title: RR930_m6Am_mouse_adult_Testes_input_KO

data_processing:
For gene expression profiling the reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (Ensembl release 95) using salmon v0.12.0 (salmon quant with options -l A  --validateMappings --gcBias)(Patro et al., 2017).  Further analysis was performed using R version 3.6.2  (R Core Team, 2017) and Bioconductor (Huber et al., 2015). The DESeq function of DESeq2_1.25.10 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression between wild-type and mutant samples and the adjusted p-values. Adjusted p-value 0.1 was used as a threshold for statistical significance. The individual mouse tissues were analyzed separately.
Analysis of ribosome footprinting data: To analyze the translational differences between the mutant and wild-type brain samples for individual genes, we compared the ratio of footprint vs. the input reads (i.e. translation efficiency) for individual genes.  We tested the differences in translation efficiency for individual genes using DESeq2 design: '~ assay(input/footprint) + condition(KO/WT) + assay:condition' and applying the likelihood ratio test which removes the interaction term in the reduced model.  For each gene we obtained log2 fold changes of gene translation efficiency difference between wild-type and mutant samples and the adjusted p-value.
Analysis of ribosome m6Am-Exo-Seq data: Reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (Ensembl release 95) using STAR (ref: PMID: 23104886) with parameters ?--outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000?. The genomic coverages for individual samples were created in R using GenomicAlignments::coverage method.
For individual genes we tested the differences in m6A enrichment of their TSSs using matrix of read counts covering TSS of individual genes and DESeq2 design: '~ assay(input/m6A_IP) + condition(KO/HET) + assay:condition' and applying the likelihood ratio test which removes the interaction term in the reduced model.  For each gene we obtained log2 fold m6A enrichment difference between wild-type and mutant samples and the adjusted p-value. We identified 1370 genes which had significantly lower m6A TSS enrichment in the mutants. "
Genome_build: Ensembl release 95
Supplementary_files_format_and_content:
Gene expression data file contains information about gene expression changes in the KO.
Ribosome profiling file contains information about differences in footprint enrichment in the KO and control.
m6Am-Exo-Seq data files contains information about differences in m6A TSS enrichment in the KO and control.

source_name: Testes

extract_protocol:
Total RNA from biological triplicates of 2 months-old wildtype (WT) and Pcif1 KO mice were used for the experiment with mouse brain, spleen and testis samples. The tissues were snap-frozen in liquid nitrogen. Total RNA was isolated from tissues using TRIzol (Thermo Fisher Scientific) according to manufacturer instructions.
For ribosomal profiling brains from three adult wildtype (WT) controls and three Pcif1 KO mice were isolated and snap-frozen in liquid nitrogen. Frozen brain (~400 mg) was homogenized in 1300 µL (3x weight of the tissue in miligrams) of ice cold polysome lysis buffer (20 mM Tris?HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 5 mM DTT, 100 ?g/ml Cycloheximide, 40 U/ml RNasin plus, (Promega), Complete EDTA-free protease inhibitor (Thermo Scientific), 1% TritonX?100, 0.5% Sodium deoxycholate) using a glass homogenizer (6-8 strokes). The lysate was transferred to a 1.5 mL Eppendorf tube and incubated on ice for 10 minutes with intermittent mixing. The lysate was centrifuged at 3000 rpm for 3 minutes at 4°C. Supernatant was carefully collected in a new 1.5 mL Eppendorf tube. The OD260 of the lysate was measured with a Nanodrop instrument and approximately 15 OD260 (which correspond to 100 µL of lysate), was used for ribosome footprint preparation, and 50 µL was directly transferred to TriZol (Ambion) for total input RNA extraction. The remaining lysate was divided in aliquots of 150 µL and was snap frozen in liquid nitrogen and stored in -80°C freezer for later use. For ribosome footprint preparation, 100 µL of the supernatant was treated with 2.5 µL (5 units) of Turbo-DNase (Ambion) and 6.5 µL (650 units) of RNase I at 23°C for 45 minutes with rotation at 300rmp in a thermoblock. In meantime, the s-400 HR columns (GE healthcare) were washed three times with 700 µL polysome buffer (20 mM Tris?HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 5 mM DTT, 100 ?g/mL Cycloheximide, 40U/mL RNasin plus, (Promega), Complete EDTA-free protease inhibitor (Thermo Scientific)) plus 20U/mL SUPERaseIn (Ambion). During each wash columns with polysome buffer were spun at 2000rpm for 1 minute in a cold centrifuge. The columns were stored on ice with the polysome buffer in it (last wash). Once the RNaseI-treatment of lysate completed, 8.7 µL of SUPERaseIn RNase inhibitor was added to the reaction, gently mixed with the help of a pipette and stored on ice. The S-400 HR columns were spun at 2000 rpm for 1 minute to remove the polysome buffer. RNaseI-treated lysate was applied on the top of the column and spun at 2400 rpm for two minutes. The flow through was transferred to a fresh Eppendorf tube and RNA was extracted using 1.0 mL TriZol reagent. The RNA contain ribosome protected fragments (RPF) of mRNA as well as ribosomal RNA.
Approximately 20-25 µg of RNaseI-treated RNAs were separated on 15% UREA-PAGE to purify RPF which are in the range of 26-34 nt. Radiolabelled RNA marker of length 28 and 30 nt were used to size select the ribosome protected RNA fragment (RPF). The urea polyacrylamide gel was run at 16 W for 1 hour with the samples. Once the bromophenol blue reached the bottom of the gel, the power was switched off and the gel was taken out of the running apparatus. One glass plate was removed and the gel was wrapped in saran wrap and exposed to Storage Phosphor Screens (GE Healthcare; BAS IP MS 2025 E, Cat no. 28-9564-75) for 30 minutes, and scanned (GE Healthcare; Typhoon FLA 9500 IP, Cat no. 29-1885-90). Based on the position of markers, the gel piece corresponding to approximately 26-34 nt was excised and transfer to an RNase-free Eppendorf tube. The gel piece was ground to a fine powder and 600 µL of RNA extraction buffer (0.5 M Ammonium Acetate, 1 mM EDTA pH 8.0, and 0.1% SDS) was added and the tubes were incubated at 25°C overnight. Next day, the slurry was transferred to filter tubes (from Art-seq kit) and spun for 5 minutes at 5000 rpm. The flow-through was collected in a new RNase-free Eppendorf tube and precipitated with 1.0 µL of glycogen and 900 µL isopropanol overnight in -20°C freezer. The RNA solution was centrifuged at 13000 rpm for 20 minutes in a cold centrifuge to pellet RNA. RNA pellet was washed with 80% ethanol once, air dried and resuspended in 20 µL of RNase-free water.
m6Am-Exo-Seq (Sendinc et al., 2019) is a variation of m6A-IP seq. In this protocol, first, the m7G-capped RNA fragments (~100-200 nt) from poly(A)+ RNAs are enriched by multiple enzymatic treatments followed by m6A IP-seq to get m6A modification near the 5´  end of the mRNAs.  Approximately 8.0 µg of poly(A)+ RNAs from biological triplicates from Pcif1+/- and Pcif1-/- mouse testes were fragmented with RNA fragmentation buffer (Ambion) in a total volume of 20 µL for 7.30 minutes at 70°C in a thermcycler to obtain RNA fragments of ~100-200nt length. Fragmentation reaction was stopped by transferring the RNAs quickly to ice and adding 2.2 µL 10x stop solution (Ambion). The fragmented RNAs were purified with RNA Clean & Concentrator-5 (Zymo Research, R1014) and eluted in 17 µL water. Fragmented RNAs were 5´ phosphorylated by adding 10x, 2 µL T4 DNA ligase buffer (NEB) and 20 units of T4 PNK (ThermoScientific) in a final reaction volume of 20 µL. The phosphorylation reaction was carried out for 1.30 hour at 37°C. The 5´ phosphorylated RNA fragments were degraded by Terminator? 5´-Phosphate-Dependent Exonuclease (Epibio). To the phosphorylation reaction, 14 µL of water, 4 µL 10x Exonuclease buffer A and 2 µL Terminator exonuclease was added and the reaction mixture was incubated at 30°C for 3 hours. RNAs were purified from above reaction with RNA Clean & Concentrator-5 and eluted in 15 µL water. At this point we get 300-400 ng of m7G-cap-enriched RNA fragments from each sample.
The RNA obtained from above reaction were directly used for m6A-IP (Wojtas et al., 2017) with some modifications. First, 100 µL of protein A dynabeads (Life Technologies; 10002D) were washed twice with PXL buffer (1X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% NP-40) and blocked with 1 µg/µL BSA in 400 µL PXL buffer for 45 minutes. Blocked beads were then incubated with 5 µg of anti-m6A antibody (Synaptic Systems, Cat. no. 202003) in 200 µL PXL buffer supplemented with 4 µL of RNasin RNase inhibitor (Promega; N2611) for one hour at room temperature. Antibody-conjugated beads were washed twice with PXL buffer and finally resuspended in 400 µL PXL buffer plus 4 µL RNAsin RNase inhibitor. Fragmented m7G-cap enriched RNAs were added and beads were incubated at 4°C for two hours with rotation. 10% of the RNA was kept separately and used to prepare input libraries. After two hours incubation, the beads were washed twice by ice-cold Nelson low-salt buffer (15 mM Tris at pH 7.5, 5 mM EDTA), once by ice-cold Nelson high-salt buffer (15 mM Tris at pH 7.5, 5 mM EDTA, 2.5 mM EGTA, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, 1 M NaCl), once by ice-cold Nelson stringent wash buffer (15 mM Tris at pH 7.5, 5 mM EDTA, 2.5 mM EGTA, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, 120 mM NaCl, 25 mM KCl), and last by ice-cold NT-2 buffer (50 mM Tris at pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40). Antibody-bound RNAs were eluted by adding 1mL TRIzol (Invitrogen) directly to the beads. RNAs were extracted and precipitated with Glycogen and ethanol overnight in -20°C, and used directly for the library preparation.
The TruSeq Stranded Total RNA kit with Ribo-Zero Gold (Illumina, Cat. No. 20020612) was used for library preparation with 400 ng of total RNA as input. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were diluted at 2 nM and pooled before the clustering process on a HiSeq 4000 Single Read flow cell. Paired-end reads of 100 bases were generated using the TruSeq SBS reagents on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva).
For ribosomal profiling the ribosomal RNAs were depleted from both input RNAs (400 ng) and RPF RNAs with mouse ribosomal RNAs probe from siTOOLs (mouse riboPOOLs) following their protocol. The ribosomal RNA-depleted input and RPF RNAs were used to make next generation sequencing library with TruSeq Ribo Profile (mammalian) kit from illumina. The libraries were sequenced at Genomics platform (University of Geneva).
The m6Am-Exo-Seq libraries were prepared with NEBNext® Ultra? II Directional RNA Library Prep Kit for Illumina® (E7765) according to the protocol 3 of the kit (Protocol for use with FFPE RNA, step 3.5 onwards). The final PCR was performed for 15 cycles (98°C ? 30 s, 12 cycle of 98°C ? 10 s, 65°C ? 75 s and final extension at 65°C ? 5 minutes). The libraries were sequenced on HiSeq4000 machine at genomics platform (University of Geneva)"

