro myelinating cultures were either untreated or treated with hFGF2, wtFGF2 or F2V2. Samples were collected at 24 hours from the untreated and treated myelinating cultures.

value: Sprague-Dawley

value: Control


title: Mock IP ChIP-exo replicate 2

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description: Replicate 2

data_processing:
Library strategy: ChIP-exo
Basecalls were performed using Bcl2fastq version 2.20.
ChIP-exo reads were aligned to sacCer3 genome assembly using bwa mem version 0.7.12 for paired reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab, tag extraction from 5' end of uniquely mapped sequencing reads, tab-delimited

organism: Saccharomyces cerevisiae

source_name: Yeast Mock IP ChIP-exo

growth_protocol: Cells were cultured using YPD media at 25°C to an O.D600 of 0.8-1.0.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols with a minor modification; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: tissue

value: yeast

tag: chip antibody

value: Non-specific antibody (Sigma, i5006)


title: Mock IP ChIP-exo replicate 4

description: Replicate 4


title: GFOGERhMSC rep 1

city: Atlanta

first: Andres

middle: Jose

last: Garcia

state: GA

address: 1106 IBB Building

institute: Georgia Institute of Technology

data_processing:
Normalization and data analysis were performed using the JMP Genomics Basic Expression Workflow
Target gene signals normalized to mean of all genes for particular sample using the mean normalization method in JMP Genomics Basic Expression Workflow

label: EvaGreen

organism: Homo sapiens

source_name: Explanted tissue from a radial segmental defect treated with peptide-functionalized, hMSC-laden hydrogels for 1 week

label_protocol: PCR assays were performed using a custom array of Taqman primers (ThermoFisher) following the Manufacturer’s instructions. cDNA synthesis was performed on total RNA (100 ng) using the High-Capacity RNA-to-cDNA Kit (Thermo Fisher). Quantitative PCR was performed using Fluidigm 96×96 nanofluidic arrays.

extract_protocol: Total RNA was extracted with RNeasy Plus Micro Kit

tag: peptide

value: GFOGER


title: Mock IP ChIP-exo replicate 3

description: Replicate 3


title: Control, rep 3


title: BRF1 ChIP-exo replicate 1

description: Replicate 1

source_name: Yeast ChIP-exo

value: BRF1-TAP (Sigma, i5006)


title: BDP1 ChIP-exo replicate 1

description: Replicate 1

value: BDP1-TAP (Sigma, i5006)


title: Mock IP ChIP-exo replicate 1

description: Replicate 1


title: NPC.CL31.UT


title: TFC4 ChIP-exo replicate 1

description: Replicate 1

value: TFC4-TAP (Sigma, i5006)


title: TFC3 ChIP-exo replicate 1

description: Replicate 1

value: TFC3-TAP (Sigma, i5006)


title: TFC8 ChIP-exo replicate 1

description: Replicate 1

value: TFC8-TAP (Sigma, i5006)


title: ARD

city: Dresden

first: Stefanie

last: Reim

state: Saxony

address: Pillnitzer Platz 3a

department: Institut for Breeding Research on Fruits

country: Germany

institute: Julius Kühn Institut

description: Test

data_processing:
The reference genes were validated according to their stability using NormFinder (Andersen et al., 2004). The data analysis were performed according to the manufacturers instructions using the software program SAS ver. 9.4.
For the normalization it uses the average of five reference genes: Elongation factor 1-α [MDP0000304140], Elongation factor 1β-like [MDP0000903484], Tubulin beta chain [MDP00009551799], Ubiquitin-conjugating enzyme E2 10-like [MDP0000140755] and Actin-7 [MDP0000774288]
Candidate gene signals normalized to reference genes; primer ∆Cq = ∆Cq candidate gene – ∆Cq reference gene
Quality of gene expression data was analyzed using the Fluidigm Real-Time PCR Analysis Software v. 4.3.1 (Fluidigm, South San Francisco, CA, USA) by setting a quality threshold of 0.65 and linear base correction. Considering the quality threshold and the quantification cycle (Cq), separate ∆Cq values were calculated
fold_change.txt reports test/control (ARD/gamma) ratios.

label: SYBR Green

organism: Malus sp.

source_name: ARD infected soil

label_protocol: First strand cDNA synthesis was performed using the RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific, Waltham, MA, USA) together with oligo dT primers and 1 µg RNA as template.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: root tissue

tag: soil treatment

value: Apple Replant Disease (ARD)-infected soil

tag: time

value: 7 days


title: TFC7 ChIP-exo replicate 1

description: Replicate 1

value: TFC7-TAP (Sigma, i5006)


title: CS-0d-1

city: Shanghai

first: Xianghui

last: Chen

address: No. 325 Guohe Rd

department: Department of Pharmaceutical Botany, School of Pharmacy

country: China

institute: Second Military Medical University

description:
ALL_Unigene.FA
ALL_Rpkm.txt

library_source: transcriptomic

data_processing:
Illumina CASAVA(v1.8.2) software used for basecalling.
Adapter sequences, low quality bases and undetected bases were removed using Trimmomatic (v0.30)
Short reads were assembled by trinity (http://trinityrnaseq.sourceforge.net/). Contigs were clustered by CD-HIT to produce longer contigs (unigenes)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: TXT file of RPKM for all Sample, FASTA file of unigene for all sample

organism: Crocus sativus

source_name: Stigma

extract_protocol:
Total RNA from the three stages of stigmas (RED, -2DAY, and 0DAY) were extracted by grinding the tissue in liquid nitrogen to fine powder and isolated in three biological replicates using 1ml TRIzol reagent. Illumina NEBNext Ultra RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: 0 DAY

value: stigma

tag: age

value: day of anthesis, dark red stigma outside the perianth tubes

tag: genotype

value: wild type


title: RPC17 ChIP-exo replicate 1

description: Replicate 1

value: RPC17-TAP (Sigma, i5006)


title: Control, rep 2

value: Sprague-Dawley

value: Control


title: TFC1 ChIP-exo replicate 1

description: Replicate 1

value: yeast

value: TFC1-TAP (Sigma, i5006)


title: Basal 2

city: Santiago de Compostela

first: Carmen

last: Conde

state: A Coruña

address: Choupana s/n

country: Spain

institute: Hospital Clinico Universitario

description: Gene expression in pool of culture FLS from RA patients after 12h of indicated treatment

hyb_protocol: 600 ng of Cy3-labelled cRNA was hybridized at 65°C for 19h at 10 rpms using SureHyb hybridization chambers (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA), using default parameters (profile AgilentG3_GX_1Color).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE1-107_Sep09_mod and Grid: 072363_D_F_20150612.
Remove Control probes (negatives and positives): 58201 biological probes.
Filter Probesets based on Detected or Not Detected Flags: Use flag spot information in data files. Entities retained in which 100% of samples in 1 out of any 4 conditions (Basal, ATRA, TNF, TNF+ATRA) have Detected or Not Detected Flag.
Probes that are not detected in any of the 8 samples are removed. Probes pass the filter if it is detected in the two samples of at least one of the four groups. 23824 filtered probes.

source_name: Pool FLS from three RA patients

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the Low Input Quick Amp Labeling kit, One-Color (Agilent), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the Speedtools Total RNA extraction kit (Biotools, Madrid, Spain). Its integrity was assessed with Agilent 2100 Bioanalyzer in combination with Agilent RNA 6000 Nano Chips.

treatment_protocol: FLS from six different RA patients were culture for 12h with 0.05% DMSO (Basal), 5mM ATRA, 10ng/ml TNF or 5mM ATRA+10ng/ml TNF in the serum-deprived medium.

value: Culture FLS


title: Control, rep 1


title: Gamma

description: Control

source_name: Gamma disinfected ARD-soil

value: gamma-irradiated (disinfected) soil


title: RPO31 ChIP-exo replicate 1

description: Replicate 1

value: RPO31-TAP (Sigma, i5006)


title: TFC6 ChIP-exo replicate 1

description: Replicate 1

value: TFC6-TAP (Sigma, i5006)


title: Basal 1


title: Input_PGCLC

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
The library sequence quality in demultiplexed fastq files was checked by FastQC (v0.11.5) and the low-quality reads and adaptor sequences were removed by Trim Galore (v0.4.1) using the default parameters.
The trimmed ChIP-seq reads were aligned to the human reference genome (UCSC hg38) by the Burrows-Wheeler Aligner (0.7.15-r1142-dirty).
Samtools (version: 1.3.1) was used to remove unmapped and low mapping quality reads (options: view -F 4 -q 20). Subsequently, duplicated reads and reads mapped to unlocalized contig (random), unplaced contigs (ChrUn) and blacklisted regions (obtained from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/) were removed using Samtools rmdup.
Before peak calling, all libraries were downsampled to 25 million reads. Peaks were then called using macs2 callpeak against the corresponding inputs (options: -g 3e9 --keep-dup all --nomodel –extsize 157).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_peaks.narrowPeak: Peak files are in the macs2 narrowpeak format (refers to https://github.com/taoliu/MACS).

source_name: Primordial germ cell-like cells

growth_protocol: PGC-competent 4i hESCs (WIS2-NANOS3-T2A-tdTomato) were cultured on irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem) in 4i medium. Media were replaced every day. hESCs were passaged by single-cell dissociation using 0.25% Trypsin-EDTA (GIBCO). 10 μM ROCK inhibitor (Y-27632, TOCRIS) was added for 24 hours after passaging. To induce hPGCLCs, 4i hESCs were trypsinized, filtered and plated into 6-well EZSPHERE microplates (ReproCELL) (500,000 cells/well in 3 mL PGCLC medium). The plates were centrifuged at 300g for 3 minutes and placed into a 37 °C 5% CO2 incubator until embryoid body (EB) collection.

