title: KO_52h

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real  time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
After adaptor sequence trimming using Trimmomatic (version 0.36),  the sequence reads were mapped to the mouse genome (GRCm38/mm10) using STAR (2.5.4b). To obtain reliable alignments, the reads with a mapping quality of less than 10 were removed by SAMtools. The University of California, Santa Cruz (UCSC) known canonical gene set (32,989 genes) was used for annotation, and the reads mapped to the exons were quantified using Homer.
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. Tab-delimited text files include RPKM values for each Sample.

source_name: differentiated mES cells (KO)

growth_protocol: Mouse ES cells were seeded in low-attachment 96-well plates and cultured for 2 days for embryoid body EB formation. EBs were then plated onto gelatin-coated 24-well plates and cultured for 26 days.

extract_protocol:
Total RNA samples were prepared using RNeasy Mini Kit (Qiagen) with RNase-Free DNase Set (Qiagen). Total RNA from differentiated cells from three embryoid bodies were pooled and used for the analysis.
PolyA RNA selection, library construction using TruSeq RNA Sample Prep Kit v2, and sequencing were performed by Macrogen Japan (Kyoto) using Illumina NovaSeq6000 with 101-bp paired-end reads according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 100 nM dexamethasone and frozen at the indicated time points.

value: differentiated ES cells

value: Per2::Luciferase knock-in, Rev-erba/Rev-erbb deficient

tag: hours after dexamethasone stimulation


title: Neurons7_Prep1

status: Public on Jul 29 2019

type: SRA

city: La Jolla

first: Daria

last: Merkurjev

state: CA

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

country: USA

institute: UCSD

description: Induced neuronal differentiation from hiPSCs

library_source: transcriptomic

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph

molecule: polyA RNA

organism: Homo sapiens

source_name: single-cell CVB derived hiPSC#7 subline (genome editing: APP V717 -/-, IIIB12)

growth_protocol: hiPSCs were seeded onto PA6 cells in PA differentiation medium for 12 days. Between days 12-14, when rosettes were visible, after dissociation, were  FACS-sorted based on the  CD184+/CD271-/CD44-/CD24+ cell-surface signature. Sorted NPCs were cultured on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated plates in NPC medium until confluency was reached. To generate neurons, NPCs grown in 10 cm-plates at confluency were switched to NPC medium without FGF (day 1), and cultured afterwards for 3 weeks. Around day 21, neurons were sorted based on the CD184-/CD44-/CD24+ signature. For RNAseq experiments 1x106 CD24+ sorted neurons were plated on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated 24-well plates in NPC media supplemented with 0.5mM dbcAMP from Sigma, and 20ng/µL BDNF and 20 ng/µL GDNF.

extract_protocol:
Total RNA was extracted using RNeasy Assay (Qiagen) and converted into cDNA using SuperScript First-Strand Synthesis System (Invitrogen) following manufacture’s protocols.
RNA quality was calculated on TapeStation (Agilent Technologies). Most of samples showed a RIN >7.0 and 7 out of 24 had an RIN between 6 and 7. PolyA+ RNA-seq libraries were generated using the Illumina TruSeq Stranded RNA LT kit and following manufacturer’s detailed instructions.

treatment_protocol: No particular treatment was applied after differentiation.

tag: cell line

value: Craig Venter-B (CVB) hiPSC subline

tag: cell type

value: single-cell derived from CVB line prior to neuronal differentiation, preparation 1


title: KO_48h

molecule: total RNA

organism: Mus musculus

tag: genotype


title: KO_56h


title: KO_44h


title: Neurons6_Prep2

source_name: single-cell CVB derived hiPSC#6 subline (genome editing: APP V717 +/-, IV8)

value: single-cell derived from CVB line prior to neuronal differentiation, preparation 2


title: Pax7 (Flag) ChIPseq in αT3 cells expressing Pax7

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

country: Canada

institute: IRCM

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

molecule: genomic DNA

growth_protocol: AtT-20 cells and αT3 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and antibiotics (penicillin/streptomycin)

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2500 following the manufacturer's protocols to obtain 50bp paired end reads.

tag: genotype/variation

value: expressing Pax7

tag: chip antibody

value: Pax7 (Flag)


title: Flag (control) ChIPseq in αT3 cells expressing Neo

value: expressing Neo

value: Flag (control)


title: Sample1_450K_rep2

type: genomic

city: Singapore

first: LI

last: ZHOU

address: 11 Mandalay Road

country: Singapore

institute: Lee Kong Chian School of Medicine, Nanyang Technological University

description: sample1 replicate 2

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip v1.2 and Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

scan_protocol: Illumina HiScan for Illumina HumanMethylation450 BeadChip and iScan for Illumina Infinium HumanMethylation850 BeadChip using standard recommended Illumina scanner setting.

data_processing:
Custom R scripts.
Raw data provided as Unmethylated and methylated signal intensities as well as in IDAT files.
Procesesd data files include raw BETA values.

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).

tag: tissue

value: whole blood


title: Neurons8_Prep1

source_name: single-cell CVB derived hiPSC#8 subline (failed genome editing, IB7)


title: Input DNA in αT3 cells expressing Pax7


title: KO_40h


title: KO_36h


title: Neurons5_Prep2

source_name: single-cell CVB derived hiPSC#5 subline (genome editing: PSEN1 deltaE9 -/-, IIA12)


title: Neurons6_Prep1


title: ATACseq in AtT-20 cells expressing Pax7 replicate 2

data_processing:
ATAC-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

source_name: ATACseq in AtT-20 cells expressing Pax7

extract_protocol:
Mouse pituitary intermediate or anterior lobes were dissected pituitaries were separated into intermediate and anterior lobes and kept during the dissections in 300µl of dissection buffer (DMEM, 10% FBS, HEPES 10mM and DNase 100 U/ml). Anterior lobes were cut in pieces using a scalpel to facilitate tissue dissociation and digested at 37°C using 5mg/ml Trypsin for 10 minutes. We then added 2mM EDTA and incubated 5 minutes more. 50 000 cells were washed in PBS and incubated on ice for 30 minute in a hypotonic cell lysis buffer (0.1% w/v sodium citrate tribasic dehydrate and 0.1% v/v Triton X100) and centrifuged (5 minutes at 2000g at 4°C). Cells were then incubated 30 minutes on ice in cell lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% v/v IGEPAL CA-630). After centrifugation, the nuclei pellets were resuspended in transposase Master Mix (1.25 µl 10x TD buffer, 5 µl H2O and 6.5 µl of Tn5: Illumina Nextera Kit; FC-121-1031) and incubated for 30 minutes at 37°C. Samples were purified using the DCC purification columns (Zymo).
The eluted DNA was barcoded for multiplexing of samples using Nextera barcodes and PCR-enriched using the Phusion kit. Libraries were recovered with GeneRead Purification columns. Samples were then evaluated by qPCR to test enrichments and sequenced on Illumina Hiseq 2500 with 50bp or 125bp paired-end reads according to Illumina’s recommendation.

tag: tissue/cell type


title: Neurons5_Prep3

value: single-cell derived from CVB line prior to neuronal differentiation, preparation 3


title: Neurons5_Prep1


title: ATACseq in AtT-20 cells expressing Neo replicate 2

source_name: ATACseq in AtT-20 cells expressing Neo


title: KO_28h


title: Neurons4_Prep3

source_name: single-cell CVB derived hiPSC#4 subline (genome editing: PSEN1 deltaE9 -/-, IB12)


title: ATACseq in AtT-20 cells expressing Neo replicate 1


title: ATACseq in αT3 cells expressing Pax7

source_name: ATACseq in αT3 cells expressing Pax7


title: KO_24h


title: Sample8_EPIC


title: Neurons4_Prep2


title: KO_20h


title: Sample7_EPIC

source_name: Neutrophils

value: Neutrophils


title: Neurons4_Prep1


title: ATACseq in αT3 cells expressing Neo

source_name: ATACseq in αT3 cells expressing Neo


title: KO_16h


title: Sample6_EPIC


title: Neurons3_Prep3

source_name: single-cell CVB derived hiPSC#3 subline (genome editing: PSEN1 deltaE9 +/-, IID12)


title: ATACseq in AtT-20 cells expressing Pax7 replicate 1


title: Sample5_EPIC


title: WT_56h

source_name: differentiated mES cells (control)

value: Per2::Luciferase knock-in


title: Neurons3_Prep2


title: KO_12h


title: KO_32h


title: ATACseq in Tpit Knockout intermediate pituitary rep2

tag: strain background

value: mixed background 129sv X Balb/C

value: Neuro-intermediate pituitary


title: Neurons3_Prep1


title: ATACseq in Pax7 and Tpit double Knockout intermediate pituitary rep1


title: ATACseq in Tpit Knockout intermediate pituitary rep1


title: ATACseq in Pax7 Knockout intermediate pituitary rep1


title: Neurons2_Prep3

source_name: single-cell CVB derived hiPSC#2 subline (genome editing: PSEN1 deltaE9 +/-, IIA11)


title: ATACseq in Pax7 Knockout intermediate pituitary rep2


title: WT_48h


title: WT_52h


title: WT_44h


title: ATACseq in Pax7 Het;Tpit Het intermediate pituitary rep2


title: Neurons2_Prep1


title: Neurons1_Prep3

source_name: single-cell CVB derived hiPSC#1 subline (failed genome editing, IID4)


title: WT_40h


title: ATACseq in Pax7 Het;Tpit Het intermediate pituitary rep1


title: WT_36h


title: Neurons1_Prep2


title: ATACseq in wild type intermediate pituitary rep2

value: WT


title: WT_32h


title: Neurons1_Prep1


title: ATACseq in wild type intermediate pituitary rep1


title: WT_28h


title: ATACseq in purified gonadotropes

source_name: ATACseq in purified gonadotropes

value: Gonadotropes


title: ATACseq in purified anterior pituitary

description: HI.4191.001_AL_noGonado_ATAC_12cycles_rep1

source_name: ATACseq in purified anterior pituitary

value: Anterior pituitary


title: WT_20h

value: differentiated ES cells


title: WT_24h


title: Neurons2_Prep2

value: Craig Venter-B (CVB) hiPSC subline


title: HnRNP C Input

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

description:
protein crosslinked RNA
crosslink over the background
iCLIP-Seq

data_processing:
Library strategy: iCLIP-Seq
Fastq files were demultiplexed and aligned using the iCount server
Reads were filtered to remove any peaks within 50 nt of a repeatMasker-annotated repeat or a short non-coding RNA
High-confidence peaks were identified using the 'peaks' option on the iCount server, with the parameters regionAsOne, flank 50, random perms 100 and fdr 0.05
Genome_build: mm9

source_name: mESC

growth_protocol: Cells were cultured on  0.1% gelatin-coated surfaces with KO-DMEM medium, 10% FCS, 5% knockout serum replacement, nonessential amino acids, L-glutamine, 2-mercaptoethanol, antibiotics (Invitrogen), and 1000 U/ml of leukaemia inhibitory factor (Abcam).