tag: age

value: adult

value: KO


title: RNAseq_hMADS_shGFP_h2_2

status: Public on Aug 28 2020

type: SRA

city: Huddinge

first: Serena

last: Barilla

state: Huddinge

address: Hälsovägen 7C

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
RNA-seq raw files (fastq files) were aligned to GRCh38 version of the human reference genome, using HISAT2 with defalt settings. SAM files were converted to BAM files and then sorted using SAMtools. featureCounts were then used to count tag in all exons.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq subreads counts files are in txt format and contain gene id and tag counts  in the indicated samples.

molecule: total RNA

organism: Homo sapiens

source_name: human adipose-derived stem cells

growth_protocol: hMADS cells were maintained in DMEM (Lonza, low glucose) supplemented with 10% fetal calf serum (Eurobio), 15 mM Hepes (Lonza), 2 mM L-Glutamine (Lonza), 1% penicillin/streptomycin and 2.5 ng/ml hFGF2 (Peprotech).

extract_protocol:
Total RNA was extracted from cells  using Trizol Reagent and RNeasy RNA Mini Kit. RNA quality was assessed by Agilent TapeStation 2200.
PolyA RNA selection was performed using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol. RNA-seq libraries were prepared and sequenced on the Illumina HiSeq 2000.

treatment_protocol: Two days post-confluence (day 0), cells were induced to differentiate in DMEM/Ham’s F12 (Lonza) media supplemented with 1 μM dexamethasone, 500 μM 3-isobutyl-1-methylxanthine (IBMX), 5 μg/ml insulin, 10 μg/ml transferrin and 0.2 nM triiodothyronine (T3). After two days of induction, dexamethasone and IBMX were omitted from the media, and 100 nM of rosiglitazone was added until day 9. The differentiation was continued until day 14 when full white adipocytes were developed.

tag: cell line

tag: genotype

value: shGFP

tag: timepoint

value: 2 hours


title: RNAseq_hMADS_shGFP_h2_1


title: ADU.021

type: protein

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

country: Italy

institute: GSK Vaccines

description:
NCT00560313
FS00005383-ADU.021

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit Sunnyvale, CA 94085, USA). The array was then incubated 1h a room temperature with human sera diluted 1:500 for anti-human IgG-specific analysis. After washing with 0.1% Tween 20 in PBS buffer (PBST), arrays were incubated with an AlexaFluor®647-labelled anti-human IgG, fab specific secondary antibody (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a Powerscanner (Tecan Trading AG, Switzerland) and the 16-bit images were generated with Powerscanner software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data was performed using in-house developed software and R scripts. For each sample, the mean fluorescence intensity (MFI) of replicated spots was determined, after subtraction of the background value surrounding each spot.

label: AlexaFluor®647-labelled anti-human secondary antibody

molecule: protein

source_name: vaccinated_Adult_serum-post III 4CmenB doses

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol: Human sera collected from different clinical trials

tag: subject group

value: Adult

tag: tissue

value: blood

tag: tissue subtype

value: serum-post III 4CmenB doses


title: ADU.020

description:
NCT00560313
FS00005382-ADU.020


title: ADU.018

description:
NCT00560313
FS00005376-ADU.018


title: ADU.019

description:
NCT00560313
FS00005380-ADU.019


title: ADU.017

description:
NCT00560313
FS00007543-ADU.017


title: ADU.022

description:
NCT00560313
FS00007685-ADU.022


title: VSMC_ATAC-seq_2

city: Bronx

first: Yizhou

last: Zhu

state: NY

address: Price469 1301 Morris Park Ave

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

description: Baseline

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Raw fq files were processed with kundaje pipeline (Github https://github.com/kundajelab/atac_dnase_pipelines) using defalt settings
Genome_build: hg19
Supplementary_files_format_and_content: Called peaks in NarrowPeak format. Signal in Fold Change (fc) in bigWig format

molecule: genomic DNA

source_name: Embryonic stem cell-derived VSMC

growth_protocol: hESC cells were maintained in feeder-free E8 system. To differentiate to VSMCs, cells were treated with N2B27 medium with 10 μM CHIR99021 and 25 ng/ml BMP4 for three days, followed by N2B27 supplied with 10ng/ml PDGF-BB and 2ng/ml Activin A for 5 days. Cells were maintained in N2B27 medium supplied with 10  ng/ml PDGF-BB

extract_protocol:
50,000 cells were trypsinized and washed with cold PBS twice and pelleted.
Performed as described in Current Protocols in Molecular Biology 21.29.1-21.29.9, January 2015

tag: cell type

value: H7-derived vascular smooth muscle cell

tag: passages

tag: method

value: ATAC-seq


title: KO-HEK293

city: Concepción

first: Carlos

last: Farkas

state: Biobío

address: Chacabuco 1140, 1808

department: Bioquímica y Biología Molecular

country: Chile

institute: Universidad de Concepción (UDEC)

data_processing:
Illumina ChIP-seq reads of SALL2 wild type, E1A-knockout cells and SALL2 total KO performed in HEK293 cells were imported to the Galaxy platform (usegalaxy.org) and aligned to the human genome (hg19 assembly) by using bowtie2 aligner with default settings [23]. Correspondent BAM files were sorted (Galaxy Version 1.7) and alignments were filtered with a sliding quality window of Q20 by using SAMtools (Galaxy Version 1.7) [23]. MACS2 program was used to call peaks in these BAM files by using an effective genome size of 2700000000, read extension size of 151, and peak detection based on p-value cutoff of 0.005. Additionally, bigwig files from aligned bam files were obtained by using deeptools bamCoverage tool (Galaxy Version 3.1.2)[24]. Each bigwig file was normalized to 1x method by using the referred effective genome size and a bin length of 50 bp
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: HEK293 cells

growth_protocol: cells were grown in 100-mm dishes at one million cells per plate

extract_protocol:
Cell nuclei were sonicated to shear DNA in 300 μl of sonication buffer, using a Bioruptor Plus (Diagenode) (18 times, 15 sec on /20 sec off each time, 9 W potency), obtaining lengths between 300 and 600 bp. Immunoprecipitations were carried out overnight at 4 °C using 40 μg of chromatin and 5 μg of SALL2 (anti-SALL2; Bethyl). The SALL2 total knockout was used as a negative control of antibody binding
To prepare each library was used the KAPA Hiper Prep kit and 7 adapters from the KAPA SI Adapters kit, both according to the manufacturer’s protocols. Briefly, the first step in library preparation was to convert any overhangs in the ChIP DNA into phosphorylated blunt ends. The 3′ ends were then adenylated, and adaptors ligated onto the ends of the fragments. The library size (348 bp) and the DNA concentration (14,486 nM) was obtained by using an Agilent 2100 Bioanalyzer

tag: chip antibody

value: Sall2 (Bethyll)


title: IMR90Induced_ATAC-seq_2

description: IFNB1 induced

source_name: Lung

growth_protocol: IMR90 cellswas maintained in EMEM with 10% FBS

treatment_protocol: To induce IFNB1 expression, cells were treated with 20 µM 2’3’-cyclic GMP-AMP, 100 ng/mL IFN?, and 10 ng/mL TNF? for 24 hours

value: Lung Fibroblast

tag: strain


title: HEK_DMSO treated rep1

type: RNA

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description:
SAMPLE 1
replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using RMA normalisation affy package (v.1.32.1) in R/Bioconductor (v.2.14.1).

label: biotin

source_name: human embryonic kidney DMSO treated

label_protocol: Standard Affymetrix labeling protocol

growth_protocol: RAS-ROSE abd ROSE cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) supplemented with 10 % fetal calf serum (FCS) (Sigma-Aldrich), 2 mM Ultraglutamine 1 (Lonza, BioWhittaker), and 100 units/ml penicillin/streptomycin (Biochrom AG) (standard medium). The medium was supplemented with G418 (400 μg/μl). 45000 RAS-ROSE cells were seeded into 6-well plates (BD Falcon) in standard medium 24 h prior to transient transfection of siRNA.

extract_protocol: Total RNA was isolated from cell lines using the mirVanaTM miRNA Isolation Kit from Ambion® (Austin, TX, USA) according to the manufacturer’s instructions. In order to avoid cross-labeling of premature miRNA we used the gel purification option. Subsequently the quality of the small RNA fraction was controlled on a 15% PAAG gel stained with ethidium bromide.

treatment_protocol: The HRASG12V-transformed human embryonal kidney cells (HA1ER) and their immortalized origin cell line HA1EB were described by [Hahn et al. Nature 400, 464-468 (1999)] . They were cultivated in Minimum Essential Medium Eagle, Alpha Modification (MEM Alpha) from Sigma, supplemented with 10% IFS, 2 mM ultraglutamine, 1%  penicillin/streptomycin,  0,1mg/ml hygromycin and  0,5µg/ml puromycin.  G418 was freshly added to a final concentration of 0,4 mg/ml . ROSE199, rat ovary epithelial cell line and their KRAS transformed derivative cell line ROSEA25 were described in [Tchernitsa et al. Oncogene 23, 4536-4555 (2004)]. Inducible RAS studies were done in HEK cell line transfected with a constuct bearing Ha-RAS under ER promoter. Cells were treated with tamoxifen before RNA was extracted. U0126 MEK inhibitor was dissolved in DMSO and used in 10µM final concentration for 48h before RNA was extracted.