extract_protocol:
The following samples were included in the analysis (one replicate per condition): 4i hESCs (cl11 no IAA), 4i+IAA hESCs (cl11+IAA) and hPGCLCs (cl11 and cl21 pooled; no IAA). For each ChIP, 2.5 million unsorted 4i hESCs or 4 million unsorted hPGCLCs (D4 EBs containing 60-70% PGCLCs as assessed by flow cytometry) were used. The cells were washed in PBS, filtered through 50 μm strainer and fixed in 1% formaldehyde at RT for 10 min. Formaldehyde was quenched by adding 450 μl of 10x glycine at RT for 10 min, followed by centrifugation at 500 g, 4 ºC for 5 minutes. The cells were then washed twice in ice-cold PBS with protease inhibitor cocktail (PIC) and the pellets were snap frozen on dry ice and stored at -80 ºC. ChIP was performed using SimpleChIP Enzymatic Chromatin IP Kit (with Magnetic Beads) from Cell Signalling Technology (CST) following manufacturer’s recommendations with modifications.
ChIP-seq libraries were prepared using KAPA HyperPrep Kit following the manufacturer’s instructions. Briefly, the protocol contains the following steps: end-repair and A-tailing; sequencing adapter (index) ligation; product purification using AMPure beads; library amplification using KAPA real-time Library Amplification Kit (11 cycles were used for ChIP libraries and 7 for input libraries to achieve similar concentration range); product purification using AMPure beads. Libraries were then quantified by qPCR using NEBNExt Library Quant Kit for Illumina (NEB) on QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems). Fragment size distribution and the absence of adapter dimers were checked using Agilent TapeStation 2200 and High Sensitivity D1000 ScreenTape.

tag: cell type

value: Primordial germ cell-like cells

value: No auxin

value: Input


title: Input_ESC_4i

source_name: Embryonic stem cells

value: Embryonic stem cells


title: GFP_PGCLC_noIAA_r2

value: anti-GFP (abcam ab290)


title: GFP_ESC_4i_noIAA_cl11


title: GFP_ESC_4i_IAA_cl11

value: With Auxin


title: PGCLC_PRDM14AID_noIAA_c11

description: processed data file: DEseq2_log2_normalized_count.txt.gz

data_processing:
The library sequence quality in demultiplexed fastq files was checked by FastQC (v0.11.5) and the low-quality reads and adaptor sequences were removed by Trim Galore (v0.4.1) using the default parameters.
The pre-processed RNA-seq reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR (2.6.0a) (--outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100) guided by the ENSEMBL (Release 87) gene models.
Read counts per gene were extracted using TEtranscripts and normalized by DEseq2 in R.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: DEseq2_log2_normalized_count.txt.gz: Tab-delimited text file containing ensemble_gene_id, hgnc_symbol, biotype, gene coordinate and DEseq2 normalized expression level of each sample [log2(normalized counts +1)].

growth_protocol: PGC-competent 4i hESCs (WIS2-NANOS3-T2A-tdTomato) were cultured on irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem) in 4i medium. Media were replaced every day. hESCs were passaged by single-cell dissociation using 0.25% Trypsin-EDTA (GIBCO). 10 μM ROCK inhibitor (Y-27632, TOCRIS) was added for 24 hours after passaging. To induce hPGCLCs, 4i hESCs were trypsinized, filtered and plated into ultra-low cell attachment U-bottom 96-well plates (Corning, 7007) at 4,000 cells/well density in 100 μl PGCLC medium. The plates were centrifuged at 300g for 3 minutes and placed into a 37 °C 5% CO2 incubator until embryoid body (EB) collection.

extract_protocol:
RNA-seq was performed on PRDM14-AID-Venus competent 4i hESCs and hPGCLCs induced therefrom. Two biological replicates were used for each condition. For IAA-sensitive cells, two clones (cl11 and cl21) from the same hESC passage or the same hPGCLC induction were used as replicates. For the parental (“no TIR1”) control, the same cell line was used at different passages or inductions to yield two independent replicates. 10,000 AP+ 4i hESCs or 10,000 NANOS3-tdTomato+AP+ hPGCLCs (with the exception of hPGCLC cl21 replicate, where 3,000 cells were used) were sorted directly into 100 μl of extraction buffer from PicoPure RNA Isolation Kit (Applied Biosystems) for subsequent total RNA extraction according to manufacturer’s protocol. RNA was stored at -80 ºC and its quality and quantity were checked by Agilent RNA 6000 Pico Kit with Bioanalyzer (Agilent Technologies) and Qubit (Thermo Fisher Scientific).
RNA-seq library was prepared from 10 ng input RNA using the end-to-end Trio RNA-seq library prep kit (Nugen) following the manufacturer’s protocol but omitting the AnyDeplete step. In short, the protocol contains the following steps: DNase treatment to remove DNA from RNA; first strand and second strand cDNA synthesis to produce the reverse complement of the input RNAs; cDNA purification using Agencourt AMPure XP beads (Backman Coulter); single primer isothermal amplification (SPIA) to stoichiometrically amplify cDNAs; enzymatic fragmentation and end repair; sequencing adaptor (index) ligation; product purification using AMPure beads; library amplification (4 cycles were used); library purification using AMPure beads. Libraries were then quantified by qPCR using NEBNExt Library Quant Kit (NEB) for Illumina on QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems). Fragment size distribution and the absence of adapter dimers was checked using Agilent TapeStation 2200 and High Sensitivity D1000 ScreenTape. Finally, RNA-seq libraries were subjected to single-end 50 bp sequencing on HiSeq 4000 sequencing system (Illumina). 24 indexed libraries (including samples from this work and 8 others) were multiplexed together and sequenced in two lanes of a flowcell, resulting in >30 million reads per sample.

tag: line

value: PRDM14-AID clone c11


title: PGCLC_PRDM14AID_IAA_c21

value: PRDM14-AID clone c21

value: With auxin


title: RPC40 ChIP-exo replicate 1

description: Replicate 1

value: RPC40-TAP (Sigma, i5006)


title: Liv_ko4_6d

city: Rehovot

first: Gal

last: Manella

state: Israel

address: 234 Herzel St.

country: Israel

institute: Weizmann Institute of Science

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_6d.raw

data_processing:
Illumina bcl2fastq software used for basecalling.
The rest of analysis was done through the UTAP pipline. Reads were trimmed using cutadapt
Reads were mapped to genome (/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index) using STAR (default parameters)
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
Counting was done using htseq-count (union mode)
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing the raw counts for each gene and sample

growth_protocol: 3mo mice were housed under standard light-dark conditions (12h/12h) for 2 weeks before the experiment. For constant darkness (DD) regimen, mice were moved to constant dark 2 days before the experiment.

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by dispenser (IKA-T18), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

treatment_protocol: The system hypoxia system is constructed from a standard, sealed-top cage (Techniplast), connected by tubing to a gas cylinder of either 6% O2 + 94% N2 mixture, or 21% O2 + 79% N2 (synthetic air) as a control (Gordon Gas, IL). Mice were moved into the dedicated cages, and the system flew-in the gas mixtures in constant flow rate of 3.5 LPM for 4 hours. Mice were euthanized immediately after the treatment by cervical dislocation.

tag: strain background

tag: genotype/variation

value: Per1,2 double knock-out (KO)