extract_protocol:
Input Individual-nucleotide resolution UV crosslinking and immunoprecipitation protocols were based in  modification of protocols available at Huppertz et al. Cells were irradiated with 0.2 J/cm2  of UV light in a Strataliker 2400 (Stratagene) with bulbs emitting at 254nm, and 25 x106 cells  per sample were lysed in 50μL of Lysis buffer (see iCLIP section). Lysates were syringed with a 27G needle and incubated in a Thermomixer at 37°C and 1100 rpm for three minutes after addition of 200U/mL of DNase Turbo and of 20 U/mL of RNase I. Sample was mixed with Nupage loading buffer with reducing agent and run on a 4-12% NuPAGE Bis-Tris gel (Invitrogen) in MOPS buffer according to the manufacturer's instructions. Protein-RNA complexes were transferred to a nitrocellμlose membrane (Hybond, GE Healthcare) washed 2x with PBS1x and exposed to a Fuji film. Using the auto-radiograph previously used for iCLIP as a mask RNA-protein complexes  attached to the membrane were isolated and treated with 200 μl PK buffer (100 mM Tris-HCl pH 7.4; 50 mM NaCl; 10 mM EDTA) and 10 μl proteinase K (Roche, 03115828001)  for 20 minutes at 1,100 rpm and 37°C. 200 μl of PKurea buffer (100 mM Tris-HCl pH 7.4; 50 mM NaCl; 10 mM EDTA; 7 M urea) was added and a second incubation was performed for 20 minutes at 37°C and 1100 rpm. Solution was collected and RNA was isolated by phenol; chloroform extraction and ethanol precipitation over night at -20°C.
RNA pellet was resuspended in 20 μl PNK mix (15 μl water; 4 μl 5x PNK pH 6.5 buffer [350mMTris-HCl, pH 6.5; 50mMgCl2 25mMdithiothreitol]; 0.5 μl PNK enzyme; 0.5 μl RNasin [Promega]) and incubated 30 min at 37°C 1100 rpm. Solution was collected and RNA was isolated by phenol; chloroform extraction and ethanol precipitation over night at -20°C. Pellet was resuspended in 20 μl ligation mix (9 μl water; 4 μl 4x ligation buffer [200 mMTris-HCl; 40m MM gCl2; 40 mM dithiothreitol]; 1 μl RNA ligase [NEB]; 0.5 μl RNasin [Promega]; 1.5 μl pre-adenylated linker L3 [20 μM]; 4 μl PEG400 [81170, Sigma]), ligation was performed over night at 16°C and 1100 rpm. L3-RNA was isolated by phenol; chloroform extraction and ethanol precipitation over night at -20°C and pellet were resuspended in 13 μl of H20, reverse transcription was performed using specific oligo and Superscript III (Thermo) according instructions.
cDNA was isolated by phenol; chloroform extraction and ethanol precipitation over night at -20°C and pellet were resuspended in 10 μl of H20+ TBE-Urea buffer. cDNA was fractionated by running samples on a precast 6% TBE-urea gel at 180 V for 40 min and cDNA bands running between 250-180 nt (top), 120-180 nt (high), 85-120 nt (medium) and 70-85 nt (low) isolated. cDNA was isolated Tris-EDTA gel resuspension and separation by phenol; chloroform extraction and ethanol precipitation over night at -20°C. cDNA was circularised using Circligase II (CamBio) and digested after hybridization with annealing oligo with BamHI. cDNA was isolated by phenol; chloroform extraction and ethanol precipitation over night at -20°C and pellet were resuspended and amplification was performed using 10 μl cDNA; 1 μl primer mix P5/P3 solexa, 10 μM each; 20 μl Accuprime Supermix 1 enzyme [Invitrogen], 9H20  and the following PCR programme: 94°C for 2 min, [94°C for 15 sec, 65°C for 30 sec, 68°C for 30 sec]n cycles, 68°C for 3 min, 4°C, with a number of cycles optimized previously. Library integrity was analysed using 8 μl PCR product with 2 μl of 5x TBE loading buffer and loading on a precast 6% TBE gel (Invitrogen). Gel was stained with Sybrgreen I (Invitrogen) and analyse with a gel imager. Concentration was determined using KAPPA kit according manufacturer instructions.

value: mESC

tag: strain

value: m ESC Ezh2 fl/fl

tag: treatment

value: No Tamoxifen

value: Ezh2 wild type

tag: ip antibody


title: WT_16h


title: WT_12h


title: FUS Input


title: Spring Castrated Hypothalamus sample

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

data_processing:
Adapter trimming was done using Universal adaptor sequences by Trimmomatic
The HQ reads so obtained were further processed as per Kallisto protocol (Bray et al., 2016)
Genome_build: FicAlb_1.4
Supplementary_files_format_and_content: m8 file (tab separated)

organism: Emberiza bruniceps

source_name: Caught from wild

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

value: Hypothalamus

tag: group

value: Spring Castrated


title: Spring Intact Hypothalamus sample

value: Spring Intact


title: Autumn Castrated Hypothalamus sample

value: Autumn Castrated


title: Autumn Intact Hypothalamus sample

value: Autumn Intact


title: HPgV-negative PBMCs_rep2

status: Public on Jul 28 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: HPgV-negative peripheral blood mononuclear cells

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: HPgV-negative PBMCs

extract_protocol:
Total RNA was extracted from PBMCs using the PureLink RNA Mini Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using the TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina, San Diego, CA, USA). according to the manufacturer’s instructions.

value: PBMC cells


title: HPgV-negative PBMCs_rep3


title: HPgV-negative PBMCs_rep1


title: HPgV-positive PBMCs_rep3

description: HPgV-positive peripheral blood mononuclear cells

source_name: HPgV-positive PBMCs


title: HPgV-positive PBMCs_rep2


title: Suz12 Input


title: 2C-3

city: Wuhan

first: Ce

last: Shi

address: Bayi Road

country: China

institute: Wuhan University

description: Amplified with SMART-Seq Ultra Low Input RNA Kit

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Nicotiana tabacum genome Ntab-TN90 using Tophat2.
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization).
Genome_build: Nicotiana tabacum genome Ntab-TN90
Supplementary_files_format_and_content: text file including FPKM value of each gene.

organism: Nicotiana tabacum

source_name: 2-celled proembryo

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 25 °C

extract_protocol:
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMARTer Ultra Low Input RNA Kit for Sequencing v3 (Clonetech) was used to generate cDNA library for sequencing
Libraries were constructed using TD503-01 TruePrep DNA Library Prep Kit V2 (Vazyme) for Illumina.

value: 2-celled proembryo

tag: developemntal stage

value: 4 days after pollination


title: Breast adenocarcinoma cell line MCF7 – cultured with oestrogen – rep2

type: RNA

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: microRNA expression of MCF7 cell cultured in the presence of 1 nmol/L 17β-oestradiol

hyb_protocol: RNA hybridization was performed in accordance to manufacturer’s indications.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner G2505C. Numerical raw values were obtained using Feature Extraction 10.7.3.1 software (Agilent Technologies). Grid: 253118115581_S01_grid. Protocol: miRNA_107_Sep09

data_processing: Data were normalized and analyzed using GeneSpring GX v.14.8 software (Agilent Technologies). Data transformation was applied to set all the negative raw values at 1.0, then the quantile normalization was applied. Filters on gene expression were used to keep only the miRNAs expressed in at least one sample

source_name: Breast adenocarcinoma

label_protocol: RNA labeling was performed in accordance to manufacturer’s indications.

growth_protocol: MCF7 and LTED human breast cancer cells were obtained from ATCC and cultured in phenol free-red RPMI 1640 medium supplemented with 10% foetal bovine serum and 2 mmol/L glutamine. Cells were short tandem repeat tested, amplified, stocked, routinely subjected to mycoplasma testing and once thawed were kept in culture for a maximum of 20 passages.

extract_protocol: Total RNA (including microRNA) was extracted using miRNeasy (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: MCF7- and LTED cells were maintained in sterol-deprived medium in phenol red–free RPMI1640 medium containing 10% dextran charcoal-stripped (DCC) FBS and 2 mmol/L glutamine (DCC medium). MCF7+ cells were grown as MCF7+ and LTED in the presence of 1 nM 17β-oestradiol (E2, Sigma).


title: Breast adenocarcinoma cell line MCFT – cultured without oestrogen – rep1

description: Gene expression of MCF7 cell cultured in absence of oestrogens for 3 days

scan_protocol: Arrays were scanned with Agilent Technologies Scanner G2505C. Numerical raw values were obtained using Feature Extraction 10.7.3.1 software (Agilent Technologies). Grid: 028004_D_F_20140813. Protocol: GE1_107_Sep09

data_processing: Data were normalized and analyzed using GeneSpring GX v.14.8 software (Agilent Technologies). Data transformation was applied to set all the negative raw values at 1.0, then the quantile normalization was applied. A filter on low gene expression was used to keep only the probes expressed in at least one sample.