tag: tissue/cell type

value: embryonic kidney

tag: genotype/variation

value: control

tag: treated with

value: DMSO


title: HEK RAS transformed UO126 treated rep2

description:
SAMPLE 6
replicate 2

source_name: human embryonic kidney RAS-transformed UO126 treated

value: RAS transformed


title: VSMC_ATAC-seq_1

description: Baseline


title: HEK RAS transformed UO126 treated rep1

description:
SAMPLE 5
replicate 1


title: RNAseq_hMADS_shGPS2_D0_2

value: Day 0


title: RNAseq_hMADS_shGFP_h2_4


title: RNAseq_hMADS_shGPS2_D0_3


title: HEK RAS transformed DMSO treated rep2

description:
SAMPLE 4
replicate 2

source_name: human embryonic kidney RAS-transformed DMSO treated


title: RNAseq_hMADS_shGPS2_D0_4


title: RNAseq_hMADS_shGFP_D0_4


title: HEK RAS transformed DMSO treated rep1

description:
SAMPLE 3
replicate 1


title: ADU.016

description:
NCT00560313
FS00005372-ADU.016


title: HEK_DMSO treated rep2

description:
SAMPLE 2
replicate 2


title: RNAseq_hMADS_shGFP_D0_3


title: ROSE RAS transformed FRA1 silenced rep2

description:
SAMPLE 13
replicate 2

organism: Rattus norvegicus

source_name: rat ovarian surface epithelium RAS transformed FRA1 silenced

value: ovarian surface epithelium cells

value: RAS transformed; FRA1 silenced


title: ROSE RAS transformed FRA1 silenced rep1

description:
SAMPLE 12
replicate 1


title: ADU.015

description:
NCT00560313
FS00005371-ADU.015


title: IMR90Induced_ATAC-seq_1

description: IFNB1 induced


title: ROSE RAS transformed PI3K control

description: replicate 1

data_processing: The data were normalised using dchip (Build date April 9 2009) normalized

source_name: rat ovarian surface epithelium RAS transformed PI3K control

treatment_protocol: The HRASG12V-transformed human embryonal kidney cells (HA1ER) and their immortalized origin cell line HA1EB were described by [Hahn et al. Nature 400, 464-468 (1999)] . They were cultivated in Minimum Essential Medium Eagle, Alpha Modification (MEM Alpha) from Sigma, supplemented with 10% IFS, 2 mM ultraglutamine, 1%  penicillin/streptomycin,  0,1mg/ml hygromycin and  0,5µg/ml puromycin.  G418 was freshly added to a final concentration of 0,4 mg/ml . ROSE199, rat ovary epithelial cell line and their KRAS transformed derivative cell line ROSEA25 were described in [Tchernitsa et al. Oncogene 23, 4536-4555 (2004)]. Inducible RAS studies were done in HEK cell line transfected with a constuct bearing Ha-RAS under ER promoter. Cells were treated with tamoxifen before RNA was extracted. U0126 MEK inhibitor was dissolved in DMSO and used in 10µM final concentration for 48h before RNA was extracted. LY294002 PI3K inhibitor was dissolved in ethanol and used at final concentration of 50µM.

value: RAS transformed; PI3K control

tag: treatment

value: LY294007 treated control


title: IMR90C_ATAC-seq_2

description: Baseline


title: RNAseq_hMADS_shGPS2_D0_1


title: IMR90C_ATAC-seq_1

description: Baseline


title: ROSE RAS transformed PI3K_inhibited

description: replicate 1

source_name: rat ovarian surface epithelium RAS transformed PI3K inhibited

value: RAS transformed; PI3K inhibited

value: LY294007 treated


title: ADU.013

description:
NCT00560313
FS00007535-ADU.013

value: Adult

value: blood


title: ADU.014

description:
NCT00560313
FS00005369-ADU.014

value: serum-post III 4CmenB doses


title: ROSE RAS transformed scrambled

description:
SAMPLE 11
replicate 1

source_name: rat ovarian surface epithelium RAS transformed treated with scrambled siRNA

value: RAS transformed; scrambled_siRNA treated


title: ROSE RAS transformed mir22 mimic rep1

description:
SAMPLE 9
replicate 1

source_name: rat ovarian surface epithelium RAS transformed mir22 mimic

value: RAS transformed; mir22 mimic


title: IMR90C_Csp6I_MLLT3_2

description: Baseline

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were filtered using padding sequence indicated (Zhu, Suh)
Viewpoint sequence was trimmed using fastx_trimmer -f N, where N equals to viewpoint length
Processed reads were aligned to the hg19 genome assembly using bwa mem with default setting
Data were filtered with MAPQ>0. Reads aligned -1k to +2k from viewpoint were removed
Duplication reads were filtered using custom awk script (Zhu, Suh)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph with 100 bp bin size. Score for each bin indicate read count aligned to 500 bp interval (+-250 bp)

extract_protocol:
Cells were fixed with 1% (v/v) formaldehyde in PBS for 10 min at room temperature. Fixation was quenched 0.2M glycene. Cells were washed with cold PBS twice and pelleted.
Cell pellet was resuspended in a premixture of 250 µl cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) and 50 µl protease inhibitors. Suspension was incubated on ice for 15 min and centrifuged. The pellet was washed once with 500 µl of cold lysis buffer, and carefully resuspended in 50 µl of 0.5% SDS. The suspension was then incubated in a 62 oC heating block for 7 min, followed by mixing with 145 µl water and 25 µl 10% Triton X-100, and incubated at 37 oC for 15 min. The suspension was mixed with 50 µl of buffer G, 120 U MboI (DpnII), 120 U Csp6I (CviQI), and 100 U Hin1II, and filled the total volume to 500 µl. For Single RE UMI-4C experiments, the suspension was mixed with 50 µl of buffer R, buffer B, and buffer G, respectively, for digestion with 100 U MboI, 100 U Csp6I, and 100 U Hin1II   in 500 µl final volume. All digestions were conducted at 37 oC overnight with rotation. The restriction enzymes were inactivated by incubating at 65 oC for 20 min. After cooling to room temperature, end blunting was performed by adding 3 µl of 10 mM dNTP, 8 µl of DNA polymerase I Klenow, and 4 µl of T4 DNA polymerase, and incubating at 37 oC for 1 hour with rotation. The suspension was then mixed with 460 µl water, 120 µl T4 ligase buffer, 100 µl 10% Triton X-100, 6 µl 20 mg/ml BSA, and 5 µl of 400 U/µl T4 ligase, and incubated for 4 hours at room temperature with rotation. The processed nuclei were pelleted and resuspended in 500 µl 1x T4 ligation buffer supplied with 50 µl 20 mg/ml proteinase K and 50 µl 10% SDS, and incubated at 55 oC for 30 min. For de-crosslinking, 60 µl 5M sodium chloride was added and the mixture was incubated at 68 oC for 2 hours. DNA was recovered using phenol-cholorform extraction.The re-arranged genomic DNA was sonicated to 300-400 bp fragments using Covaris S2 ultrasonicator. The fragmented DNA was double size-selected using 0.40x/1.0x of SPRI beads to remove reads below 100 bp and above 1000 bp, and eluted with a final volume of 70 µl of 10 mM Tris-HCl. The eluent was mixed with 10 µl 10x T4 ligation buffer , 10 µl 100 mM ATP, 5 µl 10 mM dNTP mix, 4 µl T4 DNA polymerase , 1 µl DNA polymerase Klenow, and 5 µl T4 PNK, and incubated for 30 min at room temperature. The repaired DNA was purified by using 1.0x SPRI beads, and eluted with a master mix of 94.5 µl 1x NEB buffer 2 and 0.5 µl 100 mM dATP. After removing the beads, 5 µl of Klenow exo- was added, and the mixture was incubated at 37 oC for 30 min for dA tailing. The processed DNA was purified by using 1.0x SPRI beads, and eluted with 20 µl 10 mM Tris-HCl. After dA-tailing, a custom Y shape adaptor was ligated to the fragments. For amplification, eight 100 µl reactions, each containing 400 µg preamplification library, 2 µM universal primer, 0.5 µM viewpoint-specific outer primer for each multiplexed viewpoint, and 1x SuperFi PCR master mix with 20% GC enhancer, was performed at following condition: 98 oC for 30s, 28 cycles of 98 oC for 10s, 62 oC for 10s, and 72 oC for 60s, and final extention at 72 oC for 5 min. The product was pooled and purified with 1.0x SPRI beads.
4C, Tri-4C

value: Lung Fibroblast

tag: digestion


title: RNAseq_hMADS_shGFP_D0_2

data_processing:
ChIP-seq raw files (fastq files) were aligned to the GRCh38  version of the human reference genome, using Bowtie  with parameters "-m 1". Only sequences mapping to exactly one location were kept. SAM files were then imported to HOMER to construct tag directories and HOMER was used for peak calling, annotation and extractraction of raw tag counts.
Genome_build: hg38
Supplementary_files_format_and_content: Raw tag counts files are in txt format and contain the merged peaks, annotation and raw tag counts of the respective peaks in the indicated samples.
RNA-seq raw files (fastq files) were aligned to GRCh38 version of the human reference genome, using HISAT2 with defalt settings. SAM files were converted to BAM files and then sorted using SAMtools. featureCounts were then used to count tag in all exons.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq subreads counts files are in txt format and contain gene id and tag counts  in the indicated samples.

treatment_protocol: hMADS differentiation to adipocytes

value: shGFP


title: OCI-AML2 R50+ROMI-1

city: Gainesville

first: Yi

last: Qiu

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Sequenced reads were mapped to hg19 whole genome using Tophat
output from Cufflinks, Cuffdiff
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: OCI-AML2 R50

growth_protocol: OCI-AML2 R50 cells were cultured in MEMα medium with 15% FBS and 50µM Ara-C.