tag: oxygen level

tag: light regimen

value: DD

tag: time of day


title: Liv_ko16_21a

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_21a.raw


title: Liv_ko16_21d

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_21d.raw


title: Liv_ko16_6a

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_6a.raw


title: Liv_ko16_21b

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_21b.raw


title: Liv_ko16_21c

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_21c.raw


title: PGCLC_PRDM14AID_IAA_c11

tag: treatment


title: PGCLC_Par_noIAA_r1

value: Parental


title: Liv_ko4_6b

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_6b.raw


title: PGCLC_PRDM14AID_noIAA_c21


title: Liv_ko16_6c

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_6c.raw


title: Liv_ko16_6b

description:
processed data file:
Liver_KO_countData.csv
Liv_ko16_6b.raw


title: Liv_ko4_6c

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_6c.raw


title: Liv_ko4_6a

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_6a.raw


title: PGCLC_Par_IAA_r2


title: PGCLC_Par_noIAA_r2


title: PGCLC_Par_IAA_r1


title: Liv_ko4_21d

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_21d.raw


title: Liv_ko4_21c

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_21c.raw


title: Liv_ko4_21b

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_21b.raw


title: ESC_4i_PRDM14AID_noIAA_c21


title: ESC_4i_PRDM14AID_noIAA_c11


title: Liv_ko4_21a

description:
processed data file:
Liver_KO_countData.csv
Liv_ko4_21a.raw


title: ESC_4i_PRDM14AID_IAA_c21


title: Liv_wt16_6d

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_6d.raw

value: WT


title: ESC_4i_PRDM14AID_IAA_c11

description: processed data file: DEseq2_log2_normalized_count.txt.gz


title: Liv_wt16_6c

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_6c.raw


title: Liv_wt16_6b

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_6b.raw


title: ESC_4i_Par_noIAA_r2


title: ESC_4i_Par_noIAA_r1


title: Liv_wt16_21b

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_21b.raw


title: ESC_4i_Par_IAA_r2


title: Liv_wt16_6a

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_6a.raw


title: Liv_wt4_6d

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_6d.raw


title: Liv_wt16_21d

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_21d.raw


title: Liv_wt4_6c

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_6c.raw


title: ESC_4i_Par_IAA_r1


title: Liv_wt16_21a

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_21a.raw


title: Liv_wt4_21b

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_21b.raw


title: Liv_wt4_21a

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_21a.raw


title: Liv_wt4_6a

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_6a.raw


title: Liv_wt4_21d

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_21d.raw


title: Lung_ZT16_6A

description:
processed data file:
lung_countData.csv
Lung_ZT16_6A.raw

value: LD


title: Lung_ZT16_6C

description:
processed data file:
lung_countData.csv
Lung_ZT16_6C.raw


title: Lung_ZT16_6B

description:
processed data file:
lung_countData.csv
Lung_ZT16_6B.raw


title: Lung_ZT16_6D

description:
processed data file:
lung_countData.csv
Lung_ZT16_6D.raw


title: serum_normal_rep1

city: Xi'an

first: Yat

last: Handsome

address: Changle Road

institute: Tissue engineering center

description: microRNA expression in serum of young normal participants

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: serum

tag: gender

value: male and female

value: young

tag: disease state

value: normal


title: Lung_ZT16_21D

description:
processed data file:
lung_countData.csv
Lung_ZT16_21D.raw


title: serum_osteoporosis_rep1

description: microRNA expression in serum of old osteoporotic participants

tag: tissue

value: old

value: osteoporosis


title: Liv_wt16_21c

description:
processed data file:
Liver_WT_countData.csv
Liv_wt16_21c.raw


title: Lung_ZT16_21B

description:
processed data file:
lung_countData.csv
Lung_ZT16_21B.raw


title: Lung_ZT16_21C

description:
processed data file:
lung_countData.csv
Lung_ZT16_21C.raw


title: Liv_wt4_21c

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_21c.raw


title: Liv_wt4_6b

description:
processed data file:
Liver_WT_countData.csv
Liv_wt4_6b.raw


title: serum_osteopenia_rep1

description: microRNA expression in serum of mid-age osteopenic participants

value: mid-age

value: osteopenia


title: Lung_ZT16_21A

description:
processed data file:
lung_countData.csv
Lung_ZT16_21A.raw


title: Lung_ZT4_6B

description:
processed data file:
lung_countData.csv
Lung_ZT4_6B.raw


title: Lung_ZT4_6A

description:
processed data file:
lung_countData.csv
Lung_ZT4_6A.raw


title: Lung_ZT4_6C

description:
processed data file:
lung_countData.csv
Lung_ZT4_6C.raw


title: Lung_ZT4_21C

description:
processed data file:
lung_countData.csv
Lung_ZT4_21C.raw


title: Lung_ZT4_21B

description:
processed data file:
lung_countData.csv
Lung_ZT4_21B.raw


title: Lung_ZT4_21A

description:
processed data file:
lung_countData.csv
Lung_ZT4_21A.raw


title: Kid_ZT16_6C

description:
processed data file:
kidney_countData.csv
Kid_ZT16_6C.raw


title: Kid_ZT16_6A

description:
processed data file:
kidney_countData.csv
Kid_ZT16_6A.raw


title: Kid_ZT16_21D

description:
processed data file:
kidney_countData.csv
Kid_ZT16_21D.raw


title: Kid_ZT16_21C

description:
processed data file:
kidney_countData.csv
Kid_ZT16_21C.raw


title: Kid_ZT16_21A

description:
processed data file:
kidney_countData.csv
Kid_ZT16_21A.raw


title: Kid_ZT16_21B

description:
processed data file:
kidney_countData.csv
Kid_ZT16_21B.raw


title: Kid_ZT4_6D

description:
processed data file:
kidney_countData.csv
Kid_ZT4_6D.raw


title: Kid_ZT4_6C

description:
processed data file:
kidney_countData.csv
Kid_ZT4_6C.raw


title: Kid_ZT4_6B

description:
processed data file:
kidney_countData.csv
Kid_ZT4_6B.raw


title: Lung_ZT4_6D

description:
processed data file:
lung_countData.csv
Lung_ZT4_6D.raw


title: SCII rep2

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks and the read counts of each gene were obtained by htseq-count.
The result of alignment with the reference genome was stored in a binary file, called a bam file. Using the Stringtie software to assemble the reads, the new transcript was spliced. Then the candidate lncRNA transcripts were selected by comparing the gene annotation information of the reference sequence produced by Cuffcompare software. Finally, transcripts with coding potential were screened out by CPC, CNCI, Pfam and PLEK to obtain lncRNA predicted sequences.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values
Supplementary_files_format_and_content: LncRNA ids NONRATT* can be queried in the NONCODE database (http://www.noncode.org); A fasta file was provided for other lncRNA identifiers.

source_name: spinal cord

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: ischemia-reperfusion injury

tag: strain

value: Sprague-Dawley

value: spinal cord

tag: weight


title: Kid_ZT4_6A

description:
processed data file:
kidney_countData.csv
Kid_ZT4_6A.raw


title: SCII rep3


title: Kid_ZT4_21D

description:
processed data file:
kidney_countData.csv
Kid_ZT4_21D.raw


title: Sham rep1

value: sham


title: Sham rep2


title: Kid_ZT4_21C

description:
processed data file:
kidney_countData.csv
Kid_ZT4_21C.raw


title: SCII rep1


title: Lung_ZT4_21D

description:
processed data file:
lung_countData.csv
Lung_ZT4_21D.raw


title: Kid_ZT4_21B

description:
processed data file:
kidney_countData.csv
Kid_ZT4_21B.raw


title: Sham rep3


title: Kid_ZT16_6D

description:
processed data file:
kidney_countData.csv
Kid_ZT16_6D.raw


title: Liver2_ZT16_6D

description:
processed data file:
liver_countData.csv
Liver2_ZT16_6D.raw


title: Liver2_ZT16_6A

description:
processed data file:
liver_countData.csv
Liver2_ZT16_6A.raw


title: Kid_ZT16_6B

description:
processed data file:
kidney_countData.csv
Kid_ZT16_6B.raw


title: Liver2_ZT16_21C

description:
processed data file:
liver_countData.csv
Liver2_ZT16_21C.raw


title: Liver2_ZT16_21B

description:
processed data file:
liver_countData.csv
Liver2_ZT16_21B.raw


title: Kid_ZT4_21A

description:
processed data file:
kidney_countData.csv
Kid_ZT4_21A.raw


title: Liver2_ZT16_6C

description:
processed data file:
liver_countData.csv
Liver2_ZT16_6C.raw


title: Liver2_ZT16_21A

description:
processed data file:
liver_countData.csv
Liver2_ZT16_21A.raw


title: Liver2_ZT4_6B

description:
processed data file:
liver_countData.csv
Liver2_ZT4_6B.raw


title: Liver2_ZT4_6D

description:
processed data file:
liver_countData.csv
Liver2_ZT4_6D.raw


title: Liver2_ZT4_21D

description:
processed data file:
liver_countData.csv
Liver2_ZT4_21D.raw


title: Liver2_ZT4_6C

description:
processed data file:
liver_countData.csv
Liver2_ZT4_6C.raw


title: Liver2_ZT4_21B

description:
processed data file:
liver_countData.csv
Liver2_ZT4_21B.raw


title: Liver2_ZT16_6B

description:
processed data file:
liver_countData.csv
Liver2_ZT16_6B.raw


title: Liver2_ZT4_21A

description:
processed data file:
liver_countData.csv
Liver2_ZT4_21A.raw


title: Liver2_ZT4_6A

description:
processed data file:
liver_countData.csv
Liver2_ZT4_6A.raw


title: Liver2_ZT16_21D

description:
processed data file:
liver_countData.csv
Liver2_ZT16_21D.raw


title: Liver2_ZT4_21C

description:
processed data file:
liver_countData.csv
Liver2_ZT4_21C.raw


title: Choudhary-2018-TW_HIC217

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description: Choudhary-2018-LTR41-Clone001-Region2capture

data_processing:
All libraries were sequenced on Illumina NextSeq 500 platform.
in situ HiC reads were aligned to hg19 genome using the Juicer pipeline (as described in Rao et al. 2014)
in situ HiC^2 reads were aligned to hg19 genome using the Juicer pipeline (as described in Sanborn et al. 2015)
Genome_build: hg19
Supplementary_files_format_and_content: .hic files were generated for all in situ HiC and in situ HiC^2 fastq files using the Juicer (as described in Rao et al, 2014)

source_name: GM12878 cell line

growth_protocol: GM12878 cells were grown in T25 tissue culture flask with 10-20 ml medium containing RPMI 1640 (+2mM L-glutamine) + 15% fetal bovine serum + 1x P/S at 37°C under 5% carbon dioxide

extract_protocol:
As detailed in In situ Hi-C: Protocol and Quality Control Standards, 4D Nucleome Consortium (https://drive.google.com/file/d/1wEAR_yGKMFBZ6BQ6CRRtBa8USYdRZahM/view)
As detailed in In situ Hi-C: Protocol and Quality Control Standards, 4D Nucleome Consortium (https://drive.google.com/file/d/1wEAR_yGKMFBZ6BQ6CRRtBa8USYdRZahM/view)
in situ HiC, in situ HiC^2

treatment_protocol: 1% v/v formaldehyde for 10mins with mixing at RT

value: LTR41 deletion

value: female

value: blood lymphoblastoid


title: Choudhary-2018-TW_HIC210

description: Choudhary-2018-L1M3f-Clone002-Region2capture

value: LTR41 WT


title: Choudhary-2018-TW_HIC213

description: Choudhary-2018-L1M3f-Clone003-Region2capture


title: Choudhary-2018-TW_HIC215


title: Choudhary-2018-TW_HIC206

description: Choudhary-2018-L1M3f-Clone002-Region1capture

value: L1M3f deletion


title: Choudhary-2018-TW_HIC212


title: Choudhary-2018-TW_HIC204

description: Choudhary-2018-LTR41-Clone002-Region1capture

value: L1M3f WT


title: Choudhary-2018-TW_HIC207


title: Choudhary-2018-TW_HIC216

description: Choudhary-2018-LTR41-Clone002-Region2capture


title: Choudhary-2018-TW_HIC211


title: Choudhary-2018-TW_HIC208

description: Choudhary-2018-L1M3f-Clone003-Region1capture


title: Choudhary-2018-TW_HIC203

description: Choudhary-2018-LTR41-Clone001-Region1capture


title: Choudhary-2018-TW_HIC218


title: Choudhary-2018-TW_HIC014


title: Choudhary-2018-TW_HIC202


title: C4_SpenDegron_Auxin28hDox24h_rep2

data_processing:
All data were mapped to the mouse genome mm10, using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142), and the gene annotation from ensembl (v92). Analyses were performed in R (v 3.4.2) and Bioconductor (v3.6).
Reads were trimmed using Trimgalore (v 0.4.4), mapped using STAR 10 (2.5.3a, parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD), and removed when mapping to the mitochondrial genome. Remaining reads were split by allele using SNPsplit (v 0.3.2). Allele specific and the unassigned bam files were sorted, duplicates removed using picard (v2.18.2, parameters: REMOVE_DUPLICATES=true ASSUME_SORTED=true) and pooled as the total reads. Quantification of expression was performed using featureCount (parameters: -p -t exon -g gene_id, -s 1 for stranded RNAseq of in vitro cell, -s 0 for non-stranded RNAseq of single embryo). Data were then analysed in R using DESeq2 13 (v1.18.1), calculating the sizeFactor on the count of total reads and applying it to the allele specific counts.
Genome_build: mm10

growth_protocol: Mouse ES cells (TX1072) were grown on 0.1% gelatin-coated flasks in 8% CO2 37°C incubators. For all experiments, cells were cultured in 2i + LIF serum-containing ES cell medium - DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Chemicon), CHIR99021 (3uM), PD0325901 (1uM).