value: Non-treated

value: MCFT-


title: Breast adenocarcinoma cell line MCF7 – Long Term Estrogen Deprived (LTED) – rep1

description: microRNA expression of Long Term Estrogen Deprived MCF7 cells (LTED)

value: Long Term Estrogen Deprived MCF7 cells

value: LTED


title: Breast adenocarcinoma cell line MCF7 – cultured with oestrogen – rep3


title: Breast adenocarcinoma cell line MCF7 – cultured with oestrogen – rep1


title: Gastro_26m_old3

first: Yasutomi

last: Kamei

address: 1-5 Shimogamo-Hangicho, Sakyo-ku

institute: Kyoto Prefectural University

description: Gene expression in skeletal muscle (gastrocnemius, 26 months of age)

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-028005 Whole Mouse Genome Microarray 8 × 60K G4858A was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1_1100_Jul11 and Grid: 028005_D_F_20150604) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of young mice (13 weeks of age) and aged mice (26 months of age). RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany).

value: gastrocnemius muscle

tag: gender

value: male

tag: age


description: microRNA expression of MCF7 cell cultured in absence of oestrogens for 3 days


title: Breast adenocarcinoma cell line MCFT – cultured without oestrogen – rep3

description: microRNA xpression of MCF7 cell cultured in absence of oestrogens for 3 days


title: Breast adenocarcinoma cell line MCFT – cultured without oestrogen – rep2


title: Gastro_26m_old2


title: HPgV-positive PBMCs_rep1


description: Gene expression of MCF7 cell cultured in the presence of 1 nmol/L 17β-oestradiol


title: Breast adenocarcinoma cell line MCF7 – Long Term Estrogen Deprived (LTED) – rep2


title: 2C-2


title: Gastro_26m_old1


title: 2C-1


title: Gastro_13w_young3

description: Gene expression in skeletal muscle (gastrocnemius, 13 weeks of age)


description: Gene expression of Long Term Estrogen Deprived MCF7 cells (LTED)


title: Breast adenocarcinoma cell line MCF7 – Long Term Estrogen Deprived (LTED) – rep3


title: Gastro_13w_young1


title: Gastro_13w_young2


title: Nacc-SAL/COC3-RNAseq

status: Public on Jul 27 2019

city: New York

first: Philippe

last: Melas

address: 1051 Riverside Drive

institute: Columbia University

description:
Cocaine-treated
NACC_FPKM.xlsx
sample name in processed data file:
C

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, and only reads mapping as matched pairs and being uniquely mapped (mapping quality >= 1) were used for further analysis. The 42 base pair (bp) length of the reads were used for peak-calling and the generic term “interval” was used to describe genomic regions with local enrichments in tag numbers. Intervals were defined by the chromosome number, and a start and end coordinate.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff p-value of 1e-7 and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
HISAT2 was used to map filtered sequenced reads to the reference rat genome, HTSeq was used to analyze gene expression levels (in union mode)
DESeq was used for differential gene expression analysis
rMATS (replicate multivariate analysis of transcript splicing) was used for detection of differential alternative splicing (AS)
Genome_build: RN6(Nacc-RNAseq and ATACseq), RN5(PFC-RNAseq)
Supplementary_files_format_and_content: xlsx files including FPKM value for each sample

organism: Rattus norvegicus

source_name: Cocaine-treated

extract_protocol:
Total RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
ATAC-seq: Nuclei from flash frozen PFC tissue were extracted and 100,000 nuclei were tagmented. DNA were prepared using Nextera library prep kit.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

value: Nucleus Accumbens

value: Sprague-Dawley

tag: Sex


title: PFC-COC3-RNAseq

description:
Cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
Coc_3

value: PFC


title: PFC-COC1-RNAseq

description:
Cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
Coc_1


title: PFC-COC2-RNAseq

description:
Cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
Coc_2


title: Nacc-WIN/COC3-RNAseq

description:
WIN+cocaine-treated
NACC_FPKM.xlsx
sample name in processed data file:
F

source_name: WIN+cocaine-treated


title: Nacc-WIN/COC2-RNAseq

description:
WIN+cocaine-treated
NACC_FPKM.xlsx
sample name in processed data file:
E


title: PFC-WIN+COC2-RNAseq

description:
WIN+cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
WIN_Co_2


title: PFC-WIN+COC3-RNAseq

description:
WIN+cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
WIN_Co_3


title: Nacc-WIN/COC1-RNAseq

description:
WIN+cocaine-treated
NACC_FPKM.xlsx
sample name in processed data file:
D


title: PFC-WIN+COC1-RNAseq

description:
WIN+cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
WIN_Co_1


title: Nacc-SAL/COC2-RNAseq

description:
Cocaine-treated
NACC_FPKM.xlsx
sample name in processed data file:
B


title: Nacc-SAL/COC1-RNAseq

description:
Cocaine-treated
NACC_FPKM.xlsx
sample name in processed data file:
A


title: PFC-WIN3-RNAseq

description:
WIN-treated
PFC_FPKM.xls
sample name in processed data file:
WIN_3

source_name: WIN-treated


title: PFC-Control2-RNAseq

description:
control
PFC_FPKM.xls
sample name in processed data file:
Ctrl_2

source_name: control


title: KIAA1429-rep2-RIP

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using BOWTIE software (V2.1.0).
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.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *-RIP.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: HCC cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) 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: intervention

value: KIAA1429 RNA immunoprecipitation


title: IgG-rep2-RIP

tag: cell line

value: IgG RNA immunoprecipitation


title: KIAA1429-rep1-RIP


title: PFC-Control3-RNAseq

description:
control
PFC_FPKM.xls
sample name in processed data file:
Ctrl_3


title: IgG-rep1-RIP


title: Fulvestrant rep 3

city: Solna

first: Jordi

last: Carreras-Puigvert

state: Stockholm

address: Tomtebodavägen 23A, SciLifeLab, Alfa 4

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
Replicate 3
normal_vs_treatment_2.gene_expression_table.tsv

data_processing:
RNA-seq reads aligned to reference genome or transcriptome using Bowtie v2.3.3.1
Identification of potential exon-exon splice junctions by TopHat v2.0.14
Identification and quantification of transcripts from the preprocessed RNA-Seq alignment-assembly by Cufflinks
Merging of the identified transcript pieces to full length transcripts and annotate the transcripts based on the given annotations by Cuffmerge
Cuffdiff is used to merge transcripts from two or more samples/conditions to then determine the expression levels at transcript and gene level including a measure of significance between samples/conditions
Genome_build: Hg38 / GRC38, UCSC. Annotations Genecode v27, Ensembl 90
Supplementary_files_format_and_content: tsv files containing gene expression values or FPKM values as well as statistical scores

growth_protocol: MCF-7 cells were routinely grown in DMEM supplemented with 10% FCS and 1% Streptomycin/Penicillin, at 37°C in a 5% CO2 humidified incubator

extract_protocol:
The cells were subsequently harvested and frozen at −80 °C, and the samples were processed by Eurofins Genomics Sweden AB, were the RNA was isolated and assessed for QC, and finally cDNA library preparation was performed
Illumina single read sequencing with a read length of 1x 50 bp and 30million reads per sample was performed
Strand-specific cDNA library  - Purification of poly-A containing mRNA molecules  - mRNA fragmentation  - Random primed cDNA synthesis (strand-specific)  - Adapter ligation and adapter specific PCR amplification

treatment_protocol: MCF-7 cells were grown in DMEM or phenol-red free SFM medium or in the presence of 1uM Fulvestrant during 20 days.

value: 1uM Fulvestrant


title: PFC-WIN2-RNAseq

description:
WIN-treated
PFC_FPKM.xls
sample name in processed data file:
WIN_2


title: PFC-Control1-RNAseq

description:
control
PFC_FPKM.xls
sample name in processed data file:
Ctrl_1


description: Gene expression of Long Term Estrogen Deprived MCF7 cells (LTED)

tag: cell type


title: Fulvestrant rep 2

description:
Replicate 2
normal_vs_treatment_2.gene_expression_table.tsv


title: Fulvestrant rep 1

description:
Replicate 1
normal_vs_treatment_2.gene_expression_table.tsv


title: Primary islet cells, quality 3, S975

city: Camperdown

first: Anand

last: Hardikar

state: NSW

address: 92-94 Parramatta Road

country: Australia

institute: University of Sydney

data_processing:
Fragments Per Kilobase of transcript sequence per Millions base pair sequenced (FPKM) were calculated for lncRNAs in each sample using Cuffdiff (v2.1.1)
In-house perl scripts were used to remove reads containing adapter, reads on containing ploy-N and low quality reads from the raw data (reads) leaving only the clean data (reads).
The index of the reference human GRCh38 (hg38) genome (//ftp.ensembl.org/pub/release-82/fasta/homo_sapiens/dna/) and the GTF files (ftp://ftp.ensembl.org/pub/release-82/gtf/homo_sapiens/) were used for annotation (obtained from the genome website) and built using Bowtie v2.0.6. TopHat v2.0.9 was used to align paired-end clean reads to the reference genome.
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs

source_name: Human Islets

growth_protocol: Human Islet Isolated sample preparations were extracted for RNA. The RNA of each islet sample preparation was used for RNA-seq.

extract_protocol:
RNA was extracted using TRIzol® RNA Isolation (Thermo Fisher Scientific, Waltham, MA) protocol with minor modification  (Joglekar et al. 2012)
Sequencing libraries were generated using the rRNA-depleted RNA with the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) through following manufacturer’s protocol.