extract_protocol:
RNA were purified by Genesee Scientific RNA purification kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Romidepsin treatment 18h

value: AML

value: OCI-AML2 R50

value: Romidepsin treatment 18h


title: ADU.011

description:
NCT00560313
FS00007527-ADU.011


title: ADU.010

description:
NCT00560313
FS00007529-ADU.010


title: OCI-AML2 R50

value: control


title: IMR90C_Csp6I_MLLT3_1

description: Baseline


title: ADU.009

description:
NCT00560313
FS00007525-ADU.009


title: ROSE RAS transformed

description:
SAMPLE 8
replicate 1

source_name: rat ovarian surface epithelium RAS transformed

value: ovarian surface epithelium cells

value: RAS transformed


title: 50R

data_processing:
Transcript level quantification of RNA-Seq data was carried out by Salmon using Ensemble release 75 as the reference.
Transcript level quantification was aggregated to gene-expression level using tximport R package
Gene length scaled TPM (transcripts per million) values were obtained by setting countsFromAbundance = “lengthScaledTPM” by tximport
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: AML

value: acute myeloid leukemia (AML)

tag: phenotype

value: Ara-C resistant


title: IMR90C_Csp6I_IFNB1_2

description: Baseline


title: IMR90C_Csp6I_IFNB1_1

description: Baseline


title: ROSE RAS transformed mir22 mimic rep2

description:
SAMPLE 10
replicate 2


title: ADU.008

description:
NCT00560313
FS00007521-ADU.008


title: 3R


title: ADU.007

description:
NCT00560313
FS00007705-ADU.007


title: IMR90C_NlaIII_IFNB1_2

description: Baseline

value: NlaIII


title: CD630_WT4-Cy3_sig544-cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 4 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: strain C630E grown 6h in TY (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E was grown for 6 hours in TY medium.

extract_protocol: Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.

value: C630E Mullany

source_name: sig54 mutant grown 6h in TY


title: ADU.012

description:
NCT00560313
FS00007534-ADU.012

source_name: vaccinated_Adult_serum-post III 4CmenB doses

value: Adult


title: IMR90C_Csp6I_Boundary_2

description: Baseline


title: RNAseq_hMADS_shGFP_D0_1

source_name: human adipose-derived stem cells

tag: cell line

value: Day 0


title: IMR90C_NlaIII_IFNB1_1

description: Baseline


title: CD630_WT3-Cy5_sig543-cy3

description: Biological replicate 3 of 4.


title: OCI-AML2 R50+ROMI-2


title: WT

value: Wild type


title: CD630_WT2-Cy3_sig542-cy5

description: Biological replicate 2 of 4.


title: CD630_WT1-Cy5_sig541-cy3

description: Biological replicate 1 of 4.


title: IMR90C_Csp6I_Boundary_1

description: Baseline


title: IMR90C_DpnII_MLLT3_2

description: Baseline

value: DpnII


title: ADU.004

description:
NCT00560313
FS00007526-ADU.004

value: blood

value: serum-post III 4CmenB doses


title: ADU.006

description:
NCT00560313
FS00007701-ADU.006


title: ADU.003

description:
NCT00560313
FS00007696-ADU.003


title: IMR90C_DpnII_MLLT3_1

description: Baseline

value: Lung Fibroblast


title: IMR90C_DpnII_IFNB1_1

description: Baseline


title: IMR90C_DpnII_IFNB1_2

description: Baseline


title: ADU.002

description:
NCT00560313
FS00007697-ADU.002


title: ADU.005

description:
NCT00560313
FS00007703-ADU.005


title: ADU.001

description:
NCT00560313
FS00005122-ADU.001


title: RNA-Seq O_T4F4

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

description: Ovary T4 Library biol. Rep. 4

data_processing:
Illumina reads were checked for quality using FastQC software. High quality reads(Q>30) were mapped to the Atlantic salmon genome ICSASG_v2 (Lien et al., 2016)using TopHat2 version 2.1.1 (Kim et al., 2013) with default parameters. Alignment files in BAM format were sorted by read name and converted into SAM format using SAMtools version 1.4 (Li et al., 2009). The Python package HTSeq version 0.7.2 (Anders et al., 2015) was applied to count unique reads mapped to exons using default parameters
Raw counts were analysed using the edgeR package (Robinson et al., 2010) in the R statistical computing environment to infer differential gene expression among tissues. The four tissues at the long photoperiod time points (T2, T3 and T4) were compared to the control samples at T1.
Further analyses were conducted on the lists of significant DEGs using normalised expression data (log2FPKM) according to Haas et al., 2013
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Salmo salar

source_name: ovary

growth_protocol: Fish were managed in a tank based experimental system to facilitate a long-light photoperiod regime known to stimulate the onset of sexual maturation

extract_protocol:
Tissue samples were preserved in RNA-Later at -80 °C and total RNA was isolated 626 using RNeasy mini kit (QIAGEN) as previously described (Mohamed et al., 2018). Tissues were lysed twice in 450 μL of lysis solution on a Precellys 24 homogenizer for 30s at 4.0 ms−1. RNA was bound to a column and washed twice before elution with 40 μL at room temperature. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrometer, Qubit 2.0 fluorometer and Agilent 2100 631 bioanalyzer. Messenger RNA (mRNA) was isolated from 1 μg of total RNA.
64 RNA-Seq libraries (4 time points x 4 tissues x 4 biological replicates) were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). Libraries were sequenced on 634 Illumina Nova-Seq 6000 sequencing platform

treatment_protocol: Fish from a single management group were sacrificed at a timepoint immediately before initiation of the long-light regime (throughout referred to as T1) and at three timepoints afterwards (T2, T3 and T4).


title: IMR90C_DpnII_Boundary_1

description: Baseline

source_name: Lung


title: RNA-Seq O_T4F3

description: Ovary T4 Library biol. Rep. 3


title: IMR90C_DpnII_Boundary_2

description: Baseline


title: Control RecCtrl_RecCFPm_rep2

city: Odense

first: Ines

last: Block

address: J.B. Winsløws Vej 4

department: Department of Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Biological replicate 2 of 4. Control RecCtrl with empty vector plasmid; RecCFPm

hyb_protocol: The hybridization was conducted with the Hybridization Gasket Slide Kit (G2534-60014, Agilent technologies) and the Gene Expression Hybridization Kit (5188-5242, Agilent technologies) following the manufacturer’s instructions and the samples were hybridized on the SurePrint G3 Custom Gene Expression Microarray 8x60K (G4102A, Agilent technologies)

scan_protocol: SurePrint G3 Custom Gene Expression Microarray, 8x60K (G4102A, Agilent Technologies) was scanned in the Agilent 2505C DNA Microarray Scanner with Sure-Scan High Resolution Technology. Images were quantified using Agilent Feature Extraction Software version 10.7.3.1.

data_processing:
Raw data were processed using the limma R package. Background normalization was performed using normexp with an offset of 50. Each slide was normalized using LOESS. Between array quantile normalization was performed last.
Quantile (between arrays) and loess (within arrays) normalized M values.

source_name: Inducible MCF7 RecCtrl cancer cell line

label_protocol: 1 µg of total RNA were treated with a Spike-In control (5188-5279, Agilent technologies); cDNA synthesis, cRNA synthesis/amplification and cRNA purification was conducted according to the manufacturer`s instructions: Two-Color Microarray-Based Gene Expression Analysis for Low Input Quick Amp Labeling (5190-2306, Agilent technologies)

growth_protocol: Recombinant RecCtrl, RecCFP and RecCFPm breast cancer cell lines were cultivated under optimal growth conditions and gene expression was induced with 50ng/ml doxycycline for 48 h; a cell pellet was harvested and total RNA was purified according to the extract protocol

extract_protocol: Total RNA was extracted using the mirVana™ miRNA Isolation Kit with phenol from Ambion™ (AM1561, Life technologies) following manufacturer's instructions. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).

value: Induced for 48h with doxycycline

value: RecCtrl

source_name: Inducible MCF7 CFPm2 cancer cell line


title: RNA-Seq O_T4F2

description: Ovary T4 Library biol. Rep. 2


title: GHMT/TAZ-4SA_2

city: Tokyo

first: Shota

last: Kurotsu

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Cardiology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with Affymetrix Expression Console software version 1.4 for normalization.

organism: Mus musculus

source_name: GHMT/TAZ-4SA transduced MEFs on 8 kPa

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit User Manual,  Affymetrix). Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: MEFs cultured on 8 kPa or 126 kPa hydrogel were transduced with the retrovirus (Gata4, Hand2, Mef2c, Tbx5, YAP-5SA, TAZ-4SA) and lentivirous (Scramble shRNA, shYAP, shTAZ) mixtures as indicated. The medium was replaced with DMEM/M199/10%FBS medium, which contained DMEM (high glucose) with L-glutamate and phenol red (Wako, Tokyo, Japan, 044-29765); Medium199 with Earle’s Salts, L-glutamate and 22 g/L sodium bicarbonate (Gibco, 11150-059); and 10% Hyclone Characterized FBS (Thermo Scientific, SV30014.03) after 24 hr of infection. Cells were collected after 2 weeks. The medium was changed two times a week.

extract_protocol: RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012). The RNA quality was determined by the RNA Integrity Number (RIN) value with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)). Only specimens with RIN>7.0 were used in this study.

value: mouse embryonic fibroblast

tag: culture condition

value: 8 kPa hydrogel


title: RecCFPm_Control RecCtrl_rep4

description: Biological replicate 4 of 4. Control RecCtrl with empty vector plasmid; RecCFPm

source_name: Inducible MCF7 RecCFPm cancer cell line

value: RecCFPm


title: RecCFPm_Control RecCtrl_rep3

description: Biological replicate 3 of 4. Control RecCtrl with empty vector plasmid; RecCFPm


title: GHMT/TAZ-4SA_1


title: IMR90Induced_Tri4C_MLLT3_2

description: IFNB1 induced

value: Triple


title: GHMT/YAP-5SA_2

source_name: GHMT/YAP-5SA transduced MEFs on 8 kPa


title: Control-2-Input(C2-Input)