extract_protocol:
RNA extraction was performed using the RNeasy kit and on-column DNAse digestion (Qiagen). Reverse transcription was performed on 1ug total RNA using Super Script III (Life Technologies). To quantify allelic skewing, cDNA was amplified using biotinylated primers and subsequently sequenced using Q24 Pyromark (Qiagen). Only samples showing a RIN score above 9 were used to prepare RNAseq libraries (TruSeq).
Library were prepared using TruSeq 2 kit.

treatment_protocol: X chromosome inactivation was induced through Xist expression upon administration of doxycycline (1ug/mL). Auxin mediated depletion of target proteins was achieved through supplementing culture media with auxin (Sigma) at the recommended concentration of 500uM. Auxin containing medium was renewed every 24 hours.

value: Spen-AID

value: BL/6J x CAST-EiJ


title: Choudhary-2018-TW_HIC013


title: C4_SpenDegron_Dox24h_rep2


title: hepatocyte_metformin_24hrs_rep1

city: Hamilton

first: Emily

middle: Anne

last: Day

state: Ontario

address: McMaster University, 1200 Main St W, Department of Medicine HSC 4N71

department: Medical Sciences

country: Canada

institute: McMaster University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw microarray probe data underwent background correction, log2 transformation, and normalization using the neqc function in the limma package (version 3.26.9) for R (version 3.2.3, 64bit platform).

source_name: Primary Mouse Hepatocyte isolated by collagenase profusion

label_protocol: Standard Illumina protocol

extract_protocol: Total RNA was isolated using trizol RNA extraction

tag: Sex

value: male

tag: cell

value: Primary Mouse Hepatocytes

value: Treated with 500uM metformin


title: hepatocyte_metformin_24hrs_rep3


title: hepatocyte_metformin_24hrs_rep4


title: hepatocyte_metformin_24hrs_rep2


title: hepatocyte_control_24hrs_rep3

value: control


title: C4_SpenDegron_Dox24h_rep1


title: C4_SpenDegron_Auxin28h_rep2


title: hepatocyte_control_24hrs_rep1


title: hepatocyte_control_24hrs_rep2


title: Choudhary-2018-TW_HIC012


title: Choudhary-2018-TW_HIC010


title: C4_SpenDegron_t0_rep2

value: UT


title: C2_WT_Auxin28hDox24h_rep1

value: WT


title: Choudhary-2018-TW_HIC008


title: C4_SpenDegron_t0_rep1


title: C4_SpenDegron_Auxin28hDox24h_rep1


title: C2_WT_Auxin28h_rep2


title: Choudhary-2018-TW_HIC011


title: C2_WT_Auxin28h_rep1


title: C2_WT_Auxin28hDox24h_rep2


title: C4_SpenDegron_Auxin28h_rep1


title: C2_WT_Dox24h_rep1


title: C2_WT_Dox24h_rep2


title: C2_WT_t0_rep2


title: C2_WT_t0_rep1


title: Choudhary-2018-TW_HIC002


title: Choudhary-2018-TW_HIC001


title: Choudhary-2018-TW_HIC006


title: embryo_spenKO_f2_1

data_processing:
All data were mapped to the mouse genome mm10, using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142), and the gene annotation from ensembl (v92). Analyses were performed in R (v 3.4.2) and Bioconductor (v3.6).
RNAseq data were processed similarly as ChIPseq, except for the mapping when the following parameters were used: --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD. Quantification of expression was performed using featureCount (parameters: -p -t exon -g gene_id, -s 1 for stranded RNAseq of in vitro cell, -s 0 for non-stranded RNAseq of single embryo). Data were then analysed in R using DESeq2 13 (v1.18.1), calculating the sizeFactor on the count of total reads and applying it to the allele specific counts.
Genome_build: mm10

growth_protocol: Timed natural matings were used for all experiments. Noon of the day when the vaginal plugs of mated females were identified was scored as E0.5. For Spen matings a published  conditional allele was used . For oocyte deletions published Rosa26:Zp3-Cre allele was  used 4 . F1 hybrid Spen +/- males were obtained by crossing Spen +/+ CAST/EiJ females with  Spen +/- C57BL/6J males. For Spen maternally deleted embryos, Spen flox/flox Zp3-Cre +ve  C57BL/6J females were crossed with Spen +/- F1 hybrid males. For Spen control embryos,  Spen flox/flox Zp3-Cre -ve C57BL/6J females were crossed with Spen +/- F1 hybrid males. All  husbandry and experiments involving mice were carried out in agreement with the guidelines  from French legislation and institutional policies.

extract_protocol:
RNA was extracted according to the manufacturer’s recommendations using RNeasy Mini Kit (Qiagen) with on-column DNAse digestion (Qiagen). Only samples showing a RIN score above 9 were used to prepare RNAseq libraries (TruSeq). Libraries were sequenced using NovaSeq 6000 at PE100 settings.
cDNA were fragmented to ~200 bp with Focused-ultrasonicator (Covaris, Woburn, MA) and adaptor ligated libraries were generated using NEBNext Ultra DNA library Prep Kit for illumina (New England Labs, Ipswich, MA)

treatment_protocol: E3.5 embryos were collected and morphologically assessed to ensure only viable samples were collected. Zona pellucida was removed by treatment with acidified Tyrode’s solution. Single embryos were picked into individual tubes and cDNA was prepared and amplified.


title: embryo_CN_f1_1


title: embryo_CN_f2_13


title: embryo_spenKO_f3_9


title: embryo_spenKO_f4_4


title: embryo_spenKO_f1_4


title: hepatocyte_control_24hrs_rep4


title: NPC_CL31_Aux24h

extract_protocol:
RNA was extracted according to the manufacturer’s recommendations using RNeasy Mini Kit (Qiagen) with on-column DNAse digestion (Qiagen). Only samples showing a RIN score above 9 were used to prepare RNAseq libraries (TruSeq). Libraries were sequenced using NovaSeq 6000 at PE100 settings.
Library were prepared using TruSeq RNA kit v2.

treatment_protocol: Cells were treated with auxin (500uM) for 0h, 24h or 48h.

value: neural progenitor cells


title: embryo_spenKO_f1_2


title: Choudhary-2018-TW_HIC004


title: embryo_spenKO_f4_1


title: embryo_spenKO_f1_1


title: NPC_CL31_Aux48h


title: NPC_CL30_UT

value: untreated


title: NPC_CL31_UT


title: TxCL63_Dox24h_rep1_CutRun_Spen

data_processing:
Library strategy: CUT&RUN
All data were mapped to the mouse genome mm10, using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142), and the gene annotation from ensembl (v92). Analyses were performed in R (v 3.4.2) and Bioconductor (v3.6).
Reads were trimmed using Trimgalore (v 0.4.4), mapped using STAR 10 (2.5.3a, parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 1 --alignMatesGapMax 2000 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD), and removed when mapping to the mitochondrial genome. Remaining reads were split by allele using SNPsplit (v 0.3.2). Allele specific and the unassigned bam files were sorted, duplicates removed using picard (v2.18.2, parameters: REMOVE_DUPLICATES=true ASSUME_SORTED=true) and pooled as the total reads. BigWig of coverage files were done using DeepTools 11 bamCoverage (parameters: --extendReads --binSize 1, with --extendReads 200 for single end data). A scaling factor was calculated as 106 / total number of reads, and the same factor was given as the parameter --scaleFactor for both allelic signals.
Genome_build: mm10

source_name: ESC

growth_protocol: Spen-degron mouse ES cells (TX1072) were seeded in 0.1% gelatin-coated T75 flasks (2.5*106 cells/flask). Cells were grown in 2i + LIF serum-containing ES cell medium - DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Chemicon), CHIR99021 (3uM), PD0325901 (1uM) in 8% CO2 37°C incubators.