treatment_protocol: Not applicable (n/a)

tag: quality (group)


title: Primary islet cells, quality 3, S745


title: PFC-WIN1-RNAseq

description:
WIN-treated
PFC_FPKM.xls
sample name in processed data file:
WIN_1


title: Primary islet cells, quality 3, S976


title: Primary islet cells, quality 2, S726


title: Primary islet cells, quality 1, S396


title: Primary islet cells, quality 2, S574


title: Primary islet cells, quality 1, S321


title: Primary islet cells, quality 2, S462


title: DMEM rep 3

description: Replicate 3

value: DMEM


title: DMEM rep 2

description: Replicate 2


title: Primary islet cells, quality 3, S298


title: SFM (steroid free medium) rep 1

description:
Replicate 1
normal_vs_treatment_1.gene_expression_table.tsv

value: phenol-red free SFM


title: Primary islet cells, quality 1, S712


title: Primary islet cells, quality 3, S458


title: Primary islet cells, quality 2, S263


title: Primary islet cells, quality 2, S234


title: DMEM rep 1

description: Replicate 1


title: SFM (steroid free medium) rep 2

description:
Replicate 2
normal_vs_treatment_1.gene_expression_table.tsv


title: LuCaP_173-2A_ET1554_ET2232_LCM_SCC

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 173.2 PDX tumor, LCM squamous pearl cells

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.  For PDX samples, sequences aligning to the mm10 mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from laser capture microdissected (LCM) LuCaP tumors with Arcturus PicoPure RNA Isolation Kit including the optional Dnase treatment.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: cell line source

value: LuCaP

value: prostate cancer

tag: sample type

value: LuCaP 173.2 PDX tumor

value: LCM squamous pearl cells

tag: molecular phenotype


title: Primary islet cells, quality 1, S177


title: LuCaP_173-2A_ET1554_LCM_CaP

description: LuCaP 173.2 PDX tumor, LCM adenocarcinoma

value: LCM adenocarcinoma


title: rep3 50mM MgSO4 presort

city: Cambridge

first: Conor

middle: James

last: McClune

state: MA

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

description: plasmid DNA

data_processing:
Library strategy: PCR amplicon sequencing
Reads with errors outside of the variable/barcode and mutated nucleotides were discarded to remove low quality reads
The frequency of each mutant in each bin was calculated as a function of the total reads in each bin and the total number of cells sorted into each bin (McClune et al., 2018)
Variants with fewer than 25 total reads were discarded
Gaussian functions were fit to each distribution (in log10YFP units), from both the ON and OFF sorts (SciPy optimize package).
The standard deviation error on the estimated log(YFP) mean was used as a metric to filter poorly fit sequences (sequences were removed if  ONstdev + OFFstdev > 2)
Fold induction was calculated as the ratio of the fit means between the induced (10uM MgSO4) and uninduced  (50mM MgSO4) states.
Supplementary_files_format_and_content: csv file. First line contains column titles

organism: Escherichia coli str. K-12 substr. MG1655

source_name: rep3 50mM MgSO4 presort

growth_protocol: Cells were grown in the indicated conditons for 6hr, then sorted into consecutive bins based on their YFP fluorescence. E. coli libraries were grown overnight in 2xYT media

extract_protocol:
plasmid DNA was extracted with the Quiagen plasmid Miniprep Kit
For the two mutagenized regions of the plasmid to be brought into close enough proximity (< 790 bp) for paired-end Illumina sequencing, plasmids were digested with XhoI and then self-ligated (T4 ligase, 4 hr). To isolate only self-ligation products, and not cross-ligation products, ligation reactions were cleaned (Zymo PCR Clean Up) and gel purified to select for the correct size on FlashGels (Lonza). Two PCR reactions were performed, both using KAPA HiFi Hotstart, to add Illumina sequencing adaptors and barcodes. First, ligation reaction products were amplified for 30 cycles (95 °C for 30 s, 65 °C for 15 s, 72 °C for 120 s) with primers CJM642 and CJM643 in an emulsion PCR (Micellula Emulsion PCR) to avoid PCR chimeras. Second, purified PCR product from the first reaction was subjected to a second PCR with barcoding primers for 9 cycles (95 °C for 30 s, 65 °C for 15 s, 72 °C for 60 s). Final products were quantified (NanoDrop), normalized, combined, and sequenced on an Illumina NextSeq.

treatment_protocol: After sorint, before plasmid extraction, E. coli libraries were grown overnight in 2xYT media

tag: replicate

value: replicate 3

tag: agent

value: 50mM MgSO4

tag: facs gate

value: presort


title: self-ligation control

description: plasmid DNA

source_name: self-ligation control


title: LuCaP_173-2A_ET2148_LCM_SCC

source_name: LuCaP 173.2 PDX tumor, LCM squamous pearl cells

value: male


title: rep2 50mM MgSO4 presort

description: plasmid DNA

source_name: rep2 50mM MgSO4 presort

value: replicate 2


title: Primary islet cells, quality 1, S164


title: Primary islet cells, quality 3, S118


title: Primary islet cells, quality 2, S75


title: SFM (steroid free medium) rep 3

description:
Replicate 3
normal_vs_treatment_1.gene_expression_table.tsv

tag: treatment


title: rep3 10uM MgSO4 presort

description: plasmid DNA

source_name: rep3 10uM MgSO4 presort

value: 10microM MgSO4


title: rep1 50mM MgSO4 presort

description: plasmid DNA

source_name: rep1 50mM MgSO4 presort

value: replicate 1


title: rep2 10uM MgSO4 presort

description: plasmid DNA

source_name: rep2 10uM MgSO4 presort


title: rep3 50mM MgSO4 gate 8

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 8


title: rep1 10uM MgSO4 presort

description: plasmid DNA

source_name: rep1 10uM MgSO4 presort


title: rep3 50mM MgSO4 gate 7

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 7


title: Primary islet cells, quality 3, S178


title: Bleomycin-WT4

city: Los Angeles

first: Tanyalak

last: Parimon

address: 127 San Vicente

institute: Cedars-Sinai Medical Center

data_processing:
miRNA sequencing short reads were aligned to human reference genome (GRCh38) using Bowtie2 (v2.2.3) ;
Aligned sequences were mapped to mature miRNAs with annotation from miRBase (v.21);
The relative expression abundances of miRNAs were calculated as Count-Per-Million (CPM).

source_name: Extracellular vesicles

extract_protocol:
Total RNAs were isolated from bronchoalveolar lavage fluid extracellular vesicles using miRNAeasy QIAGEN isolation protocol
Libraries were prepared according to standard Ilumina's instructions

treatment_protocol: Animals received bleomycin for 21 days, PBS-treated animals served as controls.

tag: strain

tag: condition

value: Bleomycin-injured

tag: source of extracellular vesicles

value: Bronchoalveolar lavage fluid


title: Bleomycin-KO4


title: Bleomycin-WT3


title: Bleomycin-WT2


title: Bleomycin-KO1


title: Bleomycin-KO2


title: Bleomycin-KO3


title: Bleomycin-WT1


title: rep3 50mM MgSO4 gate 3

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 3


title: rep3 50mM MgSO4 gate 6

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 6


title: rep3 50mM MgSO4 gate 2

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 2


title: rep3 50mM MgSO4 gate 4

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 4


title: rep3 50mM MgSO4 gate 5

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 5


title: Normal-KO4

value: Normal


title: rep3 50mM MgSO4 gate 1

description: plasmid DNA

source_name: rep3 50mM MgSO4 gate 1


title: LuCaP_173-2A_ET2232_LCM_CaP

source_name: LuCaP 173.2 PDX tumor, LCM adenocarcinoma

tag: gender


title: Normal-KO3


title: Normal-KO2


title: Normal-KO1


title: Normal-WT4


title: rep2 50mM MgSO4 gate 6

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 6


title: rep2 50mM MgSO4 gate 7

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 7


title: Normal-WT3


title: Normal-WT2


title: rep2 50mM MgSO4 gate 5

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 5


title: rep2 50mM MgSO4 gate 4

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 4


title: Normal-WT1


title: rep2 50mM MgSO4 gate 3

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 3


title: rep2 50mM MgSO4 gate 2

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 2


title: rep1 50mM MgSO4 gate 8

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 8


title: rep1 50mM MgSO4 gate 7

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 7


title: HSA-LR_NT_Quad_rep2

city: Paris

first: Arnaud

middle: F

last: Klein

address: 47 bld de l'hopital - Bab Babinski

department: U974 - Centre de Recherche en Myologie

country: France

institute: Sorbonne université, Inserm, institut de Myologie

data_processing:
Sequencing on HiSeq2500 2x150bp; Basecalls with CASAVA
Alignment with hisat on GRCm38
Read counts with FeatureCounts version 1.5.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Feature counts for each sample
Supplementary_files_format_and_content: DEXseq counts for sample (txt)

source_name: Quadriceps muscle

extract_protocol:
Trizol + DNAse
Illumina TruSeq Stranded mRNA Library Prep kit ; mRNA isolated by polyA selection

treatment_protocol: Intraveinous injection of pip6a-PMO or Saline (160µL/mouse)