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

country: China

institute: Shanghai Jiaotong University

data_processing:
MBD-seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.1.0.
R package MEDIPS was used to analyze data and count reads overlapping a sliding window (200 bp)
Genome_build: mm10
Supplementary_files_format_and_content: Xlsx file includes matrix table with raw read counts and RPKM values for every window and every sample

source_name: mouse ovary

extract_protocol:
Genomic DNA from ovarian tissues of PCOS mice and control group mice was extracted by using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Up to 1μg Genomic DNA was fragmented with M220 Focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA). The fragmented DNA with methylated CpGs was enriched by using the MethylMiner™ Kit (Invitrogen, Waltham, Massachusetts, USA) as recommended by the manufacturer. The MBD-enriched DNA fractions were used to generate indexed libraries with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, San Diego, California, USA). The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

value: ICR

value: No treatment

tag: age

value: 8 weeks


title: IMR90Induced_Tri4C_MLLT3_1

description: IFNB1 induced


title: Control RecCtrl_RecCFPm_rep1

description: Biological replicate 1 of 4. Control RecCtrl with empty vector plasmid; RecCFPm


title: GHMT/shTAZ_2

source_name: GHMT/shTAZ transduced MEFs on 126 kPa

value: 126 kPa hydrogel

value: GHMT/shTAZ


title: GHMT/shTAZ_1


title: RecCFP_Control RecCtrl_rep4

description: Biological replicate 4 of 4. Control RecCtrl with empty vector plasmid; RecCFP

source_name: Inducible MCF7 RecCFP cancer cell line

value: RecCFP


title: RecCFP_Control RecCtrl_rep3

description: Biological replicate 3 of 4. Control RecCtrl with empty vector plasmid; RecCFP


title: RNA-Seq O_T4F1

description: Ovary T4 Library biol. Rep. 1

tag: timepoint


title: Control RecCtrl_RecCFP_rep1

description: Biological replicate 1 of 4. Control RecCtrl with empty vector plasmid; RecCFP

source_name: Inducible MCF7 CFP cancer cell line


title: Control RecCtrl_RecCFP_rep2

description: Biological replicate 2 of 4. Control RecCtrl with empty vector plasmid; RecCFP


title: Control-1-Input(C1-Input)


title: GHMT/YAP-5SA_1


title: IMR90Induced_Tri4C_IFNB1_1

description: IFNB1 induced


title: Control-2-MBD(C2-MBD)


title: RNA-Seq O_T3F4

description: Ovary T3 Library biol. Rep. 4


title: GHMT/shYAP_2

source_name: GHMT/shYAP transduced MEFs on 126 kPa

value: GHMT/shYAP


title: IMR90Induced_Tri4C_IFNB1_2

description: IFNB1 induced


title: IMR90Induced_Tri4C_Boundary_1

description: IFNB1 induced


title: GHMT/Scramble_2

source_name: GHMT/Scramble shRNA transduced MEFs on 126 kPa

value: GHMT/Scramble shRNA


title: RNA-Seq O_T3F2

description: Ovary T3 Library biol. Rep. 2


title: IMR90Induced_Tri4C_Boundary_2

description: IFNB1 induced


title: PCOS-Treatment-4-INput(T4-Input)

value: Offspring born in DHT exposure during pregnancy


title: PCOS-Treatment-4-MBD(T4-MBD)


title: PCOS-Treatment-2-Input(T2-Input)


title: IMR90C_Tri4C_MLLT3_2

description: Baseline


title: RNA-Seq O_T2F4

description: Ovary T2 Library biol. Rep. 4


title: IMR90C_Tri4C_MLLT3_1

description: Baseline


title: GHMT/shYAP_1


title: RNA-Seq O_T3F3

description: Ovary T3 Library biol. Rep. 3


title: GHMT/Scramble_1


title: Control-1-MBD(C1-MBD)


title: IMR90C_Tri4C_IFNB1_2

description: Baseline


title: PCOS-Treatment-2-MBD(T2-MBD)


title: RNA-Seq O_T2F3

description: Ovary T2 Library biol. Rep. 3


title: RNA-Seq O_T2F2

description: Ovary T2 Library biol. Rep. 2


title: Fixed species mixing

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: FD-seq species mixing of PFA-fixed cells

data_processing:
Base calling was done automatically in Illumina's BaseSpace platform
Single-cell data was processed using Drop-seq tools v1.13 and STAR aligner according to the online manual
Bulk data was aligned using STAR aligner, and counted using featureCounts.
Single-cell count data was analyzed with monocle 2 and Seurat 3
Bulk data count data was analyzed with DESeq2
Genome_build: GRCh38, hg19 and mm10 mixed, OC43 genome NC_006213.1
Supplementary_files_format_and_content: Single-cell data: tab-delimited text file of UMI counts per single cell
Supplementary_files_format_and_content: Bulk data: tab-delimited text file of read counts per sample

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: BC3 and 3T3 cell lines

growth_protocol: BC3 cells were grown in RPMI media with 20% FBS, 2 mM GlutaMax and 1% P/S. HEK293T cells were grown in DMEM with 10% FBS, 2 mM GlutaMAX and 1% P/S. A549 cells were grown in DMEM with 10% FBS. 3T3 cells were grown in DMEM with 10% FBS, 1% GlutaMAX and 1X P/S

extract_protocol:
Single cells were captured and lysed in droplets in a microfluidic chip as per Drop-seq. Bulk RNA samples were extracted using HP Total RNA Kit.
The single-cell cDNA was tagmented using Nextera XT kit as per Drop-seq protocol. Bulk library was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Human primary effusion lymphoma and mouse embryonic fibroblast cells

tag: virus type

value: PFA fixation


title: GHMT/126 kPa_1

source_name: GHMT transduced MEFs on 126 kPa

value: GHMT


title: GHMT/8 kPa_1

source_name: GHMT transduced MEFs on 8 kPa


title: RNA-Seq O_T3F1

description: Ovary T3 Library biol. Rep. 1


title: PCOS-Treatment-1-Input(T1-input)


title: IMR90C_Tri4C_IFNB1_1

description: Baseline

value: Lung Fibroblast


title: RNA-Seq O_T2F1

description: Ovary T2 Library biol. Rep. 1


title: IMR90C_Tri4C_Boundary_2

description: Baseline


title: PCOS-Treatment-1-MBD(T1-MBD)


title: OC43 infection MOI 1

description:
FD-seq of fixed single cells from infected sample at MOI 1
ST-HVP-3S-DROP-HVP-MOI-1_S1

source_name: A549 cell line

value: Human-derived lung epithelial cancer cells

value: OC43 betacoronavirus


title: RNA-Seq O_T1F4

description: Ovary T1 Library biol. Rep. 4

source_name: ovary


title: GHMT/8 kPa_2

value: mouse embryonic fibroblast

value: 8 kPa hydrogel


title: OC43 infection mock

description:
FD-seq of fixed single cells from mock infected control sample
ST-HVP-3S-DROP-HVP-Mock_S2


title: IMR90C_Tri4C_Boundary_1

description: Baseline

source_name: Lung

value: Triple


title: RNA-Seq O_T1F3

description: Ovary T1 Library biol. Rep. 3


title: RNA-Seq O_T1F1

description: Ovary T1 Library biol. Rep. 1


title: RNA-Seq O_T1F2

description: Ovary T1 Library biol. Rep. 2


title: RNA-Seq P_T4F4

description: Pituitary T4 Library biol. Rep. 4

source_name: pituitary


title: Ovary-Control-4(C4)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5.
Raw counts were derived using stringtie v1.3.3.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Xlsx file includes matrix table with raw gene counts and FPKM values for every gene and every sample

extract_protocol:
Total RNA was extracted from ovarian tissue samples by using TRIzol reagents (Invitrogen, Waltham, Massachusetts, USA) as recommended by the manufacturer. The total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running 1.5% agarose gel electrophoresis and staining with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
1μg of total RNA was used to construct the RNA-seq libraries by the KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystem, Wilmington, Massachusetts, USA). The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

value: ICR

value: No treatment


title: Ovary-PCOS-2(P2)

value: 8 weeks


title: Live species mixing

description: Drop-seq species mixing of fresh live cells


title: Ovary-Control-1(C1)


title: RNA-Seq P_T4F3

description: Pituitary T4 Library biol. Rep. 3


title: Ovary-PCOS-4(P4)


title: ATAC-Seq T4L3

description: Liver T4 library biol. rep. 3

data_processing:
Raw reads were mapped to the Atlantic salmon reference genome ICSASG_v2 (Lin et al., 2016) using BOWTIE2 version 2.3.5.1 with the --very-sensitive parameter (Langmead & Salzberg, 2012). Duplicate reads were removed using the MarkDuplicates function in Picard (http://broadinstitute.github.io/picard/). Multi-mapped reads and mitochondrial reads were filtered and only uniquely mapped reads (MAPQ > 10) were extracted from alignment files using SAMTOOLS for downstream analyses
For peak calling, the model-based analysis of ChIP-Seq (MACS2) (https://github.com/macs3-project/MACS) was used to identify read enrichment regions “peaks” using default parameters. Only peaks detected in at least two replicates per condition were used for downstream analyses. Peaks for all of the time points were merged together to a unique peak list per tissue. The number of raw reads mapped to each peak was quantified using the Python package HTSeq version 0.11.1 (Anders et al., 2015).
Samples from the long photoperiod time points (T2, T3 and T4) were compared to control samples (T1) for each tissue. Raw counts were analysed to infer differential accessible chromatin using the R package edgeR. P-values were corrected for multiple testing using the Benjamini and Hochberg algorithm. Peaks with FDR < 0.05 and log2FC ± > 1 were considered significantly differentially accessible regions (DARs).
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1
Supplementary_files_format_and_content: Matrix table with raw counts per peak for all samples
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: liver

extract_protocol:
Tissue samples from liver were snap frozen in liquid Nitrogen and preserved at -80 °C. Frozen tissue (20 mg) was ground in liquid nitrogen using a mortar and pestle.  The pulverized tissue was transferred to a pre-chilled 2 ml dounce homogenizer containing 1mL cold 1x homogenisation buffer and homogenised with the pestle until a uniform suspension was seen (10-20 strokes).  The homogenate was filtered with a 40uM nylon cell strainer (BD Falcon) before layering onto the iodixanol solution as described previously (Corces et al., 2017).  The ratio of nuclei to enzyme concentration was optimised for each sample by performing transposition reactions containing 50000, 100000 and 200000 nuclei with 2.5ul of tagment enzyme in 50ul of transposition mix (Corces et al., 2017).  The transposed DNA was amplified with custom primers as described (Buenrostro et al., 2015).
12 liver ATAC-seq libraries arising from 3 biological replicates x 4 time points (T1-T4) were sequenced at IMB sequencing facility (University of Queensland) on an Illumina NextSeq 150 cycle (2X 75 bp).