extract_protocol:
10 million cells in suspension were fixed with 2% formaldehyde diluted in PBS for 10 minutes at room temperature. Fixation was quenched with 125mM glycine for 5 minutes and cells were washed twice with PBS. Fixed cells were then permeabilized with permeabilization buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 0.25% TritonX-100, c0mplete EDTA free) for 5 minutes and washed twice in PBS. Cells were then resuspended in washing buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, cOmplete EDTA free) and bound to concanavalin beads (50uL bead slurry used per 10 million cells), blocked in blocking buffer (wash buffer + 2mM EDTA) and incubated overnight with target antibodies diluted 1/200 in washing buffer on an end to end rotator. Cells were washed three times in washing buffer followed by 1-hour incubation with pA-MNase (1:400 in washing buffer) and washed again three times in washing buffer. After the last wash, cells were resuspended in washing buffer and left equilibrated to 0°C in a metal block for 10 minutes. To start digestion, CaCl2 was added to 1.5mM final concentration, taking care to return each sample to 0°C immediately after. Digestion was performed at 0°C for 1 hour, before being stopped by adding 2X-STOP solution (200mM NaCl, 20mM EDTA, 5mM EGTA, 0.1% NP-40, 40ug/mL glycogen). RNAse A was added to a final concentration of 50ug/mL and samples were incubated at 37°C for 20 minutes. SDS and proteinase K were then added to final concentrations of 0.1% and 300ug/mL respectively and samples were incubated at 56°C for 2 hours followed with 68°C for 16 hours to reverse crosslinking. Total DNA was extracted using phenol-chloroform followed by several rounds of ethanol precipitation and DNA size selection (using Ampure XP beads) to remove predominating large undigested DNA fragments. The selected small fragments (resulting from MNase digestion) were quantified and analyzed using Qubit and Tapestation assays.
Cut&Run libraries were prepared from 50ng DNA per samples, using the Accel-NGS 2S Plus DNA Library Kit (Swift) according to manufacturer’s protocol. Paired-end 100nt sequencing was performed on HiSeq2500 (Illumina, San Diego, CA).

treatment_protocol: 24 hours later, cells were exposed to doxycycline (1ug/mL) and/or auxin (500uM). Cells were then collected at regular intervals.

value: ESC


title: NPC_CL30_Aux24h


title: TxCL63_Dox24h_rep2_CutRun_Spen


title: embryo_spenKO_f3_5


title: Choudhary-2018-TW_HIC005


title: NPC_CL30_Aux48h


title: c-Src_24h_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Csk-/- MEFs induced c-Src for 24h_rep1

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for data processing.

source_name: Csk-/- MEFs induced c-Src for 24h_rep1

label_protocol: 500 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted with Sepazol (Nacalai Tesque), according to the manufacturer’s instructions.

treatment_protocol: CskKO (Csk-/-) MEFs  were transfected with pBKT2-c-Src. For induction of c-Src expression, cells were incubated with 1 μg/ml Dox (doxycycline; Sigma).

value: MEF

value: CskKO (Csk-/-) transfected with c-Src

tag: c-src expression duration (hours)


title: c-Src_24h_rep2

description: Csk-/- MEFs induced c-Src for 24h_rep2

source_name: Csk-/- MEFs induced c-Src for 24h_rep2

tag: genotype


title: c-Src_72h_rep1

description: Csk-/- MEFs induced c-Src for 72h_rep1

source_name: Csk-/- MEFs induced c-Src for 72h_rep1

tag: cell type


title: c-Src_72h_rep2

description: Csk-/- MEFs induced c-Src for 72h_rep2

source_name: Csk-/- MEFs induced c-Src for 72h_rep2


title: c-Src_0h_rep1

description: Csk-/- MEFs induced c-Src for 0h_rep1

source_name: Csk-/- MEFs induced c-Src for 0h_rep1


title: Choudhary-2018-TW_HIC003

value: female

value: blood lymphoblastoid


title: TxCL63_DoxAux08h_rep2_CutRun_Spen


title: c-Src_0h_rep2

description: Csk-/- MEFs induced c-Src for 0h_rep2

source_name: Csk-/- MEFs induced c-Src for 0h_rep2


title: c-Src_6h_rep1

description: Csk-/- MEFs induced c-Src for 6h_rep1

source_name: Csk-/- MEFs induced c-Src for 6h_rep1


title: TxCL63_Dox08h_rep2_CutRun_Spen


title: TxCL63_Dox08h_rep1_CutRun_Spen


title: Choudhary-2018-TW_HIC205

value: L1M3f deletion


title: Choudhary-2018-TW_HIC209

value: LTR41 WT


title: c-Src_24h_rep2_miRNA

description: Csk-/- MEFs induced c-Src for 24h_rep2

hyb_protocol: Refer to Agilent miRNA hybridisation protocol.

label_protocol: 100 ng of total RNA was first dephosphorylated by using calf intestine alkaline phosphatase (TaKaRa) and labeled by using miRNA labeling Reagent & Hybridization Kit (5190-0408, Agilent).


title: Choudhary-2018-TW_HIC201

value: L1M3f WT


title: Choudhary-2018-TW_HIC214

value: LTR41 deletion


title: Choudhary-2018-TW_HIC009


title: c-Src_72h_rep1_miRNA

description: Csk-/- MEFs induced c-Src for 72h_rep1


title: TxCL63_Dox04h_rep1_CutRun_Spen

value: BL/6J x CAST-EiJ


title: c-Src_24h_rep1_miRNA

description: Csk-/- MEFs induced c-Src for 24h_rep1


title: c-Src_6h_rep2

description: Csk-/- MEFs induced c-Src for 6h_rep2

source_name: Csk-/- MEFs induced c-Src for 6h_rep2


title: c-Src_6h_rep1_miRNA

description: Csk-/- MEFs induced c-Src for 6h_rep1


title: TxCL63_DoxAux08h_rep1_CutRun_Spen


title: Choudhary-2018-TW_HIC007


title: TxCL63_UT_rep2_CutRun_Spen


title: c-Src_72h_rep2_miRNA

description: Csk-/- MEFs induced c-Src for 72h_rep2


title: c-Src_0h_rep2_miRNA

description: Csk-/- MEFs induced c-Src for 0h_rep2


title: EOM016 Lateral ventricle wall

status: Public on Dec 07 2019

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Biological replicate 8 of 8, Dgcr8+/-, eight months

hyb_protocol: Microarray hybridization was performed at 55°C for 20 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 5μm resolution, and the array data was extracted with Agilent feature extraction software using the miRNA_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used, followed by a log transformation, percentile normalization across probes, and scaling through the samples, prior to actual analysis.

source_name: Lateral ventricle wall, 8 month-old mice

label_protocol: 100ng of total RNA were labeled with Cy3 according to Agilent's labeling protocol

extract_protocol: Total RNA was extracted with mirVana isolation kit (Ambion). RNA quality was confirmed by analysis on the Agilient 2100 Bioanalyzer.

tag: age

value: eight months


title: EOM015 Lateral ventricle wall

description: Biological replicate 7 of 8, Dgcr8+/-, eight months


title: EOM014 Lateral ventricle wall

description: Biological replicate 6 of 8, Dgcr8+/-, eight months


title: EOM013 Lateral ventricle wall

description: Biological replicate 5 of 8, Dgcr8+/-, eight months


title: EOM008 Lateral ventricle wall

description: Biological replicate 8 of 8, WT littermates

value: WT littermates


title: EOM012 Lateral ventricle wall

description: Biological replicate 4 of 8, Dgcr8+/-, eight months


title: EOM011 Lateral ventricle wall

description: Biological replicate 3 of 8, Dgcr8+/-, eight months


title: EOM007 Lateral ventricle wall

description: Biological replicate 7 of 8, WT littermates


title: EOM005 Lateral ventricle wall

description: Biological replicate 5 of 8, WT littermates


title: EOM010 Lateral ventricle wall

description: Biological replicate 2 of 8, Dgcr8+/-, eight months


title: TxCL63_UT_rep1_CutRun_Spen


title: EOM002 Lateral ventricle wall

description: Biological replicate 2 of 8, WT littermates


title: EOM006 Lateral ventricle wall

description: Biological replicate 6 of 8, WT littermates


title: EOM001 Lateral ventricle wall

description: Biological replicate 1 of 8, WT littermates


title: EOM004 Lateral ventricle wall

description: Biological replicate 4 of 8, WT littermates


title: EOM009 Lateral ventricle wall

description: Biological replicate 1 of 8, Dgcr8+/-, eight months


title: c-Src_0h_rep1_miRNA

description: Csk-/- MEFs induced c-Src for 0h_rep1


title: EOM003 Lateral ventricle wall

description: Biological replicate 3 of 8, WT littermates


title: c-Src_6h_rep2_miRNA

description: Csk-/- MEFs induced c-Src for 6h_rep2


title: Placebo [CB_56]

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: h19
Supplementary_files_format_and_content: RPKM and count values for each Sample

source_name: Placebo_Centrifuged bone needle biopsy

extract_protocol:
Bone needle biopsy was centrifuged to remove loosely adherent marrow, and homogenized in QIAZol Reagent. RNA was extracted, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared according to the manufacturer’s instructions for the NuGen Ovation RNA-Seq version 2 and Encore NGS Library Systems (San Carlos, CA).

tag: subject status

value: post-menopausal women

value: 60-79 years

value: Placebo

value: Bone biopsy


title: Placebo [CB_23]


title: Placebo [CB_38]


title: Placebo [CB_47]


title: Placebo [CB_2]


title: Placebo [CB_53]


title: Placebo [CB_8]


title: Placebo [CB_29]


title: Placebo [CB_50]


title: Placebo [CB_41]


title: Placebo [CB_62]


title: Placebo [CB_20]


title: Denosumab [CB_1]

source_name: Denosumab_Centrifuged bone needle biopsy

value: Denosumab


title: Placebo [CB_44]


title: Denosumab [CB_7]


title: Denosumab [CB_4]


title: Placebo [CB_59]


title: Denosumab [CB_22]


title: Denosumab [CB_49]


title: Placebo [CB_68]


title: TxCL63_Dox04h_rep2_CutRun_Spen

value: ESC


title: Denosumab [CB_19]


title: Denosumab [CB_46]


title: Denosumab [CB_58]


title: Denosumab [CB_16]


title: Denosumab [CB_55]


title: Denosumab [CB_64]


title: Denosumab [CB_34]


title: Denosumab [CB_43]


title: SB17

description: Centrifuged bone needle biopsy; centrifuged bone was digested twice with liberase according to manufacturer protocol (30 minutes, 37 degrees C); remaining bone was homogenized for osteocyte enriched RNA