value: fvb

tag: age

value: 20 weeks

value: untreated


title: HSA-LR_PIP6a-PMO_Quad_rep1

tag: Sex

value: PIP6a-PMO treatment


title: HSA-LR_NT_Quad_rep3


title: HSA-LR_PIP6a-PMO_Quad_rep3


title: HSA-LR_PIP6a-PMO_Quad_rep2


title: FVB_WT_Quad_rep2

value: female


title: rep1 50mM MgSO4 gate 4

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 4


title: rep1 50mM MgSO4 gate 5

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 5


title: FVB_WT_Quad_rep1


title: rep2 50mM MgSO4 gate 8

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 8


title: HSA-LR_PIP6a-PMO_Gast_rep3

source_name: gastrocnemius muscle


title: rep1 50mM MgSO4 gate 3

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 3


title: rep2 50mM MgSO4 gate 1

description: plasmid DNA

source_name: rep2 50mM MgSO4 gate 1


title: HSA-LR_PIP6a-PMO_Gast_rep2


title: rep3 10uM MgSO4 gate 8

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 8


title: HSA-LR_PIP6a-PMO_Gast_rep1


title: rep1 50mM MgSO4 gate 1

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 1


title: HSA-LR_NT_Gast_rep3


title: rep3 10uM MgSO4 gate 7

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 7


title: rep1 50mM MgSO4 gate 2

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 2


title: HSA-LR_NT_Gast_rep1


title: rep3 10uM MgSO4 gate 5

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 5


title: HSA-LR_NT_Gast_rep2


title: HSA-LR_NT_Quad_rep1


title: rep3 10uM MgSO4 gate 4

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 4


title: FVB_WT_Quad_rep3


title: rep3 10uM MgSO4 gate 2

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 2


title: FVB_WT_Gast_rep1


title: rep3 10uM MgSO4 gate 1

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 1


title: FVB_WT_Gast_rep3


title: rep2 10uM MgSO4 gate 7

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 7


title: CWb8-4: ChIP-seq WT clone 1 EZH2

city: Boston

first: Chen-Yu

last: Wang

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
ChIP-seq: ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads. The input datasets (input for WT, GSM2667230; input for Smchd1-/-, GSM2667235) have been published previously (GSE99991)(Wang et al., 2018, Cell).
Hi-C: The Hi-C summary files of WT and Smchd1-/- cells were downloaded from GEO (GSE99991), with two biological replicates combined:
WT: GSM2667262_WT1.HiC.rep1.comp.summary.txt.gz
WT: GSM2667264_WT1.HiC.rep2.comp.summary.txt.gz
Smchd1-/-: GSM2667263_KO1.HiC.rep1.comp.summary.txt.gz
Smchd1-/-: GSM2667265_KO1.HiC.rep2.comp.summary.txt.gz
The combined replicates were converted to .hic files for chromosome 2, 6, 11, 15, and 18. The .hic files can be directly loaded to the Juicebox software (Durand, et al., Cell Syst, 2016).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT1, WT clone 1. KO1, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads.

source_name: neural progenitor cells

growth_protocol: ES cell–derived neural progenitor cell clones were cultured on poly-L-ornithine (0.001%) and laminin (1μg/ml) coated plates with N2 media (DMEM/F-12, GlutaMAX™ supplement, 1X N2 supplement, 1X B27 supplement, 1X Pen/Strep) supplemented with FGF2 (20ng/ml), EGF (20ng/ml), laminin (1μg/ml), and heparin (10μg/ml).

extract_protocol:
ChIP-enriched and input DNA were extracted with phenol:chloroform.
ChIP-seq libraries were generated by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina.
Paired-end 50-cycle with Illumina HiSeq

value: ESC-derived clonal neural progenitor cells

tag: genotype

value: WT

tag: chip antibody

value: anti-EZH2 (Cell Signaling Technology, 5246S, lot:7)


title: rep3 10uM MgSO4 gate 3

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 3

value: replicate 3


title: FVB_WT_Gast_rep2


title: CWb8-1: ChIP-seq Smchd1-/- clone 1 EZH2

tag: cell type


title: rep2 10uM MgSO4 gate 6

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 6


title: rep2 10uM MgSO4 gate 3

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 3


title: CBFB-MYH11_+Dox_Chd7-rep1

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
ChIP-seq reads aligned to mm10 using bowtie2 (version  2.0.6) with extra parameters (-k 2 -N 1).
bigWig density profiles were created with in-house script incorporating UCSC's wigToBigWig utility.
Peaks were called using macs2 (version 2.0.10).
Genome_build: mm10
Supplementary_files_format_and_content: [BigWig] read density profile
Supplementary_files_format_and_content: [BED] peaks file

growth_protocol: The mouse myeloid progenitor 416B cell line (PMID: 763330) was co-transfected with: 1) a plasmid containing the tetracycline transcription silencer (tTS), the tetracycline transactivator (rtTA) and blasticidine resistance under the control of a Ef1alpha promoter; 2) a plasmid containing the entire Cbfb-Myh11 (CM) type A cDNA in frame with a F2A element and the mCherry protein under the control of a tetracycline responsive element. As a control, cells were alternatively transfected with a version of the plasmid lacking the CM protein. Transposase PL623 (PMID: 21990348, kindly donated by Pentao Liu, Sanger Institute, Cambridge), was also transiently expressed to promote simultaneous stable integration of previous constructs. Plasmids were transfected into 416B cells by electroporation using a BioRad electroporator (220V, 900 µF). After 24h, 1 µg/ml of blasticidin (InvivoGen) was added for selection. After 14 days, mCherry-negative single cells that did not stain with DAPI (Sigma) were sorted into 96-well plates using a BD Influx sorter. Cells were cultured in the presence of selection for typically 2 weeks. Clonal cultures were then tested for induction and expression levels of CM using 1 µg/ml of Doxycycline. Selected clones were expanded for further experiments. Induction of CM for ChIP experiments was confirmed by measurement of mCherry levels by FACS (BD Fortessa).

extract_protocol:
Lysates were clarified from sonicated nuclei following crosslinking with 1% formaldehyde, and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using the TruSeq Kit (Illumina) for high throughput sequencing on an Illumina HiSeq 2500, according to manufacturer’s instructions, with size selection for fragments of 150-400 bp.

treatment_protocol: Where indicated, cells were induced with 1 µg/ml Doxycycline for 24 hours before harvesting for ChIP-seq.

tag: cell line

value: myeloid progenitor 416B cell line

tag: construct

value: Doxycycline

value: Chd7 (Abcam, ab31824)


title: rep2 10uM MgSO4 gate 4

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 4

value: replicate 2

value: 10microM MgSO4


title: CBFB-MYH11_+Dox_Runx1-rep2

value: Runx1 (Abcam, ab23980)


title: CBFB-MYH11_+Dox_Runx1-rep1


title: CBFB-MYH11_+Dox_Chd7-rep2


title: CBFB-MYH11_-Dox_Chd7-rep2


title: rep2 10uM MgSO4 gate 2

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 2


title: CBFB-MYH11_-Dox_Chd7-rep1


title: rep2 10uM MgSO4 gate 1

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 1


title: rep1 10uM MgSO4 gate 8

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 8

value: replicate 1


title: CBFB-MYH11_-Dox_Runx1-rep2


title: rep1 50mM MgSO4 gate 6

description: plasmid DNA

source_name: rep1 50mM MgSO4 gate 6

value: 50mM MgSO4


title: CBFB-MYH11_-Dox_Runx1-rep1


title: rep3 10uM MgSO4 gate 6

description: plasmid DNA

source_name: rep3 10uM MgSO4 gate 6


title: Control_+Dox_Chd7-rep2

value: Control-ATG


title: F140E [miRNA]

first: Lucas

last: Pantaleao

address: 11A Glisson Road

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRC38p5 mouse transcriptome (MirGeneDBv2.0) using bowtie v1.2.3 with parameters: minimum read length = 15, minimum read count = 2, allowed number of mismatches = 2
Genome_build: GRC38p5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver

extract_protocol:
Livers were dissected, weighed, snap frozen and stored at −80 °C. Total liver RNA was extracted using a miRNeasy mini kit (Qiagen, Hilden, Germany) including a DNAse digestion protocol.
Three high quality samples from each group were randomly selected and subjected to a cDNA library preparation using TruSeq sRNA Library Preparation kit, following the manufacturer’s protocol.

treatment_protocol: Thirty-five female C57BL/6J mice were fed either a standard control diet, RM1 [7% simple carbohydrates/3% lipids (w/w)] or an energy-rich obesogenic diet [10% simple carbohydrates/20% lipids (w/w)] plus sweetened condensed milk [55% simple carbohydrates, 8% lipids, 8% protein (w/w), Nestle (Nestle, UK), supplemented with mineral and vitamin mix AIN93G]. Female mice were mated, and Pregnant mice were housed individually and maintained on their respective diets until weaning. Litter sizes were standardized to 6 pups on postnatal day 3. On post-natal day 21, male offspring were randomly weaned onto either standard chow (RM1) or the obesogenic diet.

tag: tissue

value: liver

value: post natal day 84

value: wild type

tag: maternal diet

value: Obesogenic

tag: offspring diet


title: rep2 10uM MgSO4 gate 5

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 5

tag: replicate

tag: agent


title: F176C [miRNA]


title: rep1 10uM MgSO4 gate 7

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 7

tag: facs gate


title: F155A [miRNA]

tag: strain


title: F170A [miRNA]

value: Control


title: F165A [miRNA]


title: rep1 10uM MgSO4 gate 5

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 5


title: rep1 10uM MgSO4 gate 6

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 6


title: F176A [miRNA]


title: rep2 10uM MgSO4 gate 8

description: plasmid DNA

source_name: rep2 10uM MgSO4 gate 8


title: rip_nxf3_nxf3_mut

first: Emma

last: Kneuss

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson way

department: Cancer Research UK, Cambridge University

description: Nxf3 RIP-seq using Nxf3 homozygote mutant flies

data_processing:
RNAseq, RIPseq, smallRNA seq analysis
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, the 5 first bases and the last base of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). Following removal of rRNA mapped reads, high-quality reads were aligned to transposon consensus sequences followed by alignment to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) using STAR (Dobin et al. 2013). Genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outMultimapperOrder Random' and non-mapping reads were removed. For genome-wide analyses, unique mapper reads were extracted to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million). Reads mapping to genes were counted with htseq (Anders et al. 2015) and transposon derived reads were calculated using a custom script. Differential expression analysis was performed using custom built R scripts. piRNA clusters were divided in 1 kb bin and unique reads mapping to these bins were counted using htseq. A pseudo count of 0.01 or 0.1 respectively for RNA-seq and RIP-seq experiment, was then added to each bin before calculating log2 fold-changes per bin.
For small RNA-seq, adapters were clipped from raw fastq files with fastx_clipper (adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) keeping only reads with at least 23 bp length. Then the first and last 4 bases were trimmed using seqtk (https://github.com/lh3/seqtk). After removal of cloning markers and 2S rRNA mapped reads, alignment was performed as described above and normalised to miRNA reads in the control library (set to rpm). Only high-quality small RNA reads with a length between 18 and 30 bp were used for further analysis of small RNA profiles. piRNA distribution was calculated and plotted in R. piRNA clusters were divided in 1 kb bin and unique reads mapping to these bins were counted using htseq. A pseudo count of 1 was added to each bin before calculating log2 fold-changes per bin. Small RNA size profiles were plotted in R, only unique mappers were used for small RNA distribution of piRNA clusters.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files for all dm6 alignement files, normalized to rpm (RNA-seq, RIP-seq) to miRNA (smRNA-seq). For RNA- RIP- and smallRNA-seq, sequences were split in sense- and antisense-mapping reads before normalization.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown at 25°C on cornmeal or propionic food