title: Ovary-PCOS-1(P1)


title: ATAC-Seq T4L1

description: Liver T4 library biol. rep. 1


title: RNA-Seq P_T4F1

description: Pituitary T4 Library biol. Rep. 1


title: ATAC-Seq T4L2

description: Liver T4 library biol. rep. 2


title: Ovary_phf7ey_RNAseq1

city: Boston

first: Mitzi

middle: I

last: Kuroda

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital/Harvard Medical School

description: Total mRNA from 10 day old ovaries

data_processing:
Sequencing reads were aligned to the Drosophila genome (UCSC dm6) using TopHat (2.1.0)
Differential analysis was completed using CuffDiff (2.2.1)
Processed wig files were generated using Deeptools bam coverage
Genome_build: dm6

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Drosophila were raised at 18 degrees Celcius until eclosion. Adults were transferred to 29 degrees Celcius for 10 days

extract_protocol:
RNA was extracted using standard Trizol methods
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit
Paired end RNAseq. Sequencing was completed on 2 biological replicates of each genotype with the Illumina HiSeq 2500 v2 with 100 bp reads

tag: Sex

value: Female

tag: tissue

value: Ovary

tag: genotype


title: Ovary_phf7ey_RNAseq2

description: Total mRNA from 10 day old ovaries


title: DPI14_tdTomP1

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
Samples were pooled and analyzed on 1 lanes of Illumina HiSeq with 150bp paired end reads.
The reads were mapped to the mouse transcriptome (mm10) using STAR and the influenza genome using Bowtie and samples were run on Basespace (Illumina).
Mapped reads were analyzed using DeSeq2 in R.
The library was then normalized using the DeSeq2 function and fold-change and Wald test p-values were calculated and corrected using the Benjamini-Hochberg procedure for sample comparisons.

source_name: mouse that was influenza-infected but survived and cleared the virus

extract_protocol:
Cells were sorted by FACS SONY SH800S and cDNA generated using SMART-Seq v4 Ultra Low Input RNA kit directly from cell samples.
SMART-Seq v4 Ultra Low Input RNA Kit was used to generate cDNA libraries and Nextera XT Index kit was used for library enrichment and barcoding.

treatment_protocol: Mice were infected at the indicated timepoints and olfactory epithelium was collected

value: Olfactory epithelium

tag: cell population

value: tdTomato positive cells (previously infected)

value: 14 days post-infection


title: DPI14_tdTomP2


title: DPI14_tdTomN1

value: tdTomato negative cells (never infected)


title: DPI14_tdTomN2


title: ATAC-Seq T3L2

description: Liver T3 library biol. rep. 2


title: RNA-Seq P_T3F4

description: Pituitary T3 Library biol. Rep. 4


title: RNA-Seq P_T3F3

description: Pituitary T3 Library biol. Rep. 3


title: ATAC-Seq T3L3

description: Liver T3 library biol. rep. 3


title: ATAC-Seq T3L1

description: Liver T3 library biol. rep. 1


title: DPI3_4

source_name: Olfactory epithelium

tag: infection

value: influenza


title: ATAC-Seq T2L3

description: Liver T2 library biol. rep. 3


title: RNA-Seq P_T3F2

description: Pituitary T3 Library biol. Rep. 2


title: DPI3_3


title: RNA-Seq P_T3F1

description: Pituitary T3 Library biol. Rep. 1


title: Mock_2

value: mock


title: RNA-Seq P_T2F4

description: Pituitary T2 Library biol. Rep. 4


title: RNA-Seq P_T4F2

description: Pituitary T4 Library biol. Rep. 2


title: ATAC-Seq T2L1

description: Liver T2 library biol. rep. 1


title: Mock_1


title: ATAC-Seq T1L3

description: Liver T1 library biol. rep. 3


title: RNA-Seq P_T2F3

description: Pituitary T2 Library biol. Rep. 3


title: KO MPTP 2

city: Palo Alto

first: Khoa

middle: Dinh

last: Nguyen

state: California

address: 3373 Hillview Ave

department: Pathology

institute: Stanford University

data_processing:
Illumina Casava 1.5 was used for base-calling
Low quality sequences were trimmed and aligned to mm9 genome using Bowtie 0.12.7. Read mapping (TopHat) was run with default settings and -G option
Transcripts were then assembled using Cufflinks software
Expression level estimation was reported as RPKM
RPKM values of 0 are excluded
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: KO MPTP

extract_protocol:
Microglia were isolated from the brain and sorted by flow cytometer for total RNA processing with Qiagen RNAeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Midbrain

tag: cell type

value: Brain primary microglia

value: Ppargc1a FF CreER

value: MPTP

tag: additional treatment

value: 6 weeks post Tamoxifen


title: KO MPTP 3


title: KO MPTP 1


title: RNA-Seq P_T2F1

description: Pituitary T2 Library biol. Rep. 1


title: RNA-Seq P_T1F4

description: Pituitary T1 Library biol. Rep. 4


title: ATAC-Seq T1L1

description: Liver T1 library biol. rep. 1


title: ATAC-Seq T1L2

description: Liver T1 library biol. rep. 2


title: RNA-Seq P_T2F2

description: Pituitary T2 Library biol. Rep. 2


title: KO PBS 3

source_name: KO PBS

value: PBS


title: P11_M

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
150 nt paired-end reads were assembled into transcript isoforms and mapped to the pig genome (version GRCm38) using Kallisto v0.43 (Bray et al., 2016)
Genome_build: Sus scrofa genome (version xxx)
Supplementary_files_format_and_content: csv format, comma delimited columns, including transcripts per million (TPM) values for each sample, one column per sample

organism: Sus scrofa

source_name: Amygdala

extract_protocol:
Amygdala was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000   using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Amygdala

value: PRRS

tag: gender

value: Male

value: 22 day old

tag: feeding

value: Nursed


title: RNA-Seq P_T1F3

description: Pituitary T1 Library biol. Rep. 3


title: P10_M

tag: treatment


title: KO PBS 2


title: RNA-Seq P_T1F2

description: Pituitary T1 Library biol. Rep. 2


title: P9_M


title: KO PBS 1


title: RNA-Seq P_T1F1

description: Pituitary T1 Library biol. Rep. 1


title: P8_M


title: ATAC-Seq T2L2

description: Liver T2 library biol. rep. 2


title: WT MPTP 3

source_name: WT MPTP

value: Ppargc1a FF


title: RNA-Seq B_T4F4

description: BrainT4 Library biol. Rep. 4

source_name: brain


title: P7_M


title: WT MPTP 2


title: WT MPTP 1


title: GHMT/126 kPa_2

value: mouse embryonic fibroblast

value: 126 kPa hydrogel

tag: genotype/variation

value: GHMT


title: RNA-Seq B_T4F2

description: Brain T4 Library biol. Rep. 2


title: RNA-Seq B_T4F3

description: Brain T4 Library biol. Rep. 3


title: ROSE

description:
SAMPLE 7
replicate 1

data_processing: The data were normalised using RMA normalisation affy package (v.1.32.1) in R/Bioconductor (v.2.14.1).

source_name: rat ovarian surface epithelium

tag: tissue/cell type

value: ovarian surface epithelium cells

value: control


title: WT PBS 3

source_name: WT PBS

value: Midbrain


title: KSHV K8.1 negative

description:
FD-seq of fixed, non-reactivated single cells after TPA treatment
HVP-Negative_S2

source_name: BC3 cell line

value: Human primary effusion lymphoma

value: KSHV

value: TPA, PFA fixation and Triton X permeabilization


title: P5_F

value: Female


title: RNA-Seq B_T3F4

description: Brain T3 Library biol. Rep. 4


title: P4_F


title: RNA-Seq B_T4F1

description: Brain T4 Library biol. Rep. 1


title: KSHV K8.1 positive

description:
FD-seq of fixed, reactivated single cells after TPA treatment
HVP-Positive_S1


title: WT PBS 2

value: Brain primary microglia

value: PBS

value: 6 weeks post Tamoxifen


title: WT PBS 1


title: P3_F

value: Amygdala

value: PRRS


title: RNA-Seq B_T3F3

description: Brain T3 Library biol. Rep. 3


title: P2_F

value: 22 day old

value: Nursed


title: RNAseq_OM_468

data_processing:
RNA-seq raw files (fastq files) were aligned to GRCh38 version of the human reference genome, using HISAT2 with defalt settings. SAM files were converted to BAM files and then sorted using SAMtools. featureCounts were then used to count tag in all exons.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq subreads counts files are in txt format and contain gene id and tag counts  in the indicated samples.

source_name: visceral adipose tissue

extract_protocol:
Total RNA was extracted from cells  using Trizol Reagent and RNeasy RNA Mini Kit. RNA quality was assessed by Agilent TapeStation 2200.
PolyA RNA selection was performed using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol. RNA-seq libraries were prepared and sequenced on the Illumina NextSeq 500

treatment_protocol: Visceral adipose tissue biopies were obtained from different population admittes to the Geofffroy Saint-Hilaire clinique

value: visceral adipose tissue

tag: obesity status

value: diabetic


title: RNA-Seq B_T3F2

description: Brain T3 Library biol. Rep. 2


title: RNAseq_OM_461

value: non-diabetic


title: P1_F


title: RNAseq_OM_450


title: RNA-Seq B_T3F1

description: Brain T3 Library biol. Rep. 1


title: P6_M

value: Male


title: C13_M

value: Control


title: RNA-Seq B_T2F4

description: Brain T2 Library biol. Rep. 4


title: RNAseq_OM_447


title: C12_M


title: AMX4: anammox 0.75 mM  Fe(II)

city: Suzhou

first: Jing

last: Ding

address: No 1, Kerui Road

institute: Suzhou University of Science and Technology

description: Gene expression in 0.75 mM Fe(II) culture

hyb_protocol: Then cDNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were normalized according to the cDNA concentrations and anammox bacterial qPCR results. The cDNA concnetration and anammox bacterial qPCR result of AMX2 were set as 1.