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: h19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each Sample

source_name: Centrifuged bone needle biopsy, digested 2X


title: SB27


title: SB42


title: SB33


title: SB37


title: SB20


title: SB16


title: SB44


title: SB26


title: SB66


title: SB65


title: SB41


title: SB36


title: SB2


title: SB31


title: Denosumab [CB_10]


title: SB34


title: SB59


title: Denosumab [CB_70]


title: SB38


title: SB64


title: SB29


title: SB28


title: SB15


title: SB24


title: SB61


title: SB60


title: SB13


title: SB48


title: myeloma cell line XG1 (collected at d3 after culturing)

first: Xuewei

address: 200 1st street

data_processing:
Base calling by CASAVA
Alignment by Tophat2
Gene count by featureCount
Normalization by edgeR
All above steps are wrapped in an interal workflow (MAPRSeq)
Genome_build: hg19
Supplementary_files_format_and_content: TSV file for gene rpkm values

source_name: Human myeloma cell line

growth_protocol: Cells were maintained in RPMI-1640 media, supplemented with 5% fetal calf serum and antibiotics.

extract_protocol:
Total RNA was prepared using RNeasy plus kit under the protocols of the manufacturer (Qiagen, Valencia)
RNA libraries is prepared using 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).

treatment_protocol: without treatment

tag: cell line

value: myeloma cell line XG1

tag: cell line source

value: Myeloma cell line established before from a patient sample

tag: time

value: d3 after culturing


title: myeloma cell line XG1LenRes (collected at 24hours after culturing)

value: myeloma cell line XG1LenRes

value: IMiD resistant cell line established from XG1

value: 24 hours after culturing


title: myeloma cell line XG1 (collected at 24 hours after culturing)


title: myeloma cell line XG1LenRes (collected at d3 after culturing)


title: SB8

value: female


title: SB21


title: L_MAP4

city: Sherbrooke

first: Nathalie

last: Bissonnette

state: Quebec

address: 2000 rue College

department: Sherbrooke research center

institute: Agriculture and Agri-food Canada

data_processing:
The analysis was performed on the MP2 computing cluster of Compute Canada at the Université de Sherbrooke using the RNA-seq pipeline v.1.2 developed by the McGill University and Genome Québec Innovaction center (MUGQIC) team
Trimming and clipping were done using Trimmomatic software v0.32. Trimming was performed by removing extremities that had a phred quality score below 20 in each four-nucleotide window. The same quality pass or fail criteria were also used for the entire read.
Reads with a minimum length of 32 nucleotides were aligned using TopHat software v2.0.9  to the Btau 4.6.1 reference genome , allowing for two mismatches per read. The quality of the alignment was verified by checking for high levels of duplicated reads and low transcript coverage with the RSeQC package.
The FPKM calculated by Cufflinks software v2.1.1 was used to determine the transcript expression rate.
Genome_build: Btau 4.6.1
Supplementary_files_format_and_content: All processed data files are the unmodified cufflinks output file that calculted the FPKM for each genes (genes.fpkm_tracking) renamed using the sample names

organism: Bos taurus

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from 700 mL of blood drawn from the jugular vein using two blood bags containing citrate–phosphate–dextrose–adenine anticoagulant (Animal Blood Resources International, Dixon, CA, USA). PBMCs were isolated using a Ficoll gradient and monocytes were is by adherence. PBMCs were seeded in CELLSTAR TC T-75 flasks (Greiner Bio-One North America Inc, Monroe, NC, United States) at a density of 4 × 107 cells per flask with RMPI 1640 medium (Wisent, Saint-Bruno, Quebec, Canada) supplemented by 10% bovine heat-inactivated heterologous serum from JD-negative cows and a mix of L-glutamine (Wisent) and GlutaMax (Life Technologies, Burlington, Ontario, Canada) and antibiotics/antimycotics (Wisent). After an incubation period of 2 h in a humid atmosphere at 39°C with 5% CO2, non-adherent cells were removed and cells were gently washed with complete media to only keep adherent cell (monocytes). After overnight incubation, remnants of non-adherent cells were removed and the medium was changed for a new RPMI 1640 medium containing 10% heat-inactivated FBS, the mixture of L‑glutamine and GlutaMax, and the antibiotics/antimycotics. For differentiation of monocytes into macrophages, cultures were maintained for 7 to 10 days in a humid atmosphere at 39°C with 5% CO2, with the medium being refreshed every 2 to 3 days. Once the cell displayed classical macrophage morphology, the medium was changed for complete media without the antibiotics/antimycotics. The macrophages were then incubated overnight under the same conditions for the MAP infection experiment on the following day.

extract_protocol:
The RNA was extracted using the RNeasy kit (Qiagen) with the on-column DNase treatment according to the manufacturer’s recommendations. The quality of the 72 samples (four infection and two control time points per animal) was assessed using the Bioanalyzer RNA 6000 kit.
Following rRNA removal using the Ribo-Zero Gold kit (Illumina, Victoria, British Columbia, Canada), 72 cDNA libraries (12 animals × 6 samples, including infection and control time points) were generated from 250 ng of total RNA using the Illumina TruSeq Stranded Total mRNA Sample Preparation kit (Illumina). The length of the fragments was assessed using the Agilent High Sensitivity DNA Chip (Agilent Technologies) on a 2100 Bioanalyzer (Agilent Technologies), and the concentration was determined using a NanoDrop spectrophotometer. Libraries were sequenced at the McGill University and Génome Québec Innovation Centre (MUGQIC) (McGill University, Montreal, Quebec, Canada). Samples were multiplexed in equal ratios (six libraries per two sequencing lanes, equivalent to three libraries per lane) and sequenced in the form of 50-cycle 100 bp paired-end reads on a HiSeq 2000 instrument (Illumina).

treatment_protocol: MAP ex vivo infections were performed for incubation periods of 1h, 4h, 8h, and 24h at a multiplicity of infection of 10 bacteria for each macrophages. Two uninfected control flasks were also collected at 4 h and 24 h. To stop the infection, cells were washed twice with PBS and harvested by adding 1.8 mL of RLT buffer(Qiagen) to each culture flask. Lysed cells were conserved at −80°C until required for RNA extraction.

tag: cow id

value: L

tag: johne's disease status

value: Negative

value: peripheral blood mononuclear cells  (PBMCs)

tag: cell subtype

value: monocyte-derived macrophages

tag: ex vivo infection or control

value: MAP infected

tag: time point


title: L_MAP24


title: L_CTL4

value: Control


title: L_CTL24


title: L_MAP8


title: K_CTL4

value: K


title: L_MAP1


title: J_MAP24

value: J


title: K_MAP8


title: K_MAP4


title: K_MAP1


title: K_CTL24


title: J_CTL24


title: J_MAP1


title: J_CTL4


title: K_MAP24


title: J_MAP8


title: I_MAP24

value: I


title: I_MAP8


title: I_MAP4


title: I_MAP1


title: SB6

tag: tissue

value: Bone biopsy

value: 60-79 years

tag: treatment

value: Denosumab


title: I_CTL24


title: J_MAP4


title: I_CTL4


title: H_MAP24

value: H


title: H_MAP8


title: H_CTL24


title: H_CTL4


title: H_MAP4


title: G_CTL4

value: G


title: F_MAP24

value: F

value: Positive


title: F_MAP8


title: G_MAP8


title: G_MAP1


title: G_MAP4


title: G_CTL24


title: E_MAP8

value: E


title: F_MAP4


title: E_MAP4


title: E_MAP24


title: E_MAP1


title: F_MAP1


title: G_MAP24


title: D_MAP8

value: D


title: D_MAP24


title: D_MAP4


title: D_MAP1


title: F_CTL24


title: H_MAP1

value: Negative


title: E_CTL4

value: peripheral blood mononuclear cells  (PBMCs)


title: D_CTL24

value: monocyte-derived macrophages


title: D_CTL4


title: C_MAP24

value: C

value: MAP infected


title: C_MAP4


title: C_MAP8


title: E_CTL24

value: Control


title: C_CTL24


title: C_MAP1


title: B_MAP24

value: B


title: B_MAP4


title: C_CTL4


title: B_MAP1


title: A_CTL24

value: A


title: A_MAP24


title: A_MAP4


title: A_CTL4


title: B_MAP8


title: B_CTL4


title: A_MAP1


title: Cortical bone, Prx1Cre; Piezo1fl/fl_Rep4

city: ShangHai

first: Lijun

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Hisat2
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts for each sample

source_name: cortical bone of Prx1Cre; Piezo1fl/fl mice

extract_protocol:
Cortical bones of 6-week WT and  Prx1Cre; Piezo1fl/fl mice were collected and grinded with liquid nitrogen to extract the RNA. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: 6-week WT and  Prx1Cre; Piezo1fl/fl mice.

value: cortical bone

tag: strain

value: Prx1Cre; Piezo1fl/fl


title: Cortical bone, Prx1Cre; Piezo1fl/fl_Rep5


title: Cortical bone, WT_Rep1

source_name: cortical bone of WT mice

value: WT


title: Cortical bone, Prx1Cre; Piezo1fl/fl_Rep1


title: Cortical bone, WT_Rep3


title: Cortical bone, WT_Rep5


title: Cortical bone, WT_Rep4


title: Cortical bone, Prx1Cre; Piezo1fl/fl_Rep3


title: FLASH

city: Paris

first: Charles

last: Fouillade

address: 25 rue d'Ulm

institute: Institut Curie

data_processing:
Fastq files were generated with mkfastq as part of CellRanger pipeline (10x Genomics)
Reads were aligned on mm10 reference genome and raw count matrix file was generated in HDF5 using the CellRanger pipeline.
Raw data was filtered with CellRanger V2.0 pipeline to generate processed count matrix in Market Exchange Format (MEX) supplemented with TSV files with genes and barcode sequences corresponding to rows and columns respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Each sample contains filtered gene-barcode matrix containing the number of UMIs associated with a gene and barcode in Market Exchange Format (MEX) generated by CellRanger V2.0 pipeline (10x Genomics). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

molecule: polyA RNA

source_name: Lung cells

growth_protocol: C57BL/6 female mice, 10-12 weeks old, were maintained at Institut Curie animal facility under normal day-night cycle.