extract_protocol:
RIP-seq was adapted from Hendrickson et al.,  "Widespread RNA binding by chromatin-associated proteins" Genome Biol 17: 28. February 2016
RiboGone - Mammalian (Clontech) and library preparation using the SMARTer stranded RNA-seq Kit (Clontech)

value: ovaries

tag: strain/background

value: Nxf3 ko

tag: experiement

value: RIP-seq


title: rip_nxf3_w1118

description: Nxf3 RIP-seq using w1118 flies


title: Control_+Dox_Runx1-rep2

value: myeloid progenitor 416B cell line

tag: treatment


title: Control_+Dox_Runx1-rep1

value: Doxycycline


title: smrna_boot_mut

description: small RNA seq library (19-28nt)

extract_protocol:
Tissue were homogenized in Trizol and RNA extracted using Phenol/Chloroform
Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.

value: Bootlegger ko

value: smallRNA-seq


title: RC110C [miRNA]

tag: age


title: RC131D [miRNA]


title: RC109C [miRNA]


title: Control_+Dox_Chd7-rep1

value: Chd7 (Abcam, ab31824)


title: rep1 10uM MgSO4 gate 2

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 2

value: 10microM MgSO4


title: rep1 10uM MgSO4 gate 4

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 4

value: replicate 1


title: rep1 10uM MgSO4 gate 1

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 1


title: rna_seq_nxf3_mut

description: RNA seq library

extract_protocol:
Ovaries were homogenized in Trizol and RNA extracted using Phenol/Chloroform
rRNA removal with Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina) followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)

value: RNA-seq


title: RC82A [miRNA]


title: rna_seq_boot_mut

description: RNA seq library


title: RC83A [miRNA]


title: Control_-Dox_Runx1-rep2

value: Control-ATG

value: Runx1 (Abcam, ab23980)


title: RC105A [miRNA]

value: liver

value: post natal day 84


title: Control_-Dox_Chd7-rep1


title: rna_seq_w1118

description: RNA seq library


title: Control_-Dox_Runx1-rep1


title: rep1 10uM MgSO4 gate 3

description: plasmid DNA

source_name: rep1 10uM MgSO4 gate 3


title: S25A-3 RNA-seq

city: Beijing

first: Xing

last: Chen

address: Yiheyuan Road

department: Chemical Biology

institute: Peking University

data_processing:
Base-calling was performed using CASAVA v2.19
Reads from sequencing were aligned to the mouse genome using Hisat v2.1.0, with the index built from mm10 genome and annotation files on GENCODE
The resulting SAM alignment files were quality filtered (-q 10), converted to BAM format and sorted using SAMtools v1.3
Duplicate reads were removed by Picard tools v1.140
Reads aligned to exons were counted with featureCounts v1.6.3
Differential analysis was performed with DESeq2 v1.20.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts of sequencing reads generated by featureCounts, and csv file containing differential expression analysis by DESeq2

source_name: inner cell mass

growth_protocol: R1 murine embryonic stem cells (mESCs) were grown on 0.1% gelatin (Sigma-Aldrich) coated cell culture dishes (Invitrogen).  Cells were cultured in the KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), 1× nonessential amino acids (Gibco), 1× GlutaMAXTM (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF) (Millipore), 100 μM 2-mercaptoethanol (Sigma-Aldrich), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco).  mESCs were disassociated with 0.1% trypsin (Gibco) and passaged at a split ratio of 1 to 15 every three days.

extract_protocol:
Total RNA was exracted using TRIzol Reagent
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s recommendations

treatment_protocol: We constructed mESCs stably expressing WT and Ser 25A ESRRB by the lentivirus infections.  For lentivirus packing and processing, HEK293FT cells were transfected with 10 µg plasmid of pCDH-EF1-ESRRBWT-T2A-copGFP (or pCDH-EF1-ESRRBS25A-T2A-copGFP), 8 µg plasmid of PAX2, and 4 µg plasmid of MD.2G when the cells were grown to approximately 60% confluence in a 10-cm cell culture dish.  The cell culture medium was filtered and collected after 72 h, followed by addition of Lenti-XTM Concentrator (Clontech, 631231) for lentivirus extraction based the manufacturer’s instructions.  The resulting sample was resolved in PBS (pH 7.4) and added into the cell culture of R1 mESCs when the cells were grown to approximately 30% confluence.  After incubation for 24 h, the medium was changed to fresh R1 cell culture medium.  The cells were cultured for two passages, followed by flow cytometry sorting of mESCs expressing WT or S25A ESRRB with equal GFP fluorescence intensity.

value: R1 embryonic stem cells

tag: passages

value: within 20 passages


title: F155A [RNA]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v1.2.3
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Livers were dissected, weighed, snap frozen and stored at −80 °C. Total liver RNA was extracted using a miRNeasy mini kit (Qiagen, Hilden, Germany) including a DNAse digestion protocol.
Three high quality samples from each group were randomly selected and subjected to a cDNA library preparation using TruSeq RNALibrary Preparation kit, following the manufacturer’s protocol.

tag: genotype

value: wild type

value: Obesogenic


title: Control_-Dox_Chd7-rep2

tag: chip antibody


title: smrna_nxf3_mut

description: small RNA seq library (19-28nt)

value: ovaries

value: Nxf3 ko


title: F140E [RNA]


title: S25A-1 RNA-seq


title: CO-15: MCF-7 DAXXi Rep 2

city: Maywood

first: Clodia

last: Osipo

state: Illinois

address: 2160 S. First Ave

institute: Loyola University Chicago

data_processing:
Quality control was done using FastQC (v 0.11.5) and Trimmomatic (v 0.38).  The only change from default was the min length was changed to 50 when using Trimmomatic.
Kallisto (v0.44.0) was used to quantify the RNA-Seq data.  The reference transciptome used was GRCH38.92.  Default parameters were used.
Gene expression analysis was done using DESeq2, using default values.
Genome_build: GRCh38.92
Supplementary_files_format_and_content: The processed.csv files hold the output from DESeq2, representing the gene expression analysis. They are normalized count values and the calculated fpkm.

growth_protocol: MCF-7 cells were grown in RPMI (10% FBS) + transfection reagent for 2 days

extract_protocol:
Cultured cells were removed from plates, and RNA was harvested using Trizol reagent. RNA was isolated using the ZYMO direct-zol kit (Cat#R2061) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfection reagent contained mixture of siRNA (SCBi or DAXXi), optimem, and Lipofectamine RNAiMAX reagent (Cat#13778030)

tag: cell type

value: ER+ breast cancer

value: 10-15 passages


title: CO-13: MCF-7 DAXXi Rep 1

tag: cell line


title: CO-16: MCF-7 SCBi Rep 2


title: F170A [RNA]

value: Control


title: WT-3 RNA-seq


title: F176A [RNA]


title: F176C [RNA]


title: WT-2 RNA-seq


title: CO-14: MCF-7 SCBi Rep 1


title: Control_IgG

value: myeloid progenitor 416B cell line

tag: construct

value: IgG (Sigma, I5006)


title: Cells with microRNA-489 overexpression, RNA from RISC, repeats I

city: Milwaukee

first: Pengyuan

last: Liu

state: Wisconsin

address: 8701 Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Data QC and trim with FastQ_V0.10.0 and DynamicTrim_v.1.10
Read alignment with TopHap version 2.0.5
Transcript quantification and normalization with cufflinks version 2.0.2
Differential expression analysis with cufflinks version 2.0.2
Genome_build: hg19/Homo_sapiens.GRCh37.64
Supplementary_files_format_and_content: transcript/gene abundance

source_name: HEK 293 cells

growth_protocol: Cells were cultured in normal culture medium

extract_protocol:
At 48 hours after transfection, RISCs were pulled down from cell lysate with anti-Flag resin. RNA samples were extracted with mirVana™ miRNA Isolation Kit (Life Technologies, grand Island, NY).
Libraries for RNA-Seq were prepared using TruSeq RNA Sample Preparation Kit from Illumina, following the vendor's instructions.

treatment_protocol: HEK293 cells were co-transfected with FLAG-Ago-2 plasmid (Addgene, Cambridge, MA) or control plasmid (p3xFLAG-Myc-CMV™-24 Expression Vector, Sigma, St. Louis, MO) and 100nM negative control RNA oligos, or hsa-mir-668 mimics, or hsa-mir-489 mimics (Dharmacon Research, Inc., Pittsburgh PA).

tag: mimics

tag: rna type

value: RISC RNA

value: microRNA mimic transfection


title: Cells with microRNA-489 overexpression, RNA from RISC, repeats II


title: WT-1 RNA-seq

tag: tissue


title: RC109C [RNA]

tag: maternal diet

tag: offspring diet


title: Cells with microRNA-489 overexpression, RNA from RISC, repeats III


title: RC131D [RNA]


title: S25A-2 RNA-seq


title: RC110C [RNA]


title: F165A [RNA]


title: Cells with microRNA-489 overexpression, total RNA, repeat II

value: total RNA


title: Cells with microRNA-489 overexpression, total RNA, repeat III


title: RC83A [RNA]


title: HCC_918: MRS-low

city: Guangzhou

first: Chong

last: Wu

address: 135 Xin Gang Xi Road

institute: Sun Yat-sen University

description: Gene expression in HCC tissue

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were log-transformed, and then normalized with the 'sva' R package to remove batch effects and other unwanted variations. The sva algrithm identified 5 SVs, and SV1, SV3, SV4 and SV5 were removed after careful examination.