organism: anaerobic ammonium-oxidizing bacterium enrichment culture

source_name: anammox culture, 0.75 mM Fe(II)

label_protocol: The synthetic double strand cDNAs were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: Inocula were withdrawn from a lab-scale anammox reactor that had been operated for more than two years. 35 mL anammox culture and 80 mL culture medium were mixed and then added into four groups of serum bottles (120 mL) in an anaerobic chamber, then were cultivated under 35 °C with four different Fe(II) concentrations.

extract_protocol: RNA was extracted from 15 mL samples using MoBio PowerSoil total RNA isolation kit following the manufacturer’s instructions. Concentration and quality of the extracted RNA were measured with a NanoDrop One (Thermo Fisher, USA). RNA was digested with DNase (New England Biolabs Inc, USA) to remove any DNA contamination prior to use in further assays. The processed RNA was then checked by Bioanalyzer (Agilent, USA) to determine the quality and concentration, and then was used for cDNA synthesis.

treatment_protocol: Samples were taken out of the reactors and settled naturally in an anaerobic chamber, and were then stored in -80 °C for RNA extraction.

value: enriched anammox bacteria


title: RNAseq_OM_441

city: Huddinge

first: Serena

last: Barilla

address: Hälsovägen 7C

institute: Karolinska Institutet


title: RNA-Seq B_T2F3

description: Brain T2 Library biol. Rep. 3


title: hAEC with HA treatment for 36 h

city: Zunyi

first: Nuo-Xin

last: Wang

state: Guizhou

address: 149 Dalian Road

institute: Affiliated Hospital of Zunyi Medical University

description: Test

data_processing:
the 2–∆∆Ct method was used to quantify gene expression levels
Fold Change worksheet reports test/control (i.e., without HA/with HA) ratios.

label: SYBR Green

source_name: human amniotic epithelial cells

label_protocol: cDNA was synthesized using a SuperScript III Reverse Transcriptase Kit (Invitrogen, Shanghai, China). Real-time PCR was conducted using the 2 X SuperArray PCR master mix according to the product's instructions.

growth_protocol: P1 hAECs in logarithmic growth phase were harvested, inoculated into 6-well plates at 3×105/well, and cultured with 5% CO2 at 37 °C. The medium was changed after 3 days

extract_protocol: The total RNA was purified using the RNeasy MinElute kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions

treatment_protocol: then the cells were cultured for 18 or 36 h in the presence and absence of HA (300 kDa, 1 mg/mL)

value: hAEC

tag: activation agent

value: HA 1 mg/mL

tag: time


title: hAEC without HA treatment

description: Control

value: 0 h


title: C11_M

tag: age


title: hAEC with HA treatment for 18 h

description: Test


title: AMX1: anammox 0.03 mM  Fe(II)

description: Gene expression in 0.03 mM Fe(II) culture

source_name: anammox culture, 0.03 mM Fe(II)


title: RNAseq_OM_425


title: RNA-Seq B_T2F2

description: Brain T2 Library biol. Rep. 2

tag: timepoint


title: RNAseq_OM_410


title: RNA-Seq B_T2F1

description: Brain T2 Library biol. Rep. 1


title: C10_M


title: C9_M


title: AMX2: anammox 0.09 mM  Fe(II)

description: Gene expression in 0.09 mM Fe(II) culture

source_name: anammox culture, 0.09 mM Fe(II)


title: C7_F

value: Female


title: C8_M


title: RNA-Seq B_T1F3

description: Brain T1 Library biol. Rep. 3


title: RNAseq_OM_265


title: RNA-Seq B_T1F2

description: Brain T1 Library biol. Rep. 2


title: C6_F


title: RNAseq_OM_225


title: RNA-Seq B_T1F4

description: Brain T1 Library biol. Rep. 4


title: RNA-Seq L_T4F4

description: Liver T4 Library biol. Rep. 4

source_name: liver


title: RNAseq_OM_210


title: C5_F


title: AMX3: anammox 0.12 mM  Fe(II)

description: Gene expression in 0.12 mM Fe(II) culture

source_name: anammox culture, 0.12 mM Fe(II)


title: C4_F


title: RNA-Seq L_T4F3

description: Liver T4 Library biol. Rep. 3


title: RNAseq_OM_227


title: RNAseq_OM_189


title: C3_F


title: RNAseq_OM_149


title: RNA-Seq L_T4F2

description: Liver T4 Library biol. Rep. 2


title: RNA-Seq L_T4F1

description: Liver T4 Library biol. Rep. 1


title: C2_F


title: RNA-Seq L_T3F4

description: Liver T3 Library biol. Rep. 4


title: Bisulfite-Seq Pit_T4F4

description: Pituitary T4 library biol. rep. 2

data_processing:
Raw data quality control was implemented using Trim Galore v0.5 to filter bases based on their quality (bases with Q scores > 30 were retained) and remove both universal and indexed adapter sequences. Processed high-quality data were mapped to into the bisulfite-converted version of the Atlantic salmon reference genome ICSASG_v2 (Lien et al., 2016) using BSseeker2 v2.1.8 (Guo et al., 2013) with default parameters for aligning paired-end libraries using Bowtie2 (Langmead & Salzberg 2012).
PCR duplicates were detected and removed using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Filtered (duplicates-free) reads (110 M PE reads) were retained for downstream methylation analysis with an average genome coverage of 11x in pituitary, ovary and liver.
Methylation calling was conducted using the Python script call-methylation.py within BSseeker2
CG position with 10x coverage were used to infer differential methylation in the R package DSS
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1
Supplementary_files_format_and_content: 10x_filtered_CG_position files

source_name: pituitary

extract_protocol:
Tissue samples were snap frozen in liquid N2 and stored  at -80 °C.  gDNA was isolated using DNeasy blood and tissue kit (QIAGEN) as previously described (Mohamed et al., 2018). Tissues were lysed in 360 μL of lysis solution on a Precellys 24 homogenizer for 30s at 4.0 ms−1. Samples were incubated with 40 μL of Proteinase K enzyme at 56 °C for 1 h. Following lysis, samples were treated with RNase (8 μL of RNase A incubated for 2 min at room temperature). DNA was bound to the provided columns, washed twice and eluted in 100 μL at room temperature. gDNA was fragmented (200-400bp) by sonication using Covaris S220, followed by end repair/adenylation and adapter ligation. Bisulfite modification was performed to the DNA fragments using the EZ DNA Methylation-GoldTM Kit (Zymo Research, Inc.)
12 RNA-Seq libraries (2 time points x 3 tissues x 2 biological replicates) were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). Libraries were sequenced on 634 Illumina Nova-Seq 6000 sequencing platform


title: H3K27ac_ChIPseq_shGPS2_D14_1

data_processing:
ChIP-seq raw files (fastq files) were aligned to the GRCh38  version of the human reference genome, using Bowtie 2. Only sequences mapping to exactly one location were kept. SAM files were then imported to HOMER to construct tag directories and HOMER was used for peak calling, annotation and extractraction of raw tag counts.
Genome_build: hg38
Supplementary_files_format_and_content: Raw tag counts files are in txt format and contain the merged peaks, annotation and raw tag counts of the respective peaks in the indicated samples.

source_name: human adipose-derived stem cells

extract_protocol:
Cells  were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIPed DNA was processed using Rubicon ThruPLEX DNA-seq kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

tag: cell line

value: Day 14

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_ChIPseq_shGPS2_D14_2

tag: genotype


title: C1_F

tag: tissue


title: H3K27ac_ChIPseq_shGFP_D14_2

value: shGFP


title: Bisulfite-Seq Pit_T4F2

description: Pituitary T4 library biol. rep. 1


title: RNA-Seq B_T1F1

description: Brain T1 Library biol. Rep. 1

data_processing:
Illumina reads were checked for quality using FastQC software. High quality reads(Q>30) were mapped to the Atlantic salmon genome ICSASG_v2 (Lien et al., 2016)using TopHat2 version 2.1.1 (Kim et al., 2013) with default parameters. Alignment files in BAM format were sorted by read name and converted into SAM format using SAMtools version 1.4 (Li et al., 2009). The Python package HTSeq version 0.7.2 (Anders et al., 2015) was applied to count unique reads mapped to exons using default parameters
Raw counts were analysed using the edgeR package (Robinson et al., 2010) in the R statistical computing environment to infer differential gene expression among tissues. The four tissues at the long photoperiod time points (T2, T3 and T4) were compared to the control samples at T1.
Further analyses were conducted on the lists of significant DEGs using normalised expression data (log2FPKM) according to Haas et al., 2013
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample


title: H3K27ac_ChIPseq_shGFP_D14_1


title: RNA-Seq L_T3F3

description: Liver T3 Library biol. Rep. 3


title: RNA-Seq L_T3F2

description: Liver T3 Library biol. Rep. 2


title: Bisulfite-Seq Pit_T1F4

description: Pituitary T1 library biol. rep. 2


title: H3K27ac_ChIPseq_shGPS2_D0_2

value: Day 0


title: RNA-Seq L_T3F1

description: Liver T3 Library biol. Rep. 1


title: Bisulfite-Seq Pit_T1F3

description: Pituitary T1 library biol. rep. 1


title: Bisulfite-Seq OV_T4F4

description: Ovary T4 library biol. rep. 2

source_name: ovary


title: H3K27ac_ChIPseq_shGPS2_D0_1


title: H3K27ac_ChIPseq_shGFP_D0_2


title: RNA-Seq L_T2F4

description: Liver T2 Library biol. Rep. 4


title: RNA-Seq L_T2F3

description: Liver T2 Library biol. Rep. 3


title: RNA-Seq L_T2F2

description: Liver T2 Library biol. Rep. 2


title: H3K27ac_ChIPseq_shGFP_D0_1


title: GPS2_ChIPseq_ hMADS_D14_U

value: WT


title: Bisulfite-Seq OV_T4F3

description: Ovary T4 library biol. rep. 1


title: U87MG P-bi-TAT (30 µM) Rep. 3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

source_name: GBM cell line

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human glioblastoma multiforme U87MG cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