extract_protocol:
Lungs were resected and single cell suspensions were prepared by enzymatic dissociation and sequential filtering (100 and 40 µm) before red blood cell lysis and cell counting. Single-cell 3’-RNA-Seq samples were prepared using single cell V2 reagent kit and Chromium controller (10x Genomics, PN-120237). cDNA quality control was assessed by capillary electrophoresis (Bioanalyzer, Agilent).
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol. Read 1 (26 cycles) corresponds to cell barcode and UMI, Read 2 (98 cycles) corresponds to 3'-end of RNA molecule. Index 1 (8 cycles) is single cell library barcode.

treatment_protocol: Isoflurane anesthesized C57BL6 female mouse received thoracic irradiation with a 4.5 MeV electron LINAC at a dose of 17 Gy delivered either in CONV or FLASH mode.

tag: radiation modality

value: 17 Gy FLASH

value: Lung


title: CONV

value: 17 Gy CONV


title: B_CTL24

value: Positive


title: NI

value: Non-Irradiated Control


title: F_CTL4

value: F


title: A_MAP8


title: Cysts, 8hr_1

city: Bloomington

first: Nandhini

last: Ashok

state: INDIANA

address: 212 south hawthorne drive

institute: Indiana University Bloomington

description: 8 hr after germination initiation - replicate 1

data_processing:
Trimmomatic used to trim reads off adaptors (Sliding window - 5:25; minimum read length - 40BP)
Bowtie2 used to align reads to R.centenum genome. RefSeq assembly accession :  GCF_000016185.1
HT-seq-count to detect reads per gene
De-Seq-2 package used to calculate diffrential expression between 0th hour and every other timepoint
Genome_build: GCF_000016185.1
Supplementary_files_format_and_content: tab-delimited text files include genes (features) and their raw counts for each timepoint

organism: Rhodospirillum centenum

source_name: Germinated bacterial cysts

growth_protocol: Wildtype Rhodosprillum centenum induced to form cysts, cysts purified, and induced to germinate in nutrient rich medium. Samples collected every 1/2 hour till 3rd hour and every hour after that till 8th hour.

extract_protocol:
Cells homogenized in Trizol immedietly after collection. Stored at -80C till extraction. Extracted using Zymo Directzol RNA kit
Library prepared at Univerisity of Wisconsin, Madison - Biotechnology center. Briefly, ribosomal RNA from total RNA removed using Epicentre Ribo-Zero Magnetic (Bacteria) kit with input quantity of 1.5 microgram total RNA. TruSeq RNA sample prep kit (Illumina, San Diego, CA) was used to prepare cDNA mRNA-seq libraries. Standard illumina protocol used for sinle-end sequencing

value: 60±5 hours old

value: Wildtype

value: 8hr after induction of germination


title: Cysts, 8hr_3

description: 8 hr after germination initiation - replicate 3


title: Cysts, 8hr_2

description: 8 hr after germination initiation - replicate 2


title: Cysts, 7hr_3

description: 7 hr after germination initiation - replicate 3

source_name: Germinated and germinating bacterial cysts

value: 7hr after induction of germination


title: Cysts, 6hr_3

description: 6 hr after germination initiation - replicate 3

value: 6hr after induction of germination


title: Cysts, 6hr_2

description: 6 hr after germination initiation - replicate 2


title: Cysts, 7hr_1

description: 7 hr after germination initiation - replicate 1


title: Cysts, 7hr_2

description: 7 hr after germination initiation - replicate 2


title: Cysts, 5hr_2

description: 5 hr after germination initiation - replicate 2

source_name: Germinating bacterial cysts

value: 5hr after induction of germination


title: Cysts, 4hr_2

description: 4 hr after germination initiation - replicate 2

value: 4hr after induction of germination


title: Cysts, 4hr_3

description: 4 hr after germination initiation - replicate 3


title: Cysts, 3hr_3

description: 3 hr after germination initiation - replicate 3

value: 3hr after induction of germination


title: Cysts, 4hr_1

description: 4 hr after germination initiation - replicate 1


title: Cysts, 2_5hr_3

description: 2.5 hr after germination initiation - replicate 3

value: 2.5hr after induction of germination


title: Cysts, 2hr_3

description: 2 hr after germination initiation - replicate 3

value: 2hr after induction of germination


title: Cysts, 3hr_1

description: 3 hr after germination initiation - replicate 1


title: Cysts, 2hr_2

description: 2 hr after germination initiation - replicate 2


title: Cysts, 2_5hr_2

description: 2.5 hr after germination initiation - replicate 2


title: Cysts, 1_5hr_3

description: 1.5 hrs after germination initiation - replicate 3

value: 1.5hr after induction of germination


title: Cysts, 3hr_2

description: 3 hr after germination initiation - replicate 2


title: Cysts, 1_5hr_2

description: 1.5 hrs after germination initiation - replicate 2


title: Cysts, 1hr_3

description: 1 hr after germination initiation - replicate 3

value: 1hr after induction of germination


title: Cysts, 1_5hr_1

description: 1.5 hrs after germination initiation - replicate 1


title: Cysts, 1hr_2

description: 1 hr after germination initiation - replicate 2


title: Cysts, 1hr_1

description: 1 hr after germination initiation - replicate 1


title: Cysts, 0_5hr_3

description: 0.5 hrs after germination initiation - replicate 3

value: 0.5hr after induction of germination


title: Cysts, 5hr_1

description: 5 hr after germination initiation - replicate 1


title: Cysts, 6hr_1

description: 6 hr after germination initiation - replicate 1


title: Cysts, 5hr_3

description: 5 hr after germination initiation - replicate 3


title: Cysts, 2_5hr_1

description: 2.5 hr after germination initiation - replicate 1


title: Cysts, 0hr_3

description: Cysts before intiation of germination - replicate 3

source_name: Enriched bacterial cysts

value: 0hr after induction of germination


title: Cysts, 0hr_1

description: Cysts before intiation of germination - replicate 1


title: Cysts, 2hr_1

description: 2 hr after germination initiation - replicate 1


title: control_female_R2

city: Wuhan

first: Zhen-Xia

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

description:
control female rep2
wt_5F_oA

data_processing:
High-throughput sequencing raw image data files were converted to reads using CASAVA Base Calling (bcf2fastq) analysis.
We used FastQC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9).
Reads were mapped to the corresponding reference genomes (Ensembl v93) by Hisat2 (2.0.5) with parameters “--dta -x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format (Ensembl v93)
The output of Hisat2 were converted to BAM format and sorted by Samtools (1.5) and Samtools rmdup was used for removing PCR duplicates.
HTSeq (0.9.1) was used for counting reads with parameters “-t exon –i gene_id -r pos -s reverse”.
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw_readcounts file contains matrix with not normalized (raw) read counts for 16 samples. Column names in the file correspong to sample names in the Samples table, row names correspond to Ensembl gene ID, each cell is a number of reads for the gene in the row and the sample in the column.
Supplementary_files_format_and_content: Normalized_readcounts contains matrix with normalized read counts for 16 samples. Column names in the file correspong to sample names in the Samples table, row names correspond to Ensembl gene ID, each cell is a number of reads for the gene in the row and the sample in the column.

organism: Danio rerio

source_name: control female gonad replicates2

growth_protocol: The zebrafish (AB strain) were maintained at 28.5°C in the recirculation systems with a light:dark cycle of 14 hr:10 hr according to the zebrafish book (Westerfield, M. 2000, https://zfin.org/zf_info/zfbook/zfbk.html ). The fish were fed twice daily with fish food (Zeigler AP100) for three months. The samples were obtained with the approval from National Research Council (NRC), strictly following the guidelines set for the usage of animals by this committee.

extract_protocol:
Total RNA were extracted using Trizol method. We added 1 ml Trizol (invitrogen) to the sample (4-7 million cells) stored at -80 °C and homogenized the sample by pipette. Then, 200 ul Chloroform was added to the homogenate and the sample was vigorously shaked by hand for 15 seconds until the phase separation disappeared. After standing at room temperature for 2-3 minutes, the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The colorless supernatant was transferred to another new centrifuge tube, mixed with equal volume of isopropanol thoroughly, kept standing at -20°C for 10 minutes, and then centrifuged at 12,000 g for 10 minutes at 4°C to pellet the RNA. The supernatant was carefully removed, and the pellet was gently washed with 1 ml fresh 75% ethanol for 2-3 times, dried for 2 to 3 minutes at room temperature and dissolved in 50 ul RNase-free water.
Stranded PolyA+ RNA libraries were prepared at BGI with in-house kits. The quality of the libraries were assessed by checking the distribution of the fragment size using the Agilent 2100 bioanalyzer, and the quantity of the libraries were measured using real-time quantitative PCR (TaqMan Probe). The qualified libraries were amplified on cBot to generate clusters on the flowcell, and then sequenced on the Illumina HiSeq XTen System.

treatment_protocol: Zebrafish with four treatments, including Exemestane (50ug/L), Exemestane (100ug/L), Exemestane (200ug/L) and control, were maintained in four tanks of separated recirculation systems. Each tank contained 3 males and 3 females. Exemestane (Lot#:C10070672, MACKLIN) was dissolved in Dimethyl sulfoxide (Sinopharm Chemical Reagent Co., Ltd.) before use. Drug was dissolved in system water and the water was changed every day to ensure the effective concentration of Exemestane. After 32 days drug treatment, zebrafish gonads were dissected and preserved in liquid nitrogen.