source_name: HCC

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: HCC tissues were grinded with a mortar and pestle in liquid nitrogen, and homogenized in TRIzol Reagent (Ambion). Total RNA was extracted according to the manufacturer’s instructions and quantified with a Nanodrop Instrument (Thermo Scientific). Aliquots containing 2 μg total RNA were used to generate complimentary DNA (cDNA) using the All-in-One RT MasterMix (Applied Biological Material).

value: hepatocellular carcinoma (HCC)

tag: batch

tag: prognosis

value: Poor


title: RBMX_ChIPSeq

last: Zheng

address: No. 135 West Xingang Road

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using SOAPaligner/SOAP2 (version: 2.21t) with the following setting: soap_mm_gz -p 4 -v 2 -s 35.
Data were filtered using SOAPnuke filter with the following setting:-l 5 -q 0.5 -n 0.1 -Q 2 -c 21.
Peaks were called using MACS (Model-based Analysis of ChIP-Seq) with the following setting: macs14 -s 50 -g hs -p 1e-5 -w --space 50 -m 10,30.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_peaks.txt: Tab-delimited text files include peaks generated using MACS.

source_name: 293T cells

growth_protocol: 293T cells were grown in DMEM (GIBCO) with 10% fetal bovine serum (GIBCO) and 100 U per ml penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
Cell lysates were sonicated and protein-DNA complexes were isolated with Flag-beads (Sigma Aldrich).
Libraries were prepared using Paired-End DNA Sample Prep kit (Illumina).

treatment_protocol: Cells were transfected with either Flag-RBMX or Flag-RPA1, and treated with Camptothecin (CPT) for 24 hours.

value: Embryonic kidney cell line

tag: transfection

value: Flag-RBMX

value: Anti-Flag


title: Cells with microRNA-668 overexpression, RNA from RISC, repeats I


title: HCC_795: MRS-low

description: Gene expression in HCC tissue

value: Good


title: RC105A [RNA]

tag: strain

value: liver

value: post natal day 84

value: wild type


title: HCC_971: MRS-low

description: Gene expression in HCC tissue


title: Cells with microRNA-489 overexpression, total RNA, repeat I

tag: treatment


title: selective SREBP inhibitor

city: Uji

first: Motonari

last: Uesugi

state: Kyoto

address: Gokasho

department: ICR

institute: Kyoto University

description: Sample 3

data_processing:
bcl2fastq v1. 8. 4 used for basecalling.
Sequence reads were mapped to following genome using TopHat v2. 0. 14 with parameters -m 0 --mate-std-dev 177 -p 16 -r 169 --library-type fr-firsts  trand --segment-length 25 -a 8 -g 20 --read-mismatches 2 -i 50 -l 500000 --no-coverage  -search.
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated using GeneDataExpressionist for Genomic Profiling v9.1.4a.
Genome_build: CriGri_1.0
Supplementary_files_format_and_content: gene name, FPKM values for each sample, read count for each sample, annotation type, Entrez Gene ID, description

organism: Cricetulus griseus

source_name: CHO-K1 cells

growth_protocol: CHO-K1 cells were maintained in 1:1 mixture of Ham’s F-12 medium and DMEM supplemented with 100 units/mL penicillin, 100 µg/mL streptomycin sulfate, and 5% [v/v] fetal bovine serum at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated with ISOGEN (NIPPON GENE) following the manufacturer protocol.
RNA libraries were prepared for sequencing using TruSeq Standard mRNA Sample Prep Kit.

treatment_protocol: CHO-K1 cells were added to 6-well plates at 3×10^5 cells per well and incubated for 24 hr. Then, the medium was replaced with medium (1:1 mixture of Ham’s F-12 medium and DMEM, supplemented with 100 units/mL penicillin, 100 µg/mL streptomycin sulfate, 5% [v/v] lipid-depleted serum, 50 µM compactin, and 50 µM lithium mevalonate) containing each compound and the cells were incubated for another 24 hr.

tag: chemical treatment

value: selective SREBP inhibitor


title: selective VDR activator

description: Sample 4

value: selective VDR activator


title: 25-hydroxyvitamin D3

description: Sample 2

value: 25-hydroxyvitamin D3


title: RPA1_ChIPSeq


title: Time point 4, replicate 3

city: pasco

first: aaron

last: ogden

state: wa

address: 902 battelle boulevard

department: integrative omics

institute: Pacific Northwest National Lab

data_processing:
Trimmomatic (v0.38)32 was used to remove reads with a quality score less than 28 while maintaining a minimum read length of 34 bases. The effectiveness of this procedure was evaluated with FastQC33.
Paired-end reads were then aligned using Hisat2 (v2.1.0)34,35 with an index created from the Brachypodium distachyon genome (v3.0) retrieved from EnsemblPlants36
The resulting alignment files were converted to the proper format with Samtools (v1.9)37 followed by transcript assembly and table count generation using StringTie (v1.3.5)35.
Gene-level read counts were extracted using the Python script provided in the StringTie package (prepDE.py)
DESeq2 normalization performed
We then pre-filtered and removed genes with very low read counts totaling <240 across all samples (DESeq2 rowSums function).
Genome_build: Brachypodium_distachyon_v3.0
Supplementary_files_format_and_content: Format = .GTF content=output from stringtie table counts "e.g. stringtie -e -B -p 6 -G Brady3041.gtf -o ballgown/RT1Am1/RT1Am1.gtf RT1Am1.bam"

organism: Brachypodium distachyon

source_name: Root

growth_protocol: All samples were grown in Percival Scientific Growth chambers in 9 cm pots containing Sun Gro metro-mix soil under 16 h/8h light-dark regime. Light intensity of 250 µmol m-2 s-1, temperature of 24 °C day/18 °C night, and relative humidity of 60%.

extract_protocol:
Plants were harvested at 18, 25, 32, and 36 days post sowing. Roots were quickly rinsed, excised from the stem, flash frozen in liquid nitrogen, and stored at -80°C. Frozen root tissue was homogenized in liquid nitrogen using a mortar and pestle. Approximately 100 mg of the resulting frozen root homogenate from each sample was then subjected to RNA isolation using GeneJET Plant RNA Purification Kit (ThermoFisher Scientific, Cat# K0801) according to manufacturer’s protocols.
The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit. RNA samples without degradation were used for library preparation using the TruSeq Stranded RNA Library Prep Kit (Illumina, San Diego, CA). The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit. The concentrations of RNA libraries were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA). The libraries were diluted to 2 nM with RSB (10 mM Tris-HCl, pH8.5) and denatured with 0.1 N NaOH. Eighteen pM libraries were clustered in a high-output flow cell using HiSeq Cluster Kit v4 on a cBot (Illumina). After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina). DNA was sequenced from both ends (paired-end) with a read length of 50 bp. The raw sequencing data BCL files were converted to FASTQ files using software program bcl2fastq2.17.1.14.

treatment_protocol: This is a time-course experiment, treatments are effectively stress-free roots at different growth stages.

value: Root

tag: developmental stage

value: Booting/Heading

tag: ecotype


title: HCC_1412: MRS-high

description: Gene expression in HCC tissue


title: RC82A [RNA]

source_name: Liver

tag: age

tag: genotype

value: Control


title: HCC_731: MRS-high

description: Gene expression in HCC tissue


title: HCC_895: MRS-low

description: Gene expression in HCC tissue


title: HCC_1361: MRS-high

description: Gene expression in HCC tissue


title: HCC_1530: MRS-low

description: Gene expression in HCC tissue


title: control (DMSO)

description: Sample 1

value: DMSO

tag: cell line


title: HCC_1319: MRS-low

description: Gene expression in HCC tissue


title: HCC_1373: MRS-high

description: Gene expression in HCC tissue


title: Cells with microRNA-668 overexpression, RNA from RISC, repeats II

value: RISC RNA

value: microRNA mimic transfection


title: HCC_1429: MRS-high

description: Gene expression in HCC tissue

value: hepatocellular carcinoma (HCC)


title: HCC_729: MRS-low

description: Gene expression in HCC tissue

value: Poor


title: ΔM.DraR1-2

city: Hangzhou

first: Shengjie

last: Li

address: No. 268, Yuhang Tang Road

institute: Zhejiang University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.Clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly (https://www.ncbi.nlm.nih.gov/genome/?term=Deinococcus+radiodurans+R1). Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DEGSeq R package (1.18.0)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias wascorrected. KOBAS software was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Deinococcus radiodurans

growth_protocol: All D. radiodurans strains were grown in tryptone glucose yeast extract liquid media (0.5% tryptone, 0.1% glucose and 0.3% yeast extract) at 30 oC with aeration

extract_protocol:
Strains were harvested, frozen using liquid nitrogen, and RNA was isolated using Trizol reagent. A total of 3 µg RNA per sample was used as the input material for library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stranis were grown to early exponential phase (OD600≈0.5)

tag: strain background

tag: genotype/variation

value: M.DraR1 mutant

tag: growth phase


title: ΔM.DraR1-1


title: Cells with microRNA-668 overexpression, total RNA, repeat I

tag: mimics

tag: rna type

value: total RNA


title: Time point 4, replicate 2

tag: tissue


title: HCC_1236: MRS-high

description: Gene expression in HCC tissue

tag: batch

value: Good


title: Cells with microRNA-668 overexpression, RNA from RISC, repeats III


title: Cells with microRNA-668 overexpression, total RNA, repeat II


title: Time point 3, replicate 3

value: Late Tillering


title: Time point 4, replicate 1


title: Cells with microRNA-668 overexpression, total RNA, repeat III


title: DraR1-1


title: DraR1-2


title: Time point 3, replicate 2


title: HCC_733: MRS-high

description: Gene expression in HCC tissue

tag: prognosis


title: D-1

city: guangzhou

first: zhao

last: zaoya

address: Waihuan East Road

institute: SUN YAT-SEN University

description: primary cells

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
Sequenced reads were trimmed for adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data, then mapped to 197 whole genome via software Hisat2  (v2.0.1)
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 the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Genome_build: https://www.ncbi.nlm.nih.gov/genome/197?genome_assembly_id=293496
Genome_build: transcripts.fa includes the transcript sequences.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oreochromis mossambicus

source_name: head-kidney leukocyte

growth_protocol: The tilapia head kidney leucocytes were routinely separated and cultured (typically 3–4 × 106 cells into a 24-well culture plate) on rat tail collagen coated plastic in RPMI 1640 medium (Gibco, USA) supplemented with 1% penicillin/streptomycin and 2% tilapia serum for overnight.