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

treatment_protocol: Cells were treated with P-bi-TAT (30 µM) for 24 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

value: P-bi-TAT (30 µM) for 24 h


title: Bisulfite-Seq OV_T1F3

description: Ovary T1 library biol. rep. 2


title: RNAseq_OM_415


title: U87MG P-bi-TAT (30 µM) Rep. 2


title: U87MG UNTREATED Rep. 3


title: U87MG P-bi-TAT (30 µM) Rep. 1


title: Bisulfite-Seq OV_T1F1

description: Ovary T1 library biol. rep. 1


title: RNA-Seq L_T1F4

description: Liver T1 Library biol. Rep. 4

extract_protocol:
Tissue samples were preserved in RNA-Later at -80 °C and total RNA was isolated 626 using RNeasy mini kit (QIAGEN) as previously described (Mohamed et al., 2018). Tissues were lysed twice in 450 μL of lysis solution on a Precellys 24 homogenizer for 30s at 4.0 ms−1. RNA was bound to a column and washed twice before elution with 40 μL at room temperature. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrometer, Qubit 2.0 fluorometer and Agilent 2100 631 bioanalyzer. Messenger RNA (mRNA) was isolated from 1 μg of total RNA.
64 RNA-Seq libraries (4 time points x 4 tissues x 4 biological replicates) were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). Libraries were sequenced on 634 Illumina Nova-Seq 6000 sequencing platform


title: GPS2_ChIPseq_ hMADS_D0_U


title: Bisulfite-Seq LV_T4F4

description: Liver T4 library biol. rep. 2


title: RNA-Seq L_T1F3

description: Liver T1 Library biol. Rep. 3


title: Bisulfite-Seq LV_T4F3

description: Liver T4 library biol. rep. 1


title: U87MG 021913 P-bi-TAT (30 µM) Rep. 3

data_processing:
CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Human
program-name = Expression Console
program-version = 1.4.1.46

growth_protocol: Human glioblastoma multiforme GBM 021913 cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

treatment_protocol: For 2 days prior to cell exposure to P-bi-TAT, cells were maintained in medium containing 0.25% FBS and then exposed to 30 µM P-bi-TAT for 24 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

value: P-bi-TAT (10-6 M tetrac equivalent) for 24 h


title: RNA-Seq L_T1F2

description: Liver T1 Library biol. Rep. 2


title: U87MG 021913 P-bi-TAT (30 µM) Rep. 2

value: Human glioblastoma multiforme GBM 021913


title: U87MG 021913 P-bi-TAT (30 µM) Rep. 1


title: RNA-Seq L_T1F1

description: Liver T1 Library biol. Rep. 1


title: U87MG UNTREATED Rep. 2


title: ChIPseq_hMADS_D14_Input


title: U87MG UNTREATED Rep. 1


title: RNA-Seq L_T2F1

description: Liver T2 Library biol. Rep. 1


title: Bisulfite-Seq LV_T1F3

description: Liver T1 library biol. rep. 1


title: GPS2_ChIPseq_ hMADS_D14_E


title: ChIPseq_hMADS_D0_Input


title: U87MG 021913 UNTREATED Rep. 2

source_name: U87MG 021913 UNTREATED

value: none (untreated)


title: U87MG 021913 UNTREATED Rep. 3


title: Bisulfite-Seq LV_T1F4

description: Liver T1 library biol. rep. 2


title: Mouse 4T1 Parental (BRCA WT) Untreated single cell RNA-seq Rep 3

status: Public on Aug 27 2020

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

institute: Cleveland Clinic

description:
scRNA_logcounts.csv
PARENTAL3_IGO_09605_7

data_processing:
Fastq files for Brca1 and Brca2-deficient cells as well as parental cells were aligned and pre-processed to produce a count matrix using 10X Cell Ranger version 3.0.2.  The resulting count matrix was then filtered to exclude all cells with UMI count in mitochondrial genes > than 20% of all counts as described in Azizi et al Cell 2018, and all ribosomal genes were also removed from the analysis.  We further filtered any genes that had a mean log count <= 2.5 to reduce sparsity in the final count matrix.  Following these initial filtering steps, we used Seurat version 2.4 to scale the UMI counts and perform log normalization of the data.  To mitigate batch effects, we adopted a stringent approach whereby each replicate in each condition was treated as a separate batch.  Log-normalized counts for each sample were used as input to the mnnCorrect method Haghverdi et al 2018 from the scran package. The batch-corrected PCA from mnnCorrect was used as input to Phenograph clustering at resolution 1.0. Differential expression analyses were conducted using the FindMarkers function in Seurat.
For mouse tumors, fresh frozen tissue from day 14 tumors were used for isolation of DNA and RNA and submitted to the Integrated Genomic Core for library preparation and sequencing. 3-5 replicates per condition were submitted for sequencing depending on RNA quality.
Reads were aligned against the mm10 assembly by STAR
Gene level count values were then computed by the summarizeOverlaps function from the R package "GenomicAlignments" with UCSC mm10 KnownGene as the base gene model. The Union counting mode was used and only mapped paired reads were considered.
Differentially Expressed Genes (DEG) analyses were done using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized bulk RNA-seq counts

source_name: 4T1 breast tumor mouse model

growth_protocol: 4T1 cells were grown in culture until 60% confluence in RPMI 1640 supplemented with 10% FBS

extract_protocol:
For cells lines , Qiagen RNAeasy kit was used for isolation
RNA libraries were prepared for sequencing using standard Illumina protocols
For mouse single cell analysis, orthotopic implanted tumors in the mammary fat pad were isolated at day 12 after implantation. Single cell suspensions were generated from 2 pooled tumors using the Mouse Tumor Dissociation Kit according to manufacturer instructions (Miltenyi Biotech). Singe cell suspensions were then stained with DAPI and antibodies to CD45 and live lymphoctyes (DAPI-CD45+) cells were sorted on a BD Aria cell sorter (gating strategy below). Single cell library preparation was performed according to manufacturer instructions using the mouse single cell RNAseq kit (10X genomics) with 10,000 cells input per sample. Three replicates of each condition (4T1 Parental, 4T1 Brca2null , and  4T1 Brca1null tumors) were processed although 1 Brca1null  sample failed initially quality control and was excluded.

treatment_protocol: anti PD-1 antibody was injected intraperitoneally twice a week from palpable tumos

value: untreated

tag: strain

value: Balbc/J

value: Breast

value: Brca WT


title: NSD2

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 2312 PBDB, 169 Newton Road

department: Neuroscience

institute: University of Iowa

description: Ribosome associated mRNA

data_processing:
Sequencing data was processed with the reads trimmed, aligned and quantified according to the MUGQIC RNA-seq pipeline (bitbucket.org/mugqic/genpipes/src/master/pipelines/rnaseq).
Raw reads quality trimming and removing of Illumina adapters was performed using Trimmomatic v0.36 with parameters ILLUMINACLIP:adapters-truseq.fa:2:30:15:8:true TRAILING:30 MINLEN:32
The remaining reads were then aligned to the Mus musculus reference genome (mm10) with STAR v2.7.5
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix for all the samples was generated using HTSeq-counts in txt format

source_name: Hippocampus

extract_protocol:
In all experiments, control non-sleep deprived animals were sacrificed at the same time as experimental animals. Following sleep deprivation, hippocampi were dissected from experimental and control animals and flash frozen using dry ice. RNA was harvested using Trizol reagent.
Illumina TruSeq Stranded Total RNA with Ribo-Zero gold sample preparation kit for the construction of sequencing libraries.

treatment_protocol: Animals were gently handled through tapping of the cages and cage shakes for 3 min for three days prior to the scheduled experiment. All sleep deprivation was performed starting at the beginning of the light-dark cycle to avoid circadian confounds. Sleep deprivation was performed using gentle handling through cage tapping and then cage shakes as necessary. To ensure that only the minimal amount of disturbance was used to achieve sleep deprivation, animals were monitored continuously.

tag: Sex

value: Male

tag: group

value: Non Sleep deprived

value: 2-3 months


title: SDD

description: Ribosome associated mRNA

value: Sleep deprived


title: NSD3

description: Ribosome associated mRNA


title: SD3

description: Ribosome associated mRNA


title: NSDB

description: Ribosome associated mRNA


title: SD2

description: Ribosome associated mRNA


title: SD6

description: Ribosome associated mRNA


title: NSD4

description: Ribosome associated mRNA


title: SD1

description: Ribosome associated mRNA


title: Mouse 4T1 Brca2 KO Untreated single cell RNA-seq Rep 2

description:
scRNA_logcounts.csv
BRCA2_2_IGO_09605_6

value: Brca2 KO


title: Mouse 4T1 Brca1 KO Untreated single cell RNA-seq Rep 1

description:
scRNA_logcounts.csv
BRCA1_1_IGO_09605_5

value: Brca1 KO


title: Mouse 4T1 Brca2 KO Untreated single cell RNA-seq Rep 3

description:
scRNA_logcounts.csv
BRCA2_3_IGO_09605_9


title: Mouse 4T1 Brca2 KO Untreated single cell RNA-seq Rep 1

description:
scRNA_logcounts.csv
BRCA2_1_IGO_09605_1


title: Mouse 4T1 Brca1 KO Untreated single cell RNA-seq Rep 2

description:
scRNA_logcounts.csv
BRCA1_2_IGO_09605_8


title: SD4

description: Ribosome associated mRNA


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_1_CEMBA180514_5B_2_B1_AD008_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

value: male


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_1_CEMBA180514_5B_2_B3_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G9_AD008_indexed


title: NSD5

description: Ribosome associated mRNA


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G9_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G9_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G8_AD002_indexed


title: Mouse 4T1 Parental (BRCA WT) Untreated single cell RNA-seq Rep 2

description:
scRNA_logcounts.csv
PARENTAL2_IGO_09605_4


title: Mouse 4T1 Parental (BRCA WT) Untreated single cell RNA-seq Rep 1

description:
scRNA_logcounts.csv
PARENTAL1_IGO_09605_2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G7_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G9_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G6_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G4_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G3_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G5_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G4_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G11_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G6_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G7_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G12_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G8_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G11_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G2_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G10_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F9_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G6_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G6_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G2_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F9_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G3_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G10_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G12_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F9_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F8_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F8_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F8_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F7_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F7_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F9_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F7_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F7_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F5_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_G10_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F5_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F5_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F6_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F4_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F7_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F4_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F4_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F4_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F4_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F4_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F3_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F2_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F3_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F3_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F12_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F2_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F2_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F2_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F11_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F12_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F7_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F12_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F3_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F1_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F12_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F12_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F11_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F12_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180514_5B_3_CEMBA180514_5B_4_F2_AD008_indexed


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