value: Gonad

value: AB

tag: gender

value: Female

tag: drug concentration

value: control

value: 4 month

tag: library type

value: fr-firststrand (dUTP)


title: control_female_R1

description:
control female rep1
wt_4F_oA

source_name: control female gonad replicates1

tag: age


title: EM_high_female_R2

description:
Exemastane3 female rep2
D3_5F_oA

source_name: 200ug/L exmestane female gonad replicates2

value: Exemastane


title: control_male_R1

description:
control male rep1
wt_1M_tA

source_name: control male gonad replicates1

value: Male


title: control_male_R2

description:
control male rep2
wt_3M_tA

source_name: control male gonad replicates2


title: Cysts, 0_5hr_2

description: 0.5 hrs after germination initiation - replicate 2

value: 60±5 hours old

tag: genotype

value: Wildtype


title: Fever

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

description: Thermal gradients (mean difference 15 ± 7.4 °C )

data_processing:
Illumina MiSeq reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq release 2013-5-10). Exclusions included a minimum RPKM value of 1.0 in at least two of the 16 samples (potentially duplicates of one sample group). RPKM values were log2-transformed with an offset value of 1.0.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Salmo salar

source_name: spleen

growth_protocol: S. salar’s embryos were obtained from AquaGen S.A. (Melipeuco, Chile) in December 2015. Fish embryos were maintained in a recirculating freshwater systems (temperature = 7 ± 0.7°C) with a constant photoperiod of light: dark (LD) until hatching. Then, when 95% of the embryos hatched (i.e., 30 days post-hatching), temperature was gradually incremented until reaching 15 ± 0.9°C (Figure 1). The fish were maintained for 10 months and fish were fed twice a day on a commercial diet.

extract_protocol:
Random fish were sampled for each treatment (Mock, Fever, No-Fever; n= 9 per treatment and replicate x3 N= 18) and time (24, 48, 72 and 96 hpi) and subsequently snap-frozen in liquid nitrogen and conserved at -80 °C. Total RNA was extracted from spleen with Ribo-Pure™ Kit (Ambion®, USA) according to the manufacturer’s instructions. KAPA Stranded mRNA-Seq Kit (KapaBiosystems, MA, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vivo infection of parr salmon with IPNv was performed by immersion. After 120 minutes, fish were separated in two groups and placed in the two-different experimental thermal set up per triplicate. (a) constant temperature (mean temperature 15 ± 0.9 ºC, “No-Fever”) and (b) temperature gradient (mean temperature 15 ± 7.4 ºC, “Fever”). In parallel, fish in another tank were treated by adding 100 ml virus free cell culture supernatant to the water (mean temperature 15 ± 7.4 ºC, "mock-infected"). Then, three independent experimental infection set-up were carried out  (n= 20 fish by condition, Mock, Fever, No-Fever).

tag: developmental stage

value: Parr

tag: in vivo infection

value: IPNv

tag: hours post infection


title: Mock

value: Virus free cell culture supernatant


title: Cysts, 0_5hr_1

description: 0.5 hrs after germination initiation - replicate 1

tag: time


title: EM_high_female_R1

description:
Exemastane3 female rep1
D3_4F_oA

source_name: 200ug/L exmestane female gonad replicates1


title: EM_high_male_R1

description:
Exemastane3 male rep1
D3_1M_tA

source_name: 200ug/L exmestane male gonad replicates1


title: Cysts, 0hr_2

description: Cysts before intiation of germination - replicate 2


title: SKIN_REP1

city: medellin

first: Jean

middle: Paul

last: Delgado

state: antioquia

country: Colombia

institute: University of Atioquia

data_processing:
Sequenced reads were assembly using Trinity V 2.0.6 software pipeline, and default Trimmomatic parameters to remove sequence adapters and low quality reads (Phred score < 5), The reference transcriptome was assembled from all RNA samples and all contigs with length ≥ 200 nucleotides.
Sequence reads generated from limb tissue samples were aligned to the reference transcriptome using Bowtie2 (Langmead & Salzberg 2012) and RSEM (RNA-Seq by Expectation Maximization) was used to obtain estimates of transcript abundance for all transcripts (Li & Dewey 2011). Expression levels were calculated as transcripts per million (TPM) and Fragments Per Kilobase Million (FPKM)
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample
Supplementary_files_format_and_content: reference transcriptome in fasta format

organism: Bolitoglossa vallecula

source_name: Dorsal and ventral skin

extract_protocol:
Total RNA from tissues were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of mRNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dorsal and ventral skin

value: Adult


title: Mouse_molar_E16

city: Sendai

first: Takashi

last: Nakamura

address: 4-1 Seiryomachi, Aobaku

institute: Tohoku University Graduate School of Dentistrey

description:
Small RNAs
MR025-01

hyb_protocol: Hybridization was carried out with the Genopal®-MICM DNA chips (Mitsubishi Rayon) for detection of mouse miRNAs in 100 µl of hybridization buffer [6 x SSC, 0.2% SDS and 1 µg of heat-denatured labeled RNAs] at 42℃ overnight using a hybridization chamber specific for the Genopal®-DNA chip (Mitsubishi Rayon).

scan_protocol: After hybridization, the DNA chips were washed twice in 2xSSC containing 0.2% SDS at 50℃ for 20 min followed by washing in 2xSSC at 50℃ for 10 min, and then hybridization signals were examined by means of a DNA chip reader adopting multi-beam excitation technology according to the manufacturer’s instructions (Yokogawa Electric Corporation). The Genopal™ array was  scanned, and the image was captured using a cooled charge-coupled device type Microarray Image Analyzer equipped with multibeam excitation technology (Yokogawa Electric Co., Tokyo, Japan).

data_processing: Hybridization signal intensity of each miRNA was normalized to that of the external control oligonucleotides provided by Mitsubishi Rayon.

label_protocol: Isolated small-sized RNAs (~1 µg) were subjected to direct labeling with a fluorescent dye using a PlatinumBright 647 Infrared nucleic acid labeling kit (KREATECH), according to the manufacturer’s instructions. After fluorescent labeling, the labeled RNAs were purified from free fluorescent substrates by the KREApure columns (KREATECH) and used in hybridization.

growth_protocol: Developing 1st molars was disscted from ICR mice

extract_protocol: Small RNAs were purified from ICR mice developing molars at embryonic 16.5 days (E16.5), post-natal 1 day (P1), and P3 using the mirVana miRNA isolation kitTM system (Ambion).  For preparation of cellular miRNAs, 20 µg of each isolated total RNA was mixed with 5 µl of the external control oligonucleotides provided by Mitsubishi Rayon, and subjected to isolation of small-sized RNAs containing miRNAs using an RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: no treatment

value: 1st molar

value: ICR


title: Mouse_molar_P3

description:
Small RNAs
MR025-03


title: Mouse_molar_P1

description:
Small RNAs
MR025-02


title: HEL_GRN163L_LY2784544_rep1

city: Stockholm

first: Jenny

last: Dahlström

address: Solnavägen 1

department: Medicine

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from the HEL cells treated with GRN163L and LY2784544 in the first experiment

hyb_protocol: 3ug of ss DNA target was  hybridized to  a HG 1.1 ST Array Plate and washed and stained in the Gene Titan instrument

scan_protocol: Array was scanned at the Karolinska Instituete, Bioinformatics and Expression Analysis core facility(BEA) according to Gene Titan Instrument standard protocol

data_processing: The data were analyzed with Expression Console software,using the RNA processing method，RMA = Robust Multi array Average，Summarization (Median Polish),Background Correction (RMA Background correction) and Normalization (sketch Quantile)

source_name: first experiment HEL cells treated with GRN163L and LY2784544

label_protocol: 150ng of total RNA was used to generate amplified sense strand DNA targets with Affymetrix  WT Expression Kit followed by fragmentation and biotinylation  with Affymetrix WT Terminal Labeling Kit

growth_protocol: HEL cell line was kept at cell density 0.3-1.2million/ml in RPMI 1640 meidum supplemented with 10% FBS, L-gultamine and Pencillin/streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HEL cells were treated with DMSO, 0.5uM of LY 2784544, 20uM GRN163L, the combination of the LY2784544 and GRN163L, 48 hours later,  cells were harvested.

tag: cell line

value: erythroleukemia cell line HEL


title: LIMB_REP2

source_name: forelimb

value: forelimb


title: HEL_GRN163L_LY2784544_rep2

description: Gene expression data from the HEL cells treated with GRN163L and LY2784544 in the second experiment

source_name: second experiment HEL cells treated with GRN163L and LY2784544


title: HEL_LY2784544_rep2

description: Gene expression data from the HEL cells treated with LY2784544 in the second experiment

source_name: second experiment HEL cells treated with LY2784544


title: HEL_control_rep2

description: Gene expression data from the HEL cells treated with only MDSO as a control group in the second experiment

source_name: second experiment HEL cells treated with only DMSO


title: HEL_LY2784544_rep1

description: Gene expression data from the HEL cells treated with LY2784544 in the first experiment

source_name: first experiment HEL cells treated with LY2784544


title: EM_middle_female_R2

last: Chen

description:
Exemastane2 female rep2
D2_5F_oA

source_name: 100ug/L exmestane female gonad replicates2

value: Gonad

value: AB

value: Female


title: No fever

description: Constant temperature (mean  15 ± 0.9 °C)


title: HEL_GRN163L_rep1

description: Gene expression data from the HEL cells treated with GRN163L in the first experiment

source_name: first experiment HEL cells treated with GRN163L


title: HEL_control_rep1

description: Gene expression data from the HEL cells treated with only MDSO as a control group in the first experiment

source_name: first experiment HEL cells treated with only DMSO

value: control


title: EM_high_male_R2

description:
Exemastane3 male rep2
D3_2M_tA

source_name: 200ug/L exmestane male gonad replicates2

value: Exemastane

value: 4 month

value: fr-firststrand (dUTP)


title: HEL_GRN163L_rep2

description: Gene expression data from the HEL cells treated with GRN163L in the second experiment

source_name: second experiment HEL cells treated with GRN163L