extract_protocol:
The medium were removed, the cells were collected and 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leukocytes were treated with PBS, heat-killed S.agalactiae (1 MOI), sodium nitrite (1000 μM) or heat-killed S.agalactiae (1 MOI) and sodium nitrite (1000 μM) co-treatment for 12h.

value: head-kidney

tag: cell type

value: leukocytes from tialpia head-kidney

value: treated with heat-killed Streptococcus agalactiae and Nitrite


title: Cells with negative control mimic, RNA from RISC, repeat III

value: Negative control


title: D-3

description: primary cells


title: HCC_1209: MRS-low

description: Gene expression in HCC tissue


title: D-2

description: primary cells


title: C-3

description: primary cells

value: treated with Nitrite


title: HCC_1174: MRS-high

description: Gene expression in HCC tissue


title: Time point 2, replicate 3

value: Root

value: Early Tillering


title: Time point 2, replicate 2


title: HCC_1202: MRS-high

description: Gene expression in HCC tissue


title: HCC_1158: MRS-low

description: Gene expression in HCC tissue


title: HCC_1133: MRS-high

description: Gene expression in HCC tissue


title: Cells with negative control mimic, total RNA, repeat I


title: HCC_1015: MRS-high

description: Gene expression in HCC tissue


title: Cells with negative control mimic, total RNA, repeat II


title: C-2

description: primary cells


title: Cells with negative control mimic, total RNA, repeat III


title: B-3

description: primary cells

value: treated with heat-killed Streptococcus agalactiae


title: Time point 1, replicate 2

value: Leaf development


title: Cells with negative control mimics, RNA from RISC, repeat I

value: RISC RNA


title: Time point 1, replicate 1


title: Time point 1, replicate 3


title: Cells with negative control mimics, RNA from RISC, repeat II

value: microRNA mimic transfection


title: Time point 3, replicate 1


title: WT-2

city: Seoul

first: Hyejin

last: Kim

address: 103 Daehakro

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Hippocampus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: strain

value: WT

value: Hippocampus


title: WIN-ATAC

city: New York

first: Philippe

last: Melas

address: 1051 Riverside Drive

institute: Columbia University

description:
WIN-treated
ATAC_4samples_ucsctracks.bed

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, and only reads mapping as matched pairs and being uniquely mapped (mapping quality >= 1) were used for further analysis. The 42 base pair (bp) length of the reads were used for peak-calling and the generic term “interval” was used to describe genomic regions with local enrichments in tag numbers. Intervals were defined by the chromosome number, and a start and end coordinate.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff p-value of 1e-7 and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
HISAT2 was used to map filtered sequenced reads to the reference rat genome, HTSeq was used to analyze gene expression levels (in union mode)
DESeq was used for differential gene expression analysis
rMATS (replicate multivariate analysis of transcript splicing) was used for detection of differential alternative splicing (AS)
Genome_build: RN6(Nacc-RNAseq and ATACseq), RN5(PFC-RNAseq)
Supplementary_files_format_and_content: xlsx files including FPKM value for each sample

source_name: WIN-treated

extract_protocol:
Total RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
ATAC-seq: Nuclei from flash frozen PFC tissue were extracted and 100,000 nuclei were tagmented. DNA were prepared using Nextera library prep kit.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

value: PFC

value: Sprague-Dawley

tag: Sex

value: male


title: WT-1


title: B-1

description: primary cells

tag: treatment


title: A-3

description: primary cells

value: treated with PBS


title: Time point 2, replicate 1

tag: developmental stage


title: HCC_1135: MRS-low

description: Gene expression in HCC tissue

value: hepatocellular carcinoma (HCC)

value: Good


title: PHF2 t/g-3

value: PHF2 t/g


title: A-1

description: primary cells

value: head-kidney

value: leukocytes from tialpia head-kidney


title: PHF2 t/g-2


title: Cocaine-ATAC

description:
Cocaine-treated
ATAC_4samples_ucsctracks.bed

source_name: Cocaine-treated


title: C-1

description: primary cells

value: treated with Nitrite


title: PHF2 t/g-1


title: PL-D2-1

status: Public on Jul 26 2019

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Treated sample Day 2

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: tail of pancreasta

growth_protocol: 6-12 week old mice with Lats 1 & 2 double knockout (PL) were used in the study

extract_protocol:
Total RNA was extracted from the tail of the pancreas using a lysis binding buffer (Ambion, Cat. AM1560) and Direct-zol RNA miniprep kit (Zymo Research, R2052)
RNA libraries were prepared using standard Illumina TruSeq protocol

treatment_protocol: Control and PL mice were subjected to180mg/kg/day of TAM for five consecutive days. Tails of pancreata were harvested at Days 1, 2, and 3 (n=3-5 for each time point) for RNA extraction

value: tissue

value: TAM treated

tag: day

value: mix of C57BL/6Brd-Tyr, 129S6/SvEvTac and 129X1/SvJ


title: PL-D2-3

description: Treated sample Day 2


title: PL-D3-4

description: Treated sample Day 2


title: PL-D2-2

description: Treated sample Day 2


title: PL-D3-1

description: Treated sample Day 3


title: WT-3

tag: age


title: PL-D1-3

description: Treated sample Day 1


title: PL-D1-2

description: Treated sample Day 1


title: PL-D1-4

description: Treated sample Day 1


title: B-2

description: primary cells

value: treated with heat-killed Streptococcus agalactiae


title: PL-D3-2

description: Treated sample Day 3


title: Control-5

description: control sample 5

value: untreated

value: control


title: Control-2

description: control sample 2


title: PL-D1-1

description: Treated sample Day 1


title: Control-4

description: control sample 4


title: A-2

description: primary cells


title: Control-3

description: control sample 3


title: Control-1

description: control sample 1


title: 36HAI_PBZ_rep2 [36PR2]

city: Campos Dos Goytacazes

first: Rajesh

middle: Kumar

last: Gazara

address: Avenida Alberto Lamego, 2000

department: CBB

country: Brazil

institute: Universidade Estadual do Norte Fluminense Darcy Ribeiro

data_processing:
The quality of reads was accessed by running the FastQC.
Reads were aligned on G. max 275 v2.0 genome using novoalign (V3.06.05). Gene expression level was calculated with Cufflinks v2.1.1 and normalized by reads per kilobase of transcript per million mapped reads (RPKM).
Genome_build: The Glycine max Wm82.a2.v1 genome  was used as reference.
Supplementary_files_format_and_content: 12_24_36.txt.gz : tab-separated file containing all genes mapped using the sequenced reads. Scores represent RPKM values for each soybean gene in the time-interval (12HAI, 24HAI and 36HAI) in control and PBZ conditions.

organism: Glycine max

source_name: 36HAI_PBZ_embryonic axis

growth_protocol: Soybean seeds were sown in 15 cm Petri dishes containing 2g of cotton soaked with sterile distilled water (30 mL). Seeds were allowed to germinate in a climate-controlled growth chamber at 28ºC with a 12/12 hours photo-period. We used 20 seeds per plate in a total of 60 seeds per treatment (3 plates per sample).

extract_protocol:
For RNA extraction, embryonic axes were immediately placed in RNAlater (Qiagen) until RNA extraction. Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen).
RNA-Seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 and submitted to single-end sequencing using a HiSeq 2500 instrument at LaCTAD (UNICAMP, Campinas, Brazil).

treatment_protocol: Soybean seeds were sown in 15 cm Petri dishes containing 2g of cotton soaked with sterile distilled water (30 mL) and 200 µM PBZ. Seeds were allowed to germinate in a climate-controlled growth chamber at 28ºC with a 12/12 hours photo-period. We used 20 seeds per plate in a total of 60 seeds per treatment (3 plates per sample).

tag: cultivar

value: BRS 284

value: embryonic axis

tag: time after imbibition

value: 36 hours


title: 36HAI_PBZ_rep1 [36PR1]


title: 36HAI_rep2 [36CR2]

source_name: 36HAI_embryonic axis


title: 36HAI_rep3 [36CR3]


title: 24HAI_PBZ_rep3 [24PR3]

source_name: 24HAI_PBZ_embryonic axis

value: 24 hours


title: 24HAI_PBZ_rep2 [24PR2]


title: 36HAI_rep1 [36CR1]


title: 24HAI_PBZ_rep1 [24PR1]


title: 24HAI_rep3 [24CR3]

source_name: 24HAI_embryonic axis


title: 24HAI_rep2 [24CR2]


title: 24HAI_rep1 [24CR1]


title: PL-D3-3

description: Treated sample Day 3


title: 12HAI_PBZ_rep1 [12PR1]

source_name: 12HAI_PBZ_embryonic axis

value: 12 hours


title: 12HAI_PBZ_rep2 [12PR2]


title: 12HAI_rep2 [12CR2]

source_name: 12HAI_embryonic axis


title: 12HAI_rep3 [12CR3]


title: 12HAI_rep1 [12CR1]


title: 36HAI_PBZ_rep3 [36PR3]


title: 12HAI_PBZ_rep3 [12PR